Hao Huang, Russel Keathley, Ujin Kim, Horacio Cardenas, Ping Xie, Jianjun Wei, Ernst Lengyel, Kenneth P Nephew, Guangyuan Zhao, Zhen Fu, Emma L Barber, Masha Kocherginsky, Victoria Bae-Jump, Bin Zhang, Daniela Matei
{"title":"Comparative transcriptomic, epigenomic and immunological analyses identify drivers of disparity in high-grade serous ovarian cancer.","authors":"Hao Huang, Russel Keathley, Ujin Kim, Horacio Cardenas, Ping Xie, Jianjun Wei, Ernst Lengyel, Kenneth P Nephew, Guangyuan Zhao, Zhen Fu, Emma L Barber, Masha Kocherginsky, Victoria Bae-Jump, Bin Zhang, Daniela Matei","doi":"10.1038/s41525-024-00448-2","DOIUrl":"10.1038/s41525-024-00448-2","url":null,"abstract":"<p><p>Black women face the highest mortality-to-incidence ratio from high grade serous ovarian cancer (HGSOC). This study investigated biological differences in HGSOC tumors from Black vs. White women. HGSOC from 35 Black and 31 White patients were analyzed by Infinium Methyation-EPIC array and RNA sequencing. 191 CpG sites were differentially methylated (FDR < 0.05, β value change> 10%) and 277 genes were differentially expressed (FDR < 0.05). Gene Ontology identified enriched pathways related to DNA damage response, p53/apoptosis signaling, and cholesterol/lipid metabolism directly connected with genes like INSR, FOXA1 and FOXB1. INSR and FOXA1 knockdown enhanced cisplatin sensitivity and inhibited cell proliferation and colony formation. Tumors from Black patients were infiltrated by fewer CD4+ naïve and regulatory T-cells. Overall, differences in DNA methylation, transcriptomic profiles and immune cell infiltration were detected in tumors from Black vs. White patients. Further investigation is warranted into how these differences may affect treatment response and outcomes in Black women.</p>","PeriodicalId":19273,"journal":{"name":"NPJ Genomic Medicine","volume":"9 1","pages":"64"},"PeriodicalIF":4.7,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11612190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142770760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Courtney E French, Nancy C Andrews, Alan H Beggs, Philip M Boone, Catherine A Brownstein, Maya Chopra, Janet Chou, Wendy K Chung, Alissa M D'Gama, Ryan N Doan, Darius Ebrahimi-Fakhari, Richard D Goldstein, Mira Irons, Christina Jacobsen, Margaret Kenna, Ted Lee, Jill A Madden, Amar J Majmundar, Nina Mann, Sarah U Morton, Annapurna Poduri, Adrienne G Randolph, Amy E Roberts, Stephanie Roberts, Matthew G Sampson, Diane D Shao, Wanqing Shao, Aditi Sharma, Eliot Shearer, Akiko Shimamura, Scott B Snapper, Siddharth Srivastava, Jay R Thiagarajah, Mary C Whitman, Monica H Wojcik, Shira Rockowitz, Piotr Sliz
{"title":"Hospital-wide access to genomic data advanced pediatric rare disease research and clinical outcomes.","authors":"Courtney E French, Nancy C Andrews, Alan H Beggs, Philip M Boone, Catherine A Brownstein, Maya Chopra, Janet Chou, Wendy K Chung, Alissa M D'Gama, Ryan N Doan, Darius Ebrahimi-Fakhari, Richard D Goldstein, Mira Irons, Christina Jacobsen, Margaret Kenna, Ted Lee, Jill A Madden, Amar J Majmundar, Nina Mann, Sarah U Morton, Annapurna Poduri, Adrienne G Randolph, Amy E Roberts, Stephanie Roberts, Matthew G Sampson, Diane D Shao, Wanqing Shao, Aditi Sharma, Eliot Shearer, Akiko Shimamura, Scott B Snapper, Siddharth Srivastava, Jay R Thiagarajah, Mary C Whitman, Monica H Wojcik, Shira Rockowitz, Piotr Sliz","doi":"10.1038/s41525-024-00441-9","DOIUrl":"10.1038/s41525-024-00441-9","url":null,"abstract":"<p><p>Boston Children's Hospital has established a genomic sequencing and analysis research initiative to improve clinical care for pediatric rare disease patients. Through the Children's Rare Disease Collaborative (CRDC), the hospital offers CLIA-grade exome and genome sequencing, along with other sequencing types, to patients enrolled in specialized rare disease research studies. The data, consented for broad research use, are harmonized and analyzed with CRDC-supported variant interpretation tools. Since its launch, 66 investigators representing 26 divisions and 45 phenotype-based cohorts have joined the CRDC. These studies enrolled 4653 families, with 35% of analyzed cases having a finding either confirmed or under further investigation. This accessible and harmonized genomics platform also supports additional institutional data collections, research and clinical, and now encompasses 13,800+ patients and their families. This has fostered new research projects and collaborations, increased genetic diagnoses and accelerated innovative research via integration of genomics research with clinical care.