1
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Chettle J, Louie RJ, Larner O, Best R, Chen K, Morris J, Dedeic Z, Childers A, Rogers RC, DuPont BR, Skinner C, Küry S, Uguen K, Planes M, Monteil D, Li M, Eliyahu A, Greenbaum L, Mor N, Besnard T, Isidor B, Cogné B, Blesson A, Comi A, Wentzensen IM, Vuocolo B, Lalani SR, Sierra R, Berry L, Carter K, Sanders SJ, Blagden SP. LARP1 haploinsufficiency is associated with an autosomal dominant neurodevelopmental disorder. HGG ADVANCES 2024; 5:100345. [PMID: 39182167 PMCID: PMC11418108 DOI: 10.1016/j.xhgg.2024.100345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder (NDD) that affects approximately 4% of males and 1% of females in the United States. While causes of ASD are multi-factorial, single rare genetic variants contribute to around 20% of cases. Here, we report a case series of seven unrelated probands (6 males, 1 female) with ASD or another variable NDD phenotype attributed to de novo heterozygous loss of function or missense variants in the gene LARP1 (La ribonucleoprotein 1). LARP1 encodes an RNA-binding protein that post-transcriptionally regulates the stability and translation of thousands of mRNAs, including those regulating cellular metabolism and metabolic plasticity. Using lymphocytes collected and immortalized from an index proband who carries a truncating variant in one allele of LARP1, we demonstrated that lower cellular levels of LARP1 protein cause reduced rates of aerobic respiration and glycolysis. As expression of LARP1 increases during neurodevelopment, with higher levels in neurons and astrocytes, we propose that LARP1 haploinsufficiency contributes to ASD or related NDDs through attenuated metabolic activity in the developing fetal brain.
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Affiliation(s)
- James Chettle
- Department of Oncology, University of Oxford, Oxford, UK
| | | | - Olivia Larner
- University of South Carolina School of Medicine Greenville, Greenville, SC, USA
| | - Robert Best
- University of South Carolina School of Medicine Greenville, Greenville, SC, USA
| | | | | | - Zinaida Dedeic
- Department of Oncology, University of Oxford, Oxford, UK
| | | | | | | | | | - Sébastien Küry
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut du thorax, 44000 Nantes, France
| | - Kevin Uguen
- Service de Génétique Médicale et Biologie de la Reproduction, CHRU de Brest, Brest, France
| | - Marc Planes
- Service de Génétique Médicale et Biologie de la Reproduction, CHRU de Brest, Brest, France
| | | | - Megan Li
- Invitae, San Francisco Corp., San Francisco, CA, USA
| | - Aviva Eliyahu
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Nofar Mor
- The Genomic Unit, Sheba Cancer Research Centre, Sheba Medical Center, Tel Hashomer, Israel
| | - Thomas Besnard
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut du thorax, 44000 Nantes, France
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut du thorax, 44000 Nantes, France
| | - Benjamin Cogné
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut du thorax, 44000 Nantes, France
| | | | - Anne Comi
- Kennedy Krieger Institute, Baltimore, MD, USA
| | | | | | | | | | - Lori Berry
- Baylor College of Medicine, Houston, TX, USA
| | - Kent Carter
- University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Stephan J Sanders
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK; Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
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2
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Schraiber JG, Edge MD, Pennell M. Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations. PLoS Biol 2024; 22:e3002847. [PMID: 39383205 DOI: 10.1371/journal.pbio.3002847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 09/17/2024] [Indexed: 10/11/2024] Open
Abstract
In both statistical genetics and phylogenetics, a major goal is to identify correlations between genetic loci or other aspects of the phenotype or environment and a focal trait. In these 2 fields, there are sophisticated but disparate statistical traditions aimed at these tasks. The disconnect between their respective approaches is becoming untenable as questions in medicine, conservation biology, and evolutionary biology increasingly rely on integrating data from within and among species, and once-clear conceptual divisions are becoming increasingly blurred. To help bridge this divide, we lay out a general model describing the covariance between the genetic contributions to the quantitative phenotypes of different individuals. Taking this approach shows that standard models in both statistical genetics (e.g., genome-wide association studies; GWAS) and phylogenetic comparative biology (e.g., phylogenetic regression) can be interpreted as special cases of this more general quantitative-genetic model. The fact that these models share the same core architecture means that we can build a unified understanding of the strengths and limitations of different methods for controlling for genetic structure when testing for associations. We develop intuition for why and when spurious correlations may occur analytically and conduct population-genetic and phylogenetic simulations of quantitative traits. The structural similarity of problems in statistical genetics and phylogenetics enables us to take methodological advances from one field and apply them in the other. We demonstrate by showing how a standard GWAS technique-including both the genetic relatedness matrix (GRM) as well as its leading eigenvectors, corresponding to the principal components of the genotype matrix, in a regression model-can mitigate spurious correlations in phylogenetic analyses. As a case study, we re-examine an analysis testing for coevolution of expression levels between genes across a fungal phylogeny and show that including eigenvectors of the covariance matrix as covariates decreases the false positive rate while simultaneously increasing the true positive rate. More generally, this work provides a foundation for more integrative approaches for understanding the genetic architecture of phenotypes and how evolutionary processes shape it.
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Affiliation(s)
- Joshua G Schraiber
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Michael D Edge
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
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3
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Nguyen DD, Hooper WF, Liu W, Chu TR, Geiger H, Shelton JM, Shah M, Goldstein ZR, Winterkorn L, Helland A, Sigouros M, Manohar J, Moyer J, Al Assaad M, Semaan A, Cohen S, Madorsky Rowdo F, Wilkes D, Osman M, Singh RR, Sboner A, Valentine HL, Abbosh P, Tagawa ST, Nanus DM, Nauseef JT, Sternberg CN, Molina AM, Scherr D, Inghirami G, Mosquera JM, Elemento O, Robine N, Faltas BM. The interplay of mutagenesis and ecDNA shapes urothelial cancer evolution. Nature 2024:10.1038/s41586-024-07955-3. [PMID: 39385020 DOI: 10.1038/s41586-024-07955-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/14/2024] [Indexed: 10/11/2024]
Abstract
Advanced urothelial cancer is a frequently lethal disease characterized by marked genetic heterogeneity1. In this study, we investigated the evolution of genomic signatures caused by endogenous and external mutagenic processes and their interplay with complex structural variants (SVs). We superimposed mutational signatures and phylogenetic analyses of matched serial tumours from patients with urothelial cancer to define the evolutionary dynamics of these processes. We show that APOBEC3-induced mutations are clonal and early, whereas chemotherapy induces mutational bursts of hundreds of late subclonal mutations. Using a genome graph computational tool2, we observed frequent high copy-number circular amplicons characteristic of extrachromosomal DNA (ecDNA)-forming SVs. We characterized the distinct temporal patterns of APOBEC3-induced and chemotherapy-induced mutations within ecDNA-forming SVs, gaining new insights into the timing of these mutagenic processes relative to ecDNA biogenesis. We discovered that most CCND1 amplifications in urothelial cancer arise within circular ecDNA-forming SVs. ecDNA-forming SVs persisted and increased in complexity, incorporating additional DNA segments and contributing to the evolution of treatment resistance. Oxford Nanopore Technologies long-read whole-genome sequencing followed by de novo assembly mapped out CCND1 ecDNA structure. Experimental modelling of CCND1 ecDNA confirmed its role as a driver of treatment resistance. Our findings define fundamental mechanisms that drive urothelial cancer evolution and have important therapeutic implications.
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Affiliation(s)
- Duy D Nguyen
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Weisi Liu
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | | | | | | | - Michael Sigouros
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jyothi Manohar
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jenna Moyer
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Majd Al Assaad
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alissa Semaan
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sandra Cohen
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Florencia Madorsky Rowdo
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - David Wilkes
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mohamed Osman
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Rahul R Singh
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrea Sboner
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Henkel L Valentine
- Nuclear Dynamics and Cancer program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Phillip Abbosh
- Nuclear Dynamics and Cancer program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Department of Urology, Einstein Healthcare Network, Philadelphia, PA, USA
| | - Scott T Tagawa
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Urology, Weill Cornell Medicine, New York, NY, USA
| | - David M Nanus
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Urology, Weill Cornell Medicine, New York, NY, USA
| | - Jones T Nauseef
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Cora N Sternberg
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ana M Molina
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Douglas Scherr
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Urology, Weill Cornell Medicine, New York, NY, USA
| | - Giorgio Inghirami
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Juan Miguel Mosquera
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Bishoy M Faltas
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA.
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Sun H, Chen Y, Ma L. MDVarP: modifier ~ disease-causing variant pairs predictor. BioData Min 2024; 17:39. [PMID: 39379981 PMCID: PMC11460193 DOI: 10.1186/s13040-024-00392-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 09/28/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND Modifiers significantly impact disease phenotypes by modulating the effects of disease-causing variants, resulting in varying disease manifestations among individuals. However, identifying genetic interactions between modifier and disease-causing variants is challenging. RESULTS We developed MDVarP, an ensemble model comprising 1000 random forest predictors, to identify modifier ~ disease-causing variant combinations. MDVarP achieves high accuracy and precision, as verified using an independent dataset with published evidence of genetic interactions. We identified 25 novel modifier ~ disease-causing variant combinations and obtained supporting evidence for these associations. MDVarP outputs a class label ("Associated-pair" or "Nonrelevant-pair") and two prediction scores indicating the probability of a true association. CONCLUSIONS MDVarP prioritizes variant pairs associated with phenotypic modulations, enabling more effective mapping of functional contributions from disease-causing and modifier variants. This framework interprets genetic interactions underlying phenotypic variations in human diseases, with potential applications in personalized medicine and disease prevention.
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Affiliation(s)
- Hong Sun
- Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Center for Biomedical Informatics, School of Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China.
| | - Yunqin Chen
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, 200237, China
| | - Liangxiao Ma
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Science, Shanghai, 200031, China
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5
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Chan ER, Benchek P, Miller G, Brustoski K, Schaffer A, Truitt B, Tag J, Freebairn L, Lewis BA, Stein CM, Iyengar SK. Importance of copy number variants in childhood apraxia of speech and other speech sound disorders. Commun Biol 2024; 7:1273. [PMID: 39369109 PMCID: PMC11455877 DOI: 10.1038/s42003-024-06968-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 09/25/2024] [Indexed: 10/07/2024] Open
Abstract
Childhood apraxia of speech (CAS) is a severe and rare form of speech sound disorder (SSD). CAS is typically sporadic, but may segregate in families with broader speech and language deficits. We hypothesize that genetic changes may be involved in the etiology of CAS. We conduct whole-genome sequencing in 27 families with CAS, 101 individuals in all. We identify 17 genomic regions including 19 unique copy number variants (CNVs). Three variants are shared across families, but the rest are unique; three events are de novo. In four families, siblings with milder phenotypes co-inherited the same CNVs, demonstrating variable expressivity. We independently validate eight CNVs using microarray technology and find many of these CNVs are present in children with milder forms of SSD. Bioinformatic investigation reveal four CNVs with substantial functional consequences (cytobands 2q24.3, 6p12.3-6p12.2, 11q23.2-11q23.3, and 16p11.2). These discoveries show that CNVs are a heterogeneous, but prevalent, cause of CAS.
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Affiliation(s)
- E Ricky Chan
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Penelope Benchek
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Gabrielle Miller
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Kim Brustoski
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Ashleigh Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Barbara Truitt
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Jessica Tag
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Lisa Freebairn
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Barbara A Lewis
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Catherine M Stein
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
| | - Sudha K Iyengar
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA.
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6
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Wang X, Yang B, Wu S, Fan Q, Wang Q, Zhang D, Wang H, Feng T, Lv H, Chen T. UBTF haploinsufficiency associated with UBTF-related global developmental delay and distinctive facial features without neuroregression. J Med Genet 2024:jmg-2024-110061. [PMID: 39366741 DOI: 10.1136/jmg-2024-110061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 09/25/2024] [Indexed: 10/06/2024]
Abstract
BACKGROUND The Upstream Binding Transcription Factor (UBTF) gene encodes two nucleolar proteins, UBTF1 and UBTF2. UBTF1 regulates rRNA transcription by RNA polymerase I, while UBTF2 regulates mRNA transcription by RNA polymerase II. A recurrent de novo dominant mutation c.628G>A (p.Glu210Lys) has been identified as a gain-of-function mutation associated with childhood onset neurodegeneration with brain atrophy (CONDBA). Evidence from large-scale population databases and Ubtf+/- mouse models indicates that UBTF haploinsufficiency is not tolerated. METHODS Three unrelated patients with global developmental delay and distinctive facial features were recruited for the study. Whole exome sequencing (WES) was performed to identify potential genetic abnormalities. Additionally, copy number variation analysis was conducted based on the WES data. RESULTS All three patients exhibited intellectual disabilities, social challenges and developmental delays in language and gross motor skills. Distinctive facial features included a wide forehead, sparse eyebrows, hypertelorism, narrow palpebral fissures, single-fold eyelids, a flat nasal bridge, anteverted nares, a long philtrum and a thin upper lip. Additionally, patient C presented with more severe language delay, recurrent hepatic dysfunction and an atrial septal defect. Patient A was found to have a nonsense variant, c.1327C>T (p.R443Ter), in the exon 13 of UBTF. Patients B and C both carried a heterozygous deletion encompassing the UBTF gene. CONCLUSION In this study, we analysed the detailed phenotypes associated with UBTF haploinsufficiency, which, to our knowledge, have not been previously reported. We propose that UBTF haploinsufficiency-related global developmental delay and distinctive facial features, without neuroregression, constitute a new syndrome distinct from CONDBA.
