HGG AdvancesPub Date : 2024-10-10Epub Date: 2024-08-29DOI: 10.1016/j.xhgg.2024.100348
Ralf Tambets, Anastassia Kolde, Peep Kolberg, Michael I Love, Kaur Alasoo
{"title":"Extensive co-regulation of neighboring genes complicates the use of eQTLs in target gene prioritization.","authors":"Ralf Tambets, Anastassia Kolde, Peep Kolberg, Michael I Love, Kaur Alasoo","doi":"10.1016/j.xhgg.2024.100348","DOIUrl":"10.1016/j.xhgg.2024.100348","url":null,"abstract":"<p><p>Identifying causal genes underlying genome-wide association studies (GWASs) is a fundamental problem in human genetics. Although colocalization with gene expression quantitative trait loci (eQTLs) is often used to prioritize GWAS target genes, systematic benchmarking has been limited due to unavailability of large ground truth datasets. Here, we re-analyzed plasma protein QTL data from 3,301 individuals of the INTERVAL cohort together with 131 eQTL Catalog datasets. Focusing on variants located within or close to the affected protein identified 793 proteins with at least one cis-pQTL where we could assume that the most likely causal gene was the gene coding for the protein. We then benchmarked the ability of cis-eQTLs to recover these causal genes by comparing three Bayesian colocalization methods (coloc.susie, coloc.abf, and CLPP) and five Mendelian randomization (MR) approaches (three varieties of inverse-variance weighted MR, MR-RAPS, and MRLocus). We found that assigning fine-mapped pQTLs to their closest protein coding genes outperformed all colocalization methods regarding both precision (71.9%) and recall (76.9%). Furthermore, the colocalization method with the highest recall (coloc.susie - 46.3%) also had the lowest precision (45.1%). Combining evidence from multiple conditionally distinct colocalizing QTLs with MR increased precision to 81%, but this was accompanied by a large reduction in recall to 7.1%. Furthermore, the choice of the MR method greatly affected performance, with the standard inverse-variance-weighted MR often producing many false positives. Our results highlight that linking GWAS variants to target genes remains challenging with eQTL evidence alone, and prioritizing novel targets requires triangulation of evidence from multiple sources.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100348"},"PeriodicalIF":3.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11416642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142112846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
HGG AdvancesPub Date : 2024-10-10Epub Date: 2024-08-02DOI: 10.1016/j.xhgg.2024.100339
Zhaotong Lin
{"title":"A novel framework with automated horizontal pleiotropy adjustment in mendelian randomization.","authors":"Zhaotong Lin","doi":"10.1016/j.xhgg.2024.100339","DOIUrl":"10.1016/j.xhgg.2024.100339","url":null,"abstract":"<p><p>The presence of horizontal pleiotropy in Mendelian randomization (MR) analysis has long been a concern due to its potential to induce substantial bias. In recent years, many robust MR methods have been proposed to address this by relaxing the \"no horizontal pleiotropy\" assumption. Here, we propose a novel two-stage framework called CMR, which integrates a conditional analysis of multiple genetic variants to remove pleiotropy induced by linkage disequilibrium, followed by the application of robust MR methods to model the conditional genetic effect estimates. We demonstrate how the conditional analysis can reduce horizontal pleiotropy and improve the performance of existing MR methods. Extensive simulation studies covering a wide range of scenarios of horizontal pleiotropy showcased the superior performance of the proposed CMR framework over the standard MR framework in which marginal genetic effects are modeled. Moreover, the application of CMR in a negative control outcome analysis and investigation into the causal role of body mass index across various diseases highlighted its potential to deliver more reliable results in real-world applications.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100339"},"PeriodicalIF":3.