️ Episode 210: Tumour-Reactive CD8 T Cell Clusters in Human Melanoma In this episode of PaperCast Base by Base, we explore how tumour-reactive CD8 T cells organize into stable clusters with melanoma cells and antigen-presenting cells, and how these structures can be isolated from patient samples to boost anti-tumour immunity. Study Highlights:The authors used conventional and imaging flow cytometry to identify heterotypic clusters in which CD8 T cells were physically conjugated to tumour cells and antigen-presenting cells across 21 human melanoma metastases. Single-cell RNA and TCR sequencing showed that clustered CD8 T cells were more clonally expanded and displayed gene expression signatures of tumour reactivity, activation and exhaustion, whereas single CD8 T cells were enriched for naive and bystander-like states. Specific melanoma and myeloid subpopulations with strong antigen-presentation, interferon signalling and chemokine expression were preferentially engaged in these clusters, highlighting non-random, ligand–receptor-driven interactions in the tumour microenvironment. When expanded ex vivo, T cells derived from clusters produced more cytokines and showed markedly higher cytotoxicity against autologous melanoma cells than T cells from singlets. In mouse models bearing patient-derived melanomas, adoptive transfer of cluster-derived T cells led to stronger T cell infiltration, activation and tumour control than transfer of T cells expanded from single-cell gates. Conclusion:Heterotypic CD8 T cell clusters represent a powerful and previously overlooked source of tumour-reactive T cells and TCRs that could be harnessed to refine and enhance adoptive T cell therapies, including TIL-based treatment strategies. Music:Enjoy the music based on this article at the end of the episode. Reference:Ibáñez-Molero S, Veldman J, Nieto JS, Traets JJH, George A, Hoefakker K, Karomi A, Harkes R, van den Broek B, Pack SM, Tas L, Visser NL, van Hal-van Veen SE, Alóndiga-Mérida P, Alkemade M, Seignette IM, Tissier R, Nieuwland M, van Baalen M, Poźniak J, Mul E, Tol S, Stenqvist S, Nilsson LM, Nilsson JA, Haanen JBAG, van Houdt WJ, Peeper DS. Tumour-reactive heterotypic CD8 T cell clusters from clinical samples. Nature. 2025. https://doi.org/10.1038/s41586-025-09754-w 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/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com Castos player https://basebybase.castos.com

️ Episode 209: PERT: Prime Editing tRNAs for Nonsense Mutations In this episode of PaperCast Base by Base, we explore how prime editing can reprogram endogenous tRNAs into potent suppressor tRNAs, enabling a single therapeutic strategy to rescue many different genetic diseases caused by premature stop codons. Study Highlights:The authors introduce PERT, a prime editing-mediated strategy that permanently converts selected endogenous tRNAs into optimized suppressor tRNAs capable of reading through premature termination codons. Through large-scale screening of thousands of engineered tRNA variants and careful tuning of promoter, leader, terminator and tRNA sequence elements, they identify sup-tRNAs that efficiently restore protein production even when expressed from a single genomic copy. In human cell models of Batten disease, Tay–Sachs disease, Niemann–Pick type C1 and cystic fibrosis, installation of a single optimized sup-tRNA restores substantial fractions of enzyme activity or full-length protein across many different nonsense mutations. In mouse models, including a Hurler syndrome model carrying a pathogenic stop codon, in vivo delivery of a prime editor that converts a native tRNA into a suppressor tRNA leads to durable enzyme restoration and broad correction of disease pathology, while transcriptome, proteome and off-target analyses show minimal detectable disruption of normal stop codons or global gene expression. Conclusion:This work positions PERT as a promising, disease-agnostic genome-editing platform in which a single, well-characterized prime editing agent could eventually treat diverse genetic disorders caused by nonsense mutations. Music:Enjoy the music based on this article at the end of the episode. Reference:Pierce SE, Erwood S, Oye K, An M, Krasnow N, Zhang E, Raguram A, Seelig D, Osborn MJ, Liu DR. Prime editing-installed suppressor tRNAs for disease-agnostic genome editing. Nature. 2025. https://doi.org/10.1038/s41586-025-09732-2 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/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com Castos player https://basebybase.castos.com Episode Slug: pert-prime-editing-suppressor-trnas On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Keywords: prime editing, suppressor tRNA, nonsense mutations, therapeutic genome editing, disease-agnostic strategy