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Affiliation(s)
- Xueqian Wang
- Suzhou Clinical Center for Rare Diseases in Children, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Medical Genetics and Prenatal Diagnosis, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, Jiangsu, China
| | - Bingyu Yang
- Suzhou Clinical Center for Rare Diseases in Children, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Shengnan Wu
- Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, Shanghai, China
| | - Qisang Fan
- Suzhou Clinical Center for Rare Diseases in Children, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Qing Wang
- Suzhou Clinical Center for Rare Diseases in Children, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Dandan Zhang
- Suzhou Clinical Center for Rare Diseases in Children, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Hongying Wang
- Suzhou Clinical Center for Rare Diseases in Children, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Tao Feng
- Suzhou Clinical Center for Rare Diseases in Children, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Haitao Lv
- Suzhou Clinical Center for Rare Diseases in Children, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Cardiology, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Ting Chen
- Suzhou Clinical Center for Rare Diseases in Children, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Pediatrics, Kunshan Sixth People's Hospital, Suzhou, Jiangsu, China
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7
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Liu HK, Hao HL, You H, Feng F, Qi XH, Huang XY, Hou B, Tian CG, Wang H, Yang HM, Wang J, Wu R, Fang H, Zhou JN, Zhang JG, Zhang ZX. A Cysteinyl-tRNA Synthetase Mutation Causes Novel Autosomal-Dominant Inheritance of a Parkinsonism/Spinocerebellar-Ataxia Complex. Neurosci Bull 2024; 40:1489-1501. [PMID: 38869703 PMCID: PMC11422396 DOI: 10.1007/s12264-024-01231-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 12/22/2023] [Indexed: 06/14/2024] Open
Abstract
This study aimed to identify possible pathogenic genes in a 90-member family with a rare combination of multiple neurodegenerative disease phenotypes, which has not been depicted by the known neurodegenerative disease. We performed physical and neurological examinations with International Rating Scales to assess signs of ataxia, Parkinsonism, and cognitive function, as well as brain magnetic resonance imaging scans with seven sequences. We searched for co-segregations of abnormal repeat-expansion loci, pathogenic variants in known spinocerebellar ataxia-related genes, and novel rare mutations via whole-genome sequencing and linkage analysis. A rare co-segregating missense mutation in the CARS gene was validated by Sanger sequencing and the aminoacylation activity of mutant CARS was measured by spectrophotometric assay. This pedigree presented novel late-onset core characteristics including cerebellar ataxia, Parkinsonism, and pyramidal signs in all nine affected members. Brain magnetic resonance imaging showed cerebellar/pons atrophy, pontine-midline linear hyperintensity, decreased rCBF in the bilateral basal ganglia and cerebellar dentate nucleus, and hypo-intensities of the cerebellar dentate nuclei, basal ganglia, mesencephalic red nuclei, and substantia nigra, all of which suggested neurodegeneration. Whole-genome sequencing identified a novel pathogenic heterozygous mutation (E795V) in the CARS gene, meanwhile, exhibited none of the known repeat-expansions or point mutations in pathogenic genes. Remarkably, this CARS mutation causes a 20% decrease in aminoacylation activity to charge tRNACys with L-cysteine in protein synthesis compared with that of the wild type. All family members carrying a heterozygous mutation CARS (E795V) had the same clinical manifestations and neuropathological changes of Parkinsonism and spinocerebellar-ataxia. These findings identify novel pathogenesis of Parkinsonism-spinocerebellar ataxia and provide insights into its genetic architecture.
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Affiliation(s)
- Han-Kui Liu
- BGI Genomics and BGI Research, Shenzhen, 518083, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Clin Lab, BGI Genomics, Shijiazhuang, 050011, China
| | - Hong-Lin Hao
- Department of Neurology, Clinical Epidemiology Unit, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Hui You
- Department of Neurology, Clinical Epidemiology Unit, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Feng Feng
- Department of Neurology, Clinical Epidemiology Unit, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiu-Hong Qi
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | | | - Bo Hou
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | | | - Han Wang
- Department of Neurology, Clinical Epidemiology Unit, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | | | - Jian Wang
- BGI Genomics and BGI Research, Shenzhen, 518083, China
| | - Rui Wu
- Department of Pathology, Beijing Key Laboratory of Biomarker Research and Transformation for Neurodegenerative Diseases, Peking University Third Hospital, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Hui Fang
- Anhui Provincial Children's Hospital, Children's Hospital of Fudan University, Hefei, 230051, China
| | - Jiang-Ning Zhou
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Institute of Brain Science, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Jian-Guo Zhang
- BGI Genomics and BGI Research, Shenzhen, 518083, China.
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Clin Lab, BGI Genomics, Shijiazhuang, 050011, China.
| | - Zhen-Xin Zhang
- Department of Neurology, Clinical Epidemiology Unit, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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Chong JX, Berger SI, Baxter S, Smith E, Xiao C, Calame DG, Hawley MH, Rivera-Munoz EA, DiTroia S, Bamshad MJ, Rehm HL. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing. Genet Med 2024; 26:101199. [PMID: 38944749 PMCID: PMC11456385 DOI: 10.1016/j.gim.2024.101199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
Since the first novel gene discovery for a Mendelian condition was made via exome sequencing, the rapid increase in the number of genes known to underlie Mendelian conditions coupled with the adoption of exome (and more recently, genome) sequencing by diagnostic testing labs has changed the landscape of genomic testing for rare diseases. Specifically, many individuals suspected to have a Mendelian condition are now routinely offered clinical ES. This commonly results in a precise genetic diagnosis but frequently overlooks the identification of novel candidate genes. Such candidates are also less likely to be identified in the absence of large-scale gene discovery research programs. Accordingly, clinical laboratories have both the opportunity, and some might argue a responsibility, to contribute to novel gene discovery, which should, in turn, increase the diagnostic yield for many conditions. However, clinical diagnostic laboratories must necessarily balance priorities for throughput, turnaround time, cost efficiency, clinician preferences, and regulatory constraints and often do not have the infrastructure or resources to effectively participate in either clinical translational or basic genome science research efforts. For these and other reasons, many laboratories have historically refrained from broadly sharing potentially pathogenic variants in novel genes via networks such as Matchmaker Exchange, much less reporting such results to ordering providers. Efforts to report such results are further complicated by a lack of guidelines for clinical reporting and interpretation of variants in novel candidate genes. Nevertheless, there are myriad benefits for many stakeholders, including patients/families, clinicians, and researchers, if clinical laboratories systematically and routinely identify, share, and report novel candidate genes. To facilitate this change in practice, we developed criteria for triaging, sharing, and reporting novel candidate genes that are most likely to be promptly validated as underlying a Mendelian condition and translated to use in clinical settings.
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Affiliation(s)
- Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA; Brotman-Baty Institute for Precision Medicine, Seattle, WA.
| | - Seth I Berger
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Erica Smith
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA
| | - Changrui Xiao
- Department of Neurology, University of California Irvine, Orange, CA
| | - Daniel G Calame
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Neurosciences, Baylor College of Medicine, Houston, TX
| | | | | | - Stephanie DiTroia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Michael J Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA; Brotman-Baty Institute for Precision Medicine, Seattle, WA; Department of Pediatrics, Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
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9
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Kolawole OU, Huang A, Gregory-Evans CY, Shunmugam M, Weaver T, Gregory-Evans K. Molecular genetic diagnostics for inherited retinal dystrophies in the clinical setting. CANADIAN JOURNAL OF OPHTHALMOLOGY 2024; 59:e575-e581. [PMID: 37678418 DOI: 10.1016/j.jcjo.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/09/2023]
Abstract
OBJECTIVE To evaluate the success of diagnostic genetic testing in inherited retinal dystrophy (IRD) patients in the clinical setting. DESIGN Retrospective cohort analysis. PARTICIPANTS A total of 446 consecutive participants from diverse ethnic backgrounds living in western Canada. METHODS Clinical information was collected from participants, including family history, and they underwent a full ophthalmic examination with chart review. Those with a suspected IRD were offered panel-based genetic testing of 351 genes between March 1, 2019, and February 28, 2022. The main outcome measure was effect of the genetic testing results on clinical diagnosis. RESULTS Genetic testing established a conclusive molecular diagnosis in 249 of 446 cases (55.8%), a clearly negative result in 90 of 446 cases (20.1%), and an inconclusive diagnosis in 108 of 446 cases (24.2%). Conclusive disease-causing variants were identified in 69 genes, and the most commonly affected genes were ABCA4 (31 variants), USH2A (25 variants), and RPGR (19 variants). The inconclusive group included likely novel autosomal dominant variants or a pathogenic variant with a variant of uncertain significance in the same gene for a recessive phenotype. Notably, an inconclusive molecular genetic diagnosis was seen in as many as 47.3% of East Asian participants with an outer retinal dystrophy. CONCLUSIONS This study represents the largest review of molecular genetic testing in IRDs in Canada. That negative or inconclusive results obtained in approximately 45% of cases demonstrates that there is an important need for new research into molecular genetic causes of IRDs. This is particularly true in addressing the problem of interpreting a variant of uncertain significance in ethnic minorities.
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Affiliation(s)
- Olubayo U Kolawole
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC
| | - Albert Huang
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC
| | - Cheryl Y Gregory-Evans
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC
| | - Maheshver Shunmugam
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC
| | - Travers Weaver
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC
| | - Kevin Gregory-Evans
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC..
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10
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Kernfeld E, Yang Y, Weinstock J, Battle A, Cahan P. A systematic comparison of computational methods for expression forecasting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.28.551039. [PMID: 37577640 PMCID: PMC10418073 DOI: 10.1101/2023.07.28.551039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Expression forecasting methods use machine learning models to predict how a cell will alter its transcriptome upon perturbation. Such methods are enticing because they promise to answer pressing questions in fields ranging from developmental genetics to cell fate engineering and because they are a fast, cheap, and accessible complement to the corresponding experiments. However, the absolute and relative accuracy of these methods is poorly characterized, limiting their informed use, their improvement, and the interpretation of their predictions. To address these issues, we created a benchmarking platform that combines a panel of 11 large-scale perturbation datasets with an expression forecasting software engine that encompasses or interfaces to a wide variety of methods. We used our platform to systematically assess methods, parameters, and sources of auxiliary data, finding that performance strongly depends on the choice of metric, and especially for simple metrics like mean squared error, it is uncommon for expression forecasting methods to out-perform simple baselines. Our platform will serve as a resource to improve methods and to identify contexts in which expression forecasting can succeed.
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11
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Wismayer R, Matthews R, Whalley C, Kiwanuka J, Kakembo FE, Thorn S, Wabinga H, Odida M, Tomlinson I. Determination of the frequency and distribution of APC, PIK3CA, and SMAD4 gene mutations in Ugandan patients with colorectal cancer. BMC Cancer 2024; 24:1212. [PMID: 39350061 PMCID: PMC11440721 DOI: 10.1186/s12885-024-12967-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 09/19/2024] [Indexed: 10/04/2024] Open
Abstract
Uganda is a developing low-income country with a low incidence of colorectal cancer, which is steadily increasing. Ugandan colorectal cancer (CRC) patients are young and present with advanced-stage disease. In our population, there is a scarcity of genetic oncological studies, therefore, we investigated the mutational status of CRC tissues, focusing in particular on the adenomatous polyposis coli (APC), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), and SMAD4 genes. Our objective was to determine whether there were any differences between other populations and Ugandan patients. We performed next-generation sequencing on the extracted DNA from formalin-fixed paraffin-embedded adenocarcinoma samples from 127 patients (mean (SD) age: 54.9 (16.0) years; male:female sex ratio: 1.2:1). Most tumours were located in the rectum 56 (44.1%), 14 (11%) tumours were high grade, and 96 (75.6%) were moderate grade CRC. Stage III + IV CRC tumours were found in 109 (85.8%) patients. We identified 48 variants of APC, including 9 novel APC mutations that were all pathogenic or deleterious. For PIK3CA, we found 19 variants, of which 9 were deleterious or pathogenic. Four PIK3CA novel pathogenic or deleterious variants were included (c.1397C > G, c.2399_2400insA, c.2621G > C, c.2632C > G). Three SMAD4 variants were reported, including two pathogenic or deleterious variants (c.1268G > T, c.556dupC) and one tolerant (c.563A > C) variant. One novel SMAD4 deleterious mutation (c.1268G > T) was reported. In conclusion, we provide clinicopathological information and new genetic variation data pertinent to CRC in Uganda.
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Affiliation(s)
- Richard Wismayer
- Department of Surgery, Masaka Regional Referral Hospital, Masaka, Uganda.
- Department of Surgery, Faculty of Health Sciences, Equator University of Science and Technology, Masaka, Uganda.
- Department of Surgery, Faculty of Health Sciences, Habib Medical School, IUIU University, Kampala, Uganda.
- Department of Pathology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda.
- Institute of Genetics and Cancer, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK.
| | - Rosie Matthews
- Institute of Genetics and Cancer, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Celina Whalley
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Julius Kiwanuka
- Department of Epidemiology and Biostatistics, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fredrick Elishama Kakembo
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
- African Centre of Excellence in Bioinformatics and Data Intensive Sciences, Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Steve Thorn
- Institute of Genetics and Cancer, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Henry Wabinga
- Department of Pathology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Michael Odida
- Department of Pathology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Pathology, Faculty of Medicine, Gulu University, Gulu, Uganda
| | - Ian Tomlinson
- Institute of Genetics and Cancer, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
- Department of Oncology, University of Oxford, Oxford, UK
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12
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Dinneen TJ, Ní Ghrálaigh F, Ormond C, Heron EA, Kirov G, Lopez LM, Gallagher L. Polygenic scores stratify neurodevelopmental copy number variant carrier cognitive outcomes in the UK Biobank. NPJ Genom Med 2024; 9:43. [PMID: 39341812 PMCID: PMC11438881 DOI: 10.1038/s41525-024-00426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 09/04/2024] [Indexed: 10/01/2024] Open
Abstract
Rare copy-number variants associated with neurodevelopmental conditions (ND-CNVs) exhibit variable expressivity of clinical, physical, behavioural outcomes. Findings from clinically ascertained cohorts suggest this variability may be partly due to additional genetic variation. Here, we assessed the impact of polygenic scores (PGS) and rare variants on ND-CNV carrier fluid intelligence (FI) scores in the UK Biobank. Greater PGS for cognition (PSCog) and educational attainment (PSEA) is associated with increased FI scores in all ND-CNVs (n = 1317), 15q11.2 del. (n = 543), and 16p13.11 dup. carriers (n = 275). No association of rare variants associated with intellectual disability, autism, or putatively loss-of-function, brain-expressed genes was found. Positive predictive values in the first deciles of PScog and PSEA showed a two- to five-fold increase in the rate of low FI scores compared to baseline rates. These findings demonstrate that PGS can stratify ND-CNV carrier cognitive outcomes in a population-based cohort.
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Affiliation(s)
- Thomas J Dinneen
- Trinity College Dublin, Department of Psychiatry, School of Medicine, Trinity Centre for Health Sciences, St. James' Hospital, Dublin 8, Ireland.
