Base by Base

Gustavo Barra
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Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time. Powered by AI, Base by Base offers a new way to learn on the go. Special thanks to authors who publish under CC BY 4.0, making open-access science faster to share and easier to explore.

  1. há 13 h

    457: A deletion that raises Alzheimer risk, a duplication that lowers it

    Quenez O et al., The American Journal of Human Genetics - Rare copy-number variants were called from 22,319 exomes covering early-onset Alzheimer disease, late-onset disease and unaffected controls, then tested gene by gene for a dosage effect. One locus came back with the cleanest signal in the field: at the central 22q11.21 region, deletions appeared only in early-onset cases, including one that arose de novo, while duplications piled up in controls, with late-onset cases sitting in between. Replication in nearly 400,000 further individuals confirmed it, and overexpressing SCARF2, one of the genes in the narrowed interval, increased amyloid-beta uptake in cells - the direction the protective duplications would predict. Key terms: copy-number variants, Alzheimer disease, 22q11.21, SCARF2, gene dosage. Study Highlights: The authors called rare copy-number variants from 22,319 harmonized exomes, comprising 4,150 early-onset Alzheimer cases at 65 years or younger, 8,519 late-onset cases and 9,650 unaffected controls, and found that early-onset cases carried an excess burden of rare CNVs affecting coding genes, driven particularly by deletions in genes already implicated in the disease. Pooling short truncating variants with deletions into a single loss-of-function analysis implicated ABCA1 with an odds ratio of 5.77 and ABCA7 deletions with an odds ratio of 2.29, and raised CTSB as a new candidate at an odds ratio of 5.03. An exome-wide gene-level dosage analysis then flagged 18 genes across five loci below a 10 percent false discovery rate, of which the central 22q11.21 region stood out: deletions were restricted to early-onset cases and absent from all 9,559 controls, duplications were enriched in controls, and late-onset cases fell in between, a gradient the authors narrowed to the SCARF2-KLHL22-MED15 interval. Replication across 33,977 additional cases and 362,322 controls confirmed the association at exome-wide significance, with duplications carrying an odds ratio of 0.34 and a mega-analysis p value of 5.52 times ten to the minus seven. Transfecting SCARF2 into microglial cells significantly increased uptake of fluorescent amyloid-beta with a p value of 2.2 times ten to the minus five, while uptake of inert latex beads did not change, arguing the effect is specific rather than a general boost in cell appetite. Conclusion: The same stretch of chromosome 22 pushes Alzheimer risk in opposite directions depending on how many copies you carry: losing one raises risk, gaining one lowers it. Duplications of the central 22q11.21 region emerge as one of the strongest risk-decreasing genetic factors described so far in terms of effect size, behind only the ultra-rare Icelandic APP variant, and unlike that variant they are found across multiple ancestries. The authors are careful about what this does not mean: the deletions are extremely rare, protection is relative rather than absolute, and they show it directly by pointing to duplication carriers who developed late-onset disease anyway while carrying other risk factors. Power is the central constraint, because each genome carries hundreds of rare coding point variants but typically only one rare coding CNV, and the analysis was restricted to individuals of European ancestry. Music: Enjoy the music based on this article at the end of the episode. Article title: Exome analysis of 22,319 individuals links extremely rare copy-number variants and 22q11.21 dosage to Alzheimer risk First author: Quenez O Journal: The American Journal of Human Genetics DOI: 10.1016/j.ajhg.2026.07.013 Reference: Quenez O, Schramm C, Cassinari K, Nicolas A, Groeneveld J, Huguet G, et al. Exome analysis of 22,319 individuals links extremely rare copy-number variants and 22q11.21 dosage to Alzheimer risk. The American Journal of Human Genetics. 2026;113(10):1-19. doi:10.1016/j.ajhg.2026.07.013 Li...

