Explore every episode of the podcast Base by Base

🎙️ Episode 54: Temporal Immune Landscapes — A Multi-Omic Lens on COVID-19 in End-Stage Kidney Disease

🧬 In this new Base by Base episode we unpack a 2025 Cell Genomics study by Stephenson et al. that followed 61 haemodialysis patients through two waves of the pandemic. Using single-cell multi-omics (CITE-seq, VDJ-seq) across 580 000 immune cells, the team captured how SARS-CoV-2 reshapes the blood compartment over time, why some patients spiral into critical illness, and how routine dexamethasone therapy rewires monocyte behaviour.

🔍 Main highlights
Longitudinal immune-gene trajectories diverge sharply between mild/moderate and severe/critical COVID-19.
Interferon-stimulated genes rise early after symptom onset and peak higher in severe cases.
Rapidly expanding T-cell clones are enriched for SARS-CoV-2-specific TCRs that converge on shared, MHC-II-restricted motifs.
Glucocorticoid therapy triggers a CD163-high monocyte subset with an M2-like, anti-inflammatory transcriptome that is absent without steroid exposure.

🧠 Conclusion
By marrying temporal sampling, single-cell transcriptomics, surface proteomics and immunoreceptor sequencing, the study maps an immune storyline in which early interferon pressure, B-cell hyper-proliferation and selective T-cell expansion set the stage for outcome, while dexamethasone adds a late anti-inflammatory twist. The dataset is a blueprint for understanding COVID-19 in clinically vulnerable populations and for refining immunomodulatory strategies.

📖 Reference
Stephenson, E., Macdonald-Dunlop, E., Dratva, L.M. et al. (2025). Temporal multi-omics analysis of COVID-19 in end-stage kidney disease. Cell Genomics, 5, 100918. https://doi.org/10.1016/j.xgen.2025.100918

📜 License
This episode is based on an open-access article distributed under the Creative Commons Attribution 4.0 International license (CC BY 4.0).

🎙️ Episode 53: Weighing the Evidence — A Systematic Review of Polygenic Risk Score Economic Evaluations
🧬 In this episode of Base by Base, we explore the systematic review by Siena et al. (2025) in The American Journal of Human Genetics, which examines the methods used to quantify the costs and benefits of polygenic risk–based strategies in clinical practice. The authors conducted a comprehensive search of PubMed, Web of Science, and Scopus, identifying 24 full economic evaluations—predominantly cost-utility analyses—spanning cancer screening programs, cardiovascular disease prevention, type 2 diabetes risk stratification, and glaucoma screening. Each study was assessed using the QHES instrument, and findings were synthesized narratively to highlight key methodological features, cost components, and analytic perspectives .

🔍 Study Highlights:
This review integrates evidence from cost-utility analyses across oncology, cardiology, endocrinology, and ophthalmology to reveal that many polygenic risk–stratified interventions demonstrate favorable cost-effectiveness outcomes, yet results are highly heterogeneous depending on the disease context and modelling approach; the widespread reliance on hypothetical cohorts and the scarce incorporation of real-world implementation data limit generalizability and risk underestimating delivery costs; analytic frameworks varied markedly in perspective (healthcare system, societal, payer), time horizon (5-year to lifetime), discount rates, and included cost categories (genotyping, diagnostics, treatment, indirect costs), complicating direct comparisons; indirect and non-health benefits—such as productivity gains—were infrequently evaluated; and critical gaps remain in representing diverse ancestries, accounting for long-term outcomes, and integrating comprehensive cost-benefit dimensions.

🧠 Conclusion:
Siena et al. conclude that polygenic risk–based approaches hold significant promise for enhancing precision prevention and personalized screening strategies. However, future economic evaluations must embrace real-world evidence, include diverse populations, and adopt broader cost and benefit frameworks to generate robust, actionable insights for policymakers and clinicians.

📖 Reference:
Siena, L. M., Baccolini, V., Riccio, M., Rosso, A., et al. (2025). Weighing the evidence on costs and benefits of polygenic risk-based approaches in clinical practice: A systematic review of economic evaluations. The American Journal of Human Genetics, 112(1), 1–19. https://doi.org/10.1016/j.ajhg.2025.05.012

📜 License:
This episode is based on an open access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) license (https://creativecommons.org/licenses/by/4.0/).

🎙️ Episode 52: Human Genetic Variation Reveals FCRL3 as a Lymphocyte Receptor for Yersinia pestis
🧬 In this episode of Base by Base, we dive into a cellular genome-wide association study (GWAS) of nearly 1,000 lymphoblastoid cell lines published by Keener et al. (2025) in Cell Genomics, which uncovers Fc receptor-like 3 (FCRL3) as a previously unrecognized surface receptor that mediates attachment and invasion of Yersinia pestis into human B cells. Employing the Hi-HOST platform, the authors identify a nonsynonymous SNP (rs2282284, N721S) in FCRL3 that modulates bacterial uptake, then validate that overexpression of FCRL3 in non-phagocytic HeLa cells is sufficient to trigger both adhesion and internalization of unopsonized bacteria. Through mutational analyses, they pinpoint the critical role of the first Ig-like domain for binding and define an ITAM together with an adjacent ITIM-like motif around Y722 that orchestrate SYK kinase recruitment and phagocytic signaling. Direct binding assays with purified FCRL5 extracellular domains confirm a specific interaction with Y. pestis, and phenome-wide association studies link the same FCRL3 variant to altered risk of chronic hepatitis C infection, suggesting pleiotropic effects on human infectious disease susceptibility.
🔍 Main highlights: The Hi-HOST cellular GWAS leverages global human genetic diversity to pinpoint rs2282284 in FCRL3 as a determinant of Y. pestis invasion; FCRL3 overexpression in HeLa cells drives both GFPlow bacterial attachment and GFPhigh intracellular uptake in a gentamicin-protection assay; mutagenesis of Ig-like domain 1 abolishes binding while tyrosine-to-phenylalanine substitutions in the ITAM and Y722 motif impair SYK-dependent internalization; FCRL5 extracellular domain fusion proteins bind Y. pestis directly under high-salt washes; pheWAS in BioBank Japan shows the C allele of rs2282284 is associated with reduced chronic hepatitis C risk, colocalizing with the invasion phenotype.
🧠 Conclusion: This work inaugurates a new paradigm in bacterial pathogenesis by revealing how Y. pestis exploits lymphocyte-specific Fc receptor-like proteins to create an intracellular niche, and it underscores the impact of human genetic variation on susceptibility to both ancient and modern infectious threats.
📖 Reference: Keener, R. M., Shi, S., Dalapati, T., Wang, L., Reinoso-Vizcaíno, N. M., Luftig, M. A., Miller, S. I., Wilson, T. J., & Ko, D. C. (2025). Human genetic variation reveals FCRL3 is a lymphocyte receptor for Yersinia pestis. Cell Genomics, 5, 100917. https://doi.org/10.1016/j.xgen.2025.100917
📜 License: This episode is based on an open access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) license – http://creativecommons.org/licenses/by/4.0/

🎙️ Episode 51: Diagnosing the Undiagnosed — A Phenotype-Driven Pipeline for Mitochondrial DNA Discovery

🧬 In this episode of Base by Base, we dive into a powerful phenotype-guided strategy to uncover mitochondrial DNA (mtDNA) diseases in large-scale rare disease cohorts. Ratnaike et al. (2025), publishing in The American Journal of Human Genetics, present the results of a systematic reanalysis of 10,157 exome and genome datasets from the European Solve-RD project, applying a semi-automated pipeline that filters mtDNA variants and prioritizes them based on phenotype similarity using the HPO-driven MitoPhen database.

🔍 Study Highlights:
The researchers developed and validated a workflow combining the MToolBox pipeline for mtDNA variant calling and the MitoPhen similarity scoring system to assess the match between patient-reported symptoms and known mtDNA disease profiles.
They applied this approach to over 9,900 undiagnosed individuals and identified 135 candidates with rare mtDNA variants, leading to 37 confirmed or likely mtDNA diagnoses — an increase of 0.4% in diagnostic yield in a cohort where mitochondrial disease was not suspected.
Importantly, 92% of these new diagnoses had phenotype similarity scores above 0.3, validating the use of structured phenotypic data as a sensitive filter.
The model proved robust across sequencing platforms and heterogeneous datasets, highlighting the potential of incorporating phenotype similarity into routine rare disease genomics.
This work also underscores the importance of complete and specific phenotype data (e.g., ≥5 detailed HPO terms), which was associated with higher diagnostic success.

🧠 Conclusion:
By integrating automated mtDNA variant filtering with HPO-based phenotype similarity scoring, this study demonstrates a scalable and clinically relevant method to boost diagnostic rates for mitochondrial diseases. This approach is especially valuable in genomic datasets not initially enriched for suspected mitochondrial conditions and offers a roadmap for future phenotype-genotype analyses in rare disease diagnostics.

📖 Reference:
Ratnaike, T., Paramonov, I., Olimpio, C., et al. (2025). Mitochondrial DNA disease discovery through evaluation of genotype and phenotype data: The Solve-RD experience. The American Journal of Human Genetics, 112, 1376–1387. https://doi.org/10.1016/j.ajhg.2025.04.003

🌐 License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 50: The Microbiome for Clinicians — Bridging Research and Practice

🧬 In this episode of Base by Base, we explore a Perspective article by Porcari et al. (2025) in Cell titled “The microbiome for clinicians,” which examines the current disconnect between microbiome research and its implementation in medical practice, and outlines a strategic roadmap to overcome the barriers preventing its clinical adoption.

🔍 Key Highlights:
The authors categorize translational barriers into biological complexity, methodological variability, logistical hurdles, and cultural factors that hinder reproducibility and clinician confidence ; they review diagnostic applications of gut microbiome profiling for colorectal cancer screening, inflammatory bowel disease detection, and prediction of response to immunotherapies and standard treatments ; they discuss therapeutic potentials—including fecal microbiota transplantation, live biotherapeutic consortia, engineered probiotics, and phage therapy—highlighting both the successes in recurrent C. difficile infection and the challenges in chronic disease contexts ; and they propose a multifaceted action plan—standardizing research protocols, enhancing clinical trial design with rigorous statistical frameworks, deepening mechanistic understanding of host–microbiome interactions, and fostering interdisciplinary education and communication—to accelerate the integration of microbiome science into clinical care .

🧠 Conclusion:
Porcari et al. argue that while microbiome research has delivered promising diagnostic and therapeutic insights, realizing its full potential in precision medicine requires coordinated efforts in protocol standardization, trial methodology refinement, mechanistic validation, and targeted training of healthcare professionals to transform microbiome discoveries into practical clinical tools.

📖 Reference:
Porcari S, Ng SC, Zitvogel L, Sokol H, Weersma RK, Elinav E, Gasbarrini A, Cammarota G, Tilg H, Ianiro G. (2025). The microbiome for clinicians. Cell, 188, 2836–2844. https://doi.org/10.1016/j.cell.2025.04.016

📜 License:
This episode is based on an open access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 49: Chitin as a Reservoir for Horizontal Gene Transfer — Environmental DNA Adsorption and Natural Transformation in Vibrio cholerae

🧬 In this episode of Base by Base, we explore the study by Holt et al. (2025) in Proceedings of the National Academy of Sciences, which uncovers how extracellular DNA from the marine environment binds to chitin surfaces and becomes accessible to Vibrio cholerae for natural transformation. Through the use of microfluidic flow chambers mimicking realistic ocean conditions and high-resolution confocal microscopy, the authors reveal that chitin particles act as hotspots for horizontal gene transfer, offering new insights into microbial evolution in aquatic ecosystems.

🔍 Study highlights: Under a continuous flow of artificial seawater supplemented with trace amounts of fluorescently labeled DNA, chitin flakes rapidly accumulate DNA on their outer surfaces, as quantified by fluorescence intensity heatmaps and surface-area–normalized measurements. Following a rigorous wash step that removes unbound DNA from the bulk medium, V. cholerae reporter strains carrying a repairable GFP construct integrate chitin-bound DNA and form GFP-positive transformants within 48 hours, demonstrating retrieval of surface-adsorbed DNA for recombination. The retraction ATPase PilU is shown to be indispensable for efficient natural transformation on chitin-bound substrates, whereas deletion of PilU has no effect when DNA is freely soluble, highlighting a biophysical requirement for pilus-mediated force in accessing immobilized genetic material. Remarkably, transformation frequencies on chitin are comparable to those observed with free DNA in liquid culture, underscoring the ecological significance of chitin particles as reservoirs of genetic diversity.

🧠 Conclusion: Holt et al. establish a novel paradigm in which chitin surfaces in marine habitats concentrate environmental DNA and enable pilus-dependent natural transformation, shaping the genetic landscape of V. cholerae and potentially other chitin-associated microbes. This mechanism illuminates how environmental biomaterials drive horizontal gene transfer and may inform strategies to predict and mitigate the emergence of new pathogenic variants.