- The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay St., Toronto, ON, M5G 0A4, Canada.
| | - Fiana Ní Ghrálaigh
- Department of Biology, Maynooth University, Maynooth, Co, Kildare, Ireland
| | - Cathal Ormond
- Trinity College Dublin, Department of Psychiatry, School of Medicine, Trinity Centre for Health Sciences, St. James' Hospital, Dublin 8, Ireland
| | - Elizabeth A Heron
- Trinity College Dublin, Department of Psychiatry, School of Medicine, Trinity Centre for Health Sciences, St. James' Hospital, Dublin 8, Ireland
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Lorna M Lopez
- Department of Biology, Maynooth University, Maynooth, Co, Kildare, Ireland
| | - Louise Gallagher
- Trinity College Dublin, Department of Psychiatry, School of Medicine, Trinity Centre for Health Sciences, St. James' Hospital, Dublin 8, Ireland
- The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay St., Toronto, ON, M5G 0A4, Canada
- Centre for Addiction and Mental Health, 80 Workman Way, Toronto, ON, M6J 1H4, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A1, Canada
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13
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Schuetz RJ, Ceyhan D, Antoniou AA, Chaudhari BP, White P. CNVoyant a machine learning framework for accurate and explainable copy number variant classification. Sci Rep 2024; 14:22411. [PMID: 39333267 PMCID: PMC11437066 DOI: 10.1038/s41598-024-72470-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 09/09/2024] [Indexed: 09/29/2024] Open
Abstract
The precise classification of copy number variants (CNVs) presents a significant challenge in genomic medicine, primarily due to the complex nature of CNVs and their diverse impact on rare genetic diseases (RGDs). This complexity is compounded by the limitations of existing methods in accurately distinguishing between benign, uncertain, and pathogenic CNVs. Addressing this gap, we introduce CNVoyant, a machine learning-based multi-class framework designed to enhance the clinical significance classification of CNVs. Trained on a comprehensive dataset of 52,176 ClinVar entries across pathogenic, uncertain, and benign classifications, CNVoyant incorporates a broad spectrum of genomic features, including genome position, disease-gene annotations, dosage sensitivity, and conservation scores. Models to predict the clinical significance of copy number gains and losses were trained independently. Final models were selected after testing 29 machine learning architectures and 10,000 hyperparameter combinations each for deletions and duplications via fivefold cross-validation. We validate the performance of CNVoyant by leveraging a comprehensive set of 21,574 CNVs from the DECIPHER database, a highly regarded resource known for its extensive catalog of chromosomal imbalances linked to clinical outcomes. Compared to alternative approaches, CNVoyant shows marked improvements in precision-recall and ROC AUC metrics for binary pathogenic classifications while going one step further, offering multi-classification of clinical significance and corresponding SHAP explainability plots. Additionally, when provided germline CNV calls from real-world RGD cases with diagnostic CNV(s), CNVoyant correctly classified all diagnostic CNVs as having pathogenic significance with high confidence. This large-scale validation demonstrates CNVoyant's superior accuracy and underscores its potential to aid genomic researchers and clinical geneticists in interpreting the clinical implications of real CNVs.
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Affiliation(s)
- Robert J Schuetz
- The Office of Data Sciences, The Abigail Wexner Research Institute at Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH, 43215, USA
| | - Defne Ceyhan
- The Office of Data Sciences, The Abigail Wexner Research Institute at Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH, 43215, USA
| | - Austin A Antoniou
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH, 43215, USA
| | - Bimal P Chaudhari
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH, 43215, USA.
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
- Divisions of Neonatology, Genetics and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
- Center for Clinical and Translational Science, The Ohio State University and Nationwide Children's Hospital, Columbus, OH, USA.
| | - Peter White
- The Office of Data Sciences, The Abigail Wexner Research Institute at Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH, 43215, USA.
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH, 43215, USA.
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
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14
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Lee AS, Ayers LJ, Kosicki M, Chan WM, Fozo LN, Pratt BM, Collins TE, Zhao B, Rose MF, Sanchis-Juan A, Fu JM, Wong I, Zhao X, Tenney AP, Lee C, Laricchia KM, Barry BJ, Bradford VR, Jurgens JA, England EM, Lek M, MacArthur DG, Lee EA, Talkowski ME, Brand H, Pennacchio LA, Engle EC. A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders. Nat Commun 2024; 15:8268. [PMID: 39333082 PMCID: PMC11436875 DOI: 10.1038/s41467-024-52463-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 09/04/2024] [Indexed: 09/29/2024] Open
Abstract
Unsolved Mendelian cases often lack obvious pathogenic coding variants, suggesting potential non-coding etiologies. Here, we present a single cell multi-omic framework integrating embryonic mouse chromatin accessibility, histone modification, and gene expression assays to discover cranial motor neuron (cMN) cis-regulatory elements and subsequently nominate candidate non-coding variants in the congenital cranial dysinnervation disorders (CCDDs), a set of Mendelian disorders altering cMN development. We generate single cell epigenomic profiles for ~86,000 cMNs and related cell types, identifying ~250,000 accessible regulatory elements with cognate gene predictions for ~145,000 putative enhancers. We evaluate enhancer activity for 59 elements using an in vivo transgenic assay and validate 44 (75%), demonstrating that single cell accessibility can be a strong predictor of enhancer activity. Applying our cMN atlas to 899 whole genome sequences from 270 genetically unsolved CCDD pedigrees, we achieve significant reduction in our variant search space and nominate candidate variants predicted to regulate known CCDD disease genes MAFB, PHOX2A, CHN1, and EBF3 - as well as candidates in recurrently mutated enhancers through peak- and gene-centric allelic aggregation. This work delivers non-coding variant discoveries of relevance to CCDDs and a generalizable framework for nominating non-coding variants of potentially high functional impact in other Mendelian disorders.
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Affiliation(s)
- Arthur S Lee
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Lauren J Ayers
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Wai-Man Chan
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Lydia N Fozo
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Brandon M Pratt
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Thomas E Collins
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Boxun Zhao
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Matthew F Rose
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Medical Genetics Training Program, Harvard Medical School, Boston, MA, USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jack M Fu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Isaac Wong
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Xuefang Zhao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alan P Tenney
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cassia Lee
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Harvard College, Cambridge, MA, USA
| | - Kristen M Laricchia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brenda J Barry
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Victoria R Bradford
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Julie A Jurgens
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eleina M England
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Eunjung Alice Lee
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Harrison Brand
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Elizabeth C Engle
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Medical Genetics Training Program, Harvard Medical School, Boston, MA, USA.
- Department of Ophthalmology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
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15
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Sjursen W, Hyldebrandt HK, Lavik LAS, Haukanes BI, Ariansen S, Briskemyr S, Sylvander AE, Haavind MT, Olsen MF, Røyset ES, Vetti H, Stormorken A, Grindedal EM. PMS2 mutation spectra in Norway and risk of cancer for carriers of pathogenic variants. Hered Cancer Clin Pract 2024; 22:20. [PMID: 39334433 PMCID: PMC11438158 DOI: 10.1186/s13053-024-00292-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 09/13/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND In Norway, we have offered testing of PMS2 since 2006, and have a large national cohort of carriers. The aim of this study was to describe all PMS2 variants identified, and to describe frequency, spectrum and penetrance of cancers in carriers of class 4/5 variants. METHODS All detected PMS2 variants were collected from the diagnostic laboratories and reclassified according to ACMG criteria and gene specific guidelines. Data on variant, gender, cancer diagnosis, age at diagnosis, and age at last known follow-up was collected on all carriers of class 4/5 variants from electronic patient records. The Kaplan-Meier algorithm was used to calculate cumulative risk of any cancer, colorectal cancer and endometrial cancer. RESULTS In total, 220 different PMS2 variants were detected. Twenty nine class 4/5 variants were identified in 482 carriers. The most common pathogenic variant was the founder mutation c.989-1G > T, detected in 204 patients from 58 families. Eighty seven out of 482 (18.0%) had been diagnosed with colorectal cancer, 10 of these (11.8%) before 40 years. Cumulative risk at 70 years in our cohort was 34.7% for colorectal cancer and 26.1% for endometrial cancer. CONCLUSIONS After 15 years of genetic testing, 29 different class 4/5 variants have been detected in Norway. Almost half of Norwegian PMS2 carriers have the founder variant 989-1G > T. Penetrance of colorectal cancer in our cohort was moderate but variable, as 11.5% of those diagnosed were younger than 40 years.
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Affiliation(s)
- Wenche Sjursen
- Department of Medical Genetics, St Olavs University Hospital, Trondheim, Norway.
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Hanne K Hyldebrandt
- Department of Medical Genetics, Oslo University Hospital, Trondheim, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Liss Anne S Lavik
- Department of Medical Genetics, St Olavs University Hospital, Trondheim, Norway
| | - Bjørn Ivar Haukanes
- Department of Medical Genetics, Haukeland University Hospital, Trondheim, Norway
| | - Sarah Ariansen
- Department of Medical Genetics, Oslo University Hospital, Trondheim, Norway
| | - Siri Briskemyr
- Department of Medical Genetics, University Hospital of Northern Norway, Tromsø, Norway
| | - Anna E Sylvander
- Department of Medical Genetics, St Olavs University Hospital, Trondheim, Norway
| | - Marianne T Haavind
- Department of Medical Genetics, Haukeland University Hospital, Trondheim, Norway
| | - Maren F Olsen
- Department of Medical Genetics, St Olavs University Hospital, Trondheim, Norway
| | - Elin S Røyset
- Department of Pathology, St Olavs University Hospital, Trondheim, Norway
| | - Hildegunn Vetti
- Department of Medical Genetics, Haukeland University Hospital, Trondheim, Norway
| | - Astrid Stormorken
- Department of Medical Genetics, Oslo University Hospital, Trondheim, Norway
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16
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Seo ES, Lee JW, Lim J, Shin S, Cho HW, Ju HY, Yoo KH, Sung KW, Park WY. Germline functional variants contribute to somatic mutation and outcomes in neuroblastoma. Nat Commun 2024; 15:8360. [PMID: 39333105 PMCID: PMC11437149 DOI: 10.1038/s41467-024-52128-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/27/2024] [Indexed: 09/29/2024] Open
Abstract
Germline genetic context may play a significant role in the development and evolution of cancer, particularly in childhood cancers such as neuroblastoma. This study investigates the role of putatively functional germline variants in neuroblastoma, even if they do not directly increase disease risk. Our whole-exome sequencing analysis of 125 patients with neuroblastoma reveals a positive correlation between germline variant burden and somatic mutations. Moreover, patients with higher germline variant burden exhibit worse outcomes. Similar findings are observed in the independent neuroblastoma cohort where a higher germline variant burden correlates with a higher somatic mutational burden and a worse overall survival outcome. However, contrasting results emerge in adult-onset cancer, emphasizing the importance of germline genetics in neuroblastoma. The enrichment of putatively functional germline variants in cancer predisposition genes is borderline significant when compared to healthy populations (P = 0.077; Odds Ratio, 1.45; 95% confidence intervals, 0.94-2.21) and significantly more pronounced against adult-onset cancers (P = 0.016; Odds Ratio, 2.13; 95% confidence intervals, 1.10-3.91). Additionally, the presence of these variants proves to have prognostic significance in neuroblastoma (log-rank P < 0.001), and combining germline with clinical risk factors notably improves survival predictions.
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Affiliation(s)
- Eun Seop Seo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
- Department of Digital Health, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University, Seoul, South Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Ji Won Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jinyeong Lim
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Sunghwan Shin
- Department of Laboratory Medicine, Inje University Ilsan Paik Hospital, Goyang, South Korea
| | - Hee Won Cho
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hee Young Ju
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Keon Hee Yoo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Ki Woong Sung
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Woong-Yang Park
- Department of Digital Health, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University, Seoul, South Korea.
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea.
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17
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Quinlan A, Rodan L, Barkoudah E, Tam A, Saffari A, Shammas I, Ranatunga W, Morava-Kozicz E, Oglesbee D, Berry G, Ebrahimi-Fakhari D, Srivastava S. Case Report of Friedreich's Ataxia and ALG1-Related Biochemical Abnormalities in a Patient With Progressive Spastic Paraplegia. Am J Med Genet A 2024:e63890. [PMID: 39324476 DOI: 10.1002/ajmg.a.63890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 09/05/2024] [Accepted: 09/14/2024] [Indexed: 09/27/2024]
Abstract
Frataxin is an evolutionarily conserved mitochondrial protein responsible for iron homeostasis and metabolism. A deficiency of frataxin (encoded by FXN) leads to Friedreich's ataxia (FRDA), a progressive disorder that affects both the central and peripheral nervous systems, most commonly via a pathogenic GAA trinucleotide expansion. In contrast, pathogenic variants in ALG1 in humans cause a form of congenital disorder of glycosylation. Here, we present a 15-year-old boy with a clinical presentation that raised concern for complex hereditary spastic paraplegia (HSP), with motor features including progressive spastic paraparesis, cervical dystonia, cerebellar dysfunction, and diminished lower extremity reflexes. The proband was initially found to have a novel compound heterozygous variant in ALG1 on exome sequencing, along with N-glycan profiling revealing evidence of defective mannosylation and Western blot analysis demonstrating an 84% reduction in ALG1 expression. Although several of his clinical features could be explained by the ALG1 variant specifically or considered as part of the presentation of CDGs in general, there were additional phenotypes that suggested an alternative, or additional, genetic diagnosis. Subsequently, he was found to have biallelic pathogenic GAA repeat expansions in FXN on genome sequencing, leading to a diagnosis of FRDA. Given that FRDA explained all his clinical features, the ALG1 variant may have been a hypomorphic form and/or a biochemical phenotype. Our findings underscore the importance of considering FRDA as a differential diagnosis in cases of complex HSP and demonstrate the utility of unbiased genome sequencing approaches that include detection of trinucleotide repeat expansions for progressive motor disorders.
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Affiliation(s)
- Aisling Quinlan
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Lance Rodan
- Department of Genetics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Elizabeth Barkoudah
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
- Cerebral Palsy and Spasticity Center, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Amy Tam
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Afshin Saffari
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Ibrahim Shammas
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Wasantha Ranatunga
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Eva Morava-Kozicz
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Devin Oglesbee
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Gerald Berry
- Department of Genetics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Darius Ebrahimi-Fakhari
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Siddharth Srivastava
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts, USA
- Cerebral Palsy and Spasticity Center, Boston Children's Hospital, Boston, Massachusetts, USA
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18
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Soto DC, Uribe-Salazar JM, Kaya G, Valdarrago R, Sekar A, Haghani NK, Hino K, La GN, Mariano NAF, Ingamells C, Baraban AE, Turner TN, Green ED, Simó S, Quon G, Andrés AM, Dennis MY. Gene expansions contributing to human brain evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.26.615256. [PMID: 39386494 PMCID: PMC11463660 DOI: 10.1101/2024.09.26.615256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Genomic drivers of human-specific neurological traits remain largely undiscovered. Duplicated genes expanded uniquely in the human lineage likely contributed to brain evolution, including the increased complexity of synaptic connections between neurons and the dramatic expansion of the neocortex. Discovering duplicate genes is challenging because the similarity of paralogs makes them prone to sequence-assembly errors. To mitigate this issue, we analyzed a complete telomere-to-telomere human genome sequence (T2T-CHM13) and identified 213 duplicated gene families likely containing human-specific paralogs (>98% identity). Positing that genes important in universal human brain features should exist with at least one copy in all modern humans and exhibit expression in the brain, we narrowed in on 362 paralogs with at least one copy across thousands of ancestrally diverse genomes and present in human brain transcriptomes. Of these, 38 paralogs co-express in gene modules enriched for autism-associated genes and potentially contribute to human language and cognition. We narrowed in on 13 duplicate gene families with human-specific paralogs that are fixed among modern humans and show convincing brain expression patterns. Using long-read DNA sequencing revealed hidden variation across 200 modern humans of diverse ancestries, uncovering signatures of selection not previously identified, including possible balancing selection of CD8B . To understand the roles of duplicated genes in brain development, we generated zebrafish CRISPR "knockout" models of nine orthologs and transiently introduced mRNA-encoding paralogs, effectively "humanizing" the larvae. Morphometric, behavioral, and single-cell RNA-seq screening highlighted, for the first time, a possible role for GPR89B in dosage-mediated brain expansion and FRMPD2B function in altered synaptic signaling, both hallmark features of the human brain. Our holistic approach provides important insights into human brain evolution as well as a resource to the community for studying additional gene expansion drivers of human brain evolution. Abstract short Duplicated genes expanded in the human lineage likely contributed to brain evolution, yet challenges exist in their discovery due to sequence-assembly errors. We used a complete telomere-to-telomere genome sequence to identify 213 human-specific gene families. From these, 362 paralogs were found in all modern human genomes tested and brain transcriptomes, making them top candidates contributing to human-universal brain features. Choosing a subset of paralogs, we used long-read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development, we generated zebrafish CRISPR "knockout" models of nine orthologs and introduced mRNA-encoding paralogs, effectively "humanizing" larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage-mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.