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11375132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141890278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genotype-phenotype correlation over time in Angelman syndrome: Researching 134 patients.","authors":"Masanori Fujimoto, Yuji Nakamura, Kana Hosoki, Toshihiko Iwaki, Emi Sato, Daisuke Ieda, Ikumi Hori, Yutaka Negishi, Ayako Hattori, Hideaki Shiraishi, Shinji Saitoh","doi":"10.1016/j.xhgg.2024.100342","DOIUrl":"10.1016/j.xhgg.2024.100342","url":null,"abstract":"<p><p>Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by the loss of function of maternal UBE3A. The major cause of AS is a maternal deletion in 15q11.2-q13, and the minor causes are a UBE3A mutation, uniparental disomy (UPD), and imprinting defect (ID). Previous reports suggest that all patients with AS exhibit developmental delay, movement or balance disorders, behavioral characteristics, and speech impairment. In contrast, a substantial number of AS patients with a UBE3A mutation, UPD, or ID were reported not to show these consistent features and to show age-dependent changes in their features. In this study, we investigated 134 patients with AS, including 57 patients with a UBE3A mutation and 48 patients with UPD or ID. Although developmental delay was present in all patients, 20% of patients with AS caused by UPD or ID did not exhibit movement or balance disorders. Differences were also seen in hypopigmentation and seizures, depending on the causes. Moreover, patients with a UBE3A mutation, UPD, or ID tended to show fewer of the specific phenotypes depending on their age. In particular, in patients with UPD or ID, easily provoked laughter and hyperactivity tended to become more pronounced as they aged. Therefore, the clinical features of AS based on cause and age should be understood, and genetic testing should not be limited to patients with the typical clinical features of AS.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100342"},"PeriodicalIF":3.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404063/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142018950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
HGG AdvancesPub Date : 2024-10-10Epub Date: 2024-07-17DOI: 10.1016/j.xhgg.2024.100333
Andrew C Liu, Yang Shen, Carolyn R Serbinski, Hongzhi He, Destino Roman, Mehari Endale, Lindsey Aschbacher-Smith, Katherine A King, Jorge L Granadillo, Isabel López, Darcy A Krueger, Thomas J Dye, David F Smith, John B Hogenesch, Carlos E Prada
{"title":"Clinical and functional studies of MTOR variants in Smith-Kingsmore syndrome reveal deficits of circadian rhythm and sleep-wake behavior.","authors":"Andrew C Liu, Yang Shen, Carolyn R Serbinski, Hongzhi He, Destino Roman, Mehari Endale, Lindsey Aschbacher-Smith, Katherine A King, Jorge L Granadillo, Isabel López, Darcy A Krueger, Thomas J Dye, David F Smith, John B Hogenesch, Carlos E Prada","doi":"10.1016/j.xhgg.2024.100333","DOIUrl":"10.1016/j.xhgg.2024.100333","url":null,"abstract":"<p><p>Heterozygous de novo or inherited gain-of-function mutations in the MTOR gene cause Smith-Kingsmore syndrome (SKS). SKS is a rare autosomal dominant condition, and individuals with SKS display macrocephaly/megalencephaly, developmental delay, intellectual disability, and seizures. A few dozen individuals are reported in the literature. Here, we report a cohort of 28 individuals with SKS that represent nine MTOR pathogenic variants. We conducted a detailed natural history study and found pathophysiological deficits among individuals with SKS in addition to the common neurodevelopmental symptoms. These symptoms include sleep-wake disturbance, hyperphagia, and hyperactivity, indicative of homeostatic imbalance. To characterize these variants, we developed cell models and characterized their functional consequences. We showed that these SKS variants display a range of mechanistic target of rapamycin (mTOR) activities and respond to the mTOR inhibitor, rapamycin, differently. For example, the R1480_C1483del variant we identified here and the previously known C1483F are more active than wild-type controls and less responsive to rapamycin. Further, we showed that SKS mutations dampened circadian rhythms and low-dose rapamycin improved the rhythm amplitude, suggesting that optimal mTOR activity is required for normal circadian function. As SKS is caused by gain-of-function mutations in MTOR, rapamycin was used to treat several patients. While higher doses of rapamycin caused delayed sleep-wake phase disorder in a subset of patients, optimized lower doses improved sleep. Our study expands the clinical and molecular spectrum of SKS and supports further studies for mechanism-guided treatment options to improve sleep-wake behavior and overall health.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100333"},"PeriodicalIF":3.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11342114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141731490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
HGG AdvancesPub Date : 2024-10-10Epub Date: 2024-07-14DOI: 10.1016/j.xhgg.2024.100327
