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Tolezano GC, Bastos GC, da Costa SS, Scliar MDO, de Souza CFM, Van Der Linden H, Fernandes WLM, Otto PA, Vianna-Morgante AM, Haddad LA, Honjo RS, Yamamoto GL, Kim CA, Rosenberg C, Jorge AADL, Bertola DR, Krepischi ACV. Clinical Characterization and Underlying Genetic Findings in Brazilian Patients with Syndromic Microcephaly Associated with Neurodevelopmental Disorders. Mol Neurobiol 2024; 61:5230-5247. [PMID: 38180615 DOI: 10.1007/s12035-023-03894-8] [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: 07/13/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
Microcephaly is characterized by an occipitofrontal circumference at least two standard deviations below the mean for age and sex. Neurodevelopmental disorders (NDD) are commonly associated with microcephaly, due to perturbations in brain development and functioning. Given the extensive genetic heterogeneity of microcephaly, managing patients is hindered by the broad spectrum of diagnostic possibilities that exist before conducting molecular testing. We investigated the genetic basis of syndromic microcephaly accompanied by NDD in a Brazilian cohort of 45 individuals and characterized associated clinical features, as well as evaluated the effectiveness of whole-exome sequencing (WES) as a diagnostic tool for this condition. Patients previously negative for pathogenic copy number variants underwent WES, which was performed using a trio approach for isolated index cases (n = 31), only the index in isolated cases with parental consanguinity (n = 8) or affected siblings in familial cases (n = 3). Pathogenic/likely pathogenic variants were identified in 19 families (18 genes) with a diagnostic yield of approximately 45%. Nearly 86% of the individuals had global developmental delay/intellectual disability and 51% presented with behavioral disturbances. Additional frequent clinical features included facial dysmorphisms (80%), brain malformations (67%), musculoskeletal (71%) or cardiovascular (47%) defects, and short stature (54%). Our findings unraveled the underlying genetic basis of microcephaly in half of the patients, demonstrating a high diagnostic yield of WES for microcephaly and reinforcing its genetic heterogeneity. We expanded the phenotypic spectrum associated with the condition and identified a potentially novel gene (CCDC17) for congenital microcephaly.
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Affiliation(s)
- Giovanna Cantini Tolezano
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Giovanna Civitate Bastos
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Marília de Oliveira Scliar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Carolina Fischinger Moura de Souza
- Postgraduate Program in Child and Adolescent Health, Universidade Federal do Rio Grande do Sul, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | | | | | - Paulo Alberto Otto
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Angela M Vianna-Morgante
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Luciana Amaral Haddad
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Rachel Sayuri Honjo
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Guilherme Lopes Yamamoto
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Chong Ae Kim
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Alexander Augusto de Lima Jorge
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Débora Romeo Bertola
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
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Grätz C, Schuster M, Brandes F, Meidert AS, Kirchner B, Reithmair M, Schelling G, Pfaffl MW. A pipeline for the development and analysis of extracellular vesicle-based transcriptomic biomarkers in molecular diagnostics. Mol Aspects Med 2024; 97:101269. [PMID: 38552453 DOI: 10.1016/j.mam.2024.101269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 06/12/2024]
Abstract
Extracellular vesicles are shed by every cell type and can be found in any biofluid. They contain different molecules that can be utilized as biomarkers, including several RNA species which they protect from degradation. Here, we present a pipeline for the development and analysis of extracellular vesicle-associated transcriptomic biomarkers that our group has successfully applied multiple times. We highlight the key steps of the pipeline and give particular emphasis to the necessary quality control checkpoints, which are linked to numerous available guidelines that should be considered along the workflow. Our pipeline starts with patient recruitment and continues with blood sampling and processing. The purification and characterization of extracellular vesicles is explained in detail, as well as the isolation and quality control of extracellular vesicle-associated RNA. We point out the possible pitfalls during library preparation and RNA sequencing and present multiple bioinformatic tools to pinpoint biomarker signature candidates from the sequencing data. Finally, considerations and pitfalls during the validation of the biomarker signature using RT-qPCR will be elaborated.