️ Episode 208: ZAK, Collided Ribosomes, and the Stress Switch In this episode of PaperCast Base by Base, we explore how collided ribosomes activate the MAP3K ZAK to drive the ribotoxic stress response and shape cell fate decisions under translational stress. Study Highlights:Using biochemistry, cryo-electron microscopy and crosslinking-based RNA mapping, the authors define how ZAK is constitutively recruited to ribosomes and how this engagement changes upon stress-induced ribosome collisions. They show that ZAK contacts the 40S subunit through a C-terminal eS27 pin and rRNA patches and anchors to RACK1 via a RACK1-interacting helix, while a collision-sensitive FPxL-containing RACK1-interacting motif becomes engaged only when two ribosomes collide. Disome formation brings two RACK1 molecules into proximity, allowing ZAK SAM domains to dimerize across the collision interface and enabling kinase activation, with pathogenic and engineered SAM variants revealing how this interface tunes activity on and off the ribosome. The study also identifies the ribosome-binding protein SERBP1 as a negative regulator that competes with ZAK for the FPxL-binding site on RACK1, thereby preventing inappropriate activation during basal translation. Conclusion:This work provides a structural and mechanistic blueprint for how ribosome collisions are translated into ZAK kinase activation, offering new entry points to modulate stress signalling in disease contexts. Music:Enjoy the music based on this article at the end of the episode. Reference:Huso VL, Niu S, Catipovic MA, Saba JA, Denk T, Park E, Cheng J, Berninghausen O, Becker T, Green R, Beckmann R. ZAK activation at the collided ribosome. Nature. 2025. https://doi.org/10.1038/s41586-025-09772-8 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/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com Castos player https://basebybase.castos.com Episode Slug: zak-collided-ribosome-stress-switch On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 207: Semantic Design of de novo Genes with Evo In this episode of PaperCast Base by Base, we explore how a genomic language model called Evo can use genomic context to design entirely new DNA sequences that encode functional genes and multi-component defence systems. Study Highlights:Researchers trained the Evo genomic language model on long prokaryotic and phage DNA sequences and used genomic neighbourhoods as prompts to autocomplete new genes whose functions mirror those of their neighbours. They experimentally validated Evo-designed toxin–antitoxin systems and type III toxin–antitoxin modules, discovering novel protein toxins, protein antitoxins and RNA antitoxins that strongly modulate bacterial survival despite low or absent sequence similarity to natural proteins. Using prompts from anti-CRISPR operons, they generated diverse anti-CRISPR proteins that block SpCas9 activity and protect cells from phage infection, including candidates that cannot be confidently assigned to any known protein family. Finally, they scaled this semantic design strategy to build SynGenome, a public resource of more than 120 billion base pairs of Evo-generated DNA organised by gene ontology and domain annotations to enable function-guided exploration across many biological pathways. Conclusion:This work shows that genomic language models can move beyond imitating nature, using semantic relationships in genomes to design de novo functional genes and systems that expand the sequence space available for protein engineering and synthetic biology. Music:Enjoy the music based on this article at the end of the episode. Reference:Merchant AT, King SH, Nguyen E, Hie BL. Semantic design of functional de novo genes from a genomic language model. Nature. 2025. https://doi.org/10.1038/s41586-025-09749-7 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/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com Castos player https://basebybase.castos.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 206: Wild Birds and the North American H5N1 Epizootic In this episode of PaperCast Base by Base, we explore how wild migratory birds have shaped the ecology and spread of the 2021–2023 highly pathogenic H5N1 epizootic across North America, and what this means for wildlife conservation and poultry health. Study Highlights:Using 1,818 haemagglutinin gene sequences from wild birds, domestic birds, and mammals collected across North America, the authors reconstruct the timing and routes of highly pathogenic H5N1 spread using Bayesian phylogeographical and phylodynamic models. They show that North America experienced around nine separate virus introductions, mainly via the Atlantic and Pacific migratory flyways, and that wild migratory Anseriformes sustained long-distance transmission across flyways. Non-canonical hosts such as raptors, songbirds, owls, and mammals were often infected but rarely acted as sources for onward transmission, functioning largely as dead-end hosts. In agriculture, the study estimates at least 46 and up to 113 independent introductions from wild birds into domestic poultry, with viral lineages persisting on farms for several months but rarely spilling back into wildlife. Comparisons between backyard and commercial flocks suggest that backyard birds tend to be infected slightly earlier and more frequently than commercial poultry, highlighting their potential value as early sentinels of increased viral circulation. Conclusion:Together, these findings indicate that managing future H5N1 waves in North America will require sustained surveillance in wild migratory birds and stronger measures at the wild–agriculture interface, rather than relying solely on rapid culling of infected farms. Music:Enjoy the music based on this article at the end of the episode. Reference:Damodaran L, Jaeger AS, Moncla LH. Ecology and spread of the North American H5N1 epizootic. Nature. 