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19
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Qiao L, Welch CL, Hernan R, Wynn J, Krishnan US, Zalieckas JM, Buchmiller T, Khlevner J, De A, Farkouh-Karoleski C, Wagner AJ, Heydweiller A, Mueller AC, de Klein A, Warner BW, Maj C, Chung D, McCulley DJ, Schindel D, Potoka D, Fialkowski E, Schulz F, Kipfmuller F, Lim FY, Magielsen F, Mychaliska GB, Aspelund G, Reutter HM, Needelman H, Schnater JM, Fisher JC, Azarow K, Elfiky M, Nöthen MM, Danko ME, Li M, Kosiński P, Wijnen RMH, Cusick RA, Soffer SZ, Cochius-Den Otter SCM, Schaible T, Crombleholme T, Duron VP, Donahoe PK, Sun X, High FA, Bendixen C, Brosens E, Shen Y, Chung WK. Common variants increase risk for congenital diaphragmatic hernia within the context of de novo variants. Am J Hum Genet 2024:S0002-9297(24)00334-3. [PMID: 39332409 DOI: 10.1016/j.ajhg.2024.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 08/24/2024] [Accepted: 08/30/2024] [Indexed: 09/29/2024] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly often accompanied by other structural anomalies and/or neurobehavioral manifestations. Rare de novo protein-coding variants and copy-number variations contribute to CDH in the population. However, most individuals with CDH remain genetically undiagnosed. Here, we perform integrated de novo and common-variant analyses using 1,469 CDH individuals, including 1,064 child-parent trios and 6,133 ancestry-matched, unaffected controls for the genome-wide association study. We identify candidate CDH variants in 15 genes, including eight novel genes, through deleterious de novo variants. We further identify two genomic loci contributing to CDH risk through common variants with similar effect sizes among Europeans and Latinx. Both loci are in putative transcriptional regulatory regions of developmental patterning genes. Estimated heritability in common variants is ∼19%. Strikingly, there is no significant difference in estimated polygenic risk scores between isolated and complex CDH or between individuals harboring deleterious de novo variants and individuals without these variants. The data support a polygenic model as part of the CDH genetic architecture.
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Affiliation(s)
- Lu Qiao
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Carrie L Welch
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rebecca Hernan
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Usha S Krishnan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jill M Zalieckas
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Anesthesiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Terry Buchmiller
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Julie Khlevner
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aliva De
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Amy J Wagner
- Children's Hospital of Wisconsin, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Andreas Heydweiller
- Department of General, Visceral, Vascular, and Thoracic Surgery, Unit of Pediatric Surgery, University Hospital Bonn, Bonn, Germany
| | - Andreas C Mueller
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Brad W Warner
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Dai Chung
- Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN 37232, USA
| | - David J McCulley
- Department of Pediatrics, San Diego Medical School, University of California, San Diego, San Diego, CA 92092, USA
| | | | | | | | - Felicitas Schulz
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Florian Kipfmuller
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Foong-Yen Lim
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Frank Magielsen
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | | | - Gudrun Aspelund
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Heiko Martin Reutter
- Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Howard Needelman
- University of Nebraska Medical Center College of Medicine, Omaha, NE 68114, USA
| | - J Marco Schnater
- Department of Pediatric Surgery, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Jason C Fisher
- New York University Grossman School of Medicine, Hassenfeld Children's Hospital at NYU Langone, New York, NY 10016, USA
| | - Kenneth Azarow
- Oregon Health and Science University, Portland, OR 97239, USA
| | | | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Melissa E Danko
- Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN 37232, USA
| | - Mindy Li
- Rush University Medical Center, Chicago, IL 60612, USA
| | - Przemyslaw Kosiński
- Department of Obstetrics, Perinatology and Gynecology, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Rene M H Wijnen
- Department of Pediatric Surgery, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Robert A Cusick
- University of Nebraska Medical Center College of Medicine, Omaha, NE 68114, USA
| | | | - Suzan C M Cochius-Den Otter
- Department of Neonatology and Pediatric Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Thomas Schaible
- Department of Neonatology, University Children's Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | | | - Vincent P Duron
- Department of Surgery (Pediatrics), Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Patricia K Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Xin Sun
- Department of Pediatrics, San Diego Medical School, University of California, San Diego, San Diego, CA 92092, USA
| | - Frances A High
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Charlotte Bendixen
- Department of General, Visceral, Vascular, and Thoracic Surgery, Unit of Pediatric Surgery, University Hospital Bonn, Bonn, Germany
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA; JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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20
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Li X, Yao Y, Xing S, Zheng YH, Zhou Y, Yu X, Su J, Chen S, Jin ZB. Trio-based whole-exome sequencing of 200 Chinese patients with keratoconus. Exp Eye Res 2024; 248:110109. [PMID: 39326774 DOI: 10.1016/j.exer.2024.110109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 09/09/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
Abstract
Keratoconus (KC) is a complex corneal disorder with a well-recognized genetic component. In this study, we aimed to expand the genetic spectrum of 200 Chinese patients with keratoconus and their unaffected parents. Trio-based whole-exome sequencing was performed in 200 patients with sporadic keratoconus and their unaffected parents. The variants identified in candidate genes for keratoconus were analyzed using multiple bioinformatics tools. Finally, we identified 7 variants in 5 candidate genes for keratoconus in 5 patients. The c.T464C variant in the IMPDH1 gene was defined as likely pathogenic according to the guidelines of the American College of Medical Genetics and Genomics, and the remaining variants in candidate genes (TRANK1, SLC4A11, CERKL, IFT172) were defined as uncertain significance. Our results expand the genetic spectrum in KC, highlight the genetic heterogeneity of this disease and provide important clues for future functional validation.
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Affiliation(s)
- Xingyong Li
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; Taizhou Ophthalmology and Optometry Hospital, Taizhou 318001, China
| | - Yinghao Yao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), The Eye Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Shilai Xing
- Institute of PSI Genomics, Wenzhou Global Eye & Vision Innovation Center, Wenzhou, 325024, Zhejiang, China
| | - Yi-Han Zheng
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Yang Zhou
- Taizhou Ophthalmology and Optometry Hospital, Taizhou 318001, China
| | - Xiaoguang Yu
- Institute of PSI Genomics, Wenzhou Global Eye & Vision Innovation Center, Wenzhou, 325024, Zhejiang, China
| | - Jianzhong Su
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), The Eye Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
| | - Shihao Chen
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; Taizhou Ophthalmology and Optometry Hospital, Taizhou 318001, China.
| | - Zi-Bing Jin
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China; Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing, 100005, China
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21
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Gomez-Arroyo J, Houweling AC, Bogaard HJ, Aman J, Kitzmiller JA, Porollo A, Dooijes D, Meijboom LJ, Hale P, Pauciulo MW, Hong J, Zhu N, Welch C, Shen Y, Zacharias WJ, McCormack FX, Aldred MA, Weirauch MT, Graf S, Rhodes C, Chung WK, Whitsett JA, Martin LJ, Kalinichenko VV, Nichols WC. Role of Forkhead box F1 in the Pathobiology of Pulmonary Arterial Hypertension. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.611448. [PMID: 39345371 PMCID: PMC11429893 DOI: 10.1101/2024.09.18.611448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Rationale Approximately 80% of patients with non-familial pulmonary arterial hypertension (PAH) lack identifiable pathogenic genetic variants. While most genetic studies of PAH have focused on predicted loss-of-function variants, recent approaches have identified ultra-rare missense variants associated with the disease. FOXF1 encodes a highly conserved transcription factor, essential for angiogenesis and vasculogenesis in human and mouse lungs. Objectives We identified a rare FOXF1 missense coding variant in two unrelated probands with PAH. FOXF1 is an evolutionarily conserved transcription factor required for lung vascular development and vascular integrity. Our aims were to determine the frequency of FOXF1 variants in larger PAH cohorts compared to the general population, study FOXF1 expression in explanted lung tissue from PAH patients versus control (failed-donor) lungs, and define potential downstream targets linked to PAH development. Methods Three independent, international, multicenter cohorts were analyzed to evaluate the frequency of FOXF1 rare variants. Various composite prediction models assessed the deleteriousness of individual variants. Bulk RNA sequencing datasets from human explanted lung tissues were compared to failed-donor controls to determine FOXF1 expression. Bioinformatic tools identified putative FOXF1 binding targets, which were orthogonally validated using mouse ChIP-seq datasets. Measurements and Main Results Seven novel or ultra-rare missense coding variants were identified across three patient cohorts in different regions of the FOXF1 gene, including the DNA binding domain. FOXF1 expression was dysregulated in PAH lungs, correlating with disease severity. Histological analysis showed heterogeneous FOXF1 expression, with the lowest levels in phenotypically abnormal endothelial cells within complex vascular lesions in PAH samples. A hybrid bioinformatic approach identified FOXF1 downstream targets potentially involved in PAH pathogenesis, including BMPR2 . Conclusions Large genomic and transcriptomic datasets suggest that decreased FOXF1 expression or predicted dysfunction is associated with PAH.
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22
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Schraiber JG, Spence JP, Edge MD. Estimation of demography and mutation rates from one million haploid genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.613708. [PMID: 39345369 PMCID: PMC11429810 DOI: 10.1101/2024.09.18.613708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
As genetic sequencing costs have plummeted, datasets with sizes previously un-thinkable have begun to appear. Such datasets present new opportunities to learn about evolutionary history, particularly via rare alleles that record the very recent past. However, beyond the computational challenges inherent in the analysis of many large-scale datasets, large population-genetic datasets present theoretical problems. In particular, the majority of population-genetic tools require the assumption that each mutant allele in the sample is the result of a single mutation (the "infinite sites" assumption), which is violated in large samples. Here, we present DR EVIL, a method for estimating mutation rates and recent demographic history from very large samples. DR EVIL avoids the infinite-sites assumption by using a diffusion approximation to a branching-process model with recurrent mutation. The branching-process approach limits the method to rare alleles, but, along with recent results, renders tractable likelihoods with recurrent mutation. We show that DR EVIL performs well in simulations and apply it to rare-variant data from a million haploid samples, identifying a signal of mutation-rate heterogeneity within commonly analyzed classes and predicting that in modern sample sizes, most rare variants at sites with high mutation rates represent the descendants of multiple mutation events.
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23
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Ma K, Huang S, Ng KK, Lake NJ, Joseph S, Xu J, Lek A, Ge L, Woodman KG, Koczwara KE, Cohen J, Ho V, O'Connor CL, Brindley MA, Campbell KP, Lek M. Saturation mutagenesis-reinforced functional assays for disease-related genes. Cell 2024:S0092-8674(24)00976-0. [PMID: 39326416 DOI: 10.1016/j.cell.2024.08.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 07/29/2024] [Accepted: 08/23/2024] [Indexed: 09/28/2024]
Abstract
Interpretation of disease-causing genetic variants remains a challenge in human genetics. Current costs and complexity of deep mutational scanning methods are obstacles for achieving genome-wide resolution of variants in disease-related genes. Our framework, saturation mutagenesis-reinforced functional assays (SMuRF), offers simple and cost-effective saturation mutagenesis paired with streamlined functional assays to enhance the interpretation of unresolved variants. Applying SMuRF to neuromuscular disease genes FKRP and LARGE1, we generated functional scores for all possible coding single-nucleotide variants, which aid in resolving clinically reported variants of uncertain significance. SMuRF also demonstrates utility in predicting disease severity, resolving critical structural regions, and providing training datasets for the development of computational predictors. Overall, our approach enables variant-to-function insights for disease genes in a cost-effective manner that can be broadly implemented by standard research laboratories.
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Affiliation(s)
- Kaiyue Ma
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
| | - Shushu Huang
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Kenneth K Ng
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Nicole J Lake
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Soumya Joseph
- Howard Hughes Medical Institute, Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Department of Molecular Physiology and Biophysics and Department of Neurology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Jenny Xu
- Yale University, New Haven, CT, USA
| | - Angela Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Muscular Dystrophy Association, Chicago, IL, USA
| | - Lin Ge
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Keryn G Woodman
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Justin Cohen
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Vincent Ho
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Melinda A Brindley
- Department of Infectious Diseases, Department of Population Health, University of Georgia, Athens, GA, USA
| | - Kevin P Campbell
- Howard Hughes Medical Institute, Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Department of Molecular Physiology and Biophysics and Department of Neurology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
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24
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Jiang J, Xu J, Ji S, Yu X, Chen J. Unraveling the mysteries of MGMT: Implications for neuroendocrine tumors. Biochim Biophys Acta Rev Cancer 2024; 1879:189184. [PMID: 39303858 DOI: 10.1016/j.bbcan.2024.189184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 07/15/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
Neuroendocrine tumors (NETs) are a diverse group of tumors that arise from neuroendocrine cells and are commonly found in various organs. A considerable proportion of NET patients were diagnosed at an advanced or metastatic stage. Alkylating agents are the primary treatment for NET, and O6-methylguanine methyltransferase (MGMT) remains the first-line of defense against DNA damage caused by these agents. Clinical trials have indicated that MGMT promoter methylation or its low/lacked expression can predict a favorable outcome with Temozolomide in NETs. Its status could help select NET patients who can benefit from alkylating agents. Therefore, MGMT status serves as a biomarker to guide decisions on the efficacy of Temozolomide as a personalized treatment option. Additionally, delving into the regulatory mechanisms of MGMT status can lead to the development of MGMT-targeted therapies, benefiting individuals with high levels of MGMT expression. This review aims to explore the polymorphism of MGMT regulation and summarize its clinical implications in NETs, which would help establish the role of MGMT as a biomarker and its potential as a therapeutic target in NETs. Additionally, we explore the benefits of combining Temozolomide and immunotherapy in MGMT hypermethylated subgroups. Future studies can focus on optimizing Temozolomide administration to induce specific immunomodulatory changes.