  2. há 1 dia

    456: Beyond exons: where heritability hides as traits get more polygenic

    Fuhrer J et al., The American Journal of Human Genetics - Across 34 complex traits and disorders, a MiXeR-based framework partitions SNP heritability over 74 functional annotations and finds that exons carry only a minority of it, and steadily less as a trait becomes more polygenic. Exonic heritability falls from about 22 percent in less-polygenic somatic diseases and biomarkers to about 13 percent in highly polygenic psychiatric and cognitive traits, intergenic heritability rises by the same logic, and intronic heritability stays put. A new annotation contribution score shows the same axis in the annotations themselves: highly polygenic traits load on conservation and variant-effect scores, less-polygenic traits on promoter, transcription and chromatin marks. Key terms: polygenicity, SNP heritability, noncoding variation, functional annotation, complex traits. Study Highlights: The authors extended the MiXeR framework to model SNP effect-size variance across 74 binary functional annotations, applied it to 34 traits spanning psychiatric, neurological, cardiometabolic, anthropometric, hematological and immune phenotypes, and introduced a likelihood-based annotation contribution score that measures how much a single annotation adds to the full model rather than how enriched it is per SNP. Exons cover 2.55 percent of base pairs and account for a mean of 14.52 percent of heritability, with introns and intergenic regions together explaining the remaining 85.49 percent; introns alone typically carry about half. Regressing regional fractions on log polygenicity, the exonic fraction falls 4.38 percentage points and the intergenic fraction rises 4.87 percentage points per ten-fold increase in polygenicity, while the intronic slope is not significant, and the illustrative spread runs from 8.51 percent exonic in schizophrenia to 29.44 percent in sex-hormone-binding globulin. The contribution score peaks for mid-sized annotations covering roughly 10 to 15 percent of SNPs, so compact conservation tracks such as phastCons, GERP, CADD and Eigen dominate in highly polygenic traits while promoter and chromatin tracks such as H3K4me3 and CpG islands dominate in less-polygenic ones. Sensitivity analyses against sLDSC and sLD4M agreed closely, with heritability fractions correlating at r equals 0.996 and polygenicity estimates at Spearman r equals 0.91. Conclusion: The functional location of heritability is not a fixed property of the genome but tracks a trait's polygenicity: less-polygenic somatic traits concentrate heritability in coding and gene-proximal regulatory regions, while highly polygenic psychiatric and cognitive traits distribute it across dispersed distal regulatory elements. Because enrichment per SNP and total contribution can point in opposite directions, the authors argue both must be read together, and they note that coding variants explain a minority of heritability throughout, which argues for sequencing designs that maximize noncoding coverage. The analysis relies on European-ancestry reference panels, uses relatively broad annotations with incomplete chromosome X coverage, and depends on polygenicity estimates from two methods that nonetheless agreed closely. Music: Enjoy the music based on this article at the end of the episode. Article title: Beyond exons: Linking noncoding heritability and polygenicity across complex human traits and disorders First author: Fuhrer J Journal: The American Journal of Human Genetics DOI: 10.1016/j.ajhg.2026.08.012 Reference: Fuhrer J, Shadrin AA, Hughes T, Parker N, Hindley G, Frei E, Nguyen D, Smeland OB, Djurovic S, Andreassen OA, Dale AM, Frei O. Beyond exons: Linking noncoding heritability and polygenicity across complex human traits and disorders. The American Journal of Human Genetics. 2026;113(10):1-13. doi:10.1016/j.ajhg.2026.08.012 License: This episode is based...