📖 Reference: Holt, J. D., Peng, Y., Dalia, T. N., Dalia, A. B., & Nadell, C. D. (2025). Environmental DNA adsorption to chitin can promote horizontal gene transfer by natural transformation. PNAS, 122(22), e2420708122. https://doi.org/10.1073/pnas.2420708122

📜 License: This episode is based on an open access article published under the Creative Commons Attribution 4.0 International license (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 48: Mainstreaming Genetic Testing — A Conceptual Framework for Expanding Genomic Medicine

🧬 In this episode of Base by Base, we explore an important policy and practice shift presented by Mackley et al. (2025) in Genetics in Medicine. The authors propose a conceptual framework for the mainstreaming of clinical genetic testing, addressing the increasing demand for genomic services across medicine and the limited growth of the clinical genetics workforce. By redefining how genetic testing responsibilities can be shared between geneticists and non-geneticist clinicians, this framework aims to make genomic care more accessible, efficient, and scalable across health systems.

🔍 Study highlights:
The proposed framework identifies four general models for mainstreaming genetic testing, each defined by the point at which responsibility transfers from the non-geneticist clinician to the clinical genetics service.
Rather than a one-size-fits-all approach, the models are adaptable to local healthcare infrastructure, clinician expertise, disease complexity, and testing resources.
It accounts for patient, clinician, test, system, and disease-specific variables that affect the feasibility of mainstreaming in each case.
The framework emphasizes clear communication, structured roles, and robust support systems (e.g., embedded genetic counselors, lab support lines) to ensure quality and safety.
By standardizing terminology and outlining core diagnostic pathway activities, the framework allows healthcare systems to design, evaluate, and scale mainstreaming programs effectively.

🧠 Conclusion:
This framework marks a critical step toward integrating genomics more deeply into routine care by expanding the capacity of non-geneticist clinicians to manage genetic testing. Through thoughtful implementation and consistent evaluation, the model supports more equitable access to precision medicine while preserving the essential role of clinical genetics experts in complex cases.

📖 Reference:
Mackley, M.P., Richer, J., Guerin, A., et al. (2025). Mainstreaming of clinical genetic testing: a conceptual framework. Genetics in Medicine. https://doi.org/10.1016/j.gim.2025.101465

🌐 License:
This episode is based on an open access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0)

🎙️ Episode 47: Selectivity and Promiscuity — Decoding the Human Chemokine-GPCR Network
🧬 In this episode of Base by Base, we explore a systems-level framework unveiled by Kleist et al. (2025) in Cell, which dissects how selectivity and promiscuity arise in the intricate network of human chemokine-GPCR interactions. By combining structural biology, evolutionary conservation, and machine learning, the study reveals the molecular grammar that encodes receptor specificity and versatility across immune signaling pathways.

🔍 Study Highlights:
Chemokine-GPCR recognition is governed by a hierarchy of determinants — conserved, semi-conserved, and variable — distributed across structured cores and flexible loop regions of both ligands and receptors.
Promiscuity and selectivity are modulated through short linear motifs (SLiMs) in unstructured regions, which serve as tunable hotspots for binding specificity.
The team developed a chemokine numbering (CCN) and receptor numbering (CRN) system to align residues across families and quantify their conservation and variability.
Mutagenesis and binding assays confirmed that even minor changes in SLiMs can rewire binding preferences, as demonstrated through rational engineering of a viral chemokine (vMIP-II) to alter GPCR targeting.
A new public web resource was created to support sequence-structure-function studies and the design of therapeutic chemokines with tailored selectivity.

🧠 Conclusion:
This study proposes a unifying model where selectivity is “encoded” like a molecular password and “decoded” by matching elements on ligands and receptors — akin to digital encryption. By uncovering this code, researchers can now manipulate chemokine-GPCR interactions to modulate immune cell migration, offering promising avenues for immunotherapies, cell engineering, and infection control.

📖 Reference:
Kleist, A. B., Szpakowska, M., Talbot, L. J., et al. (2025). Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network. Cell, 188, 1–20. https://doi.org/10.1016/j.cell.2025.03.046

🌐 License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International license – CC BY 4.0

🎙️ Episode 46: Pan-Epitranscriptomic Control — How tRNA and m6A Interact to Regulate mRNA Decay

🧬 In this episode of Base by Base, we delve into a landmark study by Linder et al. (2025), published in Cell, which uncovers a molecular interaction between two layers of RNA modifications — m6A in mRNA and mcm5s2U in tRNA — that tunes mRNA stability in a codon-specific and translation-dependent manner. The authors present a compelling model where tRNA modifications actively influence the functional outcome of m6A deposition, linking codon optimality with mRNA decay and revealing an unexpected coordination between translation and post-transcriptional regulation.

🔍 Study Highlights:
The study demonstrates that m6A marks in the coding sequence (CDS) reduce codon optimality, slowing translation and triggering mRNA decay. This effect is particularly strong at specific codons and leads to ribosome collisions, which initiate decay pathways. Importantly, the tRNA modification mcm5s2U counteracts this effect by improving decoding efficiency at these sites, especially for codons like AGA and GAA. Loss of mcm5s2U leads to exaggerated decay of m6A-modified transcripts, revealing a finely tuned epitranscriptomic axis. The researchers also show that many of the affected transcripts belong to oncogenic signaling pathways, and that the balance between m6A and mcm5s2U acts as a pan-cancer biomarker, with increased mcm5s2U linked to tumor aggressiveness and poor prognosis. This interplay offers a novel framework for understanding RNA stability, cancer progression, and potential therapeutic vulnerabilities.

🧠 Conclusion:
This work defines a new paradigm in RNA biology — a pan-epitranscriptomic system in which modifications in both mRNA and tRNA converge to control gene expression at the level of mRNA decay. By modulating translation kinetics at the codon level, the cell can fine-tune the lifespan of specific mRNAs, especially those involved in tightly regulated pathways like oncogenesis. These findings not only reshape our understanding of the epitranscriptome but also open avenues for new diagnostic and therapeutic strategies in cancer and beyond.

📖 Reference:
Linder, B., Sharma, P., Wu, J., et al. (2025). tRNA modifications tune m6A-dependent mRNA decay. Cell, 188, 1–13. https://doi.org/10.1016/j.cell.2025.04.013

📜 License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 45: Probing Nucleolar Mechanics — RNA-Dependent Viscoelasticity of Nucleolar Subcompartments

🧬 In this episode of Base por Base, we delve into a groundbreaking study by Cheng et al. (2025) in PNAS that employs micropipette aspiration to directly measure the material properties of nucleoli within living Xenopus laevis oocytes. By aspirating these large, transcriptionally active condensates, the authors distinguish the Newtonian, liquid-like behavior of the granular component (GC) from the partially solid-like, viscoelastic nature of the dense fibrillar component (DFC) and its fibrillar center (FC). Crucially, they demonstrate that targeted RNA degradation fluidizes the DFC, revealing an intimate link between nascent ribosomal RNA and nucleolar rheology .

🔍 Main highlights:
The study adapts micropipette aspiration—a label-free technique traditionally used for cells—to probe intracellular biomolecular condensates, achieving one-dimensional strain measurements under controlled suction pressure; aspiration profiles show the GC deforms with a constant strain rate, characteristic of a Newtonian fluid, whereas the DFC/FC exhibits a nonlinear, time-dependent response consistent with a viscoelastic solid; quantitative fitting yields an average GC viscosity of ~220 Pa·s and a DFC elastic modulus of ~3 Pa, with interfacial tensions estimated at 1.7 µN/m (GC–nucleoplasm) and ≤0.5 µN/m (DFC–GC); RNase A treatment dramatically accelerates DFC fusion and aspiration, producing an inverse capillary velocity two orders of magnitude lower and indicating a tenfold increase in the GC–DFC interfacial tension alongside a fluidization of the DFC phase.

🧠 Conclusion:
By linking RNA content to nucleolar material state, this work unveils how spatially organized rRNA processing underpins the viscoelastic architecture of the nucleolus. Such insights not only deepen our understanding of ribosome biogenesis dynamics but also pave the way for exploring how condensate mechanics influence cellular function and dysfunction in development and disease.

📖 Reference:
Cheng, H. H., Roggeveen, J. V., Wang, H., Stone, H. A., Shi, Z., & Brangwynne, C. P. (2025). Micropipette aspiration reveals differential RNA-dependent viscoelasticity of nucleolar subcompartments. Proceedings of the National Academy of Sciences, 122(22), e2407423122. https://doi.org/10.1073/pnas.2407423122

📜 License:
This episode is based on an open-access article distributed under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 44: Proofreading Precision — Unveiling the Cryo-EM Mechanism of Human DNA Polymerase ε Holoenzyme

🧬 In this episode of Base per Base, we delve into a groundbreaking study by Wang et al. (2025) in PNAS that illuminates the molecular choreography of the human leading-strand DNA polymerase ε (Polε) holoenzyme during mismatch proofreading. By combining in situ mismatch generation with high-resolution cryo-electron microscopy, the research captures authentic intermediates of the Polε–PCNA complex as it recognizes, backtracks, and excises replication errors, offering an unprecedented view of this essential fidelity mechanism.

🔍 Key highlights: The authors reveal that a primer containing a preformed mismatch is blocked from accessing the exonuclease site when PCNA is bound, underscoring the necessity of generating the mismatch within the polymerase active site; upon in situ synthesis of a mismatched nucleotide, three distinct proofreading states—mismatch-locking, polymerase backtracking, and mismatch-editing—are captured, showing an extended unwinding of six base pairs and out-of-register base pairing that guides the primer terminus into the exonuclease channel; detailed structural analysis uncovers how the PCNA sliding clamp imposes steric constraints that drive DNA translocation and how the unique P-domain of Polε contributes to duplex melting and primer repositioning; these findings challenge previous models derived from preformed mismatches and clamp-free systems by demonstrating a processive, clamp-retained proofreading pathway.

🧠 Conclusion: This study inaugurates a new paradigm for understanding replicative fidelity by capturing the full proofreading cycle of a DNA polymerase–clamp holoenzyme in near-physiological conditions. The insights into PCNA’s role and P-domain dynamics promise to inform future research on replication errors and their links to cancer and genetic disease.

📖 Reference:
Wang, F., He, Q., O’Donnell, M. E., & Li, H. (2025). The proofreading mechanism of the human leading-strand DNA polymerase ε holoenzyme. Proceedings of the National Academy of Sciences, 122(22), e2507232122. https://doi.org/10.1073/pnas.2507232122

📜 License: This episode is based on an open access article published under the Creative Commons Attribution 4.0 International license (CC BY 4.0). https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 43: Personalized Molecular Signatures of Insulin Resistance and Type 2 Diabetes

🧬 In this episode of Base by Base, we explore the groundbreaking work by Kjærgaard et al. (2025) in Cell, where cutting-edge proteomics and phosphoproteomics were applied to skeletal muscle biopsies from over 120 participants with normal glucose tolerance or type 2 diabetes. By combining hyperinsulinemic-euglycemic clamps with deep in vivo phenotyping, the study maps fasting and insulin-stimulated protein and phosphoprotein landscapes to uncover how these molecular signatures predict whole-body insulin sensitivity and reveal the signaling pathways that drive or preserve insulin action in human muscle .

🔍 Study Highlights: Advanced proteomics analysis reveals molecular signatures of insulin resistance; fasting muscle proteome and phosphoproteome robustly predict whole-body insulin sensitivity; the acute insulin-stimulated phosphoproteome captures selective signaling nodes that remain intact or become dysregulated in insulin-resistant states; and a comprehensive proteome–phosphoproteome atlas uncovers sex-specific differences in muscle metabolism .

🧠 Conclusion: Leveraging personalized proteomic profiling alongside precise measures of insulin sensitivity, this work delivers an unprecedented molecular atlas of skeletal muscle in type 2 diabetes. It identifies key candidate targets—such as the human-specific AMPKγ3 S65 phosphorylation site regulated by MAPKAPK2—as well as demonstrates that distinct branches of insulin signaling are differentially affected by insulin resistance. These insights lay the foundation for tailored therapeutic strategies aimed at specific molecular nodes within skeletal muscle .

📖 Reference: Kjærgaard, J., Stocks, B., Henderson, J., et al. (2025). Personalized molecular signatures of insulin resistance and type 2 diabetes. Cell, 188, 1–17. https://doi.org/10.1016/j.cell.2025.05.005

📜 License: This episode is based on an open access article published under the Creative Commons Attribution 4.0 International license (CC BY 4.0) – http://creativecommons.org/licenses/by/4.0/

🎙️ Episode 42: Amino Acids Catalyse RNA Formation — Unlocking Prebiotic Cross-Catalysis

🧬 In this episode of Base por Base, we delve into the groundbreaking 2025 Nature Communications study by Rout et al., which uncovers how simple amino acids, under ambient alkaline dry conditions, act as potent acid-base catalysts to drive non-enzymatic RNA oligomerisation from ribonucleoside-2′,3′-cyclic phosphates .

