Pub Date : 2024-06-28DOI: 10.1016/j.xhgg.2024.100323
Jannik Boos, Caspar I van der Made, Gayatri Ramakrishnan, Eamon Coughlan, Rosanna Asselta, Britt-Sabina Löscher, Luca V C Valenti, Rafael de Cid, Luis Bujanda, Antonio Julià, Erola Pairo-Castineira, J Kenneth Baillie, Sandra May, Berina Zametica, Julia Heggemann, Agustín Albillos, Jesus M Banales, Jordi Barretina, Natalia Blay, Paolo Bonfanti, Maria Buti, Javier Fernandez, Sara Marsal, Daniele Prati, Luisa Ronzoni, Nicoletta Sacchi, Joachim L Schultze, Olaf Riess, Andre Franke, Konrad Rawlik, David Ellinghaus, Alexander Hoischen, Axel Schmidt, Kerstin U Ludwig
Despite extensive global research into genetic predisposition for severe COVID-19, knowledge on the role of rare host genetic variants and their relation to other risk factors remains limited. Here, 52 genes with prior etiological evidence were sequenced in 1,772 severe COVID-19 cases and 5,347 population-based controls from Spain/Italy. Rare deleterious TLR7 variants were present in 2.4% of young (<60 years) cases with no reported clinical risk factors (n = 378), compared to 0.24% of controls (odds ratio [OR] = 12.3, p = 1.27 × 10-10). Incorporation of the results of either functional assays or protein modeling led to a pronounced increase in effect size (ORmax = 46.5, p = 1.74 × 10-15). Association signals for the X-chromosomal gene TLR7 were also detected in the female-only subgroup, suggesting the existence of additional mechanisms beyond X-linked recessive inheritance in males. Additionally, supporting evidence was generated for a contribution to severe COVID-19 of the previously implicated genes IFNAR2, IFIH1, and TBK1. Our results refine the genetic contribution of rare TLR7 variants to severe COVID-19 and strengthen evidence for the etiological relevance of genes in the interferon signaling pathway.
{"title":"Stratified analyses refine association between TLR7 rare variants and severe COVID-19.","authors":"Jannik Boos, Caspar I van der Made, Gayatri Ramakrishnan, Eamon Coughlan, Rosanna Asselta, Britt-Sabina Löscher, Luca V C Valenti, Rafael de Cid, Luis Bujanda, Antonio Julià, Erola Pairo-Castineira, J Kenneth Baillie, Sandra May, Berina Zametica, Julia Heggemann, Agustín Albillos, Jesus M Banales, Jordi Barretina, Natalia Blay, Paolo Bonfanti, Maria Buti, Javier Fernandez, Sara Marsal, Daniele Prati, Luisa Ronzoni, Nicoletta Sacchi, Joachim L Schultze, Olaf Riess, Andre Franke, Konrad Rawlik, David Ellinghaus, Alexander Hoischen, Axel Schmidt, Kerstin U Ludwig","doi":"10.1016/j.xhgg.2024.100323","DOIUrl":"10.1016/j.xhgg.2024.100323","url":null,"abstract":"<p><p>Despite extensive global research into genetic predisposition for severe COVID-19, knowledge on the role of rare host genetic variants and their relation to other risk factors remains limited. Here, 52 genes with prior etiological evidence were sequenced in 1,772 severe COVID-19 cases and 5,347 population-based controls from Spain/Italy. Rare deleterious TLR7 variants were present in 2.4% of young (<60 years) cases with no reported clinical risk factors (n = 378), compared to 0.24% of controls (odds ratio [OR] = 12.3, p = 1.27 × 10<sup>-10</sup>). Incorporation of the results of either functional assays or protein modeling led to a pronounced increase in effect size (OR<sub>max</sub> = 46.5, p = 1.74 × 10<sup>-15</sup>). Association signals for the X-chromosomal gene TLR7 were also detected in the female-only subgroup, suggesting the existence of additional mechanisms beyond X-linked recessive inheritance in males. Additionally, supporting evidence was generated for a contribution to severe COVID-19 of the previously implicated genes IFNAR2, IFIH1, and TBK1. Our results refine the genetic contribution of rare TLR7 variants to severe COVID-19 and strengthen evidence for the etiological relevance of genes in the interferon signaling pathway.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11320601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141471225","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}
Pub Date : 2024-04-11Epub Date: 2024-02-23DOI: 10.1016/j.xhgg.2024.100279
Yao Fu, Jennifer A Kelly, Jaanam Gopalakrishnan, Richard C Pelikan, Kandice L Tessneer, Satish Pasula, Kiely Grundahl, David A Murphy, Patrick M Gaffney
We designed a massively parallel reporter assay (MPRA) in an Epstein-Barr virus transformed B cell line to directly characterize the potential for histone post-translational modifications, i.e., histone quantitative trait loci (hQTLs), expression QTLs (eQTLs), and variants on systemic lupus erythematosus (SLE) and autoimmune (AI) disease risk haplotypes to modulate regulatory activity in an allele-dependent manner. Our study demonstrates that hQTLs, as a group, are more likely to modulate regulatory activity in an MPRA compared with other variant classes tested, including a set of eQTLs previously shown to interact with hQTLs and tested AI risk variants. In addition, we nominate 17 variants (including 11 previously unreported) as putative causal variants for SLE and another 14 for various other AI diseases, prioritizing these variants for future functional studies in primary and immortalized B cells. Thus, we uncover important insights into the mechanistic relationships among genotype, epigenetics, and gene expression in SLE and AI disease phenotypes.