  3. há 2 dias

    455: Agentic genomics: the bottleneck moves from code to judgment

    Corpas M et al., Cell Genomics - A Perspective arguing that autonomous AI agents which discover, configure and chain bioinformatics operations from natural-language instructions have shifted the bottleneck in computational biology from building pipelines to validating their output. The authors define four necessary conditions for a system to count as agentic, propose a perturbation test that separates genuine runtime decision-making from pre-specified branching, survey four existing systems, and set out a three-tier validation framework in which none of the surveyed systems yet reaches clinical grade. Key terms: agentic genomics, AI agents, validation, skill libraries, equity in genomics. Study Highlights: The authors define agentic genomics through four necessary conditions — autonomy, domain constraint via validated skill libraries, iterative refinement, and natural-language mediation — and offer an empirically testable criterion: a system is not agentic if perturbed intermediate outputs fail to change its execution strategy. They distinguish the paradigm from workflow managers like Nextflow and Galaxy, from AutoML, from LLM-assisted scripting, and from general-purpose biomedical copilots. Four systems are surveyed and placed against a proposed three-tier validation framework of research grade, benchmarked and clinical grade; all four currently sit at research grade, and none has published the external multi-site evidence the clinical tier requires. The paper documents a concrete silent failure: in the early weeks of ClawBio, one skill given an empty input file containing no genomic data returned all-normal results including recommended dosages for 51 drugs, a path since closed by community audit. It also reports that a randomized trial of GPT-4-augmented diagnostic reasoning found no significant improvement over conventional resources, 76 percent versus 74 percent with p equal to 0.60, even though the model alone scored well above physicians. Conclusion: The central claim is that agentic genomics expands the capacity to produce analyses without expanding the capacity to judge them, so validation frameworks must be formalized and tiered, equity-aware defaults must be engineered rather than aspired to, and regulatory frameworks must accommodate non-deterministic software. The authors argue the paradigm is already in use and advancing, and that the open question is not whether it will be adopted but whether the field will build the standards to make it trustworthy first. Music: Enjoy the music based on this article at the end of the episode. Article title: Agentic genomics: From pipeline automation to autonomous validation First author: Corpas M Journal: Cell Genomics DOI: 10.1016/j.xgen.2026.101305 Reference: Corpas M, Guio H, Fatumo S. Agentic genomics: From pipeline automation to autonomous validation. Cell Genomics. 2026;6(8):101305. doi:10.1016/j.xgen.2026.101305 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 is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming: ❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01 ☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 ▶️ Watch with chapters on YouTube: https://www.youtube.com/@basebybase More at basebybase.com On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/agentic-genomics-validation-bottleneck QC: This episode was checked against the original article PDF and publication metadat...

  4. 2 de set.

    454: Efavirenz retarda a doença priônica mexendo no colesterol do cérebro [PT]