Daphne J Smits, Jordy Dekker, Hannie Douben, Rachel Schot, Helen Magee, Somayeh Bakhtiari, Katrin Koehler, Angela Huebner, Markus Schuelke, Hossein Darvish, Shohreh Vosoogh, Abbas Tafakhori, Melika Jameie, Ehsan Taghiabadi, Yana Wilson, Margit Shah, Marjon A van Slegtenhorst, Evita G Medici-van den Herik, Tjakko J van Ham, Michael C Kruer, Grazia M S Mancini
{"title":"Biallelic NDC1 variants that interfere with ALADIN binding are associated with neuropathy and triple A-like syndrome.","authors":"Daphne J Smits, Jordy Dekker, Hannie Douben, Rachel Schot, Helen Magee, Somayeh Bakhtiari, Katrin Koehler, Angela Huebner, Markus Schuelke, Hossein Darvish, Shohreh Vosoogh, Abbas Tafakhori, Melika Jameie, Ehsan Taghiabadi, Yana Wilson, Margit Shah, Marjon A van Slegtenhorst, Evita G Medici-van den Herik, Tjakko J van Ham, Michael C Kruer, Grazia M S Mancini","doi":"10.1016/j.xhgg.2024.100327","DOIUrl":"10.1016/j.xhgg.2024.100327","url":null,"abstract":"<p><p>Nuclear pore complexes (NPCs) regulate nucleocytoplasmic transport and are anchored in the nuclear envelope by the transmembrane nucleoporin NDC1. NDC1 is essential for post-mitotic NPC assembly and the recruitment of ALADIN to the nuclear envelope. While no human disorder has been associated to one of the three transmembrane nucleoporins, biallelic variants in AAAS, encoding ALADIN, cause triple A syndrome (Allgrove syndrome). Triple A syndrome, characterized by alacrima, achalasia, and adrenal insufficiency, often includes progressive demyelinating polyneuropathy and other neurological complaints. In this report, diagnostic exome and/or RNA sequencing was performed in seven individuals from four unrelated consanguineous families with AAAS-negative triple A syndrome. Molecular and clinical studies followed to elucidate the pathogenic mechanism. The affected individuals presented with intellectual disability, motor impairment, severe demyelinating with secondary axonal polyneuropathy, alacrima, and achalasia. None of the affected individuals has adrenal insufficiency. All individuals presented with biallelic NDC1 in-frame deletions or missense variants that affect amino acids and protein domains required for ALADIN binding. No other significant variants associated with the phenotypic features were reported. Skin fibroblasts derived from affected individuals show decreased recruitment of ALADIN to the NE and decreased post-mitotic NPC insertion, confirming pathogenicity of the variants. Taken together, our results implicate biallelic NDC1 variants in the pathogenesis of polyneuropathy and a triple A-like disorder without adrenal insufficiency, by interfering with physiological NDC1 functions, including the recruitment of ALADIN to the NPC.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100327"},"PeriodicalIF":3.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11375137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141604271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
HGG AdvancesPub Date : 2024-10-10Epub Date: 2024-09-10DOI: 10.1016/j.xhgg.2024.100352
Reza Maroofian, Alistair T Pagnamenta, Alireza Navabazam, Ron Schwessinger, Hannah E Roberts, Maria Lopopolo, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Alireza Haerian, Mojtaba Soltanianzadeh, Mohammad Hadi Noori Kooshki, Samantha J L Knight, Kerry A Miller, Simon J McGowan, Nicolas Chatron, Andrew T Timberlake, Uirá Souto Melo, Stefan Mundlos, David Buck, Stephen R F Twigg, Jenny C Taylor, Andrew O M Wilkie, Eduardo Calpena
{"title":"Familial severe skeletal Class II malocclusion with gingival hyperplasia caused by a complex structural rearrangement at the KCNJ2-KCNJ16 locus.","authors":"Reza Maroofian, Alistair T Pagnamenta, Alireza Navabazam, Ron Schwessinger, Hannah E Roberts, Maria Lopopolo, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Alireza Haerian, Mojtaba Soltanianzadeh, Mohammad Hadi Noori Kooshki, Samantha J L Knight, Kerry A Miller, Simon J McGowan, Nicolas Chatron, Andrew T Timberlake, Uirá Souto Melo, Stefan Mundlos, David Buck, Stephen R F Twigg, Jenny C Taylor, Andrew O M Wilkie, Eduardo Calpena","doi":"10.1016/j.xhgg.2024.100352","DOIUrl":"10.1016/j.xhgg.2024.100352","url":null,"abstract":"<p><p>The aim of this work was to identify the underlying genetic cause in a four-generation family segregating an unusual phenotype comprising a severe form of skeletal Class II malocclusion with gingival hyperplasia. SNP array identified a copy number gain on chromosome 1 (chr1); however, this chromosomal region did not segregate correctly in the extended