Base by Base

Walker S et al., Genetics in Medicine - Genome sequencing of 78,195 participants in the 100,000 Genomes Project identified ultra-rare non-canonical FBN1 splice variants enriched among individuals recruited with familial thoracic aortic aneurysm disease (FTAAD). Experimental RNA assays confirmed aberrant splicing for most candidates, including multiple deep intronic pseudoexon events, indicating a measurable diagnostic contribution from intronic variants beyond standard clinical testing windows. Key terms: Marfan syndrome, FBN1, splicing, pseudoexon, genome sequencing.

Study Highlights:
A systematic screen of FBN1 singleton variants using SpliceAI found 20 unique candidate non-canonical splice variants in 23 families, with significant enrichment in the FTAAD cohort (OR=84, p=9.7x10^-14). Experimental validation (RT-PCR, RNAseq, minigene assays) confirmed splicing abnormalities for 16/20 variants, and nine events involved pseudoexon inclusion. Seventy percent of validated variants lay beyond the ±8 bp regions typically interrogated in clinical testing, and the authors estimate a ~3% additional diagnostic yield for unsolved FTAAD families.

Conclusion:
Expanded intronic analysis using genome sequencing combined with refined splice prediction and confirmatory RNA testing reveals non-canonical FBN1 splice variants as an important, actionable cause of previously undiagnosed Marfan/FTAAD cases and supports incorporating intronic analysis and RNA assays into clinical workflows.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Utility of genome sequencing and group-enrichment to support splice variant interpretation in Marfan syndrome

First author:
Walker S

Journal:
Genetics in Medicine

DOI:
10.1016/j.gim.2025.101477

Reference:
Walker S, Bunyan DJ, Thomas HB, Kesim Y, Kershaw CJ, Holloway J, Wai H, Day M, Smith CL, Hawkes G, Wood AR, Weedon MN, Blair E, Curtis SL, Fielden C, Evans J, Whittington R, Smithson SF, Cox H, Clift P, McEntagart M, Prapa M, Alsters S, Morris-Rosendahl D, Dean J, Morrison PJ, Dixit A, Sarkar A, Prescott K, Riazat Kesh LA, Tharakan R, Turner C, Ellard S, Shaw-Smith C, Fasham J, Clowes V, Holden S, Somarathi S, Mercer C, Berry I, O’Keefe RT, Banka S, Baralle D, Thomas NS, Baple EL, Taylor JC, Pagnamenta AT. Utility of genome sequencing and group-enrichment to support splice variant interpretation in Marfan syndrome. Genetics in Medicine (2025). DOI: https://doi.org/10.1016/j.gim.2025.101477

License:
© 2025 Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics.

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://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/decoding-hidden-signals-genome-sequencing-reveals-cryptic-splicing-variants-in-marfan-syndrome

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-06-05.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Substantive audit of the transcript’s coverage of study rationale, methods (genome sequencing, SpliceAI, RNA validation), key findings (20 variants in 23 families, 3% yield, 16/20 validations), extended analyses (windows/absolute scores), and clinical implications including cascade testing and UK Biobank replication.
- transcript topics: Marfan syndrome and FBN1 genetics; 100k Genomes Project dataset and FTAAD enrichment; SpliceAI-based variant prioritization and thresholds; Non-canonical intronic FBN1 splice variants (pseudoexons, exon extension, uORF); RNA validation approaches (RT-PCR, minigene, RNAseq limitations in blood); UK Biobank replication and phenotype specificity

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- 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:
- Non-canonical FBN1 splice variants contribute to undiagnosed Marfan syndrome/FTAAD (~3% diagnostic yield)
- 21 singleton FBN1 variants predicted to affect splicing by SpliceAI (delta score >= 0.5) in aggregate 78,195-person dataset
- 9/703 FTAAD-recruited individuals carry one of these variants; 12/77,492 in non-FTAAD; OR ~84, p ≈ 9.7×10^-14
- Secondary analysis identified 11 additional variants in 14 families; total 20 variants across 23 families (32 affected individuals)
- 70% of the 20 variants lie beyond ±8 bp from exons (deep intronic)
- 16/20 variants experimentally validated to affect splicing (RT-PCR and minigene); 9/20 show pseudoexonization

QC result: Pass.