    Ali T et al., JCI Insight - Um antirretroviral aprovado para HIV, dado por via oral em microdose, prolongou a sobrevida de camundongos que carregam a proteína priônica humana e foram infectados com príons de doença de Creutzfeldt-Jakob esporádica humana. O efavirenz age ativando a CYP46A1, a enzima cerebral que converte colesterol numa forma capaz de sair do cérebro — e não baixando a proteína priônica, como as abordagens dos episódios anteriores desta série. Termos-chave: efavirenz, CYP46A1, doença de Creutzfeldt-Jakob, metabolismo do colesterol cerebral, reposicionamento de medicamento. ⚠️ Importante: nada neste episódio é motivo para tomar efavirenz. O efavirenz é um antirretroviral de prescrição com efeitos colaterais reais, incluindo distúrbio do sono, sonhos vívidos, tontura e efeitos psiquiátricos. A dose usada neste estudo — cerca de 0,09 mg/kg por dia — é algo entre 300 e 400 vezes menor que a dose prescrita para HIV, e não é algo que alguém consiga aproximar por conta própria. Nenhum ser humano teve benefício demonstrado com efavirenz para doença priônica. Existe um ensaio de Fase 3 registrado como NCT07482085 no ClinicalTrials.gov, que ainda não reportou resultados. Se a doença priônica afeta você ou sua família, converse com um neurologista e pergunte sobre ensaios registrados — não sobre a farmácia. Este é o quarto episódio da nossa série sobre a doença de Creutzfeldt-Jakob, que começou como homenagem ao Lito Sousa. Todos os ensaios citados na série estão registrados publicamente no ClinicalTrials.gov. Destaques do estudo: Os autores inocularam camundongos tg650, que superexpressam a PrP humana, com príons MM1 de CJD esporádica humana e começaram o efavirenz oral em dose baixa aos 30 ou aos 130 dias após a infecção, prolongando a sobrevida em 17 e 23 dias respectivamente. Na fase clínica inicial, os animais tratados apresentaram menos PrPSc, menor teor de colesterol e de gotículas lipídicas no cérebro, e níveis mais altos de CYP46A1 e de 24S-hidroxicolesterol no cérebro e no soro. Superexpressar a CYP46A1 sozinha em células neuronais infectadas já reduziu a PrPSc e elevou o 24S-hidroxicolesterol, ligando o efeito antipriônico à enzima e não a outra propriedade do remédio. A dose usada foi de cerca de 0,09 mg/kg por dia, algo entre 300 e 400 vezes menor que a dose padrão prescrita para HIV. A eficácia no início tardio importa clinicamente, porque o paciente chega depois que os sintomas começaram. Conclusão: O efavirenz oral em dose baixa ativa a CYP46A1, restaura a renovação de colesterol no cérebro, reduz o acúmulo de PrPSc e prolonga a sobrevida num modelo humanizado de CJD esporádica, o que sustenta avaliar melhor esse medicamento reposicionado em doença priônica humana. Música: Ouça a música criada a partir deste artigo no final do episódio. Título do artigo: Treatment with efavirenz extends survival in a Creutzfeldt-Jakob disease model by regulating brain cholesterol metabolism Primeiro autor: Ali T Revista: JCI Insight DOI: 10.1172/jci.insight.190296 Referência: Ali T, Cashion J, Hannaoui S, Ahmed-Hassan H, Schatzl H, Gilch S. Treatment with efavirenz extends survival in a Creutzfeldt-Jakob disease model by regulating brain cholesterol metabolism. JCI Insight. 2025;10(14):e190296. doi:10.1172/jci.insight.190296 Licença: Este episódio é baseado em um artigo de acesso aberto publicado sob a Licença Creative Commons Atribuição 4.0 Internacional (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Apoie: O Base by Base é independente e sem anúncios — sem patrocinadores, sem paywall. Se o episódio valeu o seu tempo, contribua e ajude a manter os artigos auditados e as músicas originais: ❤️ Apoio mensal: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01 ☕ Doação única: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Mais em basebybase.com

  5. 31 de ago.

    453: Efavirenz slows sCJD progression by reshaping brain cholesterol

    Ali T et al., JCI Insight - Repurposed low-dose efavirenz slowed disease progression and extended survival in tg650 mice inoculated with MM1 sCJD prions by activating CYP46A1, raising 24S‑hydroxycholesterol and reducing PrPSc, brain cholesterol and lipid droplets at the early clinical stage. Key terms: efavirenz, CYP46A1, Creutzfeldt-Jakob disease, cholesterol metabolism, prion disease. ⚠️ Important: nothing in this episode is a reason to take efavirenz. Efavirenz is a prescription antiretroviral with real side effects, including sleep disturbance, vivid dreams, dizziness and psychiatric effects. The dose used in this study — about 0.09 mg/kg per day — is roughly 300 to 400 times lower than the dose prescribed for HIV, and is not something anyone can approximate on their own. No human being has yet been shown to benefit from efavirenz for prion disease. A Phase 3 trial is registered as NCT07482085 on ClinicalTrials.gov and has not reported results. If prion disease affects you or your family, talk to a neurologist and ask about registered trials — not about a pharmacy. This episode is the fourth in our series on Creutzfeldt-Jakob disease, which began as a dedication to Lito Sousa. Every trial named in the series is registered publicly on ClinicalTrials.gov. Study Highlights: Oral low-dose efavirenz given to human-PrP–overexpressing tg650 mice starting at 30 or 130 days postinoculation significantly slowed clinical progression and extended survival by 17 and 23 days, respectively. At the early clinical stage EFV-treated mice showed reduced PK-resistant PrPSc, decreased brain cholesterol and lipid droplets, and increased CYP46A1 expression with higher 24S‑hydroxycholesterol in brain and serum. Overexpression of CYP46A1 in prion-infected neuronal cells likewise reduced PrPSc, supporting a causal link between CYP46A1 activation and antiprion effects. Conclusion: Low-dose oral efavirenz activates CYP46A1, restores cholesterol turnover, reduces early PrPSc accumulation and lipid pathology, and extends survival in a humanized sCJD mouse model, supporting EFV as a candidate for further evaluation in human prion disease. Music: Enjoy the music based on this article at the end of the episode. Article title: Treatment with efavirenz extends survival in a Creutzfeldt-Jakob disease model by regulating brain cholesterol metabolism First author: Ali T Journal: JCI Insight DOI: 10.1172/jci.insight.190296 Reference: Ali T, Cashion J, Hannaoui S, Ahmed-Hassan H, Schatzl H, Gilch S. Treatment with efavirenz extends survival in a Creutzfeldt-Jakob disease model by regulating brain cholesterol metabolism. JCI Insight. 2025;10(14):e190296. https://doi.org/10.1172/jci.insight.190296. 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 is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming: ❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01 ☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 More at basebybase.com On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/efavirenz-prion-cjd-cholesterol QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-08-31. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited the transcript's core biomedical claims about EFV's e...