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Affiliation(s)
- Jianyun Jiang
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Junfeng Xu
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China.
| | - Shunrong Ji
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China.
| | - Xianjun Yu
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China.
| | - Jie Chen
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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25
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Schubert SA, Ruano D, Joruiz SM, Stroosma J, Glavak N, Montali A, Pinto LM, Rodríguez-Girondo M, Barge-Schaapveld DQCM, Nielsen M, van Nesselrooij BPM, Mensenkamp AR, van Leerdam ME, Sharp TH, Morreau H, Bourdon JC, de Miranda NFCC, van Wezel T. Germline variant affecting p53β isoforms predisposes to familial cancer. Nat Commun 2024; 15:8208. [PMID: 39294166 PMCID: PMC11410958 DOI: 10.1038/s41467-024-52551-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/06/2024] [Indexed: 09/20/2024] Open
Abstract
Germline and somatic TP53 variants play a crucial role during tumorigenesis. However, genetic variations that solely affect the alternatively spliced p53 isoforms, p53β and p53γ, are not fully considered in the molecular diagnosis of Li-Fraumeni syndrome and cancer. In our search for additional cancer predisposing variants, we identify a heterozygous stop-lost variant affecting the p53β isoforms (p.*342Serext*17) in four families suspected of an autosomal dominant cancer syndrome with colorectal, breast and papillary thyroid cancers. The stop-lost variant leads to the 17 amino-acid extension of the p53β isoforms, which increases oligomerization to canonical p53α and dysregulates the expression of p53's transcriptional targets. Our study reveals the capacity of p53β mutants to influence p53 signalling and contribute to the susceptibility of different cancer types. These findings underscore the significance of p53 isoforms and the necessity of comprehensive investigation into the entire TP53 gene in understanding cancer predisposition.
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Affiliation(s)
- Stephanie A Schubert
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Jordy Stroosma
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Nikolina Glavak
- School of Medicine, University of Dundee, Dundee, UK
- Croatian Institute of Transfusion Medicine, Zagreb, Croatia
| | - Anna Montali
- School of Medicine, University of Dundee, Dundee, UK
| | - Lia M Pinto
- School of Medicine, University of Dundee, Dundee, UK
| | - Mar Rodríguez-Girondo
- Department of Biomedical Data Sciences, Section of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Monique E van Leerdam
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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26
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Gracheva AS, Kashatnikova DA, Redkin IV, Zakharchenko VE, Kuzovlev AN, Salnikova LE. Genetics and Traumatic Brain Injury: Findings from an Exome-Based Study of a 50-Patient Case Series. Curr Issues Mol Biol 2024; 46:10351-10368. [PMID: 39329968 PMCID: PMC11430351 DOI: 10.3390/cimb46090616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 09/14/2024] [Accepted: 09/16/2024] [Indexed: 09/28/2024] Open
Abstract
Traumatic brain injury (TBI) is the leading cause of global mortality and morbidity. Because TBI is accident-related, the role of genetics in predisposing to TBI has been largely unexplored. However, the likelihood of injury may not be entirely random and may be associated with certain physical and mental characteristics. In this study, we analyzed the exomes of 50 patients undergoing rehabilitation after TBI. Patients were divided into three groups according to rehabilitation outcome: improvement, no change, and deterioration/death. We focused on rare, potentially functional missense and high-impact variants in genes intolerant to these variants. The concordant results from the three independent groups of patients allowed for the suggestion of the existence of a genetic predisposition to TBI, associated with rare functional variations in intolerant genes, with a prevalent dominant mode of inheritance and neurological manifestations in the genetic phenotypes according to the OMIM database. Forty-four of the 50 patients had one or more rare, potentially deleterious variants in one or more neurological genes. Comparison of these results with those of a 50-sampled matched non-TBI cohort revealed significant differences: P = 2.6 × 10-3, OR = 4.89 (1.77-13.47). There were no differences in the distribution of the genes of interest between the TBI patient groups. Our exploratory study provides new insights into the impact of genetics on TBI risk and is the first to address potential genetic susceptibility to TBI.
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Affiliation(s)
- Alesya S Gracheva
- The Department of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
| | - Darya A Kashatnikova
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- The Laboratory of Molecular Pathophysiology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Ivan V Redkin
- The Laboratory of Organoprotection in Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
| | - Vladislav E Zakharchenko
- The Department of Clinical Laboratory Diagnostics, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
| | - Artem N Kuzovlev
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
| | - Lyubov E Salnikova
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- The Laboratory of Molecular Immunology, National Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia
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27
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Seefried L, Petryk A, Del Angel G, Reder F, Bauer P. Whole genome sequencing in adults with clinical hallmarks of hypophosphatasia negative for ALPL variants. Mol Biol Rep 2024; 51:984. [PMID: 39276275 PMCID: PMC11401779 DOI: 10.1007/s11033-024-09906-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 09/03/2024] [Indexed: 09/16/2024]
Abstract
BACKGROUND Hypophosphatasia (HPP) is a rare disease caused by deficient activity of tissue-nonspecific alkaline phosphatase (ALP), encoded by the ALPL gene. The primary objective was to explore novel ALPL variants by whole genome sequencing (WGS) in patients with HPP who previously tested negative by standard methods for ALPL variants. The secondary objective was to search for genes beyond ALPL that may reduce ALP activity or contribute to HPP symptoms. METHODS AND RESULTS WGS was performed in 16 patients clinically diagnosed with HPP who had ALP activity below the normal range and tested negative for ALPL variants. Genetic variants in ALPL and genes possibly associated with low ALP activity or phenotypic overlap with HPP were assessed. All 16 patients had ALP activity below the normal range. WGS did not identify any novel disease-causing ALPL variants. Positive findings for other gene variants were identified in 4 patients: 1 patient presented with variants in COL1A1, NLRP12, and SCN9A, coding for collagen, type, I alpha-1 chain, nod-like receptor pyrin domain containing 12, and sodium voltage-gated channel alpha subunit 9, respectively; 1 presented with a heterozygous, likely pathogenic variant in P3H1 coding for prolyl 3 hydroxylase 1; 1 presented with a heterozygous pathogenic variant in SGCE, coding for sarcoglycan epsilon; and 1 presented with a heterozygous variant of uncertain significance in VDR, encoding vitamin D receptor. CONCLUSION Genomic analysis did not identify novel ALPL variants or a pattern of disease-causing variants in genes other than ALPL to explain the HPP phenotype in these patients. REGISTRATION Clinicaltrials.gov identifier: NCT04925804.
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Affiliation(s)
- Lothar Seefried
- Clinical Trial Unit, Orthopedic Department, University of Würzburg, Brettreichtstr. 11, 97074, Würzburg, Bavaria, Germany.
| | - Anna Petryk
- Alexion, AstraZeneca Rare Disease, Boston, MA, USA
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28
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Khan H, Muzaffar F, Salman M, Bashir R, Seo GH, Naz S. Genetic investigations on singleton school aged children reveal novel variants and new candidate genes for hearing loss. Sci Rep 2024; 14:21412. [PMID: 39271758 PMCID: PMC11399343 DOI: 10.1038/s41598-024-71407-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 08/27/2024] [Indexed: 09/15/2024] Open
Abstract
Hearing loss affects around 5% of the global population. Two preliminary studies have described genetic variants in sporadic individuals with hearing loss from Pakistan. Here we extend these studies to determine the spectrum of variants in a cohort of individuals with no previous history of hearing loss. Individuals with hearing loss born to consanguineous couples were identified from special schools. Audiograms were assessed. DNA from participants negative for GJB2 pathogenic variants was subjected to exome sequencing. Data were filtered to include variants with frequencies < 0.01 in the public databases. The effects of the missense variants on respective amino acids were analyzed by using PyMol software. Among the 44 participants, hearing loss was moderate for two individuals; 14 exhibited moderately-severe hearing loss while 25 had a severe degree of hearing loss. Hearing loss was reported to have been progressive in four participants and was currently profound in three participants. Variants were unambiguously identified in 17 genes, of which the majority affected SLC26A4. CDH23, MYO15A and OTOF were other significant contributors. Deleterious variants detected in two genes suggest new associations for hearing loss. Molecular characterization of hearing loss in our cohort revealed high genetic heterogeneity with a 75% diagnostic rate.
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Affiliation(s)
- Hina Khan
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Fariha Muzaffar
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Midhat Salman
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
- University of Health Sciences, Lahore, Pakistan
| | - Rasheeda Bashir
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | | | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
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29
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Molitor A, Lederle A, Radosavljevic M, Sapuru V, Zavorka Thomas ME, Yang J, Shirin M, Collin-Bund V, Jerabkova-Roda K, Miao Z, Bernard A, Rolli V, Grenot P, Castro CN, Rosenzwajg M, Lewis EG, Person R, Esperón-Moldes US, Kaare M, Nokelainen PT, Batzir NA, Hoffer GZ, Paul N, Stemmelen T, Naegely L, Hanauer A, Bibi-Triki S, Grün S, Jung S, Busnelli I, Tripolszki K, Al-Ali R, Ordonez N, Bauer P, Song E, Zajo K, Partida-Sanchez S, Robledo-Avila F, Kumanovics A, Louzoun Y, Hirschler A, Pichot A, Toker O, Mejía CAM, Parvaneh N, Knapp E, Hersh JH, Kenney H, Delmonte OM, Notarangelo LD, Goetz JG, Kahwash SB, Carapito C, Bajwa RPS, Thomas C, Ehl S, Isidor B, Carapito R, Abraham RS, Hite RK, Marcus N, Bertoli-Avella A, Bahram S. A pleiotropic recurrent dominant ITPR3 variant causes a complex multisystemic disease. SCIENCE ADVANCES 2024; 10:eado5545. [PMID: 39270020 PMCID: PMC11397499 DOI: 10.1126/sciadv.ado5545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 08/07/2024] [Indexed: 09/15/2024]
Abstract
Inositol 1,4,5-trisphosphate (IP3) receptor type 1 (ITPR1), 2 (ITPR2), and 3 (ITPR3) encode the IP3 receptor (IP3R), a key player in intracellular calcium release. In four unrelated patients, we report that an identical ITPR3 de novo variant-NM_002224.3:c.7570C>T, p.Arg2524Cys-causes, through a dominant-negative effect, a complex multisystemic disorder with immunodeficiency. This leads to defective calcium homeostasis, mitochondrial malfunction, CD4+ lymphopenia, a quasi-absence of naïve CD4+ and CD8+ cells, an increase in memory cells, and a distinct TCR repertoire. The calcium defect was recapitulated in Jurkat knock-in. Site-directed mutagenesis displayed the exquisite sensitivity of Arg2524 to any amino acid change. Despite the fact that all patients had severe immunodeficiency, they also displayed variable multisystemic involvements, including ectodermal dysplasia, Charcot-Marie-Tooth disease, short stature, and bone marrow failure. In conclusion, unlike previously reported ITPR1-3 deficiencies leading to narrow, mainly neurological phenotypes, a recurrent dominant ITPR3 variant leads to a multisystemic disease, defining a unique role for IP3R3 in the tetrameric IP3R complex.
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Affiliation(s)
- Anne Molitor
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Alexandre Lederle
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Mirjana Radosavljevic
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
- Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Vinay Sapuru
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Physiology, Biophysics, and Systems Biology (PBSB) Program, Weill Cornell Graduate School of Biomedical Sciences, New York, NY, USA
| | - Megan E Zavorka Thomas
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Jianying Yang
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Mahsa Shirin
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Virginie Collin-Bund
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Katerina Jerabkova-Roda
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Equipe labellisée, Ligue nationale Contre le Cancer, Strasbourg, France
| | - Zhichao Miao
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, China
- Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Alice Bernard
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
- Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Véronique Rolli
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
- Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Pierre Grenot
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Carla Noemi Castro
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michelle Rosenzwajg
- Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
- Sorbonne Université, INSERM UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | - Elyssa G Lewis
- Norton Children's Medical Group, University of Louisville School of Medicine, Louisville, KY, USA
| | | | | | - Milja Kaare
- Blueprint Genetics, A Quest Diagnostics Company, Espoo, Finland
| | | | - Nurit Assia Batzir
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikvah, Israel
| | - Gal Zaks Hoffer
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikvah, Israel
| | - Nicodème Paul
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Tristan Stemmelen
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
- Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Lydie Naegely
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Antoine Hanauer
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Sabrina Bibi-Triki
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Sarah Grün
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sophie Jung
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Centre de Référence des maladies rares orales et dentaires (O-Rares), Pôle de Médecine et de Chirurgie bucco-dentaires, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Ignacio Busnelli
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | | | | | | | | | - Eunkyung Song
- Division of Infectious Diseases and Host Defense, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Kristin Zajo
- Institute of Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Santiago Partida-Sanchez
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
| | - Frank Robledo-Avila
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
| | - Attila Kumanovics
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Aurélie Hirschler
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), Institut Pluridisciplinaire Hubert Curien (IPHC), UMR 7178, Université de Strasbourg, CNRS, Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Angélique Pichot
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Ori Toker
- Allergy and Immunology Unit, Shaare Zedek Medical Center, Jerusalem, Israel
- Faculty of Medicine Hebrew university, Jerusalem, Israel
| | | | - Nima Parvaneh
- Department of Pediatrics, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Esther Knapp
- Norton Children's Medical Group, University of Louisville School of Medicine, Louisville, KY, USA
| | - Joseph H Hersh
- Norton Children's Medical Group, University of Louisville School of Medicine, Louisville, KY, USA
| | - Heather Kenney
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jacky G Goetz
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Equipe labellisée, Ligue nationale Contre le Cancer, Strasbourg, France
| | - Samir B Kahwash
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), Institut Pluridisciplinaire Hubert Curien (IPHC), UMR 7178, Université de Strasbourg, CNRS, Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Rajinder P S Bajwa
- Division of Pediatric Hematology, Oncology and Bone Marrow Transplantation, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Caroline Thomas
- Service d'Oncologie-Hématologie et Immunologie Pédiatrique, Hôpital Enfant-Adolescent, CHU Nantes, Nantes, France
| | - Stephan Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bertrand Isidor
- Service de Génétique Médicale, Hôpital Hôtel-Dieu, CHU de Nantes, Nantes, France
| | - Raphael Carapito
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
- Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Roshini S Abraham
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Richard K Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nufar Marcus
- Allergy and Immunology Unit, Kipper Institute of Immunology, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, USA
| | | | - Seiamak Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Plateforme GENOMAX, Centre de Recherche d'Immunologie et d'Hématologie and Centre de Recherche en Biomédecine de Strasbourg (CRBS), Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Institut Thématique Interdisciplinaire (ITI) Transplantex NG de Médecine de Précision de Strasbourg, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
- Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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Ahmad RM, Ali BR, Al-Jasmi F, Al Dhaheri N, Al Turki S, Kizhakkedath P, Mohamad MS. AI-derived comparative assessment of the performance of pathogenicity prediction tools on missense variants of breast cancer genes. Hum Genomics 2024; 18:99. [PMID: 39256852 PMCID: PMC11389290 DOI: 10.1186/s40246-024-00667-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 08/22/2024] [Indexed: 09/12/2024] Open
Abstract
Single nucleotide variants (SNVs) can exert substantial and extremely variable impacts on various cellular functions, making accurate predictions of their consequences challenging, albeit crucial especially in clinical settings such as in oncology. Laboratory-based experimental methods for assessing these effects are time-consuming and often impractical, highlighting the importance of in-silico tools for variant impact prediction. However, the performance metrics of currently available tools on breast cancer missense variants from benchmarking databases have not been thoroughly investigated, creating a knowledge gap in the accurate prediction of pathogenicity. In this study, the benchmarking datasets ClinVar and HGMD were used to evaluate 21 Artificial Intelligence (AI)-derived in-silico tools. Missense variants in breast cancer genes were extracted from ClinVar and HGMD professional v2023.1. The HGMD dataset focused on pathogenic variants only, to ensure balance, benign variants for the same genes were included from the ClinVar database. Interestingly, our analysis of both datasets revealed variants across genes with varying penetrance levels like low and moderate in addition to high, reinforcing the value of disease-specific tools. The top-performing tools on ClinVar dataset identified were MutPred (Accuracy = 0.73), Meta-RNN (Accuracy = 0.72), ClinPred (Accuracy = 0.71), Meta-SVM, REVEL, and Fathmm-XF (Accuracy = 0.70). While on HGMD dataset they were ClinPred (Accuracy = 0.72), MetaRNN (Accuracy = 0.71), CADD (Accuracy = 0.69), Fathmm-MKL (Accuracy = 0.68), and Fathmm-XF (Accuracy = 0.67). These findings offer clinicians and researchers valuable insights for selecting, improving, and developing effective in-silico tools for breast cancer pathogenicity prediction. Bridging this knowledge gap contributes to advancing precision medicine and enhancing diagnostic and therapeutic approaches for breast cancer patients with potential implications for other conditions.