我们在爱泼斯坦-巴氏病毒(Epstein-Barr virus)转化的B细胞系中设计了一种大规模并行报告测定(MPRA),以直接鉴定组蛋白翻译后修饰(即组蛋白定量性状位点(hQTLs)、表达QTLs(eQTLs)以及系统性红斑狼疮和自身免疫(AI)疾病风险单倍型上的变体)以等位基因依赖方式调节调节活性的潜力。我们的研究表明,与其他被测试的变异类别(包括一组先前被证明与 hQTLs 和被测试的 AI 风险变异相互作用的 eQTLs)相比,hQTLs 作为一个群体更有可能在 MPRA 中调节调节活性。此外,我们还提名了 17 个变异(包括 11 个以前未报道的变异)为系统性红斑狼疮的假定致病变异,另外 14 个为其他各种 AI 疾病的假定致病变异,并将这些变异列为未来在原代和永生 B 细胞中进行功能研究的优先对象。因此,我们揭示了系统性红斑狼疮和人工智能疾病表型中基因型、表观遗传学和基因表达之间的机理关系。
{"title":"Massively parallel reporter assay confirms regulatory potential of hQTLs and reveals important variants in lupus and other autoimmune diseases.","authors":"Yao Fu, Jennifer A Kelly, Jaanam Gopalakrishnan, Richard C Pelikan, Kandice L Tessneer, Satish Pasula, Kiely Grundahl, David A Murphy, Patrick M Gaffney","doi":"10.1016/j.xhgg.2024.100279","DOIUrl":"10.1016/j.xhgg.2024.100279","url":null,"abstract":"<p><p>We designed a massively parallel reporter assay (MPRA) in an Epstein-Barr virus transformed B cell line to directly characterize the potential for histone post-translational modifications, i.e., histone quantitative trait loci (hQTLs), expression QTLs (eQTLs), and variants on systemic lupus erythematosus (SLE) and autoimmune (AI) disease risk haplotypes to modulate regulatory activity in an allele-dependent manner. Our study demonstrates that hQTLs, as a group, are more likely to modulate regulatory activity in an MPRA compared with other variant classes tested, including a set of eQTLs previously shown to interact with hQTLs and tested AI risk variants. In addition, we nominate 17 variants (including 11 previously unreported) as putative causal variants for SLE and another 14 for various other AI diseases, prioritizing these variants for future functional studies in primary and immortalized B cells. Thus, we uncover important insights into the mechanistic relationships among genotype, epigenetics, and gene expression in SLE and AI disease phenotypes.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10943488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139933217","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}
Pub Date : 2024-04-11Epub Date: 2024-01-30DOI: 10.1016/j.xhgg.2024.100275
Gautam K Pandey, Swarooparani Vadlamudi, Kevin W Currin, Anne H Moxley, Jayna C Nicholas, Jessica C McAfee, K Alaine Broadaway, Karen L Mohlke
Genome-wide association studies (GWASs) have identified hundreds of risk loci for liver disease and lipid-related metabolic traits, although identifying their target genes and molecular mechanisms remains challenging. We predicted target genes at GWAS signals by integrating them with molecular quantitative trait loci for liver gene expression (eQTL) and liver chromatin accessibility QTL (caQTL). We predicted specific regulatory caQTL variants at four GWAS signals located near EFHD1, LITAF, ZNF329, and GPR180. Using transcriptional reporter assays, we determined that caQTL variants rs13395911, rs11644920, rs34003091, and rs9556404 exhibit allelic differences in regulatory activity. We also performed a protein binding assay for rs13395911 and found that FOXA2 differentially interacts with the alleles of rs13395911. For variants rs13395911 and rs11644920 in putative enhancer regulatory elements, we used CRISPRi to demonstrate that repression of the enhancers altered the expression of the predicted target and/or nearby genes. Repression of the element at rs13395911 reduced the expression of EFHD1, and repression of the element at rs11644920 reduced the expression of LITAF, SNN, and TXNDC11. Finally, we showed that EFHD1 is a metabolically active gene in HepG2 cells. Together, these results provide key steps to connect genetic variants with cellular mechanisms and help elucidate the causes of liver disease.