2025. https://doi.org/10.1038/s41586-025-09737-x 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/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com Castos player https://basebybase.castos.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 205: Ancient RNA Expression Profiles from the Woolly Mammoth In this episode of PaperCast Base by Base, we explore how ancient RNA preserved in permafrost can reveal tissue-specific gene expression and regulatory dynamics in the extinct woolly mammoth. Study Highlights:Researchers analyzed skeletal muscle and skin from ten Late Pleistocene woolly mammoths preserved in Siberian permafrost, extracting both ancient DNA and RNA to assess the authenticity and quality of the recovered molecules. Using alignment strategies optimized for short, damaged transcripts and mapping primarily to the Asian elephant genome, they identified characteristic damage patterns, exonic enrichment, and expression hotspots that distinguish genuine ancient RNA from residual DNA contamination. One exceptionally well-preserved specimen, known as Yuka, yielded a detailed skeletal muscle transcriptome, including abundant sarcomeric and mitochondrial genes that indicate a predominance of slow-twitch muscle fibers and reveal preserved tissue identity after tens of thousands of years. The team also detected mammoth-specific sequence variants, muscle-enriched microRNAs, and candidate novel microRNA loci, showing that ancient RNA can capture both coding and regulatory layers of the transcriptome. Together, these results establish robust quality-control and analytical frameworks for decoding ancient transcriptomes, demonstrating that RNA can persist long enough to recover biologically meaningful expression profiles from extinct megafauna. Conclusion:Ancient RNA sequencing from permafrost-preserved mammoths opens the door to integrative paleogenomic studies that combine genomes, proteomes, and transcriptomes to reconstruct tissue biology and gene regulation in long-extinct species. Music:Enjoy the music based on this article at the end of the episode. Reference:Mármol-Sánchez E, Fromm B, Oskolkov N, Pochon Z, Dehasque M, Aslanzadeh M, Bozlak E, Brown K, van der Valk T, Kalogeropoulos P, Chacón-Duque JC, Biryukova I, Heintzman PD, Furugård C, Plotnikov V, Protopopov A, Andersson B, Ersmark E, Peterson KJ, Friedländer MR, Dalén L. Ancient RNA expression profiles from the extinct woolly mammoth. Cell. 2026;189(1):1–18. https://doi.org/10.1016/j.cell.2025.10.025 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/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com Castos player https://basebybase.castos.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 204: StealTHY CRISPR: Revealing Hidden Metastasis Regulators In this episode of PaperCast Base by Base, we explore how the StealTHY CRISPR platform sidesteps Cas9 immunogenicity to uncover metastasis drivers in immunocompetent and humanized cancer models. Study Highlights:Researchers show that standard CRISPR-Cas9 tools and xenogeneic reporters provoke strong T cell responses in syngeneic and humanized mice, reshaping clonal architecture and suppressing metastasis.To overcome this, they develop StealTHY, a “hit-and-run” knockout strategy that pairs species-autologous Thy1 reporters with transient delivery of Cas9 protein, eliminating persistent immunogenic transgenes while preserving sgRNA library complexity.Across multiple murine breast, lung, and colon carcinoma models, StealTHY restores polyclonal tumor growth, enables unbiased in vivo CRISPR screens, and reveals context-specific dependencies in receptor tyrosine kinase and TGF-β signaling pathways.Applying StealTHY to human breast cancer in humanized mice, the authors identify clinically relevant metastasis regulators and derive gene signatures whose expression stratifies prognosis in large breast, lung, and colon cancer cohorts.A central discovery is that the developmental AMH–AMHR2 axis acts as an immune-evasive driver of carcinoma metastasis, and its genetic or pharmacologic disruption enhances anti-tumor immunity, reduces circulating tumor cell clusters, and limits metastatic spread. Conclusion:Together, these findings position StealTHY as a broadly applicable, immune-compatible CRISPR screening platform that can expose metastasis vulnerabilities and nominate immunomodulatory pathways such as AMH–AMHR2 for future therapeutic targeting. Music:Enjoy the music based on this article at the end of the episode. Reference:Saini M, Castro-Giner F, Hotz A, et al. StealTHY: An immunogen-free CRISPR platform to expose concealed metastasis regulators in immunocompetent models. Cell. 2025;188:1–19. https://doi.org/10.1016/j.cell.2025.10.007 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/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com Castos player https://basebybase.castos.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. 