</p>","PeriodicalId":19273,"journal":{"name":"NPJ Genomic Medicine","volume":"9 1","pages":"60"},"PeriodicalIF":4.7,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11612168/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142770761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jong Hyeon Ahn, Jihoon G Yoon, Jaeso Cho, Seungbok Lee, Sheehyun Kim, Man Jin Kim, Soo Yeon Kim, Soon-Tae Lee, Kon Chu, Sang Kun Lee, Han-Joon Kim, Jinyoung Youn, Ja-Hyun Jang, Jong-Hee Chae, Jangsup Moon, Jin Whan Cho
{"title":"Implementing genomic medicine in clinical practice for adults with undiagnosed rare diseases.","authors":"Jong Hyeon Ahn, Jihoon G Yoon, Jaeso Cho, Seungbok Lee, Sheehyun Kim, Man Jin Kim, Soo Yeon Kim, Soon-Tae Lee, Kon Chu, Sang Kun Lee, Han-Joon Kim, Jinyoung Youn, Ja-Hyun Jang, Jong-Hee Chae, Jangsup Moon, Jin Whan Cho","doi":"10.1038/s41525-024-00449-1","DOIUrl":"10.1038/s41525-024-00449-1","url":null,"abstract":"<p><p>The global burden of undiagnosed diseases, particularly in adults, is rising due to their significant socioeconomic impact. To address this, we enrolled 232 adult probands with undiagnosed conditions, utilizing bioinformatics tools for genetic analysis. Alongside exome and genome sequencing, repeat-primed PCR and Cas9-mediated nanopore sequencing were applied to suspected short tandem repeat disorders. Probands were classified into probable genetic (n = 128) or uncertain (n = 104) origins. The study found genetic causes in 66 individuals (28.4%) and non-genetic causes in 12 (5.2%), with a longer diagnostic journey for those in the probable genetic group or with pediatric symptom onset, emphasizing the need for increased efforts in these populations. Genetic diagnoses facilitated effective surveillance, cascade screening, drug repurposing, and pregnancy planning. This study demonstrates that integrating sequencing technologies improves diagnostic accuracy, may shorten the time to diagnosis, and enhances personalized management for adults with undiagnosed diseases.</p>","PeriodicalId":19273,"journal":{"name":"NPJ Genomic Medicine","volume":"9 1","pages":"63"},"PeriodicalIF":4.7,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11604660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142751414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Achille Vc Manirakiza, Shakuntala Baichoo, Annette Uwineza, Damas Dukundane, Francois Uwinkindi, Edouard Ngendahayo, Fidel Rubagumya, Emmanuel Muhawenimana, Nicaise Nsabimana, Innocent Nzeyimana, Theoneste Maniragaba, Faustin Ntirenganya, Ephrem Rurangwa, Pacifique Mugenzi, Janviere Mutamuliza, Daniel Runanira, Brandon A Niyibizi, Eulade Rugengamanzi, Jeffrey Besada, Sarah M Nielsen, Brianna Bucknor, Robert L Nussbaum, Diane Koeller, Caroline Andrews, Leon Mutesa, Temidayo Fadelu, Timothy R Rebbeck
{"title":"Germline sequence variation in cancer genes in Rwandan breast and prostate cancer cases.","authors":"Achille Vc Manirakiza, Shakuntala Baichoo, Annette Uwineza, Damas Dukundane, Francois Uwinkindi, Edouard Ngendahayo, Fidel Rubagumya, Emmanuel Muhawenimana, Nicaise Nsabimana, Innocent Nzeyimana, Theoneste Maniragaba, Faustin Ntirenganya, Ephrem Rurangwa, Pacifique Mugenzi, Janviere Mutamuliza, Daniel Runanira, Brandon A Niyibizi, Eulade Rugengamanzi, Jeffrey Besada, Sarah M Nielsen, Brianna Bucknor, Robert L Nussbaum, Diane Koeller, Caroline Andrews, Leon Mutesa, Temidayo Fadelu, Timothy R Rebbeck","doi":"10.1038/s41525-024-00446-4","DOIUrl":"10.1038/s41525-024-00446-4","url":null,"abstract":"<p><p>Cancer genetic data from Sub-Saharan African (SSA) are limited. Patients with female breast (fBC), male breast (mBC), and prostate cancer (PC) in Rwanda underwent germline genetic testing and counseling. Demographic and disease-specific information was collected. A multi-cancer gene panel was used to identify germline Pathogenic Variants (PV) and Variants of Uncertain Significance (VUS). 