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Affiliation(s)
- Christian Grätz
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| | - Martina Schuster
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Agnes S Meidert
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany; Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
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Walton IS, McCann E, Weber A, Morton JEV, Noons P, Wilson LC, Ching RC, Cilliers D, Johnson D, Phipps JM, Shears DJ, Thomas GPL, Wall SA, Twigg SRF, Wilkie AOM. Reassessing the association: Evaluation of a polyalanine deletion variant of RUNX2 in non-syndromic sagittal and metopic craniosynostosis. J Anat 2024. [PMID: 38760592 DOI: 10.1111/joa.14052] [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: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 05/19/2024] Open
Abstract
The RUNT-related transcription factor RUNX2 plays a critical role in osteoblast differentiation, and alterations to gene dosage cause distinct craniofacial anomalies. Uniquely amongst the RUNT-related family, vertebrate RUNX2 encodes a polyglutamine/polyalanine repeat (Gln23-Glu-Ala17 in humans), with the length of the polyalanine component completely conserved in great apes. Surprisingly, a frequent 6-amino acid deletion polymorphism, p.(Ala84_Ala89)del, occurs in humans (termed 11A allele), and a previous association study (Cuellar et al. Bone 137:115395;2020) reported that the 11A variant was significantly more frequent in non-syndromic sagittal craniosynostosis (nsSag; allele frequency [AF] = 0.156; 95% confidence interval [CI] 0.126-0.189) compared to non-syndromic metopic craniosynostosis (nsMet; AF = 0.068; 95% CI 0.045-0.098). However, the gnomAD v.2.1.1 control population used by Cuellar et al. did not display Hardy-Weinberg equilibrium, hampering interpretation. To re-examine this association, we genotyped the RUNX2 11A polymorphism in 225 individuals with sporadic nsSag as parent-child trios and 164 singletons with sporadic nsMet, restricting our analysis to individuals of European ancestry. We compared observed allele frequencies to the non-transmitted alleles in the parent-child trios, and to the genome sequencing data from gnomAD v.4, which display Hardy-Weinberg equilibrium. Observed AFs (and 95% CI) were 0.076 (0.053-0.104) in nsSag and 0.082 (0.055-0.118) in nsMet, compared with 0.062 (0.042-0.089) in non-transmitted parental alleles and 0.065 (0.063-0.067) in gnomAD v.4.0.0 non-Finnish European control genomes. In summary, we observed a non-significant excess, compared to gnomAD data, of 11A alleles in both nsSag (relative risk 1.18, 95% CI 0.83-1.67) and nsMet (relative risk 1.29, 95% CI 0.87-1.92), but we did not replicate the much higher excess of RUNX2 11A alleles in nsSag previously reported (p = 0.0001).
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Affiliation(s)
- Isaac S Walton
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Emma McCann
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, England, UK
| | - Astrid Weber
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, England, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
- Birmingham Craniofacial Unit, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Peter Noons
- Birmingham Craniofacial Unit, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Louise C Wilson
- Clinical Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Rosanna C Ching
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Deirdre Cilliers
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David Johnson
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Julie M Phipps
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Deborah J Shears
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Gregory P L Thomas
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Steven A Wall
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Stephen R F Twigg
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Andrew O M Wilkie
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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Stafford IS, Ashton JJ, Mossotto E, Cheng G, Mark Beattie R, Ennis S. Supervised Machine Learning Classifies Inflammatory Bowel Disease Patients by Subtype Using Whole Exome Sequencing Data. J Crohns Colitis 2023; 17:1672-1680. [PMID: 37205778 PMCID: PMC10637043 DOI: 10.1093/ecco-jcc/jjad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Indexed: 05/21/2023]
Abstract
BACKGROUND Inflammatory bowel disease [IBD] is a chronic inflammatory disorder with two main subtypes: Crohn's disease [CD] and ulcerative colitis [UC]. Prompt subtype diagnosis enables the correct treatment to be administered. Using genomic data, we aimed to assess machine learning [ML] to classify patients according to IBD subtype. METHODS Whole exome sequencing [WES] from paediatric/adult IBD patients was processed using an in-house bioinformatics pipeline. These data were condensed into the per-gene, per-individual genomic burden score, GenePy. Data were split into training and testing datasets [80/20]. Feature selection with a linear support vector classifier, and hyperparameter tuning with Bayesian Optimisation, were performed [training data]. The supervised ML method random forest was utilised to classify patients as CD or UC, using three panels: 1] all available genes; 2] autoimmune genes; 3] 'IBD' genes. ML results were assessed using area under the receiver operating characteristics curve [AUROC], sensitivity, and specificity on the testing dataset. RESULTS A total of 906 patients were included in analysis [600 CD, 306 UC]. Training data included 488 patients, balanced according to the minority class of UC. The autoimmune gene panel generated the best performing ML model [AUROC = 0.68], outperforming an IBD gene panel [AUROC = 0.61]. NOD2 was the top gene for discriminating CD and UC, regardless of the gene panel used. Lack of variation in genes with high GenePy scores in CD patients was the best classifier of a diagnosis of UC. DISCUSSION We demonstrate promising classification of patients by subtype using random forest and WES data. Focusing on specific subgroups of patients, with larger datasets, may result in better classification.