️ Episode 203: Divergent Evolutionary Dynamics of Benign and Malignant Tumors In this episode of PaperCast Base by Base, we explore how benign and malignant tumors follow different evolutionary trajectories across birds and mammals, and what this reveals about cancer defenses across the tree of life. Study Highlights:The authors combine necropsy data on tumor prevalence from hundreds of bird and mammal species with Bayesian multivariate phylogenetic generalized linear mixed models to test how benign and malignant tumors relate to macroevolutionary processes. They show that prevalence of both benign and malignant tumors increases with body mass, confirming that larger-bodied species accumulate more neoplastic growths overall. Only malignant tumors, however, show a negative association with the rate of body size evolution, consistent with stronger adaptive cancer suppression mechanisms in rapidly evolving lineages. In birds, but not mammals, higher lineage diversification rates are linked to higher prevalence of both tumor types, suggesting that speciation-associated genomic instability can come with an increased tumor burden. Together, these patterns indicate that benign and malignant tumors respond differently to evolutionary pressures, with malignancies more tightly constrained by selection on body size evolution while benign tumors remain comparatively unconstrained. Conclusion:This work shows that treating benign and malignant tumors as distinct evolutionary phenomena can clarify how cancer resistance arises and help frame new hypotheses about why some lineages are more prone to malignancy than others. Music:Enjoy the music based on this article at the end of the episode. Reference:Butler G, Baker J, Amend SR, Pienta KJ, Venditti C. Divergent evolutionary dynamics of benign and malignant tumors. Proceedings of the National Academy of Sciences. 2025;122(45):e2519203122. https://doi.org/10.1073/pnas.2519203122 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/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com Castos player https://basebybase.castos.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 202: Stereo-seq V2: Spatial Total RNA Mapping in FFPE Tissues In this episode of PaperCast Base by Base, we explore how Stereo-seq V2 delivers high-resolution spatial mapping of total RNA in FFPE samples, from mouse brain to breast cancer and tuberculosis lung tissue. Study Highlights:The authors introduce Stereo-seq V2, a random-priming spatial transcriptomics platform that captures total RNA in situ on FFPE sections at single-cell resolution. By benchmarking against earlier Stereo-seq and other spatial methods in the mouse brain, they demonstrate improved gene detection, uniform gene body coverage, and robust profiling of non-coding RNAs and immune receptor transcripts. In long-stored triple-negative breast cancer blocks, Stereo-seq V2 maintains high sensitivity despite degraded RNA, enabling inference of copy-number alterations and spatially resolved alternative splicing events that distinguish tumor subtypes. Using Mycobacterium tuberculosis infection models in mice and human lung tissue, the study simultaneously maps host and pathogen transcriptomes and reconstructs spatial B cell receptor repertoires, revealing clonal expansion and affinity maturation around necrotic lesions. Conclusion:Stereo-seq V2 unlocks archival FFPE samples for high-resolution spatial total RNA and immune repertoire analysis, opening new avenues for translational research, infectious disease biology, and precision pathology. Music:Enjoy the music based on this article at the end of the episode. Reference:Zhao Y, Li Y, He Y, et al. (2025) Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution. Cell 188, 6554–6571. https://doi.org/10.1016/j.cell.2025.08.008 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/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com Castos player https://basebybase.castos.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 201: Sex, Smoking, and Somatic Selection in the Bladder In this episode of PaperCast Base by Base, we explore how ultradeep duplex DNA sequencing of normal human bladder tissue reveals sex- and smoking-related biases in the selection of somatic mutations and cancer driver clones. Study Highlights:Researchers applied ultradeep duplex DNA sequencing at around 5,000× coverage to 79 normal bladder urothelium samples from 45 deceased donors, targeting 16 genes known to drive clonal expansions and bladder tumors. They identified more than 64,000 somatic mutations and thousands of clonal driver events, allowing precise estimates of positive and negative selection across genes such as TP53, RBM10, STAG2, ARID1A, CDKN1A, FGFR3, and the TERT promoter. Men showed markedly stronger positive selection for truncating driver mutations in RBM10, CDKN1A, and ARID1A than women, despite similar burdens of non-protein-affecting mutations, indicating sex-specific differences in clonal evolution of the normal urothelium. Activating TERT promoter mutations were strongly associated with older age and were far more frequent in donors with a history of smoking, suggesting that tobacco exposure promotes the expansion of telomerase-activated clones rather than simply increasing overall mutation burden. By approaching “natural saturation mutagenesis” in these genes, the study maps selection at individual residues and protein domains, providing an in vivo framework to assess the functional impact of somatic mutations directly in human tissues. Conclusion:These results show that sex and smoking history leave distinct imprints on the clonal architecture of the normal bladder and highlight ultradeep sequencing of normal tissues as a powerful tool for understanding cancer risk and mapping functionally important mutations in vivo. Music:Enjoy the music based on this article at the end of the episode. Reference:Calvet F, Blanco Martinez-Illescas R, Muiños F, Tretiakova M, Latorre-Esteves ES, Fredrickson J, et al. Sex and smoking bias in the selection of somatic mutations in human bladder. Nature. 