🔍 Principais destaques:
Amino acids elevate RNA oligomer yields by more than 100-fold at pH values near their amine pKa, enabling room-temperature polymerisation of 2′,3′-cyclic phosphates into oligomers up to seven nucleotides long . Hydrophobic residues such as valine, leucine and isoleucine exert the strongest catalytic enhancement, equalising incorporation of A, U, C and G bases to generate a compositionally diverse pool capable of hybridisation . Kinetic and pH-dependence assays reveal that amino acid-driven transphosphorylation rates peak at pH 9–10, where the zwitterionic balance maximises proton transfer both as general base and general acid . Classical and ab initio molecular simulations show that selectivity arises from preferential hydrogen-bonding interactions between amino-group donors and the cyclic phosphate, rather than bulk hydrophobic effects . The work outlines plausible prebiotic scenarios—such as volcanic, alkaline wet-dry cycles—where RNA synthesis and templated ligation could proceed without reliance on divalent cations .

🧠 Conclusão:
This study forges a vital link between amino acids and RNA in a reverse catalytic direction, presenting a credible pathway for the emergence of informational polymers under early Earth conditions and inspiring new explorations of cross-catalytic networks in origin-of-life research.

📖 Referência:
Rout, S. K., Wunnava, S., Krepl, M., Cassone, G., Šponer, J.E., Mast, C.B., Powner, M.W. & Braun, D. (2025). Amino acids catalyse RNA formation under ambient alkaline conditions. Nature Communications, 16, 5193. https://doi.org/10.1038/s41467-025-60359-3

📜 Licença:
Este episódio baseia-se num artigo de acesso aberto publicado sob a licença Creative Commons Attribution 4.0 International (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 41: Public Preferences for Genomic Newborn Screening in Australia — Insights from Discrete Choice Experiments
🧬 In this episode of Base by Base, we discuss a landmark study by Peters et al. (2025) in The American Journal of Human Genetics, which surveyed 2,509 members of the Australian public to uncover how people value and would like to see genomic newborn screening (gNBS) implemented .

🔍 Highlights of the Study: Through two discrete choice experiments, the authors demonstrated that out-of-pocket cost is the single strongest determinant of gNBS uptake, with the public valuing programs that yield 10–50 additional diagnoses per 1,000 newborns at AUD 4,600–5,700 each . Respondents showed positive utility for higher diagnostic yield, greater accuracy, and availability of curative or symptom-managing treatments, but also a clear preference for more conservative screening panels when weighed against uncertainties in disease penetrance and treatment effectiveness . On service delivery, participants preferred that initial information be provided by general practitioners or obstetricians and that high-chance results be returned in person by genetics professionals, highlighting the importance of leveraging trusted healthcare relationships for sensitive communications .

🧠 Conclusion: This work reveals broad public support for gNBS in Australia—projected uptake exceeds 87%—and quantifies the trade-offs between cost, diagnostic yield, and clinical actionability that citizens are willing to make. These insights offer policymakers a robust, evidence-based foundation for designing value-driven and ethically sound gNBS programs.

📖 Reference: Peters, R., Best, S., Lynch, F., et al. (2025). Public preferences for the value and implementation of genomic newborn screening: Insights from two discrete choice experiments in Australia. The American Journal of Human Genetics, 112, 1–13. https://doi.org/10.1016/j.ajhg.2025.05.001

📜 License: This episode is based on an open access article published under the Creative Commons Attribution 4.0 International license (CC BY 4.0) – http://creativecommons.org/licenses/by/4.0/

🎙️ Episode 40: Lysosomal Proton Leak — Uncovering SLC7A11’s Role as an Unconventional H⁺ Transit Pathway

🧬 In this episode of Base by Base, we delve into a revealing study by Zhou et al. (2025) in Cell that identifies SLC7A11—long known for its function in redox homeostasis and ferroptosis—as a slow H⁺ transporter embedded in lysosomal membranes. Through a combination of CRISPR knockouts, pharmacological inhibition, ratiometric pH imaging, and assays on isolated lysosomes, the authors demonstrate that SLC7A11 mediates a constitutive proton efflux by trading luminal cystine for cytosolic glutamate, thereby fine-tuning lysosomal acidity and sustaining degradative capacity.

🔍 Key highlights of the study:
The authors reveal that SLC7A11 operates a distinct, slow H⁺ leak pathway—separate from the fast TMEM175 channel—directly coupling amino-acid exchange with pH regulation. Loss or inhibition of SLC7A11 causes lysosomal over-acidification and diminishes macromolecular degradation, resulting in accumulation of storage materials. Proper SLC7A11 function is shown to be essential for countering erastin-induced ferroptosis and preventing pathological α-synuclein aggregation in neurons. Mechanistic experiments confirm that efflux of cystine from, and influx of glutamate into, lysosomes through SLC7A11 drives its proton leak activity in immuno-isolated organelles.

🧠 Conclusion:
By unveiling SLC7A11 as an unconventional H⁺ transport conduit that integrates metabolite flux with pH homeostasis, this work expands our understanding of lysosomal physiology and suggests new therapeutic avenues for diseases involving ferroptosis, neurodegeneration, and lysosomal storage dysfunction.

📖 Reference:
Zhou, N., Chen, J., Hu, M., Wen, N., Cai, W., Li, P., Zhao, L., Meng, Y., Zhao, D., Yang, X., Liu, S., Huang, F., Zhao, C., Feng, X., Jiang, Z., Xie, E., Pan, H., Cen, Z., Chen, X., Luo, W., Tang, B., Min, J., Wang, F., Yang, J., & Xu, H. (2025). SLC7A11 is an unconventional H⁺ transporter in lysosomes. Cell, 188(1), 1–18. https://doi.org/10.1016/j.cell.2025.04.004

📜 License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International license (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 39: Whole-Genome Polygenic Score Inference — Fast and Memory-Efficient Algorithms for Scalable PRS

🧬 In this episode of Base by Base, we dive into the methodological breakthroughs of Zabad et al. (2025) in The American Journal of Human Genetics, where the authors introduce an updated variational inference framework (VIPRS v0.1) and novel data structures that together enable polygenic risk score computation across tens of millions of variants with dramatically reduced runtime and memory requirements .

🔍 Key highlights: Zabad and colleagues design a compressed sparse row (CSR) format for linkage-disequilibrium matrices that cuts storage by over 50-fold; they implement quantization and triangular-only representations to shrink memory footprint while preserving accuracy; they rewrite core inference routines in C/C++, leverage single-precision arithmetic, multithreading, and BLAS/SIMD optimizations to achieve more than an order-of-magnitude speedup per iteration; and they showcase whole-genome scoring on UK Biobank data of up to 18 million variants, completing analysis in under 20 minutes using less than 15 GB of RAM .

🧠 Conclusion: By uniting efficient LD compression, numeric optimizations, and parallel inference strategies, VIPRS v0.1 makes whole-genome polygenic scoring both accessible and practical for large-scale genomic studies, paving the way for more comprehensive and accurate genetic risk prediction .

📖 Reference: Zabad S., Haryan C. A., Gravel S., Misra S., Li Y. (2025). Toward whole-genome inference of polygenic scores with fast and memory-efficient algorithms. American Journal of Human Genetics, 112, 1–19. https://doi.org/10.1016/j.ajhg.2025.05.002

📜 License: This episode is based on an open access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 38: The Recency and Geographical Origins of Bat Viruses Ancestral to SARS-CoV and SARS-CoV-2
🧬 In this episode of Base by Base, we delve into a landmark study by Pekar et al. (2025) in Cell that harnesses recombination-aware phylogenetic and spatial analyses to trace how the closest bat coronavirus ancestors of SARS-CoV-1 and SARS-CoV-2 circulated mere years before spilling over into humans. By dissecting non-recombinant genomic segments and applying tailored molecular clock models, the authors reveal when and where these viral lineages emerged—and challenge past assumptions about transmission solely via bat host movement .

🔍 Key highlights of the study include: the discovery that fragments of human SARS coronaviruses share most recent common ancestors with bat viruses within the decade preceding each outbreak; evidence that both SARS-CoV-1-like and SARS-CoV-2-like viruses have circulated broadly across Asia for millennia; phylogeographic reconstructions pinpointing Western China (Yunnan, Sichuan, Guizhou) and Northern Laos as likely origins of the direct bat virus ancestors; and the striking finding that these ancestors moved at rates surpassing typical horseshoe bat dispersal to reach the sites of human emergence in Guangdong and Hubei provinces .

🧠 Conclusion: By integrating recombination-aware dating with continuous phylogeography, this work inaugurates a new paradigm in Mendelian spillover studies—demonstrating that human SARS viruses arose from bat reservoirs via rapid, long-distance jumps likely involving intermediate hosts or wildlife trade, rather than passive dispersal through bat populations alone .

📖 Reference: Pekar, J. E., Lytras, S., Ghafari, M., et al. (2025). The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2. Cell, 188, 1–17. https://doi.org/10.1016/j.cell.2025.03.035

📜 License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – http://creativecommons.org/licenses/by/4.0/

🎙️ Episode 37: Proteomic Clues — Prioritizing Functional Missense Variants with Chemoproteomics

🧬 In this episode of Base by Base, we highlight a new study by Palafox et al. (2025) in The American Journal of Human Genetics that bridges mass spectrometry-based chemoproteomics with variant interpretation. Missense variants—abundant and often challenging to classify—are prioritized here using measurements of amino acid reactivity, offering a protein-centric lens for clinical genomics. The authors leverage large-scale datasets on cysteine, lysine, and tyrosine reactivity to reveal that residues detected by chemoproteomics (CpDAAs) are significantly enriched in pathogenic and uncertain missense variants within genes associated with monogenic disease.

Using both linear (1D) and spatial (3D) proximity analyses, the study shows that pathogenic variants cluster near CpDAAs across clinically relevant proteins. CpDAAs were also found to be common in genes with high missense constraint and functional importance, including known drug targets. A case study on fumarate hydratase (FH) demonstrated how CpDAAs coincide with functionally disruptive variants affecting oligomerization, suggesting these chemically reactive residues may mark structural and clinical hotspots. Integration with CADD scores further supported their pathogenic potential.

🧠 Conclusion:
This work underscores the translational potential of chemoproteomics in variant interpretation and therapeutic targeting. By identifying amino acid sites with high functional relevance, especially those enriched for VUS and pathogenic variants, this approach adds an orthogonal layer of evidence to conventional genomics and may accelerate the development of precision therapies.

📖 Reference:
Palafox, M.F., Boatner, L., Wilde, B.R., et al. (2025). Prioritizing disease-associated missense variants with chemoproteomic-detected amino acids. Am J Hum Genet, 112, 1–15. https://doi.org/10.1016/j.ajhg.2025.04.017
📜 Licensed under CC BY 4.0 – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 36: Bi-allelic POPDC2 Variants: A Novel Autosomal Recessive Cardiac Syndrome
🧬 In this episode of Base by Base, we discuss a groundbreaking study by Nicastro et al. (2025) published in The American Journal of Human Genetics, which identifies bi-allelic loss-of-function variants in the POPDC2 gene as the cause of a previously unrecognized autosomal recessive syndrome characterized by cardiac conduction defects and hypertrophic cardiomyopathy. The authors sequenced affected individuals and families, performed homology modeling of POPDC2, and conducted electrophysiological and transcriptomic analyses to elucidate the molecular mechanisms underlying this syndrome .

🔍 Highlights of the study: The researchers discovered homozygous or compound heterozygous POPDC2 variants in four unrelated families, all presenting with early-onset sinus node dysfunction, atrioventricular block, and, in some cases, hypertrophic cardiomyopathy; structural models predict that these variants disrupt the cAMP-binding Popeye domain, impairing POPDC2 function; co-expression assays demonstrated that mutant POPDC2 fails to augment TREK-1 potassium channel currents, suggesting a loss of channel regulation; muscle biopsy from an affected individual revealed marked reduction of both POPDC1 and POPDC2 at the sarcolemma, along with tubular aggregates and membrane abnormalities, indicating impaired protein stability and trafficking; spatial and single-nucleus transcriptomics of adult human hearts showed that POPDC2 is highly expressed in sinoatrial and atrioventricular nodal cardiomyocytes, where it co-localizes with POPDC1; finally, population-level analyses across over one million individuals confirmed that heterozygous carriers of these variants do not exhibit related cardiac phenotypes, reinforcing a recessive mode of inheritance .

🧠 Conclusion: The identification of POPDC2 as a Mendelian gene for an autosomal recessive cardiac conduction and hypertrophic cardiomyopathy syndrome highlights the crucial role of POPDC2-mediated cAMP signaling and TREK-1 modulation in human cardiac pacemaking. This work expands our understanding of genetic causes of arrhythmia and cardiomyopathy and opens new avenues for diagnostic screening and potential therapeutic strategies.

📖 Reference: Nicastro, M., Vermeer, A. M. C., Postema, P. G., et al. (2025). Bi-allelic variants in POPDC2 cause an autosomal recessive syndrome presenting with cardiac conduction defects and hypertrophic cardiomyopathy. The American Journal of Human Genetics, 112, 1–18. https://doi.org/10.1016/j.ajhg.2025.04.016 .