Nicastro M et al., The American Journal of Human Genetics - Researchers identify bi-allelic POPDC2 variants in multiple families causing sinus-node dysfunction, atrioventricular conduction defects and, in some cases, hypertrophic cardiomyopathy, and investigate structural, electrophysiological and population-level evidence for pathogenicity. Key terms: POPDC2, cardiac conduction, TREK-1, cAMP binding, hypertrophic cardiomyopathy.

Study Highlights:
Bi-allelic POPDC2 variants were found in four unrelated families and associated with sinus node disease, AV conduction defects and HCM. Homology models predict impaired cAMP binding by POPDC2 variants and electrophysiology shows mutant POPDC2 fails to increase TREK-1 current density. Muscle biopsy and transcriptomics place POPDC1/POPDC2 dysfunction in conduction-system cells, and population analyses of >1 million individuals indicate heterozygous carriers are unlikely to develop clinical disease. Together the data support POPDC2 loss-of-function as a recessive cardiac syndrome gene.

Conclusion:
Bi-allelic loss-of-function POPDC2 variants cause an autosomal recessive cardiac syndrome marked by conduction disease and occasional hypertrophic cardiomyopathy, likely via impaired cAMP-dependent regulation of TREK-1 and disrupted POPDC1/2 stability or trafficking.

QC:
This episode was checked against the original article PDF and publication metadata.
Scope: article metadata and core scientific claims from the narration, excluding analogies, intro/outro, and music.
Factual QC score: 10/10.
Metadata QC score: 10/10.
Supported core claims: 6.
Claims flagged for review: 0.
Metadata checks passed: 4.
Metadata issues found: 0.
QC result: Pass.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Bi-allelic variants in POPDC2 cause an autosomal recessive syndrome presenting with cardiac conduction defects and hypertrophic cardiomyopathy

First author:
Nicastro M

Journal:
The American Journal of Human Genetics

DOI:
10.1016/j.ajhg.2025.04.016

Reference:
Nicastro M, Vermeer AMC, Postema PG, et al. Bi-allelic variants in POPDC2 cause an autosomal recessive syndrome presenting with cardiac conduction defects and hypertrophic cardiomyopathy. The American Journal of Human Genetics. 2025;112:1–18. doi:10.1016/j.ajhg.2025.04.016

License:
CC BY

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://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/popdc2-recessive-cardiac-syndrome

Chavez-Yenter D et al., Genetics in Medicine - A cross-sectional SEM study of 503 English-fluent Latino adults applied the Integrated Behavioral Model to identify predictors of intention for carrier screening (CS) and cancer predisposition testing (CPT). Perceived agency emerged as the strongest predictor for both testing types, with family/friend norms supporting CS and attitudes showing negative associations. Key terms: Latino, carrier screening, cancer predisposition testing, integrated behavioral model, agency.

Study Highlights:
Using confirmatory factor analysis and structural equation models, the authors assessed attitudes, norms, and perceived agency as predictors of intention to use carrier screening and cancer predisposition testing among 503 English-speaking Latino adults. Perceived agency (self-efficacy and perceived control) was the most consistent predictor for both CS (β=.381, p<.01) and CPT (β=.559, p<.01). Norms from family and friends positively predicted CS intention (β=.350, p<.01) while attitudes were negatively associated with CS (β=-.313, p=.028) and marginally negatively associated with CPT (β=-.277, p=.053). Demographic and clinical covariates (age, gender, income, subethnicity, insurance) had smaller but significant associations with intention.

Conclusion:
To improve genetic testing uptake among Latino populations, interventions should prioritize strengthening perceived agency (navigation, referral, access) and leveraging family/friend normative influences rather than focusing solely on attitude/knowledge campaigns.