2025;647:436–444. https://doi.org/10.1038/s41586-025-09521-x 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/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com Castos player https://basebybase.castos.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 200: Sperm Sequencing Reveals Extensive Positive Selection in the Male Germline In this episode of PaperCast Base by Base, we explore how ultra-accurate duplex sequencing of human sperm reveals widespread positive selection in the male germline and its consequences for mutation burden and disease risk in offspring. Study Highlights:This Nature study uses NanoSeq duplex whole-genome and exome sequencing on sperm and matched blood samples from healthy men aged 24 to 75 years to quantify how mutations accumulate in the male germline. The authors show that sperm acquire about 1.67 substitutions per year per haploid genome, several-fold fewer than blood cells, with age-related signatures SBS1 and SBS5 dominating the mutation spectrum. By modeling nonsynonymous versus synonymous variants, they identify 40 genes under significant positive selection in spermatogonial lineages, many of which are classic cancer and developmental disorder genes enriched for activating and loss-of-function mutations. Aggregating variant allele fractions across these genes, they estimate that positive selection drives a two- to threefold enrichment of likely pathogenic mutations, such that roughly 3–5% of sperm from middle-aged to older men carry a potentially disease-causing coding variant. Conclusion:Positive selection in spermatogonial stem cells subtly reshapes the male germline over the lifespan, increasing the fraction of sperm that carry pathogenic mutations and refining how we think about paternal age, reproductive risk, and the shared genetic architecture of cancer and developmental disorders. Music:Enjoy the music based on this article at the end of the episode. Reference:Neville MDC, Lawson ARJ, Sanghvi R, Abascal F, Pham MH, Cagan A, et al. Sperm sequencing reveals extensive positive selection in the male germline. Nature. 2025;647:421–428. https://doi.org/10.1038/s41586-025-09448-3 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/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com Castos player https://basebybase.castos.com

️ Episode 199: PLD4 Deficiency and Lupus: When Nuclease Failure Ignites Autoimmunity In this episode of PaperCast Base by Base, we explore how loss-of-function mutations in the endolysosomal exonuclease PLD4 cause a monogenic form of systemic lupus erythematosus, reshaping our understanding of nucleic acid sensing and interferon-driven autoimmunity. Study Highlights:This study identifies biallelic loss-of-function PLD4 mutations in five patients with systemic lupus erythematosus, all presenting with severe lupus nephritis and hematologic involvement. Using whole-exome sequencing, structural modelling and biochemical assays, the authors show that these PLD4 variants markedly impair single-stranded DNA and RNA exonuclease activity, leading to accumulation of nucleic acid ligands in endolysosomes. Patient immune profiling with bulk and single-cell RNA sequencing, flow cytometry and CyTOF reveals hyperactivation of Toll-like receptor 7 and 9 pathways, with a strong type I interferon signature centered in plasmacytoid dendritic cells and monocytes. In Pld4-deficient mice, the team demonstrates lupus-like autoimmunity with nephritis, expansion of plasmacytoid dendritic cells and plasma cells, and upregulation of interferon-stimulated genes in kidney immune and parenchymal cells. Finally, pharmacologic JAK inhibition with baricitinib dampens type I interferon signalling, reduces autoantibody levels and renal inflammation in Pld4−/− mice, and suppresses interferon and NF-κB pathway activation in patient cells ex vivo. Conclusion:By defining PLD4 deficiency as a new monogenic cause of systemic lupus erythematosus and showing that JAK inhibition can reverse key interferon-driven features in experimental models and patient cells, this work points toward precision diagnostics and targeted therapies for a subset of patients with lupus driven by dysregulated endosomal nucleic acid clearance. Music:Enjoy the music based on this article at the end of the episode. Reference:Wang Q, Zhu H, Sun X, Zhang C, Ma S, Jin Y, et al. Loss-of-function mutations in PLD4 lead to systemic lupus erythematosus. Nature. 2025;647:498–505. https://doi.org/10.1038/s41586-025-09513-x 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/ Support:Base by Base – Stripe donations- https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website - https://basebybase.com Castos player - https://basebybase.castos.