📜 License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 35: Tracing the Evolutionary History of CCR5Δ32 — Insights from Ancient and Modern Genomes
🧬 In this episode of Base by Base, we explore groundbreaking research by Ravn et al. (2025) published in Cell that reconstructs the origin, spread, and selective pressures acting on the CCR5Δ32 deletion in human populations. Through a comprehensive analysis of 934 ancient genomes and 2,504 present-day genomes, the authors trace how this 32-base-pair deletion in the CCR5 gene—known to confer resistance to HIV-1 infection and influence other immune-related traits—emerged on a specific haplotype in the Western Eurasian Steppe and underwent positive selection during the Late Neolithic and Bronze Age, ultimately shaping its modern-day frequency and geographical distribution .

🔍 Study Highlights:
The CCR5Δ32 deletion arose on a pre-existing haplotype containing 84 linked variants, allowing the authors to develop HAPI, a haplotype-aware probabilistic model that identifies the deletion even in low-coverage ancient genomes. By applying HAPI to 934 ancient DNA samples spanning the Mesolithic through the Viking Age, the study identifies the oldest carriers of CCR5Δ32—dating back more than 6,700 years in the Western Steppe—thus pushing its origin deeper into prehistory than previously appreciated . The analysis reveals that CCR5Δ32 was subject to strong positive selection between approximately 8,000 and 2,000 years before present, with ancestry-stratified tests indicating that selection primarily acted in Eastern hunter-gatherer and Caucasus hunter-gatherer populations before spreading westward. Spatial diffusion modeling shows a rapid longitudinal expansion of the allele during the Late Neolithic and Bronze Age, followed by a plateau in frequency over the past two millennia . Furthermore, modern European and Latin American haplotype patterns confirm that post-Columbian admixture introduced the CCR5Δ32 haplotype into the Americas, while the identification of multiple haplotypes (A, B, and C) clarifies why certain proxy SNPs previously used to tag CCR5Δ32 proved unreliable.

🧠 Conclusion:
Ravn et al. demonstrate that CCR5Δ32 did not simply arise in recent medieval times or spread solely through Viking-related migrations; instead, it emerged on a specific haplotype in the Western Eurasian Steppe over 6,700 years ago and rose to high frequency under positive selection during the Late Neolithic and Bronze Age. By integrating ancient and modern genomic data with innovative probabilistic and spatial models, this work illuminates how a single deletion linked to HIV resistance became a significant immunological signature in human populations, with implications for understanding past pathogens and guiding future therapeutic strategies targeting CCR5 .

📖 Reference:
Ravn, K., Cobuccio, L., Muktupavela, R.A., Meisner, J., Danielsen, L.S., Benros, M.E., Korneliussen, T.S., Sikora, M., Willerslev, E., Allentoft, M.E., Irving-Pease, E.K., & Rasmussen, S. (2025). Tracing the evolutionary history of the CCR5Δ32 deletion via ancient and modern genomes. Cell, 188, 1–17. https://doi.org/10.1016/j.cell.2025.04.015

📜 License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) — https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 34: Enzyme Replacement Therapy in Homocystinuria — Safety and Efficacy of Pegtibatinase in the Phase 1/2 COMPOSE Trial
🧬 In this episode of Base by Base, we delve into early findings from Ficicioglu et al. (2025) published in Genetics in Medicine, which evaluate pegtibatinase, a PEGylated truncated human cystathionine β-synthase enzyme replacement, in adults with classical homocystinuria (HCU). The COMPOSE Phase 1/2 trial randomized individuals with elevated total plasma homocysteine (tHcy) despite standard‐of‐care treatment to receive escalating doses of subcutaneous pegtibatinase or placebo, assessing safety, immunogenicity, and metabolic outcomes .

🔍 Key highlights of the study:
The trial enrolled 24 participants aged 12–65 years across six dose cohorts, with pegtibatinase administered up to 2.5 mg/kg twice weekly and placebo controls
Pegtibatinase was generally well tolerated, with no anaphylaxis or severe immune reactions; treatment‐emergent adverse events were mostly injection‐site reactions and mild-to-moderate urticaria managed by dose interruption and premedication
Geometric mean reductions in tHcy were dose-dependent, with the highest doses (1.5 mg/kg BIW and 2.5 mg/kg BIW) achieving 57 % and 67 % relative decreases, respectively, and all patients in these cohorts maintaining tHcy below 100 μM
One participant receiving 2.5 mg/kg BIW normalized tHcy (< 15 μM) and reduced methionine (< 14 μM), enabling dietary protein liberalization without adverse events
Quantitative measurements showed restoration of methionine-cycle metabolites, including increased cysteine and cystathionine and decreased S-adenosylhomocysteine, indicating broader pathway correction
Anti-drug antibody incidence was transient and low in titer, suggesting pegtibatinase is not highly immunogenic and that antibodies did not affect pharmacokinetics

🧠 Conclusion:
The COMPOSE trial demonstrates that pegtibatinase offers a promising enzyme replacement approach for adults with classical homocystinuria, achieving substantial and sustained reductions in plasma homocysteine with an acceptable safety profile. These findings support continued investigation in larger and longer-term studies to confirm clinical benefits and explore impacts on diet and quality of life.

📖 Reference:
Ficicioglu, C., Thomas, J. A., Ganesh, J., Kudrow, D., Lah, M., Smith, W. E., Güner, J., McDermott, S., Vaidya, S. A., Wilkening, L., & Levy, H. L. (2025). Safety and efficacy of pegtibatinase enzyme replacement therapy in adults with classical homocystinuria in the COMPOSE® phase 1/2 randomized trial. Genetics in Medicine. Advance online publication

📜 License:
This episode summary is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 33: Mis-splicing-derived Neoantigens — A New Avenue for Immunotherapy in Leukemia

🧬 In this episode of Base por Base, we examine groundbreaking research by Kim et al. (2025), recently published in Cell, that uncovers a promising immunotherapeutic strategy targeting leukemia-associated splicing factor mutations. The study identifies recurrent neoantigens arising from mis-splicing events in SRSF2 and ZRSR2 mutant myeloid leukemias, which can be exploited for T cell receptor (TCR)-based therapies.

🔍 Study highlights
The researchers discovered that somatic mutations in RNA splicing factors lead to highly stereotyped mis-splicing events, generating neoantigens shared across patients. These aberrant splicing isoforms yield peptides capable of being presented by HLA class I molecules and recognized by CD8⁺ T cells. Using high-throughput screening, the team isolated neoantigen-reactive TCRs from both healthy donors and leukemia patients. They demonstrated that T cells engineered with these TCRs could selectively recognize and kill leukemia cells harboring splicing mutations, particularly those affecting the SRSF2 gene.

Importantly, these mis-splicing-derived neoantigens are minimally expressed in healthy tissues, improving the specificity and safety profile of the proposed immunotherapy. The study also provides evidence of functional impairment in patient-derived neoantigen-reactive T cells, but shows that adoptively transferred engineered T cells retain robust cytotoxicity. In vivo models confirmed tumor control and increased survival with TCR-T cell therapy targeting the CLK3-derived neoantigen.

🧠 Conclusion
This work positions RNA mis-splicing as a fertile source of “public” neoantigens that are both recurrent and targetable across genetically defined subtypes of leukemia. It opens new doors for TCR-based therapies and possibly neoantigen vaccines, especially in the context of allogeneic stem cell transplantation. The implications for personalized immunotherapy in myeloid malignancies are profound and set the stage for future clinical translation.

📖 Reference
Kim, W. J., Crosse, E. I., De Neef, E., et al. (2025). Mis-splicing-derived neoantigens and cognate TCRs in splicing factor mutant leukemias. Cell, 188, 1–19. https://doi.org/10.1016/j.cell.2025.03.047

📜 License
This episode is based on an open access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 32: Idursulfase Beta — A New Therapeutic Option for MPS II with Strong Clinical Evidence
🧬 In this episode of Base por Base, we delve into a pivotal phase 3 clinical study published by Sohn et al. (2025) in Genetics in Medicine, evaluating the efficacy and safety of idursulfase beta in patients with mucopolysaccharidosis type II (MPS II), also known as Hunter syndrome. This two-part study compared idursulfase beta to a historical placebo group drawn from a prior trial with idursulfase (Elaprase®), providing compelling evidence to support its use as enzyme replacement therapy (ERT) in MPS II.

🔍 The study demonstrated that weekly intravenous treatment with idursulfase beta (0.5 mg/kg) led to significant improvements in key clinical outcomes. Participants receiving the drug showed an average increase of 62.2 meters in the six-minute walk test (6-MWT) at week 53, compared to only 7.3 meters in the historical placebo group. Additionally, urinary glycosaminoglycan (GAG) excretion dropped by more than 70%, and liver and spleen volumes were markedly reduced. These results reflect robust improvements in somatic burden and functional capacity.
The drug was well tolerated, with a favorable safety profile and lower rates of persistent neutralizing antibody formation compared to idursulfase. Notably, no serious adverse events occurred in patients with missense variants. Pharmacokinetic data confirmed stable drug exposure across the treatment period.
The use of a historical placebo group was justified by ethical concerns surrounding rare disease trials and validated by the consistent performance of idursulfase in both contemporary and historical settings. The reduction in urinary heparan and dermatan sulfate and the organ volume improvements reinforce the drug's biological efficacy.

🧠 Conclusion:
Idursulfase beta represents a safe and effective ERT alternative for MPS II, demonstrating superior clinical outcomes and reduced immunogenicity in this rigorously designed trial. These findings broaden therapeutic options for a complex and multisystemic rare disease, offering hope for better functional outcomes in affected individuals.

📖 Reference:
Sohn, Y.B., Yang, A., Kim, M.S., et al. (2025). Efficacy and safety of idursulfase beta in the treatment of mucopolysaccharidosis II: a phase 3, two-part study compared to a historical placebo cohort. Genetics in Medicine, [online ahead of print]. https://doi.org/10.1016/j.gim.2025.101460

📜 License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) license – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 31: Decoding Hidden Signals — Genome Sequencing Reveals Cryptic Splicing Variants in Marfan Syndrome

🧬 In this episode of Base por Base, we delve into a breakthrough study by Walker et al. (2025), published in Genetics in Medicine, which leverages whole-genome sequencing and RNA-based validation to uncover non-canonical splicing variants in the FBN1 gene, often overlooked in conventional genetic testing for Marfan Syndrome (MFS). The authors analyzed data from over 78,000 individuals in the 100,000 Genomes Project to identify ultra-rare splice-altering variants contributing to undiagnosed cases of Familial Thoracic Aortic Aneurysm Disease (FTAAD), a hallmark feature of MFS.

🔍 Study Highlights:
This study systematically identified FBN1 splice variants predicted by SpliceAI to alter mRNA splicing — even when located deep within introns beyond conventional ±8 bp thresholds.
Among individuals with FTAAD, these variants were highly enriched compared to non-FTAAD participants (OR=84, p = 9.7×10⁻¹⁴), suggesting a significant pathogenic contribution.
Experimental validation using RT-PCR, minigene assays, and RNA sequencing confirmed aberrant splicing in 16 of 20 predicted variants, many of which induced pseudoexon insertions or exon extensions that introduce premature stop codons.
Nearly 70% of the identified splice variants lay outside canonical splice regions, revealing a previously underestimated mechanism behind unexplained MFS cases.
The study illustrates how expanding the SpliceAI analysis window from 50 to 500 bp enhances sensitivity for variant detection and aids in designing confirmatory RNA tests.
A recurrent variant (c.1589-1217G>T) was identified in multiple unrelated families across the UK, demonstrating the importance of screening for deep intronic mutations in FBN1 regardless of population background.

🧠 Conclusion:
This research reframes the molecular diagnosis of Marfan Syndrome by showing that non-coding FBN1 variants with splicing effects account for ~3% of undiagnosed cases. It underscores the necessity of genome sequencing and RNA validation in clinical pipelines and provides a compelling case for integrating advanced splicing prediction tools in routine diagnostics.

📖 Reference:
Walker, S., Bunyan, D. J., Thomas, H. B., et al. (2025). Utility of genome sequencing and group-enrichment to support splice variant interpretation in Marfan syndrome. Genetics in Medicine. https://doi.org/10.1016/j.gim.2025.101477

📜 License:
This episode is based on an article provided as a pre-proof by Genetics in Medicine (Elsevier) and is subject to final editing. © 2025 Elsevier Inc. on behalf of the American College of Medical Genetics and Genomics.

Episode 30: Heart in the Genes — A New Genetic Syndrome Linked to POPDC2

🫀 In this episode of Base by Base, we delve into a groundbreaking study by Nicastro et al. (2025), published in The American Journal of Human Genetics, which identifies bi-allelic variants in the POPDC2 gene as the cause of a novel autosomal recessive cardiac syndrome. This condition manifests with sinus node dysfunction, atrioventricular (AV) block, and in some cases, hypertrophic cardiomyopathy (HCM).