400 patients (201 with BC and 199 with PC) were consented and recruited to the study. Data was available for 342 patients: 180 with BC (175 women and 5 men) and 162 men with PC. PV were observed in 18.3% fBC, 4.3% PC, and 20% mBC. BRCA2 was the most common PV. Among non-PV carriers, 65% had ≥1 VUS: 31.8% in PC and 33.6% in BC (female and male). Our findings highlight the need for germline genetic testing and counseling in cancer management in SSA.</p>","PeriodicalId":19273,"journal":{"name":"NPJ Genomic Medicine","volume":"9 1","pages":"61"},"PeriodicalIF":4.7,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11586404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Common protein-altering variant in GFAP is associated with white matter lesions in the older Japanese population.","authors":"Yoshihiko Furuta, Masato Akiyama, Naoki Hirabayashi, Takanori Honda, Mao Shibata, Tomoyuki Ohara, Jun Hata, Chikashi Terao, Yukihide Momozawa, Yasuko Tatewaki, Yasuyuki Taki, Shigeyuki Nakaji, Tetsuya Maeda, Kenjiro Ono, Masaru Mimura, Kenji Nakashima, Jun-Ichi Iga, Minoru Takebayashi, Toshiharu Ninomiya","doi":"10.1038/s41525-024-00431-x","DOIUrl":"10.1038/s41525-024-00431-x","url":null,"abstract":"<p><p>The genetic architecture of white matter lesions (WMLs) in Asian populations has not been well-characterized. Here, we performed a genome-wide association study (GWAS) to identify loci associated with the WML volume. Brain MRI and DNA samples were collected from 9479 participants in the Japan Prospective Studies Collaboration for Aging and Dementia (JPSC-AD). The GWAS confirmed three known WML-associated loci (SH3PXD2A, GFAP, and TRIM47). The lead variant of GFAP was a common missense variant (p.D295N) in East Asians. Meta-GWAS using the publicly available summary statistics of UK Biobank identified one previously unreported locus 6q23.2 (SLC2A12). Integration with expression quantitative trait locus data implied the newly identified locus affects SLC2A12 expression. The effect sizes of 20 lead variants at the WML-associated loci were moderately correlated between JPSC-AD and UK Biobank. These results indicate that the alteration in GFAP protein caused by the common missense variant in East Asians influences the WML volume.</p>","PeriodicalId":19273,"journal":{"name":"NPJ Genomic Medicine","volume":"9 1","pages":"59"},"PeriodicalIF":4.7,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561265/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Denis M Nyaga, Peter Tsai, Clare Gebbie, Hui Hui Phua, Patrick Yap, Polona Le Quesne Stabej, Sophie Farrow, Jing Rong, Gergely Toldi, Eric Thorstensen, Zornitza Stark, Sebastian Lunke, Kimberley Gamet, Jodi Van Dyk, Mark Greenslade, Justin M O'Sullivan
{"title":"Benchmarking nanopore sequencing and rapid genomics feasibility: validation at a quaternary hospital in New Zealand.","authors":"Denis M Nyaga, Peter Tsai, Clare Gebbie, Hui Hui Phua, Patrick Yap, Polona Le Quesne Stabej, Sophie Farrow, Jing Rong, Gergely Toldi, Eric Thorstensen, Zornitza Stark, Sebastian Lunke, Kimberley Gamet, Jodi Van Dyk, Mark Greenslade, Justin M O'Sullivan","doi":"10.1038/s41525-024-00445-5","DOIUrl":"10.1038/s41525-024-00445-5","url":null,"abstract":"<p><p>Approximately 200 critically ill infants and children in New Zealand are in high-dependency care, many suspected of having genetic conditions, requiring scalable genomic testing. We adopted an acute care genomics protocol from an accredited laboratory and established a clinical pipeline using Oxford Nanopore Technologies PromethION 2 solo system and Fabric GEM™ software. Benchmarking of the pipeline was performed using Global Alliance for Genomics and Health benchmarking tools and Genome in a Bottle samples (HG002-HG007). Evaluation of single nucleotide variants resulted in a precision and recall of 0.997 and 0.992, respectively. Small indel identification approached a precision of 0.922 and recall of 0.838. Large genomic variations from Coriell Copy Number Variation Reference Panel 1 were reliably detected with ~2 M long reads. Finally, we present results obtained from fourteen trio samples, ten of which were processed in parallel with a clinically accredited short-read rapid genomic testing pipeline (Newborn Genomics Programme; NCT06081075; 2023-10-12).</p>","PeriodicalId":19273,"journal":{"name":"NPJ Genomic Medicine","volume":"9 1","pages":"57"},"PeriodicalIF":4.7,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Riccardo Sangermano, Priya Gupta, Cherrell Price, Jinu Han, Julien Navarro, Christel Condroyer, Emily M Place, Aline Antonio, Shizuo Mukai, Xavier Zanlonghi, José-Alain Sahel, Stephanie DiTroia, Emily O'Heir, Jacque L Duncan, Eric A Pierce, Christina Zeitz, Isabelle Audo, Rachel M Huckfeldt, Kinga M Bujakowska