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 198: Mechanical Confinement and the Shape-Shifting Life of Melanoma Cells In this episode of PaperCast Base by Base, we explore how physical forces in the tumor microenvironment can push melanoma cells to switch from a pigment-producing, proliferative state into an invasive, drug-tolerant one, focusing on new work that links mechanical confinement, chromatin remodeling, and neuronal-like programs in cancer. Study Highlights:Using a zebrafish model of BRAFV600E-driven melanoma together with human tumor samples and single-cell transcriptomics, the authors identify a subpopulation of tumor cells at the tumor–microenvironment interface that displays elongated nuclei and a gene expression program resembling undifferentiated, neuron-like cells. In vitro confinement of human melanoma cells under a polydimethylsiloxane piston recapitulates this interface state, triggering assembly of a perinuclear cage of acetylated microtubules that protects the nucleus from mechanical stress. Mechanical confinement selectively upregulates the chromatin-bending protein HMGB2, whose increased residence time on chromatin opens neuronal and invasive gene loci and engages pathways such as Notch and BRN2 that drive a switch toward an invasive phenotype. Genetic disruption of HMGB2 in zebrafish melanomas and human melanoma cells shifts the balance back toward proliferation with larger but less invasive tumors, whereas HMGB2 overexpression enhances invasion and tolerance to BRAF and MEK inhibition in mouse xenografts. Conclusion:Mechanical confinement within the tumor microenvironment can rewire melanoma cells through HMGB2-dependent chromatin remodeling to favor an invasive, neuronal-like and drug-tolerant state over purely proliferative growth. Music:Enjoy the music based on this article at the end of the episode. Reference:Hunter MV, Joshi E, Bowker S, Montal E, Ma Y, Kim YH, Yang Z, Tuffery L, Li Z, Rosiek E, Browning A, Moncada R, Yanai I, Byrne H, Monetti M, de Stanchina E, Hamard P-J, Koche RP, White RM. Mechanical confinement governs phenotypic plasticity in melanoma. Nature. 2025;647:517–527. https://doi.org/10.1038/s41586-025-09445-6 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/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official websiteBase by Base – https://basebybase.com/ On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 197: Somatic Mutation and Selection at Population Scale In this episode of PaperCast Base by Base, we explore how ultra-accurate NanoSeq duplex sequencing reveals the hidden landscape of somatic mutations and clonal selection across blood and oral epithelium in over a thousand adults. Study Highlights:This study introduces improved whole-genome and targeted versions of NanoSeq, a duplex sequencing method with error rates below five mutations per billion base pairs, enabling reliable detection of single-molecule variants in highly polyclonal tissues. By applying targeted NanoSeq to 1,042 buccal swabs and 371 blood samples from a twins cohort, the authors map age-related somatic mutation rates and identify 46 genes under positive selection in oral epithelium, yielding more than 62,000 cancer-driver mutations. They also uncover negative selection against truncating variants in essential genes, generating in vivo saturation mutagenesis maps that distinguish activating hotspots from deleterious loss-of-function sites. Mutational signature analyses reveal a ubiquitous clock-like process and an alcohol-associated signature whose burdens vary widely between individuals and correlate with lifestyle factors such as tobacco use, alcohol consumption, and poor oral health. Twin-based and germline analyses further suggest that inherited variants, including a locus near ALDH2, can modulate somatic mutation signatures and driver landscapes. Conclusion:Accurate single-molecule sequencing at population scale shows that normal tissues are mosaics of tiny driver-mutant clones shaped by age, environment, and germline background, opening a path toward mechanistic cancer epidemiology and new biomarkers for early carcinogenesis. Music:Enjoy the music based on this article at the end of the episode. Reference:Lawson ARJ, Abascal F, Nicola PA, et al. Somatic mutation and selection at population scale. Nature. 2025;647:411–419. https://doi.org/10.1038/s41586-025-09584-w 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/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.com/  

️ Episode 196: Impact of Chromatin Accessibility QTLs Across Immune Contexts In this episode of PaperCast Base by Base, we explore how single-cell chromatin accessibility QTLs (caQTLs) reshape the interpretation of immune disease genetics by mapping regulatory variation across major immune cell types and disease-relevant states. Study Highlights:The authors harmonized ∼280,000 PBMC scATAC-seq profiles from 48 individuals—including healthy donors and COVID-19 patients—to build a unified chromatin accessibility atlas. Topic modeling uncovered continuous cell-state programs, including a CD8 effector-memory continuum associated with COVID-19, and enabled the discovery of 37,390 caQTLs plus thousands of dynamic, state-dependent effects. Compared to eQTLs, caQTLs explained roughly 50% more GWAS loci and highlighted that many regulatory variants act through chromatin without detectable steady-state expression changes in current datasets. Extensive sharing of caQTLs across immune cell types contrasted with the context specificity of eQTL colocalizations, underscoring the need to integrate chromatin, expression, enhancer–promoter links, and disease-relevant cellular states to pinpoint causal mechanisms. Conclusion:Chromatin accessibility QTLs substantially expand the fraction of disease loci with molecular support, but reliable causal gene mapping requires convergence of caQTL and eQTL signals within the same cellular context and along relevant cell-state trajectories. Music:Enjoy the music based on this article at the end of the episode. Reference:Mu Z, Randolph HE, Aguirre-Gamboa R, Ketter E, Dumaine A, Locher V, Brandolino C, Liu X, Kaufmann DE, Barreiro LB, Li YI. Impact of disease-associated chromatin accessibility QTLs across immune cell types and contexts. Cell Genomics. 2026;6:101061. https://doi.org/10.1016/j.xgen.2025.101061 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/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.com/