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Affiliation(s)
- Rahaf M Ahmad
- Health Data Science Lab, Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Tawam road, Al Maqam district, Al Ain, Abu Dhabi, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Tawam road, Al Maqam district, Al Ain, Abu Dhabi, United Arab Emirates
| | - Fatma Al-Jasmi
- Health Data Science Lab, Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Tawam road, Al Maqam district, Al Ain, Abu Dhabi, United Arab Emirates
- Division of Metabolic Genetics, Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Noura Al Dhaheri
- Health Data Science Lab, Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Tawam road, Al Maqam district, Al Ain, Abu Dhabi, United Arab Emirates
- Division of Metabolic Genetics, Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Saeed Al Turki
- Health Data Science Lab, Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Tawam road, Al Maqam district, Al Ain, Abu Dhabi, United Arab Emirates
| | - Praseetha Kizhakkedath
- Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Tawam road, Al Maqam district, Al Ain, Abu Dhabi, United Arab Emirates
| | - Mohd Saberi Mohamad
- Health Data Science Lab, Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Tawam road, Al Maqam district, Al Ain, Abu Dhabi, United Arab Emirates.
- Center for Engineering Computational Intelligence, Faculty of Engineering and Technology, Multimedia University, Melaka, Malaysia.
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31
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Ren X, Zhang J, Wang L, Zhang Y, Li J, Yu H, Zheng Z, Zhang Y, Zeng H, Chen Y, Wu J. Evaluation of plasma phytosterols in sitosterolemia, their kindreds and hyperlipidemia subjects. J Clin Lipidol 2024:S1933-2874(24)00242-3. [PMID: 39278776 DOI: 10.1016/j.jacl.2024.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 08/06/2024] [Accepted: 09/03/2024] [Indexed: 09/18/2024]
Abstract
BACKGROUND Patients suffering from sitosterolemia with ABCG5/8 mutation typically present with early-onset or rapidly progressive atherosclerosis. Their kindreds with partial genetic deficiencies of ABCG5/8 are often considered healthy. However, discerning sitosterolemia from its familial kindreds and hyperlipidemia subjects has remained challenging. METHODS Here we retrospectively recruited seven families including 8 individuals diagnosed with sitosterolemia subjects, and 14 kindreds carrying single gene mutations. Additionally, 17 individuals with hyperlipidemia and 130 healthy controls served as positive and negative controls, respectively. A total of 6 phytosterols combined with cholesterol absorption indices (including sitosterol, campesterol, stigmasterol, and cholestanol) and cholesterol synthesis markers (desmosterol and 7-dehydrocholesterol), was compared across the aforementioned four groups. RESULTS As expected, the sitosterolemia subjects with double mutations demonstrated significantly elevated levels of sitosterol and other cholesterol absorption indices. Meanwhile, sitosterolemia kindreds with single gene mutation showed a similar pattern of activated cholesterol-absorption ability to the hyperlipidemia group, but not as high as the double mutation group. Notably, the cholesterol-synthesis enzyme 7-dehydrocholesterol reductase displayed an increase in the hyperlipidemia group but a decrease in the sitosterolemia kindred group, suggesting a potential discriminative role of 7-dehydrocholesterol in distinguishing between these two groups. The combination of phytosterols was more valuable than clinical lipid index for sitosterolemia diagnosis. CONCLUSION Our study revealed mild disruptions of cholesterol absorption capacities in sitosterolemia kindreds with single mutations. Furthermore, the combination of 6 phytosterols proved effective in distinguishing between sitosterolemia, its single mutation carriers, and hyperlipidemia patients.
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Affiliation(s)
- Xuanru Ren
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430000, China.
| | - Jun Zhang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China.
| | - Luya Wang
- Beijing Anzhen Hospital, Capital Medical University, Department of Atherosclerosis, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, 100029, China.
| | - Yuxuan Zhang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430000, China.
| | - Jialu Li
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China.
| | - Hao Yu
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China.
| | - Zhaohai Zheng
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China.
| | - Yiqing Zhang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China.
| | - Hesong Zeng
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430000, China.
| | - Yan Chen
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China; The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, China.
| | - Junfang Wu
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430000, China.
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Hussain A, Zhang H, Zubair M, Shah W, Khan K, Ali I, Raza Y, Zeb A, Abbas T, Ahmed N, Rahim F, Mustafa G, Uddin M, Ullah N, Abbas M, Khan MA, Ma H, Yang B, Shi QH. A novel homozygous splicing mutation in AK7 causes multiple morphological abnormalities of sperm flagella in patients from consanguineous Pakistani families. Asian J Androl 2024:00129336-990000000-00242. [PMID: 39254435 DOI: 10.4103/aja202471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 06/12/2024] [Indexed: 09/11/2024] Open
Abstract
Multiple morphological abnormalities of the flagella (MMAF) represent a severe form of sperm defects leading to asthenozoospermia and male infertility. In this study, we identified a novel homozygous splicing mutation (c.871-4 ACA>A) in the adenylate kinase 7 (AK7) gene by whole-exome sequencing in infertile individuals. Spermatozoa from affected individuals exhibited typical MMAF characteristics, including coiled, bent, short, absent, and irregular flagella. Transmission electron microscopy analysis showed disorganized axonemal structure and abnormal mitochondrial sheets in sperm flagella. Immunofluorescence staining confirmed the absence of AK7 protein from the patients' spermatozoa, validating the pathogenic nature of the mutation. This study provides direct evidence linking the AK7 gene to MMAF-associated asthenozoospermia in humans, expanding the mutational spectrum of AK7 and enhancing our understanding of the genetic basis of male infertility.
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Affiliation(s)
- Ansar Hussain
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Huan Zhang
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Muhammad Zubair
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Wasim Shah
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Khalid Khan
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Imtiaz Ali
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Yousaf Raza
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Aurang Zeb
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Tanveer Abbas
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Nisar Ahmed
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Fazal Rahim
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Ghulam Mustafa
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Meftah Uddin
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Nadeem Ullah
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Musavir Abbas
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29220, Pakistan
| | - Hui Ma
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Bo Yang
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Qing-Hua Shi
- Center for Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
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Qiu JJ, Chang XY, Zhang N, Guo LP, Wang S, Gu WY, Yin YM, Shi ZW, Hua KQ. Genetic variation and molecular profiling of congenital malformations of the female genital tract based on whole-genome sequencing. World J Pediatr 2024:10.1007/s12519-024-00839-6. [PMID: 39251565 DOI: 10.1007/s12519-024-00839-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 08/07/2024] [Indexed: 09/11/2024]
Abstract
BACKGROUND Congenital malformations of the female genital tract (CM-FGT) are characterized by abnormal development of the fallopian tubes, uterus, and vagina, often accompanied by malformations in the urinary system, bones and hearing. However, no definitive pathogenic genes and molecular genetic causes have been identified. METHODS We present the largest whole-genome sequencing study of CM-FGT to date, analyzing 590 individuals in China: 95 patients, 442 case-controls, and 53 familial controls. RESULTS Among the patients, 5.3% carried known CM-FGT-related variants. Pedigree and case-control analyses in two dimensions of coding and non-coding regulatory regions revealed seven novel de novo copy number variations, 12 rare single-nucleotide variations, and 10 rare 3' untranslated region (UTR) mutations in genes related to CM-FGT, particularly highlighting ASH1L as a pathogenic gene. Single-cell sequencing data showed that the majority of CM-FGT-related risk genes are spatiotemporally specifically expressed early in uterus development. CONCLUSIONS In conclusion, this study identified novel variants related to CM-FGT, particularly highlighting ASH1L as a pathogenic gene. The findings provide insights into the genetic variants underlying CM-FGT, with single-cell sequencing data revealing spatiotemporal specific expression patterns of key risk genes early in uterine development. This study significantly advances the understanding of CM-FGT etiology and genetic landscape, offering new opportunities for prenatal screening.
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Affiliation(s)
- Jun-Jun Qiu
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai, 200011, China
| | - Xing-Yu Chang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai, 200011, China
| | - Ning Zhang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai, 200011, China
| | - Luo-Pei Guo
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai, 200011, China
| | - Shuai Wang
- Data and Analysis Center for Genetic Diseases, Chigene Translational Medicine Research Center, Beijing, 100032, China
| | - Wei-Yue Gu
- Data and Analysis Center for Genetic Diseases, Chigene Translational Medicine Research Center, Beijing, 100032, China
| | - Yi-Meng Yin
- Translational Research Institute of Brain and Brain-Like Intelligence, School of Medicine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, 200434, China.
| | - Zhi-Wen Shi
- Data and Analysis Center for Genetic Diseases, Chigene Translational Medicine Research Center, Beijing, 100032, China.
| | - Ke-Qin Hua
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China.
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai, 200011, China.
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Davies KC, Fearnley LG, Snell P, Bourke D, Mossman S, Kyne K, McKeown C, Delatycki MB, Bahlo M, Lockhart PJ. A multi-exon RFC1 deletion in a case of CANVAS: expanding the genetic mechanism of disease. J Neurol 2024:10.1007/s00415-024-12675-9. [PMID: 39249106 DOI: 10.1007/s00415-024-12675-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/10/2024]
Affiliation(s)
- Kayli C Davies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, 3052, Australia
| | - Liam G Fearnley
- Bruce Lefroy Centre, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, 3052, Australia
| | - Penny Snell
- Bruce Lefroy Centre, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - David Bourke
- Department of Neurology, Wellington Hospital, Wellington, 6242, New Zealand
| | - Stuart Mossman
- Department of Neurology, Wellington Hospital, Wellington, 6242, New Zealand
| | - Karen Kyne
- Capital and Coast District Health Board, Wellington Regional Hospital, Wellington, 6021, New Zealand
| | - Colina McKeown
- Genetic Health Service New Zealand, Wellington Hospital, Wellington, 6242, New Zealand
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, 3052, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, 3052, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia.
- Department of Paediatrics, The University of Melbourne, Parkville, 3052, Australia.
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Chen X, Fansler MM, Janjoš U, Ule J, Mayr C. The FXR1 network acts as a signaling scaffold for actomyosin remodeling. Cell 2024; 187:5048-5063.e25. [PMID: 39106863 PMCID: PMC11380585 DOI: 10.1016/j.cell.2024.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/24/2024] [Accepted: 07/08/2024] [Indexed: 08/09/2024]
Abstract
It is currently not known whether mRNAs fulfill structural roles in the cytoplasm. Here, we report the fragile X-related protein 1 (FXR1) network, an mRNA-protein (mRNP) network present throughout the cytoplasm, formed by FXR1-mediated packaging of exceptionally long mRNAs. These mRNAs serve as an underlying condensate scaffold and concentrate FXR1 molecules. The FXR1 network contains multiple protein binding sites and functions as a signaling scaffold for interacting proteins. We show that it is necessary for RhoA signaling-induced actomyosin reorganization to provide spatial proximity between kinases and their substrates. Point mutations in FXR1, found in its homolog FMR1, where they cause fragile X syndrome, disrupt the network. FXR1 network disruption prevents actomyosin remodeling-an essential and ubiquitous process for the regulation of cell shape, migration, and synaptic function. Our findings uncover a structural role for cytoplasmic mRNA and show how the FXR1 RNA-binding protein as part of the FXR1 network acts as an organizer of signaling reactions.
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Affiliation(s)
- Xiuzhen Chen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Mervin M Fansler
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Urška Janjoš
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; Biosciences PhD Program, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Ule
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; UK Dementia Research Institute at King's College London, London SE5 9NU, UK
| | - Christine Mayr
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA.
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36
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Sneddon TP, Gilmore KL, Xiong M, Weck KE, Powell BC, Vora NL. WDR44 Loss-of-Function Promoter Deletion in a Male Newborn With a Ciliopathy Phenotype. Am J Med Genet A 2024:e63861. [PMID: 39235309 DOI: 10.1002/ajmg.a.63861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 06/13/2024] [Accepted: 08/18/2024] [Indexed: 09/06/2024]
Abstract
Gain-of-function variants in the WDR44 gene have recently been associated with an X-linked ciliopathy-related neurodevelopmental phenotype. Here, we report on a WDR44 loss-of-function (LOF) variant identified in the genome sequence from a male fetus enrolled in the Prenatal Genetic Diagnosis by Genomic Sequencing (PrenatalSEQ) multicenter study. The phenotype is consistent with the described X-linked ciliopathy that includes developmental delay, microcephaly, congenital heart defects, kidney abnormalities, cryptorchidism, musculoskeletal abnormalities, craniofacial dysmorphism, and effusions. This is the first report of a WDR44 LOF variant in an affected individual with a prenatal presentation and supports LOF as a mechanism for the X-linked WDR44 ciliopathy-related phenotype.