🔍 Study highlights:
The research demonstrates that pathogenic variants in POPDC2 disrupt its ability to bind cyclic AMP (cAMP), compromising its interaction with the TREK-1 potassium channel and affecting cardiac electrical activity.
Through in vitro electrophysiology, mutant POPDC2 variants failed to enhance TREK-1 current density, unlike the wild-type protein.
Structural modeling showed that disease-causing mutations cluster around key functional domains critical for cAMP binding and dimerization.
Muscle biopsy from an affected individual revealed a marked reduction in both POPDC2 and POPDC1 proteins, suggesting destabilization of their membrane complex.
Single-cell and spatial transcriptomics confirmed that POPDC2 is highly expressed in specialized cardiac conduction tissues—especially in the AV node and bundle cells—where it often co-localizes with POPDC1.
Large-scale population data (>1 million individuals) showed that heterozygous carriers of these rare variants do not display the disease phenotype, indicating a recessive inheritance pattern without clinical penetrance in carriers.

🧠 Conclusion:
This study establishes POPDC2 as a new Mendelian gene responsible for a previously unrecognized cardiac syndrome. It emphasizes the importance of functional genomics and integrative modeling to unravel complex genotype–phenotype relationships in cardiogenetics. These findings expand our understanding of the molecular mechanisms underlying cardiac conduction disorders and have important implications for genetic counseling and early diagnosis in affected families.

📖 Reference:
Nicastro, M., Vermeer, A.M.C., Postema, P.G., et al. (2025). Bi-allelic variants in POPDC2 cause an autosomal recessive syndrome presenting with cardiac conduction defects and hypertrophic cardiomyopathy. The American Journal of Human Genetics, 112, 1–18. https://doi.org/10.1016/j.ajhg.2025.04.016

📜 License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 29: Rethinking Agency for Genetic Testing Intention among Latinos — Determining Predictors of Intention for Carrier Screening and Cancer Predisposition Testing

🧬 In this episode of Base por Base, we explore a pre-proof by Chavez-Yenter and Kaphingst (2025) in Genetics in Medicine that leverages the Integrated Behavioral Model to uncover how attitudes, social norms, and perceived agency drive Latino adults’ intentions to pursue both carrier screening and cancer predisposition testing .

🔍 Study Highlights:
The authors first applied confirmatory factor analysis to refine latent constructs for attitude, norms, and agency, removing indicators with loadings below .500, and then employed structural equation modeling to predict behavioral intention for carrier screening (CS) and cancer predisposition testing (CPT) . Across both outcomes, perceived agency emerged as the strongest positive driver—β = .381 (p < .01) for CS and β = .559 (p < .01) for CPT—while stronger normative beliefs from family and friends boosted CS intention and attitudes showed a modest negative association with CS intention . Sensitivity analyses excluding participants with prior genetic testing upheld these agency and norm effects for carrier screening but attenuated IBM effects for cancer testing .

🧠 Conclusion:
These findings suggest that interventions designed to empower Latino patients—by enhancing their perceived ability to access testing and engaging family and social networks—may be more effective at increasing genetic testing uptake than strategies focused solely on information provision and attitude change .

📖 Reference:
Chavez-Yenter D, Kaphingst KA. Rethinking Agency for Genetic Testing Intention among Latinos: Determining Predictors of Intention for Carrier Screening and Cancer Predisposition Testing. Genetics in Medicine. 2025. https://doi.org/10.1016/j.gim.2025.101455

📜 License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) license – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 28: Cell-Type-Resolved TWAS — scPrediXcan Integrates Deep Learning and Single-Cell Data for Transcriptome-Wide Association Studies
🧬 In this episode of Base por Base, we explore the groundbreaking framework scPrediXcan introduced by Zhou et al. (2025) in Cell Genomics. This approach combines a deep learning–based model, ctPred, with single-cell RNA-seq data to predict cell-type-specific gene expression, and then linearizes those predictions into a SNP-based model, ℓ-ctPred, for use in S-PrediXcan. By leveraging only GWAS summary statistics and in silico expression references, scPrediXcan enables transcriptome-wide association studies at unprecedented cellular resolution .

🔍 Highlights of the study:
ctPred leverages a pretrained sequence-to-epigenomics model (Enformer) to predict cell-type-specific gene expression with high accuracy across diverse scRNA-seq datasets.
The ℓ-ctPred linear model robustly approximates ctPred outputs, allowing efficient TWAS using GWAS summary statistics without individual-level data.
In type 2 diabetes, scPrediXcan identifies 222 candidate genes across 108 independent LD blocks, compared with just 12 and 111 genes recovered by pseudobulk and bulk TWAS approaches.
Applied to systemic lupus erythematosus, scPrediXcan nominates 129 genes across 24 LD blocks, uncovering cell-type-specific drivers such as PYCARD and ITGAM that bulk analyses miss.
By integrating deep learning–based prediction with cell-type resolution, the framework reveals nuanced disease mechanisms and markedly improves gene prioritization for complex traits.

🧠 Conclusion:
scPrediXcan represents a major advance in genetic epidemiology by enabling large-scale, cell-type-specific TWAS using only summary statistics and single-cell-informed prediction models. It dramatically expands the set of candidate causal genes, refines our understanding of cellular mechanisms in disease, and lays the groundwork for more targeted experimental follow-up and therapeutic discovery.

📖 Reference:
Zhou, Y., Adeluwa, T., Zhu, L., et al. (2025). scPrediXcan integrates deep learning methods and single-cell data into a cell-type-specific transcriptome-wide association study framework. Cell Genomics, 5, 100875. https://doi.org/10.1016/j.xgen.2025.100875

📜 License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) license – http://creativecommons.org/licenses/by/4.0/

🎙️ Episode 27: Nucleocytosolic Vehicles — A CRISPR RNP Delivery Breakthrough

🧬 In this episode of Base by Base, we delve into a novel virus-like particle (VLP) platform, ENVLPE, developed by Geilenkeuser et al. (2025) in Cell. This innovation harnesses nucleocytosolic shuttling and RNA aptamer recruitment to efficiently package and deliver fully assembled CRISPR ribonucleoproteins (RNPs), overcoming spatial and loading limitations of previous VLP approaches.

🔍 Main Highlights:
The ENVLPE system integrates a PP7 coat protein into the HIV-1 Gag polyprotein and appends PP7-tagged guide RNAs to selectively load base editors, prime editors, nucleases, and trans-activators as RNPs rather than mRNA or protein fusions.
Active nuclear export and localization signals shuttle editor RNPs into the cytosol, synchronizing RNP assembly with VLP budding and greatly enhancing packaging efficiency.
Co-expression of the RNA endonuclease Csy4, which remains bound to a 3′ hairpin on pegRNAs, protects guide RNAs from degradation and substantially boosts prime editing performance under low-dose conditions.
A streamlined “miniENVLPE” variant retaining only essential Gag elements and coiled-coil oligomerization domains matches full-length editing efficiency, demonstrating the platform’s modularity and scalability.
In vivo subretinal delivery of ENVLPE in mouse models achieves robust editor uptake by retinal cells and functional gene correction in inherited eye disease—with minimal off-target activity.

🧠 Conclusion:
ENVLPE represents a versatile, high-efficiency vehicle for RNP delivery of CRISPR effectors in both ex vivo and in vivo settings. By combining RNA-mediated recruitment, active transport, and modular VLP engineering, this platform opens new avenues for precise therapeutic genome editing.

📖 Reference:
Geilenkeuser, J., Armbrust, N., Steinmaßl, E., et al. (2025). Engineered nucleocytosolic vehicles for loading of programmable editors. Cell, 188, 2637–2655. https://doi.org/10.1016/j.cell.2025.03.015

📜 License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) license – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 26: Reannotation in Focus — Uncovering Functional Non-Coding Mutations in Melanoma

🧬 In this episode of Base por Base, we delve into a breakthrough study by Pepe et al. (2025) in The American Journal of Human Genetics that challenges conventional cancer mutation annotation. The authors present an automated pipeline combining RNA-seq–based transcript quantification and Ensembl VEP reannotation to map somatic variants to the transcripts actually expressed in melanoma tumors. By integrating TCGA and COSMIC datasets, deep-learning predictions, and functional assays, this framework exposes a hidden layer of non-coding promoter mutations driving melanoma pathogenesis.

🔍 Study Highlights:
The reannotation approach revealed that many mutation clusters previously labeled as synonymous or missense events in cancer databases instead reside in promoter regions of expressed genes and adjacent loci, with 22% of 52 hotspots in melanoma belonging to this non-coding category. Functional validation using CRISPR-Cas9–edited melanocyte models and luciferase reporter assays demonstrated that IRF3/BCL2L12 promoter variants downregulate IRF3, BCL2L12, and downstream TP53 signaling, and disrupt ETS and SP/E2F transcription factor binding motifs as predicted by the DeepMEL2 model and PhysBinder/FABIAN-variant analyses. Systematic reannotation of KNSTRN and SLC27A5 clusters further confirmed non-coding promoter activity alterations, underscoring the prevalence and significance of regulatory mutations overlooked by reference-transcript annotation.

🧠 Conclusion:
By anchoring mutation annotation to expressed transcripts, the BayesMRnet reannotation pipeline (Salmon + VEP) ushers in a more precise era of cancer genomics, uncovering functional non-coding drivers in melanoma and offering a scalable tool to refine driver mutation discovery and guide future therapeutic strategies.

📖 Reference:
Pepe, D., Janssens, X., Timcheva, K., Marrón-Liñares, G. M., Verbelen, B., Konstantakos, V., … De Keersmaecker, K. (2025). Reannotation of cancer mutations based on expressed RNA transcripts reveals functional non-coding mutations in melanoma. The American Journal of Human Genetics, 112, 1–21. https://doi.org/10.1016/j.ajhg.2025.04.005

📜 License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) license – http://creativecommons.org/licenses/by/4.0/

🎙️ Episode 25: Uncovering Mitochondrial DNA Diseases — The Solve-RD Experience with Genotype and Phenotype Integration

🧬 In this episode of Base por Base, we delve into a groundbreaking study by Ratnaike et al. (2025) published in The American Journal of Human Genetics, which presents a semi-automated workflow combining mtDNA variant filtering and MitoPhen-based HPO phenotype similarity scoring applied to exome and genome data from the Solve-RD cohort of undiagnosed rare disease cases .

🔍 Study highlights:
Our workflow applied MToolBox for mtDNA reconstruction and MITOMAP annotations with stringent quality filters (≥50% mtDNA assembly and ≥5× coverage) to prioritize 136 rare variants across 9,923 individuals from 9,483 families without prior suspicion of mitochondrial disease .
Phenotype similarity scoring using the curated MitoPhen database achieved 100% sensitivity at a 0.3 threshold and distinguished confirmed mtDNA disease cases from nuclear genetic diagnoses with an AUC of 0.82 .
A total of 21 confirmed and 16 likely causative mtDNA diagnoses were made, boosting the overall diagnostic yield by 0.4% and uncovering 37 new diagnoses .
The pipeline efficiently handled off-target exome sequencing data, retaining 90% of datasets for analysis and enabling detection of pathogenic variants at heteroplasmy levels as low as 1% .
Structured, phenotype-driven curation underscored the importance of comprehensive HPO annotation and highlighted the value of iterative genotype-phenotype evaluation in improving rare disease diagnostics .

🧠 Conclusion:
This study demonstrates a scalable approach to integrate mtDNA analysis into routine exome and genome reanalysis by leveraging automated bioinformatic filtering and phenotype similarity scoring, offering a powerful tool to improve diagnostic rates for mitochondrial disorders in heterogeneous cohorts .

📖 Reference:
Ratnaike, T., Paramonov, I., Olimpio, C., et al. (2025). Mitochondrial DNA disease discovery through evaluation of genotype and phenotype data: The Solve-RD experience. The American Journal of Human Genetics, 112(1), 1–12. https://doi.org/10.1016/j.ajhg.2025.04.003

📜 License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) license – http://creativecommons.org/licenses/by/4.0/

🎙️ Episode 24: The Role of the X Chromosome in Complex Trait Genetics — Unraveling Dosage-Compensation Mechanisms
🧬 In this installment of Base por Base, we delve into groundbreaking work by Fu et al. (2025) in The American Journal of Human Genetics, which systematically interrogates how the X chromosome shapes human quantitative traits. Leveraging data from over 350,000 UK Biobank participants with replication in more than 400,000 FinnGen individuals, the study quantifies the X chromosome’s contribution to trait heritability, examines sex-specific genetic variance, and elucidates the interplay between X-inactivation and upregulation processes in balancing dosage between sexes and with the autosomes .

🔍 Key Highlights: In a comprehensive analysis of 48 traits, the authors report that the X chromosome accounts for roughly 3% of the heritability explained by autosomes, demonstrating a proportional yet distinct contribution to complex trait variation; they confirm near-complete X chromosome inactivation in females and hemizygosity in males, leading to approximately double the genetic variance on X in men versus women; compelling evidence emerges for partial escape from inactivation impacting traits such as height; moreover, the study reveals that single active copies of X-linked loci exert allele effects about 1.6-fold greater than those on autosomes, supporting a model of partial transcriptional upregulation on X relative to autosomes .

🧠 Conclusion: By integrating large-scale biobank data with advanced heritability and effect-size modeling, this work inaugurates a new era in understanding X-linked genetic architecture. It highlights how near-complete inactivation, nuanced escape, and dosage compensation via allele-level upregulation collectively maintain balanced contributions of the X chromosome to human phenotypic diversity, offering vital insights for future locus discovery and sex-specific analyses in genomics .