️ Episode 195: Tiny Shields: Lymphoid Microglia in Alzheimer’s Disease In this episode of PaperCast Base by Base, we explore how a subset of brain immune cells adopts a lymphoid-like program that helps contain inflammation and protect neural circuits in Alzheimer’s disease models. Study Highlights: Using mouse models of amyloid pathology and human Alzheimer’s brain tissue, the authors identify plaque-associated microglia with reduced PU.1 expression that cluster around deposits and express an unexpected set of lymphoid receptors, including CD28. By genetically tuning PU.1 levels specifically in microglia, they show that lowering PU.1 is sufficient to trigger this lymphoid-like transcriptional program, remodel chromatin and generate microglia that compact amyloid plaques, limit tau aggregation and preserve synapses, plasticity and behaviour. These PU.1low microglia display fewer type I interferon and complement signatures, accumulate fewer lipid droplets and extend survival in Alzheimer’s model mice, indicating a broadly neuroprotective state. In contrast, microglia-specific deletion of CD28 amplifies amyloid burden and drives a widespread pro-inflammatory interferon response in the microglial pool, suggesting that a small CD28+ subset exerts outsized control over brain inflammation. Human genetic data further link a PU.1-lowering SPI1 allele with increased abundance of lymphoid-like microglia, supporting the relevance of this protective program in people with Alzheimer’s disease. Conclusion: This work positions PU.1-tuned, CD28-expressing microglia as critical regulators of neuroinflammation and suggests that selectively boosting their lymphoid-style “checkpoint” signals could inspire new immunotherapy strategies for Alzheimer’s disease. Music: Enjoy the music based on this article at the end of the episode. Reference: Ayata P, Crowley JM, Challman MF, et al. Lymphoid gene expression supports neuroprotective microglia function. Nature. 2025. https://doi.org/10.1038/s41586-025-09662-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/ Support: If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.com/ On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 194: Bayesian History of Science: Watson and Crick and the Structure of DNA In this episode of PaperCast Base by Base, we explore how Bayesian reasoning can be used to reconstruct the famous discovery of the DNA double helix by James Watson and Francis Crick, following the sequence of structural models proposed in the early 1950s and the evolving evidence that supported or undermined each hypothesis. Study Highlights:The author applies a naïve Bayes framework to four competing models of DNA proposed by Watson, Crick, and Linus Pauling, treating each model as a target theory evaluated against multiple lines of historical evidence such as X-ray diffraction patterns, base pairing rules, symmetry constraints, and stereochemical feasibility. Conditional probabilities for how well each model accounts for each piece of evidence are manually estimated from historical sources using a simple five-point scale ranging from strongly inconsistent to strongly consistent, and combined with prior probabilities to calculate posteriors and likelihood ratios. By updating priors model by model, the study reconstructs how initial triple-helix proposals were progressively disconfirmed, while intermediate double-helix attempts with incorrect base pairing achieved only modest support despite offering a plausible replication mechanism. A dramatic jump in posterior probability and in the likelihood ratio is observed for the final Watson–Crick model with complementary purine–pyrimidine base pairing, consistent bond geometry, compliance with Chargaff’s rules, and correct symmetry, which the author interprets as a form of “Bayesian surprise” that matches scientists’ retrospective sense of having made a genuine discovery. The analysis also shows how “soft” considerations, such as analogy to Pauling’s alpha helix and the promise of an explanatory replication mechanism, can be incorporated alongside hard experimental data within a Bayesian account of theory choice in the history of science. Conclusion:This work argues that Bayesian analysis provides a coherent way to track how evidence and prior expectations jointly shaped the path from early speculative DNA models to the accepted double-helix structure, offering a quantitative complement to narrative histories of scientific discovery. Reference:Small H. Bayesian history of science: The case of Watson and Crick and the structure of DNA. Quantitative Science Studies. 2023;4(1):209–228. https://doi.org/10.1162/qss_a_00233 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/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.com/