family. Exome sequencing also failed to identify a candidate causative variant but highlighted co-segregating genetic markers on chr17 and chr19. Short- and long-read genome sequencing allowed us to pinpoint and characterize at nucleotide-level resolution a chromothripsis-like complex rearrangement (CR) inserted into the chr17 co-segregating region at the KCNJ2-SOX9 locus. The CR involved the gain of five different regions from chr1 that are shuffled, chained, and inserted as a single block (∼828 kb) at chr17q24.3. The inserted sequences contain craniofacial enhancers that are predicted to interact with KCNJ2/KCNJ16 through neo-topologically associating domain (TAD) formation to induce ectopic activation. Our findings suggest that the CR inserted at chr17q24.3 is the cause of the severe skeletal Class II malocclusion with gingival hyperplasia in this family and expands the panoply of phenotypes linked to variation at the KCNJ2-SOX9 locus. In addition, we highlight a previously overlooked potential role for misregulation of the KCNJ2/KCNJ16 genes in the pathomechanism of gingival hyperplasia associated with deletions and other rearrangements of the 17q24.2-q24.3 region (MIM 135400).</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100352"},"PeriodicalIF":3.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11465088/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
HGG AdvancesPub Date : 2024-10-10Epub Date: 2024-08-27DOI: 10.1016/j.xhgg.2024.100347
Pratik Ramprasad, Nidhi Pai, Wei Pan
{"title":"Enhancing personalized gene expression prediction from DNA sequences using genomic foundation models.","authors":"Pratik Ramprasad, Nidhi Pai, Wei Pan","doi":"10.1016/j.xhgg.2024.100347","DOIUrl":"10.1016/j.xhgg.2024.100347","url":null,"abstract":"<p><p>Artificial intelligence (AI)/deep learning (DL) models that predict molecular phenotypes like gene expression directly from DNA sequences have recently emerged. While these models have proven effective at capturing the variation across genes, their ability to explain inter-individual differences has been limited. We hypothesize that the performance gap can be narrowed through the use of pre-trained embeddings from the Nucleotide Transformer, a large foundation model trained on 3,000+ genomes. We train a transformer model using the pre-trained embeddings and compare its predictive performance to Enformer, the current state-of-the-art model, using genotype and expression data from 290 individuals. Our model significantly outperforms Enformer in terms of correlation across individuals, and narrows the performance gap with an elastic net regression approach that uses just the genetic variants as predictors. Although simple regression models have their advantages in personalized prediction tasks, DL approaches based on foundation models pre-trained on diverse genomes have unique strengths in flexibility and interpretability. With further methodological and computational improvements with more training data, these models may eventually predict molecular phenotypes from DNA sequences with an accuracy surpassing that of regression-based approaches. Our work demonstrates the potential for large pre-trained AI/DL models to advance functional genomics.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100347"},"PeriodicalIF":3.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11416237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142112845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
HGG AdvancesPub Date : 2024-07-18Epub Date: 2024-05-14DOI: 10.1016/j.xhgg.2024.100307
Dominique L Brooks, Kiran Musunuru, Xiao Wang
{"title":"Response to Harding and Martinez.","authors":"Dominique L Brooks, Kiran Musunuru, Xiao Wang","doi":"10.1016/j.xhgg.2024.100307","DOIUrl":"10.1016/j.xhgg.2024.100307","url":null,"abstract":"","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":"5 3","pages":"100307"},"PeriodicalIF":3.3,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11153232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141155619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
HGG AdvancesPub Date : 2024-07-18Epub Date: 2024-05-10DOI: 10.1016/j.xhgg.2024.100306
Jocelyn N Plowman, Evanjalina J Matoy, Lavanya V Uppala, Samantha B Draves, Cynthia J Watson, Bridget A Sefranek, Mark L Stacey, Samuel P Anderson, Michael A Belshan, Elizabeth E Blue, Chad D Huff, Yusi Fu, Holly A F Stessman