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Affiliation(s)
- Tam P Sneddon
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Kelly L Gilmore
- Department of Obstetrics and Gynecology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Mai Xiong
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Karen E Weck
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Neeta L Vora
- Department of Obstetrics and Gynecology, University of North Carolina, Chapel Hill, North Carolina, USA
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Bae JH, Kang H. Identification of Sweetness Preference-Related Single-Nucleotide Polymorphisms for Polygenic Risk Scores Associated with Obesity. Nutrients 2024; 16:2972. [PMID: 39275286 PMCID: PMC11397467 DOI: 10.3390/nu16172972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/09/2024] [Accepted: 08/31/2024] [Indexed: 09/16/2024] Open
Abstract
Our study aimed to identify sweetness preference-associated single-nucleotide polymorphisms (SNPs), characterize the related genetic loci, and develop SNP-based polygenic risk scores (PRS) to analyze their associations with obesity. For genotyping, we utilized a pooled genome-wide association study (GWAS) dataset of 18,499 females and 10,878 males. We conducted genome-wide association analyses, functional annotation, and employed the weighted method to calculate the levels of PRS from 677 sweetness preference-related SNPs. We used Cox proportional hazards modeling with time-varying covariates to estimate age-adjusted and multivariable hazard ratios (HRs) and 95% confidence intervals (CIs) for obesity incidence. We also tested the correlation between PRS and environmental factors, including smoking and dietary components, on obesity. Our results showed that in males, the TT genotype of rs4861982 significantly increased obesity risk compared to the GG genotype in the Health Professionals Follow-up Study (HPFS) cohort (HR = 1.565; 95% CI, 1.122-2.184; p = 0.008) and in the pooled analysis (HR = 1.259; 95% CI, 1.030-1.540; p = 0.025). Protein tyrosine phosphatase receptor type O (PTPRO) was identified as strongly associated with sweetness preference, indicating a positive correlation between sweetness preference and obesity risk. Moreover, each 10 pack-year increment in smoking was significantly associated with an increased risk of obesity in the HPFS cohort (HR = 1.024; 95% CI, 1.000-1.048) in males but not in females. In conclusion, significant associations between rs4861982, sweetness preference, and obesity were identified, particularly among males, where environmental factors like smoking are also correlated with obesity risk.
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Affiliation(s)
- Ji Hyun Bae
- Department of Food Science and Nutrition, Keimyung University, Daegu 42601, Republic of Korea
| | - Hyunju Kang
- Department of Food Science and Nutrition, Keimyung University, Daegu 42601, Republic of Korea
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Fang J, Yang X, Tang M, Li S, Han F, Zhou L, Li M, Yang M, Cui L, Zhang S, Zhu Y, Yao M, Ni J. Rare RNF213 variants is related to early-onset intracranial atherosclerosis: A Chinese community-based study. J Stroke Cerebrovasc Dis 2024; 33:107982. [PMID: 39233284 DOI: 10.1016/j.jstrokecerebrovasdis.2024.107982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/06/2024] [Accepted: 08/27/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND The relationship between rare variants in Ring finger protein 213 (RNF213) and intracranial atherosclerosis (ICAS) remained unelucidated. Using whole-exome sequencing (WES) and high-resolution magnetic resonance imaging (HR-MRI), this study aimed at investigating the association between rare RNF213 variants and ICAS within a Chinese community-dwelling population. METHODS The present study included 821 participants from Shunyi cohort. Genetic data of rare RNF213 variants were acquired by WES and were categorized by functional domains. Intracranial and extracranial atherosclerosis were assessed by brain HR-MRI and carotid ultrasound, respectively. Logistic regression and generalized linear regression were applied to evaluate the effects of rare RNF213 variants on atherosclerosis. Stratification by age were conducted with 50 years old set as the cutoff value. RESULTS Ninety-five participants were identified as carriers of rare RNF213 variants. Carotid plaques were observed in 367 (44.7 %) participants, while ICAS was identified in 306 (37.3 %). Rare variants of RNF213 was not associated with ECAS. Employing HR-MRI, both the presence of rare variants (β = 0.150, P = 0.025) and numerical count of variants (β = 0.182, P = 0.003) were significantly correlated with ICAS within the group of age ≤50 years. Both variant existence (β = 0.154, P = 0.014) and variant count (β = 0.188, P = 0.003) were significantly associated with plaques in middle cerebral arteries within younger subgroup, rather than basilar arteries. Furthermore, a significant association was observed between variants that located outside the N-arm domain and ICAS in the younger subgroup (OR = 2.522, P = 0.030). Statistical results remained robust after adjusted for age, gender, and cardiovascular risk factors. CONCLUSIONS Rare variants of RNF213 is associated with age-related ICAS in general Chinese population, highlighting the potential role of RNF213 as a genetic contributor to early-onset ICAS.
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Affiliation(s)
- Jianxun Fang
- Department of Neurology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Xinzhuang Yang
- Center for bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Mingyu Tang
- Department of Neurology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Shengde Li
- Department of Neurology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Fei Han
- Department of Neurology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Lixin Zhou
- Department of Neurology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Mingli Li
- Department of Radiology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Meng Yang
- Department of Ultrasound, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Liying Cui
- Department of Neurology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Shuyang Zhang
- Department of Cardiology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Yicheng Zhu
- Department of Neurology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Ming Yao
- Department of Neurology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China.
| | - Jun Ni
- Department of Neurology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China.
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Takatsu H, Nishimura N, Kosugi Y, Ogawa H, Nakayama K, Colin E, Platzer K, Abou Jamra R, Redler S, Prouteau C, Ziegler A, Shin HW. De Novo Missense Variations of ATP8B2 Impair Its Phosphatidylcholine Flippase Activity. Mol Cell Biol 2024:1-16. [PMID: 39219493 DOI: 10.1080/10985549.2024.2391829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/11/2024] [Accepted: 07/27/2024] [Indexed: 09/04/2024] Open
Abstract
P4-ATPases comprise a family of lipid flippases that translocate lipids from the exoplasmic (or luminal) to the cytoplasmic leaflet of biological membranes. Of the 14 known human P4-ATPases, ATP8B2 is a phosphatidylcholine flippase at the plasma membrane, but its physiological function is not well understood. Although ATP8B2 could interact with both CDC50A and CDC50B, it required only the CDC50A interaction for its exit from the endoplasmic reticulum and subsequent transport to the plasma membrane. Three de novo monoallelic missense variations of ATP8B2 were found in patients with intellectual disability. None of these variations affected the interaction of ATP8B2 with CDC50A or its localization to the plasma membrane. However, variations of either of two amino acid residues, which are conserved in all P4-ATPases, significantly reduced the phosphatidylcholine flippase activity of ATP8B2. Furthermore, mutations in the corresponding residues of ATP8B1 and ATP11C were found to decrease their flippase activities toward phosphatidylcholine and phosphatidylserine, respectively. These results indicate that the conserved amino acid residues are crucial for the enzymatic activities of the P4-ATPases.
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Affiliation(s)
- Hiroyuki Takatsu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Narumi Nishimura
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yusuke Kosugi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Haruo Ogawa
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Estelle Colin
- Department of Medical Genetics, Angers University Hospital, Angers, France
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Silke Redler
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Clément Prouteau
- Department of Medical Genetics, Angers University Hospital, Angers, France
| | - Alban Ziegler
- Department of Medical Genetics, Angers University Hospital, Angers, France
| | - Hye-Won Shin
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
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Huggins E, Jackson DG, Young SP, Kishnani PS. Whole exome sequencing reveals a dual diagnosis of BCAP31-related syndrome and glutaric aciduria III. Mol Genet Metab Rep 2024; 40:101117. [PMID: 39101156 PMCID: PMC11296045 DOI: 10.1016/j.ymgmr.2024.101117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/28/2024] [Accepted: 07/05/2024] [Indexed: 08/06/2024] Open
Abstract
Background Biochemical testing is a common first-tier approach in the setting of genetic evaluation of patients with unexplained developmental delay. However, results can be unclear, and a plan for second-tier analysis must be determined based on the patient's biochemical results and clinical presentation - in many cases, triggering a diagnostic odyssey. Case presentation A male patient from the United States presenting with unexplained developmental delay, microcephaly, hypotonia, and feeding difficulties was referred for clinical genetic evaluation at age 8 months. Biochemical testing revealed an isolated marked elevation of glutaric acid on urine organic acid profile, without elevations of related metabolites. Further testing included GCDH sequencing, a neurometabolic gene panel, chromosomal microarray, Prader Willi/Angelman testing, and lysosomal disease enzyme panel, all of which were non-diagnostic. The patient had persistent developmental delay and hypotonia, dystonia, sensorineural hearing loss, and abnormal brain myelination on magnetic resonance imaging. Whole exome sequencing (WES) was performed and revealed a dual diagnosis of glutaric aciduria III (GA III) and BCAP31-related disorder, an X-linked intellectual disability syndrome, caused by a novel pathogenic variant. Conclusions GA III has historically been considered clinically benign, with few reported cases. This patient's presenting symptoms were similar to those commonly seen in GA I and GA II, however the biochemical abnormalities were not consistent with these disorders, prompting additional molecular and biochemical testing. Ultimately, WES confirmed a diagnosis of BCAP31-related syndrome, a rare neurological disorder, which explained the patient's presenting symptoms. WES also identified a secondary diagnosis of GA III. We present a patient with two rare genetic conditions, highlighting the importance of deep phenotyping and the utility of WES in the setting of a patient with dual genetic diagnoses.
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Affiliation(s)
- Erin Huggins
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - David G. Jackson
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Sarah P. Young
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
- Duke University Health System Biochemical Genetics Laboratory, Durham, NC, USA
| | - Priya S. Kishnani
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
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Abdelrahman HA, Akawi N, Al-Shamsi AM, Al-Gazali L, Ali BR. Pontocerebellar Hypoplasia Type 9: A New Case with a Novel Mutation and Review of Literature. J Pediatr Genet 2024; 13:215-222. [PMID: 39086442 PMCID: PMC11288706 DOI: 10.1055/s-0042-1748018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 03/07/2022] [Indexed: 10/18/2022]
Abstract
Pontocerebellar hypoplasia type 9 (PCH-9) is a very rare autosomal recessive neurodegenerative disorder. Affected infants present early with severe developmental delay, spasticity, with the unique magnetic resonance imaging picture of thin corpus callosum, atrophied pons, and cerebellum. It is caused by loss of function mutations in the AMPD2 gene, encoding for the adenosine monophosphate deaminase enzyme-paralog 2. This gene is expressed in different somatic tissues with high level of expression in cerebellum and its encoded enzyme catalyzes a critical step in de novo biosynthesis of purines and its deficiency in the developing neurons severely affects neuronal differentiation and cell viability. We clinically evaluated an Emirati patient presented with severe developmental and growth delay, as well as corpus callosum agenesis and atrophy of brainstem and cerebellum. We performed exome sequencing, Sanger sequencing, and segregation analysis to identify the genetic cause of the phenotype, followed by in silico and in vitro analysis. We identified the novel variant (NM_004037.9:c.1471G > A) in AMPD2 gene leading to a single amino acid substitution (p.Gly491Arg) in adenosine monophosphate deaminase-2 enzyme. This variant is predicted to be pathogenic using several in silico tools, and resulted in a decrease in the enzyme function in the patient's polymorphonuclear cells by 82% (95% confidence interval: 73.3-91.7%, p = 0.029) compared with the control. This data establishes that the affected child is affected by PCH-9. Furthermore, we review all reported cases in literature to summarize the main clinical features of this rare disease.
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Affiliation(s)
- Hanadi A. Abdelrahman
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
| | - Nadia Akawi
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
| | | | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bassam R. Ali
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
- Zayed Center for Health sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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Sarygina EV, Kozlova AS, Ponomarenko EA, Ilgisonis EV. The human proteome size as a technological development function. BIOMEDITSINSKAIA KHIMIIA 2024; 70:364-373. [PMID: 39324201 DOI: 10.18097/pbmc20247005364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Changes in information on the number of human proteoforms, post-translational modification (PTM) events, alternative splicing (AS), single-amino acid polymorphisms (SAP) associated with protein-coding genes in the neXtProt database have been retrospectively analyzed. In 2016, our group proposed three mathematical models for predicting the number of different proteins (proteoforms) in the human proteome. Eight years later, we compared the original data of the information resources and their contribution to the prediction results, correlating the differences with new approaches to experimental and bioinformatic analysis of protein modifications. The aim of this work is to update information on the status of records in the databases of identified proteoforms since 2016, as well as to identify trends in changes in the quantities of these records. According to various information models, modern experimental methods may identify from 5 to 125 million different proteoforms: the proteins formed due to alternative splicing, the implementation of single nucleotide polymorphisms at the proteomic level, and post-translational modifications in various combinations. This result reflects an increase in the size of the human proteome by 20 or more times over the past 8 years.
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Affiliation(s)
- E V Sarygina
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A S Kozlova
- Institute of Biomedical Chemistry, Moscow, Russia
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Gudkov M, Thibaut L, Giannoulatou E. Context-adjusted proportion of singletons (CAPS): a novel metric for assessing negative selection in the human genome. NAR Genom Bioinform 2024; 6:lqae111. [PMID: 39211329 PMCID: PMC11358819 DOI: 10.1093/nargab/lqae111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 07/24/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
Interpretation of genetic variants remains challenging, partly due to the lack of well-established ways of determining the potential pathogenicity of genetic variation, especially for understudied classes of variants. Addressing this, population genetics methods offer a practical solution by evaluating variant effects through human population distributions. Negative selection influences the ratio of singleton variants and can serve as a proxy for deleteriousness, as exemplified by the Mutability-Adjusted Proportion of Singletons (MAPS) metric. However, MAPS is sensitive to the calibration of the singletons-by-mutability linear model, which results in biased estimates for certain variant classes. Building up on the methodology used in MAPS, we introduce the Context-Adjusted Proportion of Singletons (CAPS) metric for assessing negative selection in the human genome. CAPS produces corrected estimates with more accurate confidence intervals by eliminating the mutability layer in the model. Retaining the advantageous features of MAPS, CAPS emerges as a robust and reliable tool. We believe that CAPS has the potential to enhance the identification of new disease-variant associations in clinical and research settings, offering improved accuracy in assessing negative selection for diverse SNV classes.
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Affiliation(s)
- Mikhail Gudkov
- Victor Chang Cardiac Research Institute, NSW 2010, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Australia
| | - Loïc Thibaut
- Centre for Population Genomics, Garvan Institute of Medical Research, NSW 2010, Australia
- School of Mathematics and Statistics, UNSW Sydney, NSW 2052, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, NSW 2010, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Australia
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44
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Jurgens SJ, Wang X, Choi SH, Weng LC, Koyama S, Pirruccello JP, Nguyen T, Smadbeck P, Jang D, Chaffin M, Walsh R, Roselli C, Elliott AL, Wijdeveld LFJM, Biddinger KJ, Kany S, Rämö JT, Natarajan P, Aragam KG, Flannick J, Burtt NP, Bezzina CR, Lubitz SA, Lunetta KL, Ellinor PT. Rare coding variant analysis for human diseases across biobanks and ancestries. Nat Genet 2024; 56:1811-1820. [PMID: 39210047 DOI: 10.1038/s41588-024-01894-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 08/01/2024] [Indexed: 09/04/2024]
Abstract
Large-scale sequencing has enabled unparalleled opportunities to investigate the role of rare coding variation in human phenotypic variability. Here, we present a pan-ancestry analysis of sequencing data from three large biobanks, including the All of Us research program. Using mixed-effects models, we performed gene-based rare variant testing for 601 diseases across 748,879 individuals, including 155,236 with ancestry dissimilar to European. We identified 363 significant associations, which highlighted core genes for the human disease phenome and identified potential novel associations, including UBR3 for cardiometabolic disease and YLPM1 for psychiatric disease. Pan-ancestry burden testing represented an inclusive and useful approach for discovery in diverse datasets, although we also highlight the importance of ancestry-specific sensitivity analyses in this setting. Finally, we found that effect sizes for rare protein-disrupting variants were concordant between samples similar to European ancestry and other genetic ancestries (βDeming = 0.7-1.0). Our results have implications for multi-ancestry and cross-biobank approaches in sequencing association studies for human disease.