{"title":"Liver regulatory mechanisms of noncoding variants at lipid and metabolic trait loci.","authors":"Gautam K Pandey, Swarooparani Vadlamudi, Kevin W Currin, Anne H Moxley, Jayna C Nicholas, Jessica C McAfee, K Alaine Broadaway, Karen L Mohlke","doi":"10.1016/j.xhgg.2024.100275","DOIUrl":"10.1016/j.xhgg.2024.100275","url":null,"abstract":"<p><p>Genome-wide association studies (GWASs) have identified hundreds of risk loci for liver disease and lipid-related metabolic traits, although identifying their target genes and molecular mechanisms remains challenging. We predicted target genes at GWAS signals by integrating them with molecular quantitative trait loci for liver gene expression (eQTL) and liver chromatin accessibility QTL (caQTL). We predicted specific regulatory caQTL variants at four GWAS signals located near EFHD1, LITAF, ZNF329, and GPR180. Using transcriptional reporter assays, we determined that caQTL variants rs13395911, rs11644920, rs34003091, and rs9556404 exhibit allelic differences in regulatory activity. We also performed a protein binding assay for rs13395911 and found that FOXA2 differentially interacts with the alleles of rs13395911. For variants rs13395911 and rs11644920 in putative enhancer regulatory elements, we used CRISPRi to demonstrate that repression of the enhancers altered the expression of the predicted target and/or nearby genes. Repression of the element at rs13395911 reduced the expression of EFHD1, and repression of the element at rs11644920 reduced the expression of LITAF, SNN, and TXNDC11. Finally, we showed that EFHD1 is a metabolically active gene in HepG2 cells. Together, these results provide key steps to connect genetic variants with cellular mechanisms and help elucidate the causes of liver disease.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10881423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139651843","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}
Pub Date : 2024-04-11Epub Date: 2024-02-02DOI: 10.1016/j.xhgg.2024.100274
Janelle Geist Hauserman, Chamindra G Laverty, Sandra Donkervoort, Ying Hu, Sarah Silverstein, Sarah B Neuhaus, Dimah Saade, Gabrielle Vaughn, Denise Malicki, Rupleen Kaur, Yuesheng Li, Yan Luo, Poching Liu, Patrick Burr, A Reghan Foley, Payam Mohassel, Carsten G Bönnemann
Pathogenic variants in the DES gene clinically manifest as progressive skeletal muscle weakness, cardiomyopathy with associated severe arrhythmias, and respiratory insufficiency, and are collectively known as desminopathies. While most DES pathogenic variants act via a dominant mechanism, recessively acting variants have also been reported. Currently, there are no effective therapeutic interventions for desminopathies of any type. Here, we report an affected individual with rapidly progressive dilated cardiomyopathy, requiring heart transplantation at age 13 years, in the setting of childhood-onset skeletal muscle weakness. We identified biallelic DES variants (c.640-13 T>A and c.1288+1 G>A) and show aberrant DES gene splicing in the affected individual's muscle. Through the generation of an inducible lentiviral system, we transdifferentiated fibroblast cultures derived from the affected individual into myoblasts and validated this system using RNA sequencing. We tested rationally designed, custom antisense oligonucleotides to screen for splice correction in these transdifferentiated cells and a functional minigene splicing assay. However, rather than correctly redirecting splicing, we found them to induce undesired exon skipping. Our results indicate that, while an individual precision-based molecular therapeutic approach to splice-altering pathogenic variants is promising, careful preclinical testing is imperative for each novel variant to test the feasibility of this type of approach for translation.