{"title":"Coding and non-coding variants in the ciliopathy gene CFAP410 cause early-onset non-syndromic retinal degeneration.","authors":"Riccardo Sangermano, Priya Gupta, Cherrell Price, Jinu Han, Julien Navarro, Christel Condroyer, Emily M Place, Aline Antonio, Shizuo Mukai, Xavier Zanlonghi, José-Alain Sahel, Stephanie DiTroia, Emily O'Heir, Jacque L Duncan, Eric A Pierce, Christina Zeitz, Isabelle Audo, Rachel M Huckfeldt, Kinga M Bujakowska","doi":"10.1038/s41525-024-00439-3","DOIUrl":"10.1038/s41525-024-00439-3","url":null,"abstract":"<p><p>Inherited retinal degenerations are blinding genetic disorders characterized by high genetic and phenotypic heterogeneity. In this retrospective study, we describe sixteen families with early-onset non-syndromic retinal degenerations in which affected probands carried rare bi-allelic variants in CFAP410, a ciliary gene previously associated with recessive Jeune syndrome. We detected twelve variants, eight of which were novel, including c.373+91A>G, which led to aberrant splicing. To our knowledge this is the first likely pathogenic deep-intronic variant identified in this gene. Analysis of all reported and novel CFAP410 variants revealed no clear correlation between the severity of the CFAP410-associated phenotypes and the identified causal variants. This is supported by the fact that the frequently encountered missense variant p.(Arg73Pro), often found in syndromic cases, was also associated with non-syndromic retinal degeneration. This study expands the current knowledge of CFAP410-associated ciliopathy by enriching its mutational landscape and supports its association with non-syndromic retinal degeneration.</p>","PeriodicalId":19273,"journal":{"name":"NPJ Genomic Medicine","volume":"9 1","pages":"58"},"PeriodicalIF":4.7,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Simo Li, Sanami Takada, Ghada M H Abdel-Salam, Mohamed S Abdel-Hamid, Maha S Zaki, Mahmoud Y Issa, Aida M S Salem, Eriko Koshimizu, Atsushi Fujita, Ryoko Fukai, Toshio Ohshima, Naomichi Matsumoto, Noriko Miyake
{"title":"Biallelic loss-of-function variants in GON4L cause microcephaly and brain structure abnormalities.","authors":"Simo Li, Sanami Takada, Ghada M H Abdel-Salam, Mohamed S Abdel-Hamid, Maha S Zaki, Mahmoud Y Issa, Aida M S Salem, Eriko Koshimizu, Atsushi Fujita, Ryoko Fukai, Toshio Ohshima, Naomichi Matsumoto, Noriko Miyake","doi":"10.1038/s41525-024-00437-5","DOIUrl":"10.1038/s41525-024-00437-5","url":null,"abstract":"<p><p>We identified two homozygous truncating variants in GON4L [NM_001282860.2:c.62_63del, p.(Gln21Argfs*12) and c.5517+1G>A] in two unrelated families who presented prenatal-onset growth impairment, microcephaly, characteristic face, situs inversus, and developmental delay. The frameshift variant is predicted to invoke nonsense-mediated mRNA decay of all five known GON4L isoforms resulting in the complete loss of GON4L function. The splice site variant located at a region specific to the longer isoforms; therefore, defects of long GON4L isoforms may explain the phenotypes observed in the three patients. Knockdown of Gon4l in rat PC12 cells suppressed neurite outgrowth in vitro. gon4lb knockdown and knockout zebrafish successfully recapitulated the patients' phenotypes including craniofacial abnormalities. We also observed situs inversus in gon4lb-knockout zebrafish embryo. To our knowledge, the relationship between craniofacial abnormalities or situs inversus and gon4lb has not been reported before. Thus, our data provide evidence that GON4L is involved in craniofacial and left-right patterning during development.</p>","PeriodicalId":19273,"journal":{"name":"NPJ Genomic Medicine","volume":"9 1","pages":"55"},"PeriodicalIF":4.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11538285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kheireddin Mufti, Miguel Cordova, Erika N Scott, Jessica N Trueman, Jessica M Lovnicki, Catrina M Loucks, Shahrad R Rassekh, Colin J D Ross, Bruce C Carleton