{"title":"Targeted sequencing for hereditary breast and ovarian cancer in BRCA1/2-negative families reveals complex genetic architecture and phenocopies.","authors":"Jocelyn N Plowman, Evanjalina J Matoy, Lavanya V Uppala, Samantha B Draves, Cynthia J Watson, Bridget A Sefranek, Mark L Stacey, Samuel P Anderson, Michael A Belshan, Elizabeth E Blue, Chad D Huff, Yusi Fu, Holly A F Stessman","doi":"10.1016/j.xhgg.2024.100306","DOIUrl":"10.1016/j.xhgg.2024.100306","url":null,"abstract":"<p><p>Approximately 20% of breast cancer cases are attributed to increased family risk, yet variation in BRCA1/2 can only explain 20%-25% of cases. Historically, only single gene or single variant testing were common in at-risk family members, and further sequencing studies were rarely offered after negative results. In this study, we applied an efficient and inexpensive targeted sequencing approach to provide molecular diagnoses in 245 human samples representing 134 BRCA mutation-negative (BRCAX) hereditary breast and ovarian cancer (HBOC) families recruited from 1973 to 2019 by Dr. Henry Lynch. Sequencing identified 391 variants, which were functionally annotated and ranked based on their predicted clinical impact. Known pathogenic CHEK2 breast cancer variants were identified in five BRCAX families in this study. While BRCAX was an inclusion criterion for this study, we still identified a pathogenic BRCA2 variant (p.Met192ValfsTer13) in one family. A portion of BRCAX families could be explained by other hereditary cancer syndromes that increase HBOC risk: Li-Fraumeni syndrome (gene: TP53) and Lynch syndrome (gene: MSH6). Interestingly, many families carried additional variants of undetermined significance (VOUSs) that may further modify phenotypes of syndromic family members. Ten families carried more than one potential VOUS, suggesting the presence of complex multi-variant families. Overall, nine BRCAX HBOC families in our study may be explained by known likely pathogenic/pathogenic variants, and six families carried potential VOUSs, which require further functional testing. To address this, we developed a functional assay where we successfully re-classified one family's PMS2 VOUS as benign.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100306"},"PeriodicalIF":3.3,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11166883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140909245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
HGG AdvancesPub Date : 2024-07-18Epub Date: 2024-07-02DOI: 10.1016/j.xhgg.2024.100324
Rebecca Meyer-Schuman, Allison R Cale, Jennifer A Pierluissi, Kira E Jonatzke, Young N Park, Guy M Lenk, Stephanie N Oprescu, Marina A Grachtchouk, Andrzej A Dlugosz, Asim A Beg, Miriam H Meisler, Anthony Antonellis
{"title":"A model organism pipeline provides insight into the clinical heterogeneity of TARS1 loss-of-function variants.","authors":"Rebecca Meyer-Schuman, Allison R Cale, Jennifer A Pierluissi, Kira E Jonatzke, Young N Park, Guy M Lenk, Stephanie N Oprescu, Marina A Grachtchouk, Andrzej A Dlugosz, Asim A Beg, Miriam H Meisler, Anthony Antonellis","doi":"10.1016/j.xhgg.2024.100324","DOIUrl":"10.1016/j.xhgg.2024.100324","url":null,"abstract":"<p><p>Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed, essential enzymes that complete the first step of protein translation: ligation of amino acids to cognate tRNAs. Genes encoding ARSs have been implicated in myriad dominant and recessive phenotypes, the latter often affecting multiple tissues but with frequent involvement of the central and peripheral nervous systems, liver, and lungs. Threonyl-tRNA synthetase (TARS1) encodes the enzyme that ligates threonine to tRNA<sup>THR</sup> in the cytoplasm. To date, TARS1 variants have been implicated in a recessive brittle hair phenotype. To better understand TARS1-related recessive phenotypes, we engineered three TARS1 missense variants at conserved residues and studied these variants in Saccharomyces cerevisiae and Caenorhabditis elegans models. This revealed two loss-of-function variants, including one hypomorphic allele (R433H). We next used R433H to study the effects of partial loss of TARS1 function in a compound heterozygous mouse model (R432H/null). This model presents with phenotypes reminiscent of patients with TARS1 variants and with distinct lung and skin defects. This study expands the potential clinical heterogeneity of TARS1-related recessive disease, which should guide future clinical and genetic evaluations of patient populations.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100324"},"PeriodicalIF":3.3,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11284558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141493724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}