QC:
This episode was checked against the original article PDF and publication metadata.
Scope: article metadata and core scientific claims from the narration, excluding analogies, intro/outro, and music.
Factual QC score: 10/10.
Metadata QC score: 10/10.
Supported core claims: 4.
Claims flagged for review: 0.
Metadata checks passed: 4.
Metadata issues found: 0.
QC result: Pass.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Rethinking Agency for Genetic Testing Intention among Latinos: Determining Predictors of Intention for Carrier Screening and Cancer Predisposition Testing

First author:
Chavez-Yenter D

Journal:
Genetics in Medicine

DOI:
https://doi.org/10.1016/j.gim.2025.101455

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). doi: https://doi.org/10.1016/j.gim.2025.101455

License:
© 2025 Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics.

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://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/rethinking-agency-genetic-testing-latinos

Zhou Y et al., Cell Genomics - This paper introduces scPrediXcan, which combines a deep-learning model (ctPred) built on Enformer-derived features with single-cell RNA-seq to perform cell-type-specific TWAS via a linearized SNP predictor (ℓ-ctPred), improving gene discovery for T2D and SLE. Key terms: cell-type-specific expression, deep learning, TWAS, single-cell RNA-seq, GWAS.

Study Highlights:
The authors developed ctPred, a compact deep-learning model that uses Enformer epigenomic features to predict cell-type-specific pseudobulk expression. They linearized ctPred into ℓ-ctPred (SNP-based elastic net) so predictions can be used with GWAS summary statistics in S-PrediXcan. Applied to type 2 diabetes and systemic lupus erythematosus, scPrediXcan identifies more candidate causal genes, explains more GWAS loci, and provides cell-type-resolved insights compared with canonical TWAS approaches. Models and weights for 46 cell types are released via predictdb.org for community use.

Conclusion:
scPrediXcan leverages sequence-based deep learning and single-cell data to enable cell-type-level TWAS with higher power and broader gene coverage than canonical methods, offering improved mechanistic resolution for complex traits while noting limitations related to model biases and cis-focused inference.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
scPrediXcan integrates deep learning methods and single-cell data into a cell-type-specific transcriptome-wide association study framework

First author:
Zhou Y

Journal:
Cell Genomics

DOI:
10.1016/j.xgen.2025.100875

Reference:
Zhou Y., Adeluwa T., Zhu L., Salazar-Magaña S., Sumner S., Kim H., Gona S., Nyasimi F., Kulkarni R., Powell J.E., Madduri R., Liu B., Chen M., Im H.K. scPrediXcan integrates deep learning methods and single-cell data into a cell-type-specific transcriptome-wide association study framework. Cell Genomics. 2025;5:100875. doi: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 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

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/scpredixcan-cell-type-twas

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-05-22.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript for substantive scientific content: ctPred architecture, Enformer-derived features, ℓ-ctPred linearization, S-PrediXcan integration, disease results (T2D and SLE) with cell-type specificity, limitations (directionality, distal enhancers, ancestry), and public resources.
- transcript topics: Cell-type-specific TWAS rationale vs bulk tissue TWAS; ctPred architecture and Enformer-derived epigenomic features; ℓ-ctPred linearization and S-PrediXcan integration; Comparison with PEN and scalability considerations; T2D results in islet cell types (gamma, stellate cells) and bulk vs pseudobulk; SLE results in immune cell types (T cells, monocytes; CFB, CXCR5)

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- 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:
- ctPred uses Enformer-derived epigenomic features and a lightweight four-layer MLP to predict cell-type-specific expression
- ℓ-ctPred is a SNP-based elastic net linearization enabling TWAS with GWAS summary statistics (S-PrediXcan)
- ctPred predictions are cross-validated across cell types with high Pearson correlations (0.753–0.892 reported in the article)
- Enformer input window around TSS is 196,608 bp and yields 5,313 epigenomic features
- T2D: scPrediXcan identified 222 candidate genes across 108 LD blocks vs 12 genes across 11 LD blocks (TWAS-pseudobulk) and 111 genes across 64 LD blocks (TWAS-bulk)
- SLE: scPrediXcan identified 129 genes across 24 LD blocks vs 11 (TWAS-pseudobulk) and 54 (TWAS-bulk) across LD blocks

QC result: Pass.