DES 基因的致病变体在临床上表现为进行性骨骼肌无力、伴有严重心律失常的心肌病和呼吸功能不全,统称为 DESminopathies。虽然大多数 DES 致病变异体通过显性机制发挥作用,但也有隐性作用变异体的报道。目前,对任何类型的脱敏病都没有有效的治疗干预措施。在此,我们报告了一名患有快速进展性扩张型心肌病的患者,该患者在13岁时需要进行心脏移植手术,同时还伴有儿童期发病的骨骼肌无力。我们发现了双倍序列的 DES 变体(c.640-13 T>A 和 c.1288+1 G>A),并在患者的肌肉中发现了异常的 DES 基因拼接。通过生成诱导性慢病毒系统,我们将来自受影响个体的成纤维细胞培养物转分化为肌细胞,并利用 RNA 测序对该系统进行了验证。我们测试了合理设计的定制反义寡核苷酸,以筛选这些转分化细胞中的剪接校正和功能性微型基因剪接检测。然而,我们发现这些反义寡核苷酸非但不能正确地重定向剪接,反而会诱导不希望的外显子跳转。我们的研究结果表明,虽然针对剪接改变致病变体的个体精准分子治疗方法很有前景,但必须对每种新型变体进行仔细的临床前测试,以检验这种方法转化的可行性。
{"title":"Clinical, immunohistochemical, and genetic characterization of splice-altering biallelic DES variants: Therapeutic implications.","authors":"Janelle Geist Hauserman, Chamindra G Laverty, Sandra Donkervoort, Ying Hu, Sarah Silverstein, Sarah B Neuhaus, Dimah Saade, Gabrielle Vaughn, Denise Malicki, Rupleen Kaur, Yuesheng Li, Yan Luo, Poching Liu, Patrick Burr, A Reghan Foley, Payam Mohassel, Carsten G Bönnemann","doi":"10.1016/j.xhgg.2024.100274","DOIUrl":"10.1016/j.xhgg.2024.100274","url":null,"abstract":"<p><p>Pathogenic variants in the DES gene clinically manifest as progressive skeletal muscle weakness, cardiomyopathy with associated severe arrhythmias, and respiratory insufficiency, and are collectively known as desminopathies. While most DES pathogenic variants act via a dominant mechanism, recessively acting variants have also been reported. Currently, there are no effective therapeutic interventions for desminopathies of any type. Here, we report an affected individual with rapidly progressive dilated cardiomyopathy, requiring heart transplantation at age 13 years, in the setting of childhood-onset skeletal muscle weakness. We identified biallelic DES variants (c.640-13 T>A and c.1288+1 G>A) and show aberrant DES gene splicing in the affected individual's muscle. Through the generation of an inducible lentiviral system, we transdifferentiated fibroblast cultures derived from the affected individual into myoblasts and validated this system using RNA sequencing. We tested rationally designed, custom antisense oligonucleotides to screen for splice correction in these transdifferentiated cells and a functional minigene splicing assay. However, rather than correctly redirecting splicing, we found them to induce undesired exon skipping. Our results indicate that, while an individual precision-based molecular therapeutic approach to splice-altering pathogenic variants is promising, careful preclinical testing is imperative for each novel variant to test the feasibility of this type of approach for translation.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10876619/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139742237","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}
Pub Date : 2024-04-11Epub Date: 2024-03-12DOI: 10.1016/j.xhgg.2024.100282
W Gregory Feero, Robert D Steiner, Anne Slavotinek, Tiago Faial, Michael J Bamshad, Jehannine Austin, Bruce R Korf, Annette Flanagin, Kirsten Bibbins-Domingo
{"title":"Guidance on use of race, ethnicity, and geographic origin as proxies for genetic ancestry groups in biomedical publications.","authors":"W Gregory Feero, Robert D Steiner, Anne Slavotinek, Tiago Faial, Michael J Bamshad, Jehannine Austin, Bruce R Korf, Annette Flanagin, Kirsten Bibbins-Domingo","doi":"10.1016/j.xhgg.2024.100282","DOIUrl":"10.1016/j.xhgg.2024.100282","url":null,"abstract":"","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11019354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140120983","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}
Pub Date : 2024-04-11Epub Date: 2024-01-30DOI: 10.1016/j.xhgg.2024.100273
Morad Ansari, Kamli N W Faour, Akiko Shimamura, Graeme Grimes, Emeline M Kao, Erica R Denhoff, Ana Blatnik, Daniel Ben-Isvy, Lily Wang, Benjamin M Helm, Helen Firth, Amy M Breman, Emilia K Bijlsma, Aiko Iwata-Otsubo, Thomy J L de Ravel, Vincent Fusaro, Alan Fryer, Keith Nykamp, Lara G Stühn, Tobias B Haack, G Christoph Korenke, Panayiotis Constantinou, Kinga M Bujakowska, Karen J Low, Emily Place, Jennifer Humberson, Melanie P Napier, Jessica Hoffman, Jane Juusola, Matthew A Deardorff, Wanqing Shao, Shira Rockowitz, Ian Krantz, Maninder Kaur, Sarah Raible, Victoria Dortenzio, Sabine Kliesch, Moriel Singer-Berk, Emily Groopman, Stephanie DiTroia, Sonia Ballal, Siddharth Srivastava, Kathrin Rothfelder, Saskia Biskup, Jessica Rzasa, Jennifer Kerkhof, Haley McConkey, Bekim Sadikovic, Sarah Hilton, Siddharth Banka, Frank Tüttelmann, Donald F Conrad, Anne O'Donnell-Luria, Michael E Talkowski, David R FitzPatrick, Philip M Boone
Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.