  6. 28 de ago.

    452: Reduzir a PrP funciona em todas as linhagens [PT]

    Minikel EV et al., Nucleic Acids Research - Este estudo testa a redução da proteína priônica (PrP) por oligonucleotídeos antisense (ASOs) em camundongos, variando doses, esquemas de aplicação, linhagens de príon e estágios da doença. O tratamento reduziu o RNA do Prnp, prolongou a sobrevida, atrasou os sintomas e reverteu biomarcadores de lesão neuronal e de gliose em vários cenários. O benefício apareceu mesmo com redução parcial, nas cinco linhagens testadas, e em alguns casos até depois do início dos sintomas. Termos-chave: proteína priônica, oligonucleotídeo antisense, neurodegeneração, biomarcadores, terapias. Destaques do estudo: A redução da PrP mediada por ASO prolongou a sobrevida e atrasou o início da doença tanto no esquema profilático quanto no tardio, em diferentes químicas de ASO. O benefício foi dose-dependente — uma redução de apenas cerca de 21 por cento do RNA já produziu ganho mensurável de sobrevida — e apareceu contra cinco linhagens distintas de príon adaptadas a camundongo, sem sinal de linhagens resistentes ao tratamento. Uma dose única aplicada depois da detecção da patologia reverteu a alta do neurofilamento leve no plasma e reduziu a bioluminescência de GFAP; a supressão crônica iniciada até o começo da neuropatologia alcançou benefício comparável ao de camundongos com apenas uma cópia funcional do gene da PrP. Alguns animais tratados já com sintomas francos tiveram sobrevida prolongada, embora a tolerabilidade de certas químicas de ASO em fase tardia tenha sido limitada. Conclusão: Reduzir a PrP por ASO, via mecanismo dependente de RNase H, é uma estratégia modificadora de doença amplamente eficaz nos modelos de príon em camundongo — atravessando linhagens e estágios — e justifica o desenvolvimento de terapias que baixem a PrP, com esquemas de dose apropriados. Música: Ouça a música criada a partir deste artigo no final do episódio. Título do artigo: Prion protein lowering is a disease-modifying therapy across prion disease stages, strains and endpoints Primeiro autor: Minikel EV Revista: Nucleic Acids Research DOI: 10.1093/nar/gkaa616 Referência: Minikel EV, Zhao HT, Le J, O’Moore J, Pitstick R, Graffam S, Carlson GA, Kavanaugh MP, Kriz J, Kim JB, Ma J, Wille H, Aiken J, McKenzie D, Doh-ura K, Beck M, O’Keefe R, Stathopoulos J, Caron T, Schreiber SL, Carroll JB, Kordasiewicz HB, Cabin DE, Vallabh SM. Prion protein lowering is a disease-modifying therapy across prion disease stages, strains and endpoints. Nucleic Acids Research. 2020;48(19):10615–10631. doi:10.1093/nar/gkaa616 Licença: Este episódio é baseado em um artigo de acesso aberto publicado sob a Licença Creative Commons Atribuição 4.0 Internacional (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Apoie: O Base by Base é independente e sem anúncios — sem patrocinadores, sem paywall. Se o episódio valeu o seu tempo, contribua e ajude a manter os artigos auditados e as músicas originais: ❤️ Apoio mensal: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01 ☕ Doação única: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Mais em basebybase.com No PaperCast Base by Base você acompanha o que há de mais recente em genômica, genômica funcional, genômica estrutural e proteômica. Link do episódio: https://basebybase.com/episodes/prion-protein-lowering-across-strains-pt QC: Este episódio foi conferido contra o PDF original do artigo e os metadados da publicação, para a edição publicada em 2026-08-28. Escopo do QC: - metadados do artigo e as afirmações científicas centrais da narração - exclui analogias, abertura/encerramento e música - cobertura da transcrição: Audited the transcript sections describing mechanism of action (RNase H–mediated PrP reduction), dose-response and minimal knockdown, cross-strain efficacy across five prion strains, treatmen...