️Episode 193: SARM1, DNA, and the Death Signal In this episode of PaperCast Base by Base, we explore how the axon-degenerating enzyme SARM1 acts as a double-stranded DNA sensor that triggers NAD+ loss, cell death, and chemotherapy-induced neuropathy, opening up new possibilities for neuroprotective therapies. Study Highlights:The authors show that the immune adaptor SARM1 directly binds double-stranded DNA via its TIR domain and, once activated, rapidly degrades cellular NAD+ in a sequence-independent but length-dependent manner. Using a combination of biochemical assays and structural analyses, they demonstrate that SARM1 forms multimeric complexes with linear DNA, with optimal activation occurring when DNA fragments are long enough to engage multiple SARM1 molecules. In cells, cytosolic DNA introduced by transfection or released during chemotherapy colocalizes with SARM1, driving NAD+ depletion and promoting cell death, whereas mutations that disrupt DNA binding or complete knockout of SARM1 blunt this response. In mouse models, loss of SARM1 protects against chemotherapy-induced neuropathy, linking DNA sensing by SARM1 directly to treatment-related neurotoxicity and positioning this pathway as a therapeutic target. Conclusion:By revealing SARM1 as a double-stranded DNA sensor that couples cytosolic DNA to NAD+ degradation, cell death, and chemotherapy-induced neuropathy, this study highlights a druggable axis for preserving neural function during cancer treatment. Reference:Wang L, Liu Q, Li S, et al. SARM1 senses dsDNA to promote NAD+ degradation and cell death. Cell. 2025;188:1–18. https://doi.org/10.1016/j.cell.2025.09.026 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/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/  

️Episode 192: At Base-Pair Resolution: Chromatin’s Cis-Regulatory Conversations In this episode of PaperCast Base by Base, we explore how base-pair resolution maps of chromatin contacts reveal a unified, biophysical model of communication between enhancers, promoters, and other cis-regulatory elements in mammalian cells. Study Highlights:Using Micro Capture-C ultra (MCCu), the authors generate multidimensional chromosome conformation maps with single base-pair pixels, allowing them to resolve contacts between individual transcription factor motifs within cis-regulatory elements in mouse embryonic stem, hematopoietic progenitor, and erythroid cells. They show that nucleosome-depleted regions partition chromatin into nanoscale domains and form highly localized contacts with one another, while surrounding nucleosomes produce distinct patterns of linker spacing that mark inactive regions. By acutely degrading Mediator complex subunits with degron systems, they find that Mediator is critical for fine-scale promoter architecture and transcription complex stabilization but has only minor effects on large-scale enhancer–promoter contacts. Integrating MCCu data with coarse-grained molecular dynamics simulations and super-resolution imaging, they demonstrate that the physicochemical properties of chromatin itself can recapitulate observed contact patterns and help explain how transcription factor binding and nucleosome positioning coordinate cis-regulatory interactions. Conclusion:This work provides a high-resolution framework for linking chromatin biophysics to gene regulation, offering a roadmap for dissecting how specific protein complexes and nucleosome landscapes shape enhancer–promoter communication across the genome. Reference:Li H, Dalgleish JLT, Lister G, et al. Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions. Cell. 2025;188:1–19. https://doi.org/10.1016/j.cell.2025.10.013 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/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/  

️ Episode 191: CATphishing: Synthetic Learning as an Alternative to Federated Learning in MRI In this episode of PaperCast Base by Base, we explore a Nature Communications study that proposes CATphishing—an approach that uses latent diffusion models to generate site-specific synthetic 3D brain MRIs for collaborative training without sharing raw data. The work spans seven institutions and 2,491 patients and evaluates whether models trained on synthetic data can match those trained via centralized data sharing or federated learning. Study Highlights:The authors train latent diffusion models locally at each site to capture dataset-specific MRI distributions and then aggregate only synthetic multi-contrast MRIs and tumor masks for downstream model training across centers. In IDH mutation status classification, models trained solely on synthetic data achieved performance comparable to centralized and federated approaches, with overall accuracy around 95.5% and AUC near 0.966, versus 96.2% and 0.979 for centralized training. A two‑stage tumor‑type pipeline—separating glioblastoma from IDH‑mutated tumors and then classifying oligodendroglioma versus astrocytoma—likewise showed similar end‑to‑end accuracy for synthetic versus real‑data strategies, landing near 90–92% overall. Fidelity and privacy were examined with FID and no‑reference image‑quality metrics and by a membership‑inference analysis that performed at chance, supporting the case for synthetic data as a viable, privacy‑preserving alternative in multi‑center AI development. Conclusion:CATphishing demonstrates that high‑fidelity synthetic MRI can enable cross‑institutional modeling with accuracy close to real‑data training while reducing privacy, communication, and coordination burdens in multi‑center collaborations. Reference:Truong NCD, Yogananda CGB, Wagner BC, Holcomb JM, Reddy DD, Saadat N, Bowerman J, Hatanpaa KJ, Patel TR, Fei B, Lee MD, Jain R, Bruce RJ, Madhuranthakam AJ, Pinho MC, Maldjian JA. Categorical and phenotypic image synthetic learning as an alternative to federated learning. Nature Communications. 2025;16:9384. https://doi.org/10.1038/s41467-025-64385-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/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/