{"title":"Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features.","authors":"Morad Ansari, Kamli N W Faour, Akiko Shimamura, Graeme Grimes, Emeline M Kao, Erica R Denhoff, Ana Blatnik, Daniel Ben-Isvy, Lily Wang, Benjamin M Helm, Helen Firth, Amy M Breman, Emilia K Bijlsma, Aiko Iwata-Otsubo, Thomy J L de Ravel, Vincent Fusaro, Alan Fryer, Keith Nykamp, Lara G Stühn, Tobias B Haack, G Christoph Korenke, Panayiotis Constantinou, Kinga M Bujakowska, Karen J Low, Emily Place, Jennifer Humberson, Melanie P Napier, Jessica Hoffman, Jane Juusola, Matthew A Deardorff, Wanqing Shao, Shira Rockowitz, Ian Krantz, Maninder Kaur, Sarah Raible, Victoria Dortenzio, Sabine Kliesch, Moriel Singer-Berk, Emily Groopman, Stephanie DiTroia, Sonia Ballal, Siddharth Srivastava, Kathrin Rothfelder, Saskia Biskup, Jessica Rzasa, Jennifer Kerkhof, Haley McConkey, Bekim Sadikovic, Sarah Hilton, Siddharth Banka, Frank Tüttelmann, Donald F Conrad, Anne O'Donnell-Luria, Michael E Talkowski, David R FitzPatrick, Philip M Boone","doi":"10.1016/j.xhgg.2024.100273","DOIUrl":"10.1016/j.xhgg.2024.100273","url":null,"abstract":"<p><p>Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10876629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139651833","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}
Pub Date : 2024-04-11Epub Date: 2023-12-30DOI: 10.1016/j.xhgg.2023.100261
Serena Redaelli, Francesca Romana Grati, Viviana Tritto, Giuliana Giannuzzi, Maria Paola Recalcati, Elena Sala, Nicoletta Villa, Francesca Crosti, Gaia Roversi, Francesca Malvestiti, Valentina Zanatta, Elena Repetti, Ornella Rodeschini, Chiara Valtorta, Ilaria Catusi, Lorenza Romitti, Emanuela Martinoli, Donatella Conconi, Leda Dalprà, Marialuisa Lavitrano, Paola Riva, Angela Bentivegna
The largest multi-gene family in metazoans is the family of olfactory receptor (OR) genes. Human ORs are organized in clusters over most chromosomes and seem to include >0.1% the human genome. Because 369 out of 856 OR genes are mapped on chromosome 11 (HSA11), we sought to determine whether they mediate structural rearrangements involving this chromosome. To this aim, we analyzed 220 specimens collected during diagnostic procedures involving structural rearrangements of chromosome 11. A total of 222 chromosomal abnormalities were included, consisting of inversions, deletions, translocations, duplications, and one insertion, detected by conventional chromosome analysis and/or fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (array-CGH). We verified by bioinformatics and statistical approaches the occurrence of breakpoints in cytobands with or without OR genes. We found that OR genes are not involved in chromosome 11 reciprocal translocations, suggesting that different DNA motifs and mechanisms based on homology or non-homology recombination can cause chromosome 11 structural alterations. We also considered the proximity between the chromosomal territories of chromosome 11 and its partner chromosomes involved in the translocations by using the deposited Hi-C data concerning the possible occurrence of chromosome interactions. Interestingly, most of the breakpoints are located in regions highly involved in chromosome interactions. Further studies should be carried out to confirm the potential role of chromosome territories' proximity in promoting genome structural variation, so fundamental in our understanding of the molecular basis of medical genetics and evolutionary genetics.