Geilenkeuser J et al., Cell - A Cell paper describing ENVLPE/ENVLPE+, virus-like particles engineered with nucleocytosolic-shuttling Gag-PCP to recruit aptamer-tagged (pe)gRNAs and preferentially package fully assembled CRISPR RNPs. Csy4-mediated 3' protection of pegRNAs and modular minimal budding modules boost prime and base editing in cells and restore gene function in retinal mouse models. Key terms: VLP, prime editing, pegRNA stabilization, Csy4, gene delivery.

Study Highlights:
The authors engineered nucleocytosolic-shuttling Gag-PCP VLPs (ENVLPE) that retrieve assembled Cas effector RNPs via PP7-aptamer-tagged (pe)gRNAs, increasing the fraction of functional cargo. Co-expression of Csy4 stabilizes pegRNA 3' ends and markedly improves prime editing rates during RNP delivery. A minimal homomeric “miniENVLPE” and an enhanced ENVLPE+ with GCN4 coiled coils achieve high per-particle loading of Cas9 and pegRNA. ENVLPE+ outperforms prior eVLP systems ex vivo in primary T cells and in vivo in two mouse retinal disease models, restoring protein expression and visual function.

Conclusion:
ENVLPE+ is a modular VLP platform that preferentially packages intact RNP editors via aptamer-tagged (pe)gRNAs and uses Csy4 to protect pegRNA 3' ends, producing higher per-particle editing efficiency and demonstrating therapeutic potential in ex vivo and in vivo models.

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-05-21.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- 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:
- ENVLPE enables loading of fully assembled editor RNPs by recruiting PP7-tagged gRNAs via Gag-PCP, rather than fusing Cas9 to Gag.
- Csy4/Cas6f protection fortifies the pegRNA 3' end, increasing prime editing efficiency in ENVLPE.
- ENVLPE+ improves per-particle loading and editing efficacy via GCN4 coiled-coil enhancement.
- ENVLPE+ particles carry high cargo per particle (around 78 Cas9 and 77 pegRNAs) and outperform prior VLPs per particle.
- In hiPSC-derived cortical neurons, ENVLPE/ENVLPE+ achieve about 90% base editing at the B2M locus.
- ENVLPE+ enables in vivo prime editing in inherited retinal disease models, restoring gene function and improving visual outcomes.

QC result: Pass.

Pepe D et al., The American Journal of Human Genetics (112:1–21, June 5, 2025) - Pepe et al. show that annotating cancer mutations to the transcripts actually expressed in tumors uncovers previously overlooked non-coding promoter mutations in melanoma. Using TCGA mutation calls, RNA-seq, and an automated Salmon+VEP pipeline, they reclassify multiple hotspots and validate functional effects for IRF3/BCL2L12 and KNSTRN promoter mutations with CRISPR-Cas9 and reporter assays. Key terms: melanoma, non-coding mutations, synonymous mutations, transcript annotation, CRISPR-Cas9.

Study Highlights:
The authors reannotated TCGA melanoma mutation clusters to expressed transcripts and found that 22% (11/50) of identified clusters previously labeled as coding are non-coding promoter mutations. They validated IRF3/BCL2L12 promoter mutations in isogenic CRISPR-Cas9 Mel-ST models and reporter assays, showing reduced IRF3, BCL2L12, and downstream TP53 expression. KNSTRN and SLC27A5 clusters were also reclassified as promoter mutations, and transcription-factor binding analyses implicate disruption of ETS/SP/E2F sites. The study presents a simple Salmon+VEP workflow to improve mutation annotation and notes an association between IRF3/BCL2L12 promoter mutations and poorer immunotherapy response.

Conclusion:
Integrating RNA-seq expression data into mutation annotation reveals functional non-coding promoter mutations missed by reference-transcript annotation; a Salmon+VEP reannotation workflow improves accuracy and highlights clinically relevant non-coding events in melanoma.