{"title":"Genomic variations associated with risk and protection against vincristine-induced peripheral neuropathy in pediatric cancer patients.","authors":"Kheireddin Mufti, Miguel Cordova, Erika N Scott, Jessica N Trueman, Jessica M Lovnicki, Catrina M Loucks, Shahrad R Rassekh, Colin J D Ross, Bruce C Carleton","doi":"10.1038/s41525-024-00443-7","DOIUrl":"10.1038/s41525-024-00443-7","url":null,"abstract":"<p><p>Vincristine-induced peripheral neuropathy is a common and highly debilitating toxicity from vincristine treatment that affects quality of life and often requires dose reduction, potentially affecting survival. Although previous studies demonstrated genetic factors are associated with vincristine neuropathy risk, the clinical relevance of most identified variants is limited by small sample sizes and unclear clinical phenotypes. A genome-wide association study was conducted in 1100 cases and controls matched by vincristine dose and genetic ancestry, uncovering a statistically significant (p < 5.0 × 10<sup>-8</sup>) variant in MCM3AP gene that substantially increases the risk of neuropathy and 12 variants protective against neuropathy within/near SPDYA, METTL8, PDE4D, FBN2, ZFAND3, NFIB, PAPPA, LRRTM3, NRG3, VTI1A, ARHGAP5, and ACTN1. A follow-up pathway analysis reveals the involvement of four key pathways, including nerve structure and development, myelination, neuronal transmission, and cytoskeleton/microfibril function pathways. These findings present potential actionable genomic markers of vincristine neuropathy and offer opportunities for tailored interventions to improve vincristine safety in children with cancer. This study is registered with ClinicalTrials.gov under the title National Active Surveillance Network and Pharmacogenomics of Adverse Drug Reactions in Children (ID NCT00414115, registered on December 21, 2006).</p>","PeriodicalId":19273,"journal":{"name":"NPJ Genomic Medicine","volume":"9 1","pages":"56"},"PeriodicalIF":4.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11538333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Guy Karlebach, Robin Steinhaus, Daniel Danis, Maeva Devoucoux, Olga Anczuków, Gloria Sheynkman, Dominik Seelow, Peter N Robinson
{"title":"Alternative splicing is coupled to gene expression in a subset of variably expressed genes.","authors":"Guy Karlebach, Robin Steinhaus, Daniel Danis, Maeva Devoucoux, Olga Anczuków, Gloria Sheynkman, Dominik Seelow, Peter N Robinson","doi":"10.1038/s41525-024-00432-w","DOIUrl":"10.1038/s41525-024-00432-w","url":null,"abstract":"<p><p>Numerous factors regulate alternative splicing of human genes at a co-transcriptional level. However, how alternative splicing depends on the regulation of gene expression is poorly understood. We leveraged data from the Genotype-Tissue Expression (GTEx) project to show a significant association of gene expression and splicing for 6874 (4.9%) of 141,043 exons in 1106 (13.3%) of 8314 genes with substantially variable expression in nine GTEx tissues. About half of these exons demonstrate higher inclusion with higher gene expression, and half demonstrate higher exclusion, with the observed direction of coupling being highly consistent across different tissues and in external datasets. The exons differ with respect to multiple characteristics and are enriched for hundreds of isoform-specific Gene Ontology annotations suggesting an important regulatory mechanism. Notably, splicing-expression coupling of exons with roles in JUN and MAP kinase signalling could play an important role during cell division.</p>","PeriodicalId":19273,"journal":{"name":"NPJ Genomic Medicine","volume":"9 1","pages":"54"},"PeriodicalIF":4.7,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11535429/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142576706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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