后生动物中最大的多基因家族是嗅觉受体(OR)基因家族。人类的嗅觉受体基因在大多数染色体上成群分布,似乎占人类基因组的 0.1%以上。由于 856 个 OR 基因中有 369 个被映射到 11 号染色体(HSA11)上,我们试图了解它们是否介导了涉及该染色体的结构重排。为此,我们分析了在涉及 11 号染色体结构重排的诊断过程中收集的 220 份标本。共纳入 222 例染色体异常,包括倒位、缺失、易位、重复和一个插入,均通过常规染色体分析和/或 FISH 和阵列-CGH 检测到。我们通过生物信息学和统计学方法验证了有或没有 OR 基因的细胞带中断裂点的发生情况。我们发现,OR 基因不参与 11 号染色体的相互易位,这表明基于同源或非同源重组的不同 DNA 主题和机制可导致 11 号染色体结构的改变。我们还利用保存的有关可能发生染色体相互作用的 Hi-C 数据,考虑了 11 号染色体的染色体区域与易位所涉及的伙伴染色体之间的邻近性。有趣的是,大多数断裂点都位于染色体相互作用高度涉及的区域。应开展进一步的研究,以确认染色体区域的邻近性在促进易位中的潜在作用,从而帮助理解可能与遗传疾病有关的基因组结构变异的内在机制,同时也是促进基因组进化的基础。
{"title":"Olfactory receptor genes and chromosome 11 structural aberrations: Players or spectators?","authors":"Serena Redaelli, Francesca Romana Grati, Viviana Tritto, Giuliana Giannuzzi, Maria Paola Recalcati, Elena Sala, Nicoletta Villa, Francesca Crosti, Gaia Roversi, Francesca Malvestiti, Valentina Zanatta, Elena Repetti, Ornella Rodeschini, Chiara Valtorta, Ilaria Catusi, Lorenza Romitti, Emanuela Martinoli, Donatella Conconi, Leda Dalprà, Marialuisa Lavitrano, Paola Riva, Angela Bentivegna","doi":"10.1016/j.xhgg.2023.100261","DOIUrl":"10.1016/j.xhgg.2023.100261","url":null,"abstract":"<p><p>The largest multi-gene family in metazoans is the family of olfactory receptor (OR) genes. Human ORs are organized in clusters over most chromosomes and seem to include >0.1% the human genome. Because 369 out of 856 OR genes are mapped on chromosome 11 (HSA11), we sought to determine whether they mediate structural rearrangements involving this chromosome. To this aim, we analyzed 220 specimens collected during diagnostic procedures involving structural rearrangements of chromosome 11. A total of 222 chromosomal abnormalities were included, consisting of inversions, deletions, translocations, duplications, and one insertion, detected by conventional chromosome analysis and/or fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (array-CGH). We verified by bioinformatics and statistical approaches the occurrence of breakpoints in cytobands with or without OR genes. We found that OR genes are not involved in chromosome 11 reciprocal translocations, suggesting that different DNA motifs and mechanisms based on homology or non-homology recombination can cause chromosome 11 structural alterations. We also considered the proximity between the chromosomal territories of chromosome 11 and its partner chromosomes involved in the translocations by using the deposited Hi-C data concerning the possible occurrence of chromosome interactions. Interestingly, most of the breakpoints are located in regions highly involved in chromosome interactions. Further studies should be carried out to confirm the potential role of chromosome territories' proximity in promoting genome structural variation, so fundamental in our understanding of the molecular basis of medical genetics and evolutionary genetics.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10820794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139075234","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}
Pub Date : 2024-04-11Epub Date: 2024-01-08DOI: 10.1016/j.xhgg.2024.100262
Mikhail Gudkov, Loïc Thibaut, Eleni Giannoulatou
Widespread adoption of DNA sequencing has resulted in large numbers of genetic variants, whose contribution to disease is not easily determined. Although many types of variation are known to disrupt cellular processes in predictable ways, for some categories of variants, the effects may not be directly detectable. A particular example is synonymous variants, that is, those single-nucleotide variants that create a codon substitution, such that the produced amino acid sequence is unaffected. Contrary to the original theory suggesting that synonymous variants are benign, there is a growing volume of research showing that, despite their "silent" mechanism of action, some synonymous variation may be deleterious. Here, we studied the extent of the negative selective pressure acting on different classes of synonymous variants by analyzing the relative enrichment of synonymous singleton variants in the human exomes provided by gnomAD. Using a modification of the mutability-adjusted proportion of singletons (MAPS) metric as a measure of purifying selection, we found that some classes of synonymous variants are subject to stronger negative selection than others. For instance, variants that reduce codon optimality undergo stronger selection than optimality-increasing variants. Besides, selection affects synonymous variants implicated in splice-site-loss or splice-site-gain events. To understand what drives this negative selection, we tested a number of predictors in the aim to explain the variability in the selection scores. Our findings provide insights into the effects of synonymous variants at the population level, highlighting the specifics of the role that these variants play in health and disease.