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Affiliation(s)
- Sean J Jurgens
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xin Wang
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Lu-Chen Weng
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Satoshi Koyama
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - James P Pirruccello
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Cardiology, University of California, San Francisco, CA, USA
| | - Trang Nguyen
- Metabolism Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Patrick Smadbeck
- Metabolism Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Dongkeun Jang
- Metabolism Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mark Chaffin
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Roddy Walsh
- Department of Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Carolina Roselli
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amanda L Elliott
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry and Center for Genomic Medicine, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital,Harvard Medical School, Boston, MA, USA
- Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Leonoor F J M Wijdeveld
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Physiology, Amsterdam UMC location VU, Amsterdam, The Netherlands
| | - Kiran J Biddinger
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shinwan Kany
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cardiology, University Heart and Vascular Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Joel T Rämö
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Pradeep Natarajan
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Krishna G Aragam
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason Flannick
- Metabolism Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Noël P Burtt
- Metabolism Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Connie R Bezzina
- Department of Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Steven A Lubitz
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- NHLBI and Boston University's Framingham Heart Study, Framingham, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA.
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45
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Liu H, Guan L, Su X, Zhao L, Shu Q, Zhang J. A broken network of susceptibility genes in the monocytes of Crohn's disease patients. Life Sci Alliance 2024; 7:e202302394. [PMID: 38925865 PMCID: PMC11208737 DOI: 10.26508/lsa.202302394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Genome-wide association studies have identified over 200 genetic loci associated with inflammatory bowel disease; however, the mechanism of such a large amount of susceptibility genes remains uncertain. In this study, we integrated bioinformatics analysis and two independent single-cell transcriptome datasets to investigate the expression network of 232 susceptibility genes in Crohn's disease (CD) patients and healthy controls. The study revealed that most of the susceptibility genes are specifically and strictly expressed in the monocytes of the human intestinal tract. The susceptibility genes established a network within the monocytes of health control. The robustness of a gene network may prevent disease onset that is influenced by the genetic and environmental alteration in the expression of susceptibility genes. In contrast, we showed a sparse network in pediatric/adult CD patients, suggesting the broken network contributed to the CD etiology. The network status of susceptibility genes at the single-cell level of monocytes provided novel insight into the etiology.
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Affiliation(s)
- Hankui Liu
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
| | - Liping Guan
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Su
- BGI Genomics, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lijian Zhao
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
- Hebei Medical University, Shijiazhuang, China
| | - Qing Shu
- Department of Gastroenterology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Jianguo Zhang
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Research, Shenzhen, China
- Hebei Medical University, Shijiazhuang, China
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46
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Herzeg A, Borges B, Diafos LN, Gupta N, MacKenzie TC, Sanders SJ. The Conundrum of Mechanics Versus Genetics in Congenital Hydrocephalus and Its Implications for Fetal Therapy Approaches: A Scoping Review. Prenat Diagn 2024. [PMID: 39218781 DOI: 10.1002/pd.6654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/07/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Recent advances in gene therapy, particularly for single-gene disorders (SGDs), have led to significant progress in developing innovative precision medicine approaches that hold promise for treating conditions such as primary hydrocephalus (CH), which is characterized by increased cerebrospinal fluid (CSF) volumes and cerebral ventricular dilation as a result of impaired brain development, often due to genetic causes. CH is a significant contributor to childhood morbidity and mortality and a driver of healthcare costs. In many cases, prenatal ultrasound can readily identify ventriculomegaly as early as 14-20 weeks of gestation, with severe cases showing poor neurodevelopmental outcomes. Postnatal surgical approaches, such as ventriculoperitoneal shunts, do not address the underlying genetic causes, have high complication rates, and result in a marginal improvement of neurocognitive deficits. Prenatal somatic cell gene therapy (PSCGT) promises a novel approach to conditions such as CH by targeting genetic mutations in utero, potentially improving long-term outcomes. To better understand the pathophysiology, genetic basis, and molecular pathomechanisms of CH, we conducted a scoping review of the literature that identified over 160 published genes linked to CH. Mutations in L1CAM, TRIM71, MPDZ, and CCDC88C play a critical role in neural stem cell development, subventricular zone architecture, and the maintenance of the neural stem cell niche, driving the development of CH. Early prenatal interventions targeting these genes could curb the development of the expected CH phenotype, improve neurodevelopmental outcomes, and possibly limit the need for surgical approaches. However, further research is needed to establish robust genotype-phenotype correlations and develop safe and effective PSCGT strategies for CH.
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Affiliation(s)
- Akos Herzeg
- Department of Surgery, University of California, San Francisco, San Francisco, California, USA
- UCSF Center for Maternal-Fetal Precision Medicine, University of California San Francisco, San Francisco, California, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, California, USA
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Beltran Borges
- Department of Surgery, University of California, San Francisco, San Francisco, California, USA
- UCSF Center for Maternal-Fetal Precision Medicine, University of California San Francisco, San Francisco, California, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, California, USA
| | - Loukas N Diafos
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, California, USA
- Department of Pediatrics and Benioff Children's Hospital, University of California, San Francisco, San Francisco, California, USA
| | - Nalin Gupta
- UCSF Center for Maternal-Fetal Precision Medicine, University of California San Francisco, San Francisco, California, USA
- Department of Pediatrics and Benioff Children's Hospital, University of California, San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
- Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Tippi C MacKenzie
- Department of Surgery, University of California, San Francisco, San Francisco, California, USA
- UCSF Center for Maternal-Fetal Precision Medicine, University of California San Francisco, San Francisco, California, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, California, USA
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Pediatrics and Benioff Children's Hospital, University of California, San Francisco, San Francisco, California, USA
| | - Stephan J Sanders
- UCSF Center for Maternal-Fetal Precision Medicine, University of California San Francisco, San Francisco, California, USA
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, USA
- Institute for Developmental and Regenerative Medicine, Oxford University, Oxford, UK
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47
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Guo H, Urban AE, Wong WH. Prioritizing disease-related rare variants by integrating gene expression data. PLoS Genet 2024; 20:e1011412. [PMID: 39348415 PMCID: PMC11466430 DOI: 10.1371/journal.pgen.1011412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 10/10/2024] [Accepted: 08/29/2024] [Indexed: 10/02/2024] Open
Abstract
Rare variants, comprising the vast majority of human genetic variations, are likely to have more deleterious impact in the context of human diseases compared to common variants. Here we present carrier statistic, a statistical framework to prioritize disease-related rare variants by integrating gene expression data. By quantifying the impact of rare variants on gene expression, carrier statistic can prioritize those rare variants that have large functional consequence in the patients. Through simulation studies and analyzing real multi-omics dataset, we demonstrated that carrier statistic is applicable in studies with limited sample size (a few hundreds) and achieves substantially higher sensitivity than existing rare variants association methods. Application to Alzheimer's disease reveals 16 rare variants within 15 genes with extreme carrier statistics. We also found strong excess of rare variants among the top prioritized genes in patients compared to that in healthy individuals. The carrier statistic method can be applied to various rare variant types and is adaptable to other omics data modalities, offering a powerful tool for investigating the molecular mechanisms underlying complex diseases.
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Affiliation(s)
- Hanmin Guo
- Department of Statistics, Stanford University, Stanford, California, United States of America
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, United States of America
| | - Alexander Eckehart Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, California, United States of America
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California, United States of America
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48
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Zhong Z, Dai L, Ding J, Gao Y, Su G, Zhu Y, Deng Y, Li F, Gao Y, Yang P. Molecular diagnostic yield for Blau syndrome in previously diagnosed juvenile idiopathic arthritis with uveitis or cutaneous lesions. Rheumatology (Oxford) 2024; 63:SI260-SI268. [PMID: 37941393 DOI: 10.1093/rheumatology/kead596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/24/2023] [Accepted: 10/03/2023] [Indexed: 11/10/2023] Open
Abstract
OBJECTIVE Diagnostic pitfalls often arise in the community because of potentially misleading similarities between juvenile idiopathic arthritis (JIA) and Blau syndrome, an immune-related disorder caused by NOD2 gene mutations. It remains unclear in which population and to what extent next-generation sequencing techniques can aid in diagnosis. METHODS We evaluated clinical usefulness of targeted next-generation sequencing in previously diagnosed JIA. Participants were required to have symptoms and signs suspected of Blau syndrome, including at least uveitis or cutaneous lesions in addition to arthritis. Targeted sequencing was conducted on NOD2 gene to detect diagnostic variants classified as pathogenic or likely pathogenic for Blau syndrome. We assessed the molecular diagnostic yield and clinical implications for patient care. RESULTS Between 1 May 2008 and 1 June 2021, sequencing data were accrued from 123 previously diagnosed JIA (median age: 5 years; female: 62.6%). Targeted NOD2 sequencing yielded a positive molecular diagnosis of Blau syndrome in 21.1% (95% CI: 14.9%, 29.2%), encompassing six heterozygous missense mutations classified as pathogenic variants. Among those receiving a molecular diagnosis, changes in clinical management and treatment were considered as having occurred in 38.5%. Nine predictors were identified as being associated with a higher diagnostic yield, providing clinical clues to suspect the possibility of Blau syndrome. CONCLUSION Among some patients with paediatric-onset arthritis complicated with uveitis or cutaneous lesions, reassessment of the diagnosis of JIA may be warranted. Targeted NOD2 sequencing established the molecular diagnosis of Blau syndrome in nearly one-fifth of these cases and provided clinically relevant information for patient-care decisions.
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Affiliation(s)
- Zhenyu Zhong
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, and Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Lingyu Dai
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, and Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Jiadong Ding
- The First Affiliated Hospital of Zhengzhou University, Henan Province Eye Hospital, and Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, China
| | - Yu Gao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, and Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, and Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Yunyun Zhu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, and Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Yang Deng
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, and Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Fuzhen Li
- The First Affiliated Hospital of Zhengzhou University, Henan Province Eye Hospital, and Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, China
| | - Yuan Gao
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University, and Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, and Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
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49
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D'Apolito M, Santacroce R, Vazquez DO, Cordisco G, Fantini CA, D'Andrea G, Leccese A, Colia AL, Martinez P, Zanichelli A, Josviack D, Margaglione M. DAB2IP associates with hereditary angioedema: Insights into the role of VEGF signaling in HAE pathophysiology. J Allergy Clin Immunol 2024; 154:698-706. [PMID: 38823490 DOI: 10.1016/j.jaci.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/09/2024] [Accepted: 05/24/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND In the recent years, there was an important improvement in the understanding of the pathogenesis of hereditary angioedema (HAE). Notwithstanding, in a large portion of patients with unknown mutation (HAE-UNK) the genetic cause remains to be identified. OBJECTIVES To identify new genetic targets associated with HAE, a large Argentine family with HAE-UNK spanning 3 generations was studied. METHODS Whole exome sequencing was performed on affected family members to identify potential genetic variants associated with HAE-UNK. In silico analyses and experimental studies were applied to assess the role of the identified gene variant. RESULTS A missense variant (p.D239N) in DAB2IP was identified. The variant occurred in the C2-domain, the region interacting with vascular endothelial growth factor receptor 2 (VEGFR2). It was found to be rare, and predicted to have a detrimental effect on the functionality of DAB2IP. Protein structure modeling predicted changes in the mutant p.D239N protein structure, impacting protein stability. The p.D239N variant affected the subcellular localization of VEGFR2. Cells transfected with the DAB2IP-239N transcript exhibited an intracellular distribution, and VEGFR2 remained associated with the cell membrane. The altered localization pattern indicated reduced colocalization of the mutant protein with VEGFR2, suggesting a diminished ability of VEGFR2 binding. CONCLUSIONS The study identified a novel missense variant (p.D239N) in DAB2IP in a family with HAE-UNK and highlighted the role of dysregulated VEGF-mediated signaling in altered endothelial permeability. DAB2IP loss-of-function pathogenic variants lead to the impairment of the endothelial VEGF/VEGFR2 ligand system and represent a new pathophysiologic cause of HAE-UNK.
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Affiliation(s)
- Maria D'Apolito
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Rosa Santacroce
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | | | - Giorgia Cordisco
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | | | - Giovanna D'Andrea
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Angelica Leccese
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Anna Laura Colia
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Pablo Martinez
- Universidad Nacional del Sur, Argentina Hospital Penna de Bahia Blanca, Bahia Blanca, Argentina
| | - Andrea Zanichelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy; Operative Unit of Medicine, Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Darío Josviack
- Instituto de Medicina Respiratoria, Rafaela, Santa Fe, Argentina
| | - Maurizio Margaglione
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy.
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50
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Yin L, Duan A, Zhang W, Li B, Zhao T, Xu X, Yang L, Nian B, Lu K, Chen S, Li Z, Liu J, Duan Q, Liu D, Chen H, Cui L, Chang Y, Kuang Y, Zhang D, Wang X, Zhang Y. Identification of whole-genome mutations and structural variations of bile cell-free DNA in cholangiocarcinoma. Genomics 2024; 116:110916. [PMID: 39147332 DOI: 10.1016/j.ygeno.2024.110916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/17/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024]
Abstract
Bile cell-free DNA (cfDNA) has been reported as a promising liquid biopsy tool for cholangiocarcinoma (CCA), however, the whole-genome mutation landscape and structural variants (SVs) of bile cfDNA remains unknown. Here we performed whole-genome sequencing on bile cfDNA and analyzed the correlation between mutation characteristics of bile cfDNA and clinical prognosis. TP53 and KRAS were the most frequently mutated genes, and the RTK/RAS, homologous recombination (HR), and HIPPO were top three pathways containing most gene mutations. Ten overlapping putative driver genes were found in bile cfDNA and tumor tissue. SVs such as chromothripsis and kataegis were identified. Moreover, the hazard ratio of HR pathway mutations were 15.77 (95% CI: 1.571-158.4), patients with HR pathway mutations in bile cfDNA exhibited poorer overall survival (P = 0.0049). Our study suggests that bile cfDNA contains genome mutations and SVs, and HR pathway mutations in bile cfDNA can predict poor outcomes of CCA patients.
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Affiliation(s)
- Lei Yin
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Anqi Duan
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Wei Zhang
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Bin Li
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Teng Zhao
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Xiaoya Xu
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Lixue Yang
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Baoning Nian
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Kai Lu
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Sheng Chen
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Zhikuan Li
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Jian Liu
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Qiaonan Duan
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Dongyu Liu
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Hao Chen
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Longjiu Cui
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Yanxin Chang
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Yue Kuang
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Dadong Zhang
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China.
| | - Xiang Wang
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China.
| | - Yongjie Zhang
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China.
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