📖 Reference:
Fu, Y., Kenttämies, A., Ruotsalainen, S., Pirinen, M., & Tukiainen, T. (2025). Role of X chromosome and dosage-compensation mechanisms in complex trait genetics. The American Journal of Human Genetics, 112, 1–14. https://doi.org/10.1016/j.ajhg.2025.04.004

📜 License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) license – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 23: Evaluating the Return of Additional Findings from the 100,000 Genomes Project — Participant Experiences of Secondary Genomic Findings

🧬 In this episode of Base por Base, we explore a mixed-methods study by Stafford-Smith et al. (2025) published in Genetics in Medicine, which examines how participants in England’s 100,000 Genomes Project experienced the disclosure of additional (secondary) genomic findings. By combining a cross-sectional survey of 147 adults who received either cancer- or familial hypercholesterolemia-related findings with in-depth interviews of 35 positive-finding recipients and 29 individuals with no additional findings, this research sheds light on the psychological, behavioural, and communication aspects of returning actionable genetic results through NHS pathways.

🔍 Study highlights:
Participants rated the utility of their results exceptionally high (mean 8.9/10 now; 9.0/10 for future use) and most (82%) reported that knowing their finding would influence health management. Those who learned of a cancer-related variant often felt initial shock and anxiety, whereas individuals with familial hypercholesterolemia findings described relief and readiness to act. Recipients of no additional findings welcomed the reassurance but sometimes struggled to distinguish these results from their primary diagnostic findings. Overall decisional regret was low (median score 5/100), though a minority experienced mild or high regret initially. Thematic analysis revealed that clear, tailored communication and timely clinical support were critical for helping participants adjust, share results with family, and implement risk-reducing strategies.

🧠 Conclusion:
Stafford-Smith et al. demonstrate strong participant support for routinely offering actionable secondary findings alongside genome sequencing, while emphasizing the need for condition-specific pathways, improved consent-to-result timelines, and enhanced informational resources for no-finding recipients. Their work lays the groundwork for more patient-centred genomic medicine practices and underscores the importance of psychosocial support in “genome-first” care models.

📖 Reference:
Stafford-Smith B., Daniel M., Peter M., et al. (2025). Evaluating the return of additional findings from the 100,000 Genomes Project: A mixed methods study exploring participant experiences of receiving secondary findings from genomic sequencing. Genetics in Medicine. https://doi.org/10.1016/j.gim.2025.101446

📜 License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) license – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 22: Immune Sensing Unveiled — Ribonuclease Control of Naked Extracellular RNA

🧬 In this episode of Base por Base, we explore a landmark study by Castellano et al. (2025) published in Cell Genomics that uncovers how extracellular ribonucleases regulate the immune detection and functional uptake of naked extracellular RNA (exRNA). Through strategic use of a broad-spectrum ribonuclease inhibitor, the authors demonstrate that, contrary to long-held assumptions, naked exRNAs can be spontaneously internalized by dendritic cells and macrophages, engage both endosomal Toll-like receptors and cytosolic RIG-I-like receptors, and even serve as templates for protein translation, thereby revealing a novel, nonvesicular pathway of intercellular RNA communication .

🔍 Key Highlights: Naked extracellular RNA exhibits intrinsic bioactivity when extracellular RNases are inhibited or absent, triggering pro-inflammatory transcriptional programs via endosomal TLR13 in murine cells and RIG-I/MAVS-dependent pathways in human macrophages; these naked RNAs can escape endosomes to reach the cytosol, where they activate downstream antiviral and inflammatory signaling; in vitro-transcribed mRNAs delivered as naked exRNA are taken up and translated into functional reporter proteins in both primary immune cells and epithelial cell lines in an RNase-sensitive manner; and systemic administration of naked bacterial RNA or synthetic dsRNA with ribonuclease inhibition markedly amplifies immune cell activation in vivo, whereas the high RNase activity of blood normally prevents such systemic inflammation .

🧠 Conclusion: Castellano et al. reveal that extracellular RNase activity serves as a critical barrier to the bioactivity of naked exRNAs, and that in low-RNase environments naked RNA can mediate immune communication and protein expression. These insights fundamentally challenge the prevailing view that vesicular encapsulation is required for functional RNA transfer and position extracellular RNases as key modulators of intercellular RNA signaling and immune homeostasis .

📖 Reference:
Castellano, M., Blanco, V., Li Calzi, M., Costa, B., Witwer, K., Hill, M., Cayota, A., Segovia, M., & Tosar, J.P. (2025). Ribonuclease activity undermines immune sensing of naked extracellular RNA. Cell Genomics, 5, 100874. https://doi.org/10.1016/j.xgen.2025.100874

📜 License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) license – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 21: High-Throughput Variant Discovery — Pooled Prime Editing in Human Cells

🧬 In this episode of Base by Base, we explore a cutting-edge platform for scalable functional screening of human genetic variants reported by Herger et al. (2025) in Cell Genomics. The study introduces a pooled prime editing workflow in haploid HAP1 cells that optimizes pegRNA scaffold design, employs co-selection via an ATP1A1 resistance mutation, and integrates surrogate targets to enrich and filter highly active edits—enabling interrogation of both coding and non-coding variants in their native genomic context .

🔍 Study highlights:
The platform achieves improved editing efficiencies by incorporating stabilized pegRNA scaffolds, optimized prime editor expression, and co-selection for an ATP1A1 resistance mutation in HAP1 cells .
Deep sequencing of pegRNA–surrogate target cassettes enables negative selection screening in SMARCB1 exons 8–9, accurately identifying loss-of-function single-nucleotide and multinucleotide variants that impair protein function .
Positive selection using 6-thioguanine in MLH1 screens yields precise function scores for SNVs in exon 10, with AUCs reaching 1.00 under stringent surrogate editing thresholds, demonstrating robust discrimination of pathogenic variants .
A comprehensive library covering 874 non-coding ClinVar variants across 60 kb of MLH1 reveals pathogenic splice and regulatory variants at scale, with surrogate target filtering ensuring high data quality .
Validation assays confirm that surrogate target editing correlates strongly with endogenous variant installation, supporting accurate function scoring across large genomic regions .

🧠 Conclusion:
This pooled prime editing platform offers a versatile and scalable tool for functional assessment of genetic variants across both coding and non-coding regions, paving the way for accelerated discovery and classification of disease-associated alleles .

📖 Reference:
Herger, M., Kajba, C. M., Buckley, M., Cunha, A., Strom, M., & Findlay, G. M. (2025). High-throughput screening of human genetic variants by pooled prime editing. Cell Genomics, 5, 100814. https://doi.org/10.1016/j.xgen.2025.100814

📜 License:
This episode is based on an open access article published under the Creative Commons Attribution 4.0 International license (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 20: Genotype-Specific Chemoprevention with Sulfadoxine-Pyrimethamine

🧬 In this episode of Base by Base, we examine a comprehensive analysis by Mousa et al. (2025) in Nature Communications that quantifies how mutations in the Plasmodium falciparum dihydropteroate synthase (dhps) gene affect the duration of protection conferred by sulfadoxine-pyrimethamine (SP) chemoprevention across Africa. A Bayesian multi-strain model was applied to reinfection data from seven therapeutic efficacy studies involving 1,639 participants across twelve African sites, enabling simultaneous estimation of genotype-specific protective durations and mapping of SP efficacy in diverse resistance settings .

🔍 Main highlights: Protection against dhps sulfadoxine-susceptible parasites extends beyond 42 days, while protection against the West African dhps GKA genotype lasts a median of 30.3 days (95% Credible Interval: 17.1–45.1). The East African dhps GEA and highly resistant dhps GEG genotypes reduce median protection to 16.5 days (95% CrI: 11.2–37.4) and 11.7 days (95% CrI: 8.0–21.9), respectively; model validation against intermittent preventive treatment in infants (IPTi) trials from Mozambique and Tanzania demonstrated strong agreement between predicted and observed reinfection patterns. Continent-wide predictions based on genotype frequency maps revealed 30-day protective efficacy ranging from 59.3% to 91.5% and median protection durations from 17.2 to 37.2 days, guiding targeted SP deployment strategies. Comparative analyses with SP–amodiaquine (SPAQ) and SP–chloroquine (SPCQ) combinations highlight enhanced protection against resistant genotypes where amodiaquine efficacy remains high .

🧠 Conclusion: By providing robust genotype-specific estimates of SP protective efficacy and developing an interactive prediction tool for local genomic surveillance integration, this study equips malaria control programs with actionable insights to tailor chemoprevention strategies and optimize SP-based interventions across varying transmission and resistance landscapes .

📖 Reference:
Mousa, A., Cuomo-Dannenburg, G., Thompson, H. A., et al. (2025). Impact of dhps mutations on sulfadoxine-pyrimethamine protective efficacy and implications for malaria chemoprevention. Nature Communications, 16, 4268. https://doi.org/10.1038/s41467-025-58326-z

📜 License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International license (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 19: Systematic Identification of Promoter and UTR Variants in Rare Disease Diagnostics

🧬 In this episode of Base by Base, we delve into Martin-Geary et al.’s (2025) innovative framework for uncovering disease-causing variants within promoters and untranslated regions (UTRs) in individuals with rare disorders. Leveraging genome sequencing data from 8,040 undiagnosed trios in the Genomics England 100,000 Genomes Project, the authors combine precise region definitions based on MANE transcripts and ENCODE candidate cis-regulatory elements with stringent filtering and annotation tools—including VEP with UTRannotator, SpliceAI, CADD, PhyloP, and FABIAN—to prioritize de novo non-coding variants with high likelihood of pathogenicity .

🔍 Key Highlights:
The study defines over 20 million bases of proximal promoter and UTR sequence across 1,567 dominant disease genes and excludes coding regions to focus on regulatory elements; it then filters de novo variants by allele frequency and region overlap, yielding 1,311 candidates prior to annotation . Utilizing annotation thresholds calibrated for non-coding contexts, the pipeline prioritizes eleven de novo variants, nine of which match patients’ phenotypes and include both previously confirmed diagnoses (e.g., PAX6, MEF2C) and novel findings (e.g., SLC2A1, NIPBL, ZBTB18, SETD5, GNAS). Clinical review and functional follow-up, such as RNA-seq and DNA methylation episignatures, validate the diagnostic potential of these variants. Applying the same filters to ClinVar confirms high specificity—prioritizing 53.7% of known pathogenic variants while excluding 99.3% of benign ones—though sensitivity for promoter variants remains an area for improvement. Finally, a burden test across 7,862 probands matched to controls shows no significant enrichment of prioritized promoter or UTR variants, underscoring challenges in detecting aggregate non-coding variant effects at current cohort sizes.

🧠 Conclusion:
Martin-Geary et al.’s framework demonstrates that routine interrogation of promoters and UTRs can yield actionable genetic diagnoses—albeit at modest incremental yield—and provides a reproducible, highly specific pipeline that can be integrated into clinical diagnostic workflows. As our understanding of regulatory genomics deepens and annotation tools improve, such approaches will become increasingly powerful for uncovering hidden causes of rare disease.

📖 Reference:
Martin-Geary, A. C., Blakes, A. J. M., Dawes, R., et al. (2025). Systematic identification of disease-causing promoter and untranslated region variants in 8040 undiagnosed individuals with rare disease. Genome Medicine, 17, 40. https://doi.org/10.1186/s13073-025-01464-2.

📜 License:
This episode is based on an open access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 18: Network Causality — A New Bayesian Model for Multivariable Mendelian Randomization

🧬 In this episode of Base by Base, we examine the methodological breakthrough presented by Liu et al. (2025) in Nature Communications. The authors introduce BayesMRnet, a Bayesian causal graphical model designed to perform joint Mendelian randomization (MR) across multiple exposures and outcomes. By leveraging genome-wide association study (GWAS) data, BayesMRnet constructs directed acyclic graphs (DAGs) that capture both direct and mediated causal effects among phenotypic traits, even in the presence of horizontal pleiotropy.

🔍 Key highlights: BayesMRnet departs from traditional pairwise MR by modeling causal relationships among multiple phenotypes simultaneously, using genetic variants as instrumental variables; it employs a DAG framework combined with Bayesian inference to disentangle direct and indirect effects, accommodating pleiotropic and mediated pathways; extensive simulations demonstrate that BayesMRnet achieves higher sensitivity and lower false-positive rates compared with established methods such as MR-Egger and multivariable MR; applied to real-world data on 66 metabolic and anthropometric traits, the model reconstructed biologically plausible causal networks, revealing novel pathways influencing cardiometabolic risk; and its Bayesian foundation allows quantification of uncertainty on each network edge, offering more robust interpretation in complex clinical and epidemiological settings.

🧠 Conclusion: BayesMRnet ushers in a new era for Mendelian randomization by enabling multivariate modeling of exposures and outcomes at scale. By integrating structural dependencies and uncertainty estimates, this framework provides a powerful tool for uncovering causal relationships in human genomics and guiding more effective prevention strategies.