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-05-20.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- 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:
- 22% (11/50) mutation clusters in melanoma are misannotated as coding mutations when using expressed transcripts, and are actually non-coding promoter mutations.
- IRF3/BCL2L12 promoter mutations downregulate IRF3, BCL2L12, and TP53 expression in melanoma contexts.
- KNSTRN and SLC27A5 promoter mutations were identified as functional non-coding promoter mutations in melanoma.
- CRISPR-Cas9 knockin in Mel-ST cells demonstrates that IRF3/BCL2L12 promoter mutations reduce IRF3 and BCL2L12 mRNA and protein levels, and influence TP53 pathway components.
- Promoter non-coding mutations in IRF3/BCL2L12 region are associated with a worse response to immunotherapy in melanoma patients.
- Salmon+VEP automated annotation achieves about 90% accuracy in annotating expressed transcripts for mutations in melanoma.

QC result: Pass.

Ratnaike et al et al., The American Journal of Human Genetics - A semi-automated mtDNA reanalysis pipeline using MToolBox and MitoPhen HPO-based phenotype similarity was applied to the Solve-RD cohort, identifying previously undiagnosed mtDNA variants and adding a 0.4% diagnostic uplift. Key terms: mitochondrial DNA, heteroplasmy, MitoPhen, Solve-RD, phenotype similarity.

Study Highlights:
The authors validated an mtDNA calling and prioritization workflow on 42 pre-solved exomes and then applied it to 10,157 ES/GS datasets from 9,923 individuals in Solve-RD. Automated filtering (heteroplasmy ≥1%, MITOMAP annotation, haplogroup exclusion) prioritized 136 mtDNA variants in 135 undiagnosed individuals. An HPO-based phenotype similarity score from MitoPhen (threshold >0.3) was tested and used to prioritize candidates, capturing 34 of 37 confirmed or likely causative diagnoses. The integrated genotype-phenotype pipeline yielded 37 new confirmed or likely mtDNA diagnoses, a 0.4% diagnostic uplift in this heterogeneous cohort.

Conclusion:
Incorporating structured mtDNA analysis and HPO-based phenotype similarity scoring into ES/GS reanalysis can reveal previously undiagnosed mitochondrial diagnoses and modestly increase diagnostic yield in large rare-disease cohorts.

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-05-19.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- 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:
- MToolBox/MITOMAP/MitoPhen-based reanalysis identified 136 mtDNA variants in 135 undiagnosed individuals and produced 37 confirmed or likely mtDNA diagnoses, yielding a 0.4% diagnos
- Phenotype similarity threshold of 0.3 provides high sensitivity; higher thresholds increase specificity; 92% of diagnosed/likely cases had a score > 0.3.
- All diagnostically relevant mtDNA variants were detectable in blood with heteroplasmy > 11%; lower blood heteroplasmy can hinder diagnosis.
- A homoplasmic MT-TL1 variant m.1555A>G confers risk for aminoglycoside-induced deafness; recognition enables avoidance of this drug.
- Incorporating focused mtDNA analysis and phenotype similarity scoring into routine exome/genome reanalysis can reveal actionable mitochondrial findings and modestly increase diagno
- Diversity of study populations is limited; European ancestry predominates (about 96%), underscoring the need for diverse cohorts to ensure generalizability.

QC result: Pass.

Fu Y et al., The American Journal of Human Genetics - Fu et al. (2025) analyze large biobank datasets to quantify how the X chromosome contributes to complex trait heritability and how dosage-compensation biology shapes those effects. Key terms: X chromosome, dosage compensation, X chromosome inactivation, complex trait heritability, sex differences.

Study Highlights:
The study analyzed 48 quantitative traits in 343,695 UK Biobank participants with replication in 412,181 FinnGen individuals. ChrX accounted for about 3% of autosomal heritability and showed higher heritability in males consistent with near-complete X chromosome inactivation. The authors find plausible evidence that partial escape from XCI influences height and identify a female-biased signal near ITM2A. They also report systematically larger active allele effects on chrX versus autosomes, consistent with partial X upregulation.

Conclusion:
The X chromosome makes a modest but meaningful contribution to complex trait genetics shaped by near-complete XCI and partial dosage compensation with autosomes; including chrX in GWAS improves discovery and interpretation of sex-biased effects.