  7. 25 de ago.

    451: Prion protein lowering is disease-modifying across stages and strains

    Minikel EV et al., Nucleic Acids Research - This study uses antisense oligonucleotides (ASOs) to lower prion protein (PrP) RNA in mice and shows dose-dependent extension of survival, efficacy across multiple prion strains, reversal of molecular biomarkers, and benefit even when treatment is delayed into symptomatic stages. Key terms: prion protein, antisense oligonucleotide, neurodegeneration, biomarkers, survival. Study Highlights: Using ASOs to reduce PrP RNA in intracerebrally inoculated mice produced dose-dependent extension of survival in both prophylactic and delayed dosing paradigms. Less than 25% PrP suppression was sufficient to delay symptoms and extend survival. Treatment was effective across five distinct prion strains without evidence of drug-resistant prions. Biomarkers of neuronal injury (plasma NfL) and astrocytosis (GFAP bioluminescence) were reversed after ASO treatment, and chronic early dosing matched benefits seen in heterozygous PrP knockout animals. Conclusion: ASO-mediated PrP lowering is a robust, disease-modifying approach in mouse models of prion disease across strains and disease stages, supporting advancement of PrP-lowering therapeutics and use of CSF PrP and blood NfL as pharmacodynamic biomarkers. Music: Enjoy the music based on this article at the end of the episode. Article title: Prion protein lowering is a disease-modifying therapy across prion disease stages, strains and endpoints First author: Minikel EV Journal: Nucleic Acids Research DOI: 10.1093/nar/gkaa616 Reference: Minikel EV, Zhao HT, Le J, O’Moore J, Pitstick R, Graffam S, Carlson GA, Kavanaugh MP, Kriz J, Kim JB, Ma J, Wille H, Aiken J, McKenzie D, Doh-ura K, Beck M, O’Keefe R, Stathopoulos J, Caron T, Schreiber SL, Carroll JB, Kordasiewicz HB, Cabin DE, Vallabh SM. Prion protein lowering is a disease-modifying therapy across prion disease stages, strains and endpoints. Nucleic Acids Research. 2020;48(19):10615–10631. doi:10.1093/nar/gkaa616 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 is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming: ❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01 ☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 More at basebybase.com On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/prion-protein-lowering-stages-strains-endpoints QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-08-25. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited sections include PrP biology and PrP function; ASO mechanism and RNase H action; dose-response and minimal PrP knockdown; cross-strain efficacy across five mouse prion strains; biomarkers (plasma NfL and GFAP bioluminescence); therapeutic timing (prophylactic, early/delayed, late/symptomatic); resistance and tr - transcript topics: Prion protein biology and PrP function; ASO mechanism and RNase H action; Dose-response and minimal PrP knockdown; Cross-strain efficacy across five mouse prion strains; Biomarkers: plasma neurofilament light (NfL) and GFAP bioluminescence; Behavioral readouts: rotarod and nest-building QC Summary: - factual score: 10/10 - metadata score: 10/10 - supported core claims: 5 - claims flagged for review: 0 - metadata check...