📖 Reference: Liu, Y., Xiang, Z., Han, Z., et al. (2025). Bayesian causal graphical model for joint Mendelian randomization analysis of multiple exposures and outcomes. Nature Communications, 16, 3142. https://doi.org/10.1038/s41467-024-46789-7

📜 License: This episode is based on an open access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0).

🎙️ Episode 17: The Structure of Human Sweetness — Cryo-EM of the TAS1R2+TAS1R3 Sweet Taste Receptor
🧬 In this episode of Base por Base, we explore a landmark cryo-electron microscopy study by Juen et al. (2025) published in Cell, which reveals the high-resolution structure of the human sweet taste receptor heterodimer TAS1R2+TAS1R3 bound to the artificial sweeteners sucralose and aspartame, providing the first detailed view of how a single receptor recognizes a diverse array of sweet compounds.
🔍 Highlights of the study: The TAS1R2 subunit binds sweet ligands while TAS1R3 remains in an open conformation; a common binding pocket accommodates both sucralose and aspartame via key conserved residues; site-directed mutagenesis confirms the functional importance of these residues for receptor activation; 3D variability analysis uncovers coordinated conformational changes between subunits; and structural analysis of the transmembrane and cysteine-rich domains illuminates the mechanism of G protein coupling exclusively through TAS1R2.
🧠 Conclusion: This work establishes a structural framework for designing novel taste modulators and deepens our understanding of sweet taste physiology, paving the way for targeted strategies in nutrition, health, and flavor engineering.
📖 Reference: Juen, Z., Lu, Z., Yu, R., Chang, A. N., Wang, B., Fitzpatrick, A. W. P., & Zuker, C. S. (2025). The structure of human sweetness. Cell, 188, 1–13. https://doi.org/10.1016/j.cell.2025.04.021
📜 License: This episode is based on an open access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) license – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 16: Equity in Focus: Building a Truly Global Genomic Landscape

🧬 In this episode of Base by Base, we address one of the most pressing issues in human genomics: the need to close the ancestral data gap. Published in Cell Genomics, this commentary by Ana Luiza Arruda, Andrew Morris, and Eleftheria Zeggini calls attention to how genomic medicine remains disproportionately centered on individuals of European ancestry—jeopardizing its promise of precision health for all.

The authors highlight why expanding tissue-specific, multi-ancestry molecular datasets is critical for moving genomics forward—from discovery to clinical translation—while promoting equity and inclusion in healthcare innovation.

🔍 Key insights include:

• Systemic underrepresentation: Despite global diversity, most GWAS and molecular QTL data derive from European populations—leaving African, Indigenous, South Asian, and Latin American ancestries critically underrepresented.

• Biological impact: Genetic variants specific to diverse populations often remain undiscovered or uninterpretable due to lack of relevant tissue-specific molecular data, such as gene expression, proteomics, and epigenomics.

• Tissue specificity matters: Most available molecular data come from blood samples, but disease-relevant regulation happens in diverse tissues. Without this diversity, causal variants may be missed or misinterpreted.

• Examples of progress: Initiatives like GTEx, TOPMed, and the Human Cell Atlas provide initial steps toward inclusive molecular catalogs—but sample sizes and tissue variety for non-European ancestries remain small and underpowered.

• Call to action: The authors propose increased funding, infrastructure, community engagement, and global collaboration to fill these gaps. Analytical methods must evolve to handle ancestry-aware integration of complex omics data.

This episode is a wake-up call: advancing equity in human genomics isn’t optional—it’s essential. Only by embedding diversity across every layer of genomic research can we realize the full potential of personalized medicine for all populations.

📖 Reference:
Arruda, A.L., Morris, A.P., & Zeggini, E. (2024). Advancing equity in human genomics through tissue-specific multi-ancestry molecular data. Cell Genomics, 4(2), 100485. https://doi.org/10.1016/j.xgen.2023.100485

📜 License:
This episode is based on an open access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 15: What Makes Us Human? Genetics from Neandertals to Now

🧬 In this episode of Base by Base, we travel back in time—over 600,000 years—to explore the genomic storylines of Neandertals, Denisovans, and modern humans. Published in Cell by Hugo Zeberg, Mattias Jakobsson, and Nobel Laureate Svante Pääbo, this comprehensive review deciphers the evolutionary divergences that defined—and continue to define—our species.

By comparing high-quality genomes from extinct and extant human lineages, the authors provide a sweeping analysis of the genetic variants that shaped brain function, metabolism, immunity, reproduction, and adaptation to diverse environments.

🔍 Key insights include:

• Archaic legacy: 2% of the genome in non-African individuals today comes from Neandertals; in Oceania, over 5% derives from Denisovans.

• Disease and adaptation: Some Neandertal variants increase risk for conditions like severe COVID-19 and autoimmune disease—yet others provide resistance to infections like Helicobacter pylori and HIV.

• Denisovan traces: Modern Tibetan populations inherited a Denisovan variant in EPAS1, aiding adaptation to high altitudes.

• Brain development: Modern human-specific changes in genes like TKTL1, KNL1, and KIF18A influence early neurogenesis and chromosomal segregation—potential contributors to our cognitive evolution.

• The combinatorial human: Rather than a single “modern” genetic signature, humans today carry a mosaic of derived and ancestral alleles—defining our species by combinations of variants, not absolutes.

• Experimental revival: Using CRISPR, organoids, and mouse models, researchers are now resurrecting archaic variants to study their effects in human cells and model organisms.

• Rewriting assumptions: Several variants thought to be exclusive to modern humans are found in ancestral form in present-day populations—especially in Africa and the Philippines.

This landmark review redefines human uniqueness through a genomic lens, not as a checklist of fixed traits, but as a dynamic ensemble of evolutionary possibilities. It’s a must-listen for anyone intrigued by how ancient DNA continues to shape our biology, health, and identity.

📖 Reference:
Zeberg, H., Jakobsson, M., & Pääbo, S. (2024). The genetic changes that shaped Neandertals, Denisovans, and modern humans. Cell, 187. https://doi.org/10.1016/j.cell.2023.12.029

📜 License:
This episode is based on an open access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 14: Beyond the Genome: Societal Value of National Genomics Programmes

🧬 In this episode of Base by Base, we discuss a thought-provoking report published in the European Journal of Human Genetics that tackles a crucial yet underexplored question: what is the actual value of large-scale national genomic programmes for society?

Led by Ruth Horn, Angeliki Kerasidou, Jennifer Merchant and the UK-FR+GENE consortium, this multidisciplinary workshop brought together ethicists, geneticists, economists, clinicians, and policymakers from across Europe. Their goal was to define how these programmes contribute to public good—scientifically, economically, and socially.

🔍 Key insights include:

• Trust and Transparency: Public trust is essential but fragile. While rigorous data governance can help, ongoing concerns about data privacy and public-private partnerships must be addressed transparently.

• Economic Gaps: Despite major investments, there is still a lack of robust evaluations on the cost-effectiveness of large sequencing programmes. Without economic frameworks, the opportunity costs for public health remain unquantified.

• Clinical Impacts: While many patients benefit from genomic diagnosis—especially in rare diseases—others experience uncertainty or frustration when no actionable outcome is available. Professionals often navigate this with cautious optimism.

• Scientific Caution: While technologies like polygenic risk scores and whole-genome sequencing promise precision, their predictive power is still limited in many common diseases. Interpretation challenges persist in the clinic.

• Population-Level Dilemmas: Genomic medicine has the potential to inform public health strategies, but equitable access and demonstrable outcomes are still lacking. Minority and underserved groups risk being left behind.

• Call to Action: The authors advocate for clearer criteria when rolling out large-scale genomic initiatives—avoiding overpromising, prioritizing equity, integrating cost assessments, and respecting the nuanced experiences of patients and families.

This episode explores how genomics must not only advance science, but also demonstrate meaningful, measurable benefits to society at large—especially in solidarity-based healthcare systems. Without this balance, the promise of genomic medicine risks being overshadowed by overreach.

📖 Reference:
Horn, R., Kerasidou, A., Merchant, J., et al. (2025). The value of large-scale programmes in human genomics. European Journal of Human Genetics. https://doi.org/10.1038/s41431-025-01844-7

📜 License:
This episode is based on an open access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 13: Decoding De Novo: A Multigenerational Benchmark for Human Mutation Rates

🧬 In this episode of Base by Base, we explore a monumental study published in Nature that redefines how we understand human de novo mutation (DNM) rates. By sequencing 28 individuals across four generations from the CEPH 1463 family with five complementary technologies, this study delivers the most complete pedigree reference to date.

Led by Porubsky and colleagues, the research team used a mix of short- and long-read sequencing to phase and assemble more than 95% of each diploid human genome, enabling unprecedented insight into de novo mutations—spanning single-nucleotide variants (SNVs), indels, tandem repeats, structural variants, and centromeric changes.

🔍 Key insights include:

• 98–206 DNMs per transmission were observed, with a strong paternal bias (75–81%), particularly for SNVs and structural events.

• 16% of SNVs are postzygotic, with no paternal bias, and can still be transmitted, highlighting early embryonic mosaicism.

• Tandem repeats (TRs) were highly mutable, with an average of 65.3 de novo TR events per genome, accounting for more mutated base pairs than SNVs.

• Large centromeric SVs were uncovered in ~7% of assembled centromeres, with some events causing functional shifts in the kinetochore-associated hypomethylation zone (CDR).

• Y chromosome mutations were enriched in heterochromatic satellite DNA, with a de novo mutation rate up to 30x higher than autosomal euchromatin, often driven by interlocus gene conversion.

• Sequence-resolved recombination maps enabled the identification of 1,503 meiotic breakpoints, showing recombination patterns influenced by sex and parental age.

• Nearly all variation types were cross-validated using multiple sequencing platforms, positioning this dataset as a gold standard for benchmarking new mutation discovery tools.

This study is a landmark in human genomics, offering a comprehensive “truth set” for future mutation rate models, algorithm development, and clinical benchmarking—bringing us closer to decoding the full complexity of inherited and spontaneous variation in the human genome.

📖 Reference:
Porubsky, D., Dashnow, H., Sasani, T.A., et al. (2025). Human de novo mutation rates from a four-generation pedigree reference. Nature. https://doi.org/10.1038/s41586-025-08922-2

📜 License:
This episode is based on an open access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 12: Repairing the Blueprint: Insights from MUTYH Structure and Cancer-Associated Variants

🧬 In this episode of Base by Base, we explore a pivotal study published in Nature Communications that reveals the structural and functional secrets of the human MUTYH DNA glycosylase. This landmark work provides the first crystal structure of human MUTYH bound to DNA, illuminating how its [4Fe-4S] cluster cofactor allosterically connects to the catalytic site — a critical feature for maintaining genome integrity.

Led by Trasviña-Arenas and colleagues, the study deciphers how cancer-associated variants (CAVs) disrupt the intricate hydrogen bond network bridging the [4Fe-4S] cluster and the DNA excision active site. The findings show that even subtle changes can decouple mitochondrial metal cofactors from enzymatic function, revealing an allosteric network essential for oxidative DNA damage repair and cancer prevention.

🔍 Key insights include:

• First Human MUTYH-DNA Complex Structure: The structure reveals an H-bond network connecting the [4Fe-4S] cluster to the catalytic residue Asp236, essential for efficient base excision repair.

• Functional Impact of Cancer-Associated Variants (CAVs): Variants like R241Q and N238S retain the metal cofactor and DNA binding ability but abolish glycosylase activity by disrupting the allosteric communication pathway.

• Allosteric Regulation: The study demonstrates how the [4Fe-4S] cluster not only binds DNA but actively regulates enzymatic catalysis through structural cross-talk with the active site.

• Molecular Dynamics Simulations: Computational analyses confirm that mutations alter the dynamic network between the cluster and catalytic site, changing the protein's flexibility and communication pathways.

• Clinical Implications: Highlights how mutations disrupting this allosteric network contribute to MUTYH-associated polyposis (MAP) and elevate cancer risk, offering new targets for functional variant classification and therapeutic strategies.

This episode highlights how deep structural and functional analysis of MUTYH is reshaping our understanding of DNA repair mechanisms, cancer risk, and the delicate orchestration of genome maintenance.

📖 Reference:
Trasviña-Arenas, C.H., Dissanayake, U.C., Tamayo, N., et al. (2025). Structure of human MUTYH and functional profiling of cancer-associated variants reveal an allosteric network between its [4Fe-4S] cluster cofactor and active site required for DNA repair. Nature Communications, 16, 3596. https://doi.org/10.1038/s41467-025-58361-w

📜 License: This content is distributed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). For more information, visit https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 11: Targeting Mitochondria: A Therapeutic Strategy for Dnmt3a-Mutant Clonal Hematopoiesis

🧬 In this episode of Base by Base, we dive into a compelling study published in Nature Communications that reveals a novel therapeutic vulnerability in clonal hematopoiesis driven by DNMT3A mutations. The research identifies elevated mitochondrial membrane potential (Δψm) as a selective weakness in mutant hematopoietic stem and progenitor cells (HSPCs), paving the way for targeted interventions.