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-05-18.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music

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:
- The X chromosome contributes about 3% of autosomal heritability in the general population.
- Male bias in chrX heritability reflects near-complete X chromosome inactivation (XCI) between sexes.
- Escape from XCI plausibly contributes to height, with ITM2A locus implicated and a female-biased effect near rs59648890.
- Active allele effects on chrX are larger than autosomal effects, approximately 1.6× in males and 1.3× in females.
- Two dosage-compensation mechanisms (XCI and upregulation of chrX) act in concert to balance chrX across the genome.
- Skewed XCI is associated with autoimmune diseases and occurs at higher frequencies in affected individuals.

QC result: Pass.

Stafford-Smith B et al., Genetics in Medicine - Mixed-methods evaluation of how 100,000 Genomes Project participants experienced receiving positive additional findings (PAFs) for cancer or familial hypercholesterolaemia and no additional findings (NAFs), with implications for clinical return pathways and patient support. Key terms: genome sequencing, additional findings, secondary findings, participant experiences, familial hypercholesterolemia.

Study Highlights:
This convergent mixed-methods study surveyed 147 PAF recipients and conducted interviews with 35 PAF and 29 NAF participants across 18 NHS sites. Most participants found AF results useful, expected to act on recommendations, and shared results with family, though cancer PAFs caused more initial shock and distress than FH PAFs. NAF recipients were generally relieved but some misunderstood the scope and limitations of the result and wanted follow-up. Participants supported offering AFs when optional and actionable, while recommending tailored communication and timely clinical support.

Conclusion:
Patient experiences were largely positive and supportive of routinely offering actionable additional findings, but practice should include clearer communication for NAF recipients, condition-tailored approaches, and timely, tailored clinical support for those with positive findings.

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-05-17.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- 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:
- Returning secondary findings is valued by patients and support for routine offering when actionable.
- Cancer-associated AFs produce higher distress than FH-associated AFs.
- No findings (NAF) results are generally positive but can be misunderstood, requiring additional education and follow-up.
- Decisional regret about AFs is generally low and high-regret instances decline after plan development and support.
- A large proportion share AF results with family to enable cascade testing.
- Clinical pathways for AFs must be tailored by condition; a one-size-fits-all approach is insufficient.

QC result: Pass.

Castellano M et al., Cell Genomics - This study shows that extracellular ribonucleases mask the bioactivity of naked extracellular RNA (exRNA). When RNases are inhibited or absent, naked exRNA is internalized, triggers endosomal and cytosolic RNA sensors, and can enable translation of delivered mRNAs. Key terms: extracellular RNA, ribonuclease, TLR13, gymnosis, mRNA translation.

Study Highlights:
Inhibition or absence of extracellular RNases reveals that naked exRNA is spontaneously internalized by diverse cell types and induces pro-inflammatory responses. Internalized exRNA activates endosomal Toll-like receptors (including mouse TLR13 for bacterial rRNA) and, after endosomal escape, cytosolic RIG-I–like receptors via MAVS. Stabilized naked mRNAs can be translated in recipient cells in an RNase-dependent manner. In vivo RNase inhibition amplifies systemic immune activation while RNase-poor compartments (e.g., peritoneal cavity) respond to naked exRNA without added inhibitor.

Conclusion:
Extracellular RNases are a key barrier that prevents immune sensing and functional uptake of naked exRNA; controlling RNase activity reveals that nonvesicular exRNAs can mediate intercellular signaling, activate endosomal and cytosolic RNA sensors, and serve as translatable templates in recipient cells.

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-05-16.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- 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:
- Naked exRNA is bioactive when extracellular RNases are inhibited, triggering pro-inflammatory responses via endosomal TLRs and cytosolic RLRs.
- TLR13 recognizes bacterial 23S ribosomal RNA Ec12 in endosomes; endocytosis is required for the response.
- Naked exRNA can escape endosomes to the cytosol and activate MAVS-dependent cytosolic sensors (RIG-I/MDA5 in human cells).
- Naked mRNA can be translated in recipient cells when RNases are inhibited (gymnotic uptake).
- In vivo, systemic RNases limit exRNA signaling; RI co-injection enhances systemic inflammatory activation; RNase-poor compartments (peritoneal cavity) can respond without RI.
- RNases act as a regulatory shield preventing systemic inflammation; dysregulation of RNase activity relates to autoimmune contexts like lupus.

QC result: Pass.