  8. 24 de ago.

    450: ASOs que reduzem PrP prolongam a sobrevida [PT]

    Raymond GJ et al., JCI Insight - This episode covers a 2019 study showing that sequence-specific antisense oligonucleotides (ASOs) targeting the prion protein (PrP) mRNA, delivered by bolus intracerebroventricular injection, lower PrP levels in the CNS, slow neuropathology, and markedly extend survival in prion-infected wild-type mice when given prophylactically or even near symptom onset. Key terms: antisense oligonucleotide, prion disease, prion protein, intracerebroventricular, mouse model. Study Highlights: Two PrP-targeting ASOs (active ASO 1 and 2) reduced Prnp mRNA and PrP protein across brain regions and produced robust survival benefits in RML prion–infected wild-type mice, with prophylactic extension of lifespan by 61%–98%. A single bolus dose given at 120 days post-infection (near clinical onset) extended survival by 55% and slowed symptomatic progression. A non‑targeting control ASO showed no efficacy, indicating a sequence-specific, on‑target mechanism mediated by RNase H–dependent RNA lowering. Some tolerability issues were observed with particular ASO candidates at late-stage treatment, but at least one active ASO was both tolerated and effective. Conclusion: Bolus CNS delivery of sequence-specific PrP‑lowering ASOs lowers PrP, delays prion neuropathology, and substantially extends survival in infected mice, supporting further development of PrP‑lowering therapy and use of CSF PrP as a pharmacodynamic biomarker. Music: Enjoy the music based on this article at the end of the episode. Article title: Antisense oligonucleotides extend survival of prion-infected mice First author: Raymond GJ Journal: JCI Insight DOI: 10.1172/jci.insight.131175 Reference: Raymond GJ, Zhao HT, Race B, et al. Antisense oligonucleotides extend survival of prion-infected mice. JCI Insight. 2019;4(16):e131175. doi:10.1172/jci.insight.131175. 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 is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming: ❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01 ☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 More at basebybase.com On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/450-prp-lowering-asos-prion-mice QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-08-24. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited sections describing ASOs targeting Prnp, PrP reduction, i.c.v. bolus delivery, prophylactic vs late-stage treatment in prion-infected mice, and the role of control ASOs and sequence specificity. - transcript topics: Antisense oligonucleotides targeting Prnp mRNA; PrP reduction and PrP biology; Intracerebroventricular bolus delivery vs continuous infusion; Prophylactic vs late-stage treatment in prion-infected mice; Sequence specificity and non-targeting control ASO; Pharmacodynamic biomarker: CSF PrP measurement QC Summary: - factual score: 10/10 - metadata score: 10/10 - supported core claims: 6 - claims flagged for review: 0 - metadata checks passed: 4 - metadata issues found: 0 Metadata Audited: - article_doi - article_title - article_journal - license Factual Items Audited: - ASOs targeting Prnp mRNA discussed as a therap...

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Sobre

Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time. Powered by AI, Base by Base offers a new way to learn on the go. Special thanks to authors who publish under CC BY 4.0, making open-access science faster to share and easier to explore.

Informações

  • Criado por
    Gustavo Barra
  • Anos de atividade
    2025 - 2026
  • Episódios
    458
  • Classificação
    Livre
  • Copyright
    © Gustavo Barra
  • Site do podcast
    Base by Base

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