Led by Young and colleagues, the study demonstrates that Dnmt3a-mutant HSPCs exhibit enhanced oxidative phosphorylation, mitochondrial hyperactivity, and increased Δψm, providing them a competitive advantage during aging. Exploiting this vulnerability, the researchers show that long-chain alkyl-TPP molecules like MitoQ can selectively disrupt mitochondrial function and ablate the mutant cells' fitness advantage.

🔍 Key insights include:

• Metabolic Reprogramming: Dnmt3a-mutant HSPCs display hypomethylation and upregulation of oxidative phosphorylation genes, leading to elevated mitochondrial respiration and Δψm.

• Therapeutic Targeting with MitoQ: MitoQ selectively accumulates in mitochondria of mutant HSPCs, impairing their respiration, inducing mitochondrial-driven apoptosis, and eliminating their competitive advantage both ex vivo and in vivo.

• Conserved Mechanism: The mitochondrial vulnerability and response to MitoQ are conserved in human DNMT3A-knockdown HSPCs, enhancing the translational potential of this strategy.

• Selective Action: Wild-type HSPCs are spared, with MitoQ even promoting healthy mitochondrial function in normal cells, underscoring its therapeutic promise with minimal toxicity.

• Clinical Relevance: These findings open the possibility of using mitochondrially targeted molecules to prevent the expansion of pre-malignant clones, reducing the risk of cardiovascular disease, leukemia, and other age-related conditions.

This episode underscores how precision targeting of mitochondrial metabolism can transform therapeutic approaches for age-associated clonal hematopoiesis and beyond.

📖 Reference:
Young, K.A., Hosseini, M., Mistry, J.J., et al. (2025). Elevated mitochondrial membrane potential is a therapeutic vulnerability in Dnmt3a-mutant clonal hematopoiesis. Nature Communications, 16, 3306. https://doi.org/10.1038/s41467-025-57238-2

📜 License: This content is distributed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). For more information, visit https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 10: Targeting the Genome: Guidelines for Antisense Oligonucleotide Therapy Eligibility

🧬 In this episode of Base by Base, we explore a transformative study published in The American Journal of Human Genetics that introduces the N1C VARIANT guidelines — a consensus framework for evaluating the eligibility of pathogenic DNA variants for antisense oligonucleotide (ASO) therapies. This pioneering effort addresses a critical gap for rare genetic diseases, where individualized treatments are urgently needed.

Led by Cheerie and colleagues from the N=1 Collaborative, the study outlines a systematic approach to classify variants for ASO strategies such as splice correction, exon skipping, transcript knockdown, and upregulation of wild-type alleles, providing practical tools like eligibility calculators and training materials.

🔍 Key insights include:

• Development of the N1C VARIANT Guidelines: A structured framework to assess DNA variants for ASO-based therapeutic strategies, with classifications like eligible, likely eligible, unlikely eligible, not eligible, and unable to assess.

• Innovative Tools: Creation of an interactive eligibility calculator and educational videos to streamline variant assessment and training.

• Multiple ASO Strategies Covered: Guidelines cover not only traditional splice correction and exon skipping but also emerging methods like transcript knockdown and upregulation of the wild-type allele.

• Community-Centered Approach: Built through collaboration among international experts and piloted by geneticists, researchers, and clinicians across diverse healthcare settings.

• Path to Clinical Integration: Highlights the potential to integrate variant assessments into routine clinical practice, offering rare disease patients a new avenue toward personalized treatment options.

This episode highlights how collaborative, structured frameworks are accelerating the translation of genomic diagnostics into actionable, individualized therapies for rare diseases.

📖 Reference:Cheerie, D., Meserve, M.M., Beijer, D., et al. (2025). Consensus guidelines for assessing eligibility of pathogenic DNA variants for antisense oligonucleotide treatments. The American Journal of Human Genetics, 112(5), 1–9. https://doi.org/10.1016/j.ajhg.2025.02.017

📜 License: This content is distributed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). For more information, visit https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 9: Unraveling Complexity: A Bayesian Graphical Model for Joint Mendelian Randomization

🧬 In this episode of Base by Base, we explore a groundbreaking study published in The American Journal of Human Genetics that introduces MrDAG, a Bayesian causal graphical model designed to jointly analyze multiple exposures and outcomes in Mendelian randomization (MR) studies. This innovative approach overcomes the limitations of traditional MR methods, offering a deeper understanding of complex causal networks.

Led by Zuber and colleagues, the study presents MrDAG, a framework that integrates genetic instrumental variables, structure learning, and interventional calculus to model dependencies between exposures and outcomes, even in the presence of unobserved confounders. MrDAG enables the identification of intricate causal pathways critical for understanding multifactorial traits such as mental health conditions.

🔍 Key insights include:

• Introduction of MrDAG: A novel Bayesian model that detects dependency structures and improves causal effect estimation in MR analyses using summary-level data.

• Handling Complex Relationships: MrDAG simultaneously models multiple exposures and outcomes, capturing both direct and mediated effects with greater precision.

• Superior Performance: In simulation studies, MrDAG outperformed existing methods (such as MR-BMA, MR2, and MRPC) in detecting true causal relationships and minimizing bias.

• Application to Mental Health: Using real-world data, MrDAG highlighted education and smoking as key modifiable risk factors influencing mental health phenotypes and revealed novel paths, such as the connection between smoking and genetic liability to schizophrenia.

• Robustness: MrDAG remains effective even with noisy genetic associations and misclassified exposure-outcome groupings.

This episode underscores how advanced causal modeling reshapes our understanding of complex biological relationships, offering powerful new tools for epidemiology, genetic research, and precision medicine.

📖 Reference:Zuber, V., Cronje, T., Cai, N., Gill, D., & Bottolo, L. (2025). Bayesian causal graphical model for joint Mendelian randomization analysis of multiple exposures and outcomes. The American Journal of Human Genetics, 112(5), 1–26. https://doi.org/10.1016/j.ajhg.2025.03.005

📜 License: This content is distributed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). For more information, visit https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 8: Mapping Structural Variation: A Global Reference for Clinical and Population Genomics

🧬 In this episode of Base by Base, we explore a landmark study published in Nature that presents the first high-resolution, sequence-resolved map of structural variants (SVs) across human populations. Built from 14,891 genomes analyzed through the Genome Aggregation Database (gnomAD), this study delivers a transformative resource for medical genetics, population studies, and clinical diagnostics.

Led by Collins and colleagues, the project characterizes the landscape, frequency, and functional impact of over 430,000 structural variants, spanning deletions, duplications, inversions, insertions, and complex rearrangements across diverse ancestries.

🔍 Key insights include:

• 433,371 structural variants identified, with 54% of the samples being non-European, creating an unprecedented diversity reference.

• SVs account for 25–29% of rare protein-truncating events in the human genome, underscoring their major role in genetic variation and disease.

• Strong natural selection signatures observed against damaging SVs, paralleling known patterns from single nucleotide variants (SNVs).

• Noncoding SVs in regulatory elements exhibit modest selection, revealing new insights into genome function beyond protein-coding genes.

• Rare, large SVs (>1 Mb) detected in ~3.9% of individuals, with 0.13% carrying clinically reportable findings according to ACMG criteria.

• Public access via gnomAD-SV, enabling widespread application for variant filtering, disease-association studies, and clinical screening.

This episode highlights how comprehensive SV mapping reshapes our understanding of human genetics, opening new opportunities for precision medicine and evolutionary biology.

📖 Reference:
Collins, R.L., Brand, H., Karczewski, K.J., et al. (2020). A structural variation reference for medical and population genetics. Nature, 581, 444–451. https://doi.org/10.1038/s41586-020-2287-8

📜 License: This content is distributed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). For more information, visit https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 7: Filtering with Precision: How High-Resolution Variant Frequencies Enhance Clinical Genome Interpretation

🧬 In this episode of Base by Base, we explore a landmark study published in Genetics in Medicine that presents a statistical framework for leveraging large-scale population databases to improve the interpretation of rare genetic variants in clinical genomics.

Led by Whiffin and colleagues, the 2017 study proposes a method to set disease-specific allele frequency thresholds based on prevalence, penetrance, and genetic architecture—moving beyond arbitrary cutoffs and offering a robust tool for variant filtering in Mendelian disease diagnosis.

🔍 Key insights include:

• Statistical framework defines the maximum credible allele frequency for pathogenic variants based on disease parameters, accounting for sampling variance.

• Application to ExAC: Precomputed "filtering allele frequencies" for millions of variants using the Exome Aggregation Consortium (ExAC) dataset, enabling clinicians to filter out variants that are "too common" to cause a specific disease.

• Validation in hypertrophic cardiomyopathy (HCM): The approach correctly retains nearly all known pathogenic variants while removing about two-thirds of candidate variants.

• Extension to recessive diseases and rare disorders, with flexible adaptation to different inheritance patterns.

• Public tools and resources: Online calculators and downloadable datasets to facilitate the adoption of this filtering framework in research and diagnostics.

This episode highlights how a more rigorous, disease-informed approach to variant frequency analysis can dramatically improve the specificity of clinical genome interpretation—enhancing our ability to distinguish pathogenic mutations from benign variation.

📖 Reference:
Whiffin, N., Minikel, E., Walsh, R., et al. (2017). Using high-resolution variant frequencies to empower clinical genome interpretation. Genetics in Medicine, 19(10), 1151–1158. https://doi.org/10.1038/gim.2017.26

📜 License: This content is distributed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). For more information, visit https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 6: Cracking the Code: How TRMT1 Mutations Disrupt tRNA and Drive Neurodevelopmental Disorders

🧠 In this episode of Base by Base, we dive into a 2025 study published in The American Journal of Human Genetics that sheds light on how pathogenic variants in the TRMT1 gene disrupt tRNA modification, leading to a newly characterized neurodevelopmental disorder.

Led by Efthymiou and colleagues, the study describes 43 individuals from 31 families carrying biallelic TRMT1 variants. Through human cell models, patient-derived cells, and zebrafish experiments, the authors uncover how defective TRMT1-mediated tRNA methylation can impair brain development and function.

🔍 Key insights include:

• Discovery of 24 ultra-rare TRMT1 variants (missense, frameshift, and splicing) all clustered in functional domains critical for tRNA modification.

• Aberrant splicing and loss of TRMT1 protein were observed in several variants, confirmed via minigene assays and immunoblotting.

• Deficient tRNA modifications in patient-derived cells link directly to impaired global protein synthesis.

• Zebrafish models with trmt1 knockout recapitulate key features such as developmental delay, behavioral abnormalities, and brain structural defects.

• Transcriptomic analyses revealed dysregulation of genes involved in cell cycle control, immune response, and neurodegeneration pathways.

This episode highlights how disruption of a fundamental RNA modification pathway—previously underappreciated—can drive human cognitive disorders, opening new avenues for diagnosis and potentially for future therapeutic strategies.

📖 Reference:
Efthymiou, S., Leo, C.P., Deng, C., et al. (2025). Biallelic pathogenic variants in TRMT1 disrupt tRNA modification and induce a neurodevelopmental disorder. The American Journal of Human Genetics, 112(5), 1–22. https://doi.org/10.1016/j.ajhg.2025.03.015

📜 License: This content is distributed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). For more information, visit https://creativecommons.org/licenses/by/4.0/

🎙️ Episode 5: Decoding Preterm Birth: How cfDNA Promoter Profiles Can Predict Pregnancy Risk

🩸 In this episode of Base by Base, we dive into a large-scale 2025 study published in PLOS Medicine that explores how genome-wide nucleosome footprints of plasma cell-free DNA (cfDNA) can be leveraged to predict spontaneous preterm birth (sPTB). This innovative work introduces PTerm, a promoter-profiling-based classifier built from cfDNA data routinely collected during non-invasive prenatal testing (NIPT).

Led by Guo and colleagues, the case-control study analyzed cfDNA from over 2,500 pregnant women, using whole-genome sequencing and machine learning to uncover a predictive signature of preterm birth risk—months before clinical symptoms arise.

🔍 Key insights include:

• Promoter coverage at transcriptional start sites (pTSS) in cfDNA reflects gene expression from placental and hematopoietic tissues.

• 277 genes showed differential nucleosome footprints between preterm and full-term pregnancies, linked to apoptosis, oxytocin signaling, and immune pathways.

• The PTerm classifier, based on a support vector machine model and 83 genes, achieved an AUC of 0.849 across validation cohorts.

• PTerm retained performance across spontaneous labor subtypes and gestational ages—even in external cohorts—without requiring changes to existing NIPT workflows.

• Many of the top hub genes (e.g., NFKBIA, ATF3, ERBB2) are tied to known preterm birth mechanisms like inflammation and placental dysfunction.

This episode highlights how nucleosome positioning in cfDNA can serve as a powerful non-invasive biomarker for identifying pregnancies at risk of preterm birth—offering new tools for early intervention and maternal-fetal health.

📖 Reference:
Guo Z., Wang K., Huang X., et al. (2025). Genome-wide nucleosome footprints of plasma cfDNA predict preterm birth: A case-control study. PLOS Medicine, 22(4):e1004571. https://doi.org/10.1371/journal.pmed.1004571

📜 License: This content is distributed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). For more information, visit https://creativecommons.org/licenses/by/4.0/