DNA 测序技术的广泛应用产生了大量基因变异,而这些变异对疾病的影响却不易确定。虽然已知许多类型的变异会以可预测的方式破坏细胞过程,但对于某些类别的变异,其影响可能无法直接检测到。一个特别的例子是同义变异,即那些产生密码子置换的单核苷酸变异,其产生的氨基酸序列不受影响。与最初认为同义变异是良性的理论相反,越来越多的研究表明,尽管同义变异的作用机制是 "无声 "的,但有些同义变异可能是有害的。在这里,我们通过分析 gnomAD 提供的人类外显子组中同义单子变异的相对富集程度,研究了作用于不同类别同义变异的负选择压力的程度。使用变异性调整的单子比例(MAPS)指标作为纯化选择的衡量标准,我们发现某些类别的同义变异比其他变异受到更强的负选择。例如,降低密码子最优性的变体比提高最优性的变体受到更强的选择。此外,选择也会影响剪接位点丢失或剪接位点增益事件中的同义变异。为了了解这种负选择的驱动因素,我们测试了一些预测因子,旨在解释选择得分的变化。我们的研究结果让人们深入了解了同义变异在群体水平上的影响,突出了这些变异在健康和疾病中所起作用的特殊性。
{"title":"Quantifying negative selection on synonymous variants.","authors":"Mikhail Gudkov, Loïc Thibaut, Eleni Giannoulatou","doi":"10.1016/j.xhgg.2024.100262","DOIUrl":"10.1016/j.xhgg.2024.100262","url":null,"abstract":"<p><p>Widespread adoption of DNA sequencing has resulted in large numbers of genetic variants, whose contribution to disease is not easily determined. Although many types of variation are known to disrupt cellular processes in predictable ways, for some categories of variants, the effects may not be directly detectable. A particular example is synonymous variants, that is, those single-nucleotide variants that create a codon substitution, such that the produced amino acid sequence is unaffected. Contrary to the original theory suggesting that synonymous variants are benign, there is a growing volume of research showing that, despite their \"silent\" mechanism of action, some synonymous variation may be deleterious. Here, we studied the extent of the negative selective pressure acting on different classes of synonymous variants by analyzing the relative enrichment of synonymous singleton variants in the human exomes provided by gnomAD. Using a modification of the mutability-adjusted proportion of singletons (MAPS) metric as a measure of purifying selection, we found that some classes of synonymous variants are subject to stronger negative selection than others. For instance, variants that reduce codon optimality undergo stronger selection than optimality-increasing variants. Besides, selection affects synonymous variants implicated in splice-site-loss or splice-site-gain events. To understand what drives this negative selection, we tested a number of predictors in the aim to explain the variability in the selection scores. Our findings provide insights into the effects of synonymous variants at the population level, highlighting the specifics of the role that these variants play in health and disease.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10835449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139404654","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}
Pub Date : 2024-04-11Epub Date: 2024-02-03DOI: 10.1016/j.xhgg.2024.100276
Jaeyong Choi, Seung Mi Lee, Errol R Norwitz, Ji Hoi Kim, Young Mi Jung, Chan-Wook Park, Jong Kwan Jun, Dakyung Lee, Yongjoon Jin, Sookyung Kim, Bukyoung Cha, Joong Shin Park, Jong-Il Kim
Expression quantitative trait loci (eQTL) analysis measures the contribution of genetic variation in gene expression on complex traits. Although this methodology has been used to examine gene regulation in numerous human tissues, eQTL research in solid tissues is relatively lacking. We conducted eQTL analysis on placentas collected from an East Asian population in an effort to identify gene regulatory mechanisms in this tissue. Placentas (n = 102) were collected at the time of cesarean delivery. mRNA was extracted, sequenced with NGS, and compared with matched maternal and fetal DNA arrays performed using maternal and neonatal cord blood. Linear regression modeling was performed using tensorQTL. Fine-mapping along with epigenomic annotation was used to select putative functional variants. We identified 2,703 coding genes that contained at least one eQTL with statistical significance (false discovery rate <0.05). After fine-mapping, we found 108 previously unreported eQTL variants with posterior inclusion probability >0.1. Of these, 19% were located in genomic regions with evidence from public placental epigenome suggesting that they may be functionally relevant. For example, variant rs28379289 located in the placenta-specific regulatory region changes the binding affinity of transcription factor leading to higher expression of LGALS3, which is known to affect placental function. This study expands the knowledge base of regulatory elements within the human placenta and identifies 108 previously unreported placenta eQTL signals, which are listed in our publicly available GMI eQTL database. Further studies are needed to identify and characterize genetic regulatory mechanisms that affect placental function in normal pregnancy and placenta-related diseases.
{"title":"Placental expression quantitative trait loci in an East Asian population.","authors":"Jaeyong Choi, Seung Mi Lee, Errol R Norwitz, Ji Hoi Kim, Young Mi Jung, Chan-Wook Park, Jong Kwan Jun, Dakyung Lee, Yongjoon Jin, Sookyung Kim, Bukyoung Cha, Joong Shin Park, Jong-Il Kim","doi":"10.1016/j.xhgg.2024.100276","DOIUrl":"10.1016/j.xhgg.2024.100276","url":null,"abstract":"<p><p>Expression quantitative trait loci (eQTL) analysis measures the contribution of genetic variation in gene expression on complex traits. Although this methodology has been used to examine gene regulation in numerous human tissues, eQTL research in solid tissues is relatively lacking. We conducted eQTL analysis on placentas collected from an East Asian population in an effort to identify gene regulatory mechanisms in this tissue. Placentas (n = 102) were collected at the time of cesarean delivery. mRNA was extracted, sequenced with NGS, and compared with matched maternal and fetal DNA arrays performed using maternal and neonatal cord blood. Linear regression modeling was performed using tensorQTL. Fine-mapping along with epigenomic annotation was used to select putative functional variants. We identified 2,703 coding genes that contained at least one eQTL with statistical significance (false discovery rate <0.05). After fine-mapping, we found 108 previously unreported eQTL variants with posterior inclusion probability >0.1. Of these, 19% were located in genomic regions with evidence from public placental epigenome suggesting that they may be functionally relevant. For example, variant rs28379289 located in the placenta-specific regulatory region changes the binding affinity of transcription factor leading to higher expression of LGALS3, which is known to affect placental function. This study expands the knowledge base of regulatory elements within the human placenta and identifies 108 previously unreported placenta eQTL signals, which are listed in our publicly available GMI eQTL database. Further studies are needed to identify and characterize genetic regulatory mechanisms that affect placental function in normal pregnancy and placenta-related diseases.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10883826/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139681686","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}
Tumors are intricate and heterogeneous systems characterized by mosaic cancer cell populations with diverse expression profiles. Leveraging single-cell technologies, we employed the Scissor algorithm to delineate an epithelial subpopulation associated with the aggressive phenotype in esophageal squamous cell carcinoma (ESCC). This identified subpopulation exhibited elevated expression of genes involved in critical pathways, such as epithelial-mesenchymal transition and PI3K-Akt. Key signature genes within this subpopulation, namely CAV1, COL3A1, COL6A1, POSTN, and TAGLN, demonstrated significant upregulation concomitant with both tumorigenesis and tumor progression across independent single-cell datasets. Furthermore, we selected 1,450 expression quantitative trait loci of the top 62 signature genes of this cell subpopulation to investigate their potential in predicting ESCC risk. The results showed that the POSTN loci were predominantly associated with ESCC susceptibility. Through functional annotation and replication analyses, we identified that the rs1028728 in the POSTN promoter was significantly associated with increased ESCC risk in 7,049 ESCC cases and 8,063 controls (odds ratio = 1.29, 95% confidence interval: 1.18-1.42, p = 4.03 × 10-8). Subsequent biochemical experiments showed that the rs1028728[T] allele enhanced POSTN expression by affecting the binding of PRRX1 in the POSTN promoter. In summary, our meticulous single-cell analysis delineates an invasive epithelial subpopulation in ESCC, with POSTN emerging as an important marker for the aggressive phenotype. These findings offer more insights into potential strategies for the prevention and intervention of ESCC, enriching our understanding of this complex cancer landscape.
{"title":"Single-cell analysis identified POSTN<sup>+</sup> cells associated with the aggressive phenotype and risk of esophageal squamous cell carcinoma.","authors":"Yuqian Tan, Lina Song, Jialing Ma, Miaoxin Pan, Siyuan Niu, Xinying Yue, Yueping Li, Linglong Gu, Shasha Liu, Jiang Chang","doi":"10.1016/j.xhgg.2024.100278","DOIUrl":"10.1016/j.xhgg.2024.100278","url":null,"abstract":"<p><p>Tumors are intricate and heterogeneous systems characterized by mosaic cancer cell populations with diverse expression profiles. Leveraging single-cell technologies, we employed the Scissor algorithm to delineate an epithelial subpopulation associated with the aggressive phenotype in esophageal squamous cell carcinoma (ESCC). This identified subpopulation exhibited elevated expression of genes involved in critical pathways, such as epithelial-mesenchymal transition and PI3K-Akt. Key signature genes within this subpopulation, namely CAV1, COL3A1, COL6A1, POSTN, and TAGLN, demonstrated significant upregulation concomitant with both tumorigenesis and tumor progression across independent single-cell datasets. Furthermore, we selected 1,450 expression quantitative trait loci of the top 62 signature genes of this cell subpopulation to investigate their potential in predicting ESCC risk. The results showed that the POSTN loci were predominantly associated with ESCC susceptibility. Through functional annotation and replication analyses, we identified that the rs1028728 in the POSTN promoter was significantly associated with increased ESCC risk in 7,049 ESCC cases and 8,063 controls (odds ratio = 1.29, 95% confidence interval: 1.18-1.42, p = 4.03 × 10<sup>-8</sup>). Subsequent biochemical experiments showed that the rs1028728[T] allele enhanced POSTN expression by affecting the binding of PRRX1 in the POSTN promoter. In summary, our meticulous single-cell analysis delineates an invasive epithelial subpopulation in ESCC, with POSTN emerging as an important marker for the aggressive phenotype. These findings offer more insights into potential strategies for the prevention and intervention of ESCC, enriching our understanding of this complex cancer landscape.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10924139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139900533","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}