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Affiliation(s)
- Imogen S Stafford
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research, University Hospital Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - James J Ashton
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Enrico Mossotto
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - Guo Cheng
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research, University Hospital Southampton, Southampton, UK
| | - Robert Mark Beattie
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
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Lewis MA, Schulte J, Matthews L, Vaden KI, Steves CJ, Williams FMK, Schulte BA, Dubno JR, Steel KP. Accurate phenotypic classification and exome sequencing allow identification of novel genes and variants associated with adult-onset hearing loss. PLoS Genet 2023; 19:e1011058. [PMID: 38011198 PMCID: PMC10718637 DOI: 10.1371/journal.pgen.1011058] [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: 05/17/2023] [Revised: 12/13/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
Adult-onset progressive hearing loss is a common, complex disease with a strong genetic component. Although to date over 150 genes have been identified as contributing to human hearing loss, many more remain to be discovered, as does most of the underlying genetic diversity. Many different variants have been found to underlie adult-onset hearing loss, but they tend to be rare variants with a high impact upon the gene product. It is likely that combinations of more common, lower impact variants also play a role in the prevalence of the disease. Here we present our exome study of hearing loss in a cohort of 532 older adult volunteers with extensive phenotypic data, including 99 older adults with normal hearing, an important control set. Firstly, we carried out an outlier analysis to identify genes with a high variant load in older adults with hearing loss compared to those with normal hearing. Secondly, we used audiometric threshold data to identify individual variants which appear to contribute to different threshold values. We followed up these analyses in a second cohort. Using these approaches, we identified genes and variants linked to better hearing as well as those linked to worse hearing. These analyses identified some known deafness genes, demonstrating proof of principle of our approach. However, most of the candidate genes are novel associations with hearing loss. While the results support the suggestion that genes responsible for severe deafness may also be involved in milder hearing loss, they also suggest that there are many more genes involved in hearing which remain to be identified. Our candidate gene lists may provide useful starting points for improved diagnosis and drug development.
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Affiliation(s)
- Morag A. Lewis
- Wolfson Centre for Age-Related Diseases, King’s College London, United Kingdom
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Jennifer Schulte
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Lois Matthews
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Kenneth I. Vaden
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Claire J. Steves
- Department of Twin Research and Genetic Epidemiology, King’s College London, School of Life Course and Population Sciences, London, United Kingdom
| | - Frances M. K. Williams
- Department of Twin Research and Genetic Epidemiology, King’s College London, School of Life Course and Population Sciences, London, United Kingdom
| | - Bradley A. Schulte
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Judy R. Dubno
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Karen P. Steel
- Wolfson Centre for Age-Related Diseases, King’s College London, United Kingdom
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
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Harvey DC, Verma R, Sedaghat B, Hjelm BE, Morton SU, Seidman JG, Kumar SR. Mutations in genes related to myocyte contraction and ventricular septum development in non-syndromic tetralogy of Fallot. Front Cardiovasc Med 2023; 10:1249605. [PMID: 37840956 PMCID: PMC10569225 DOI: 10.3389/fcvm.2023.1249605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/08/2023] [Indexed: 10/17/2023] Open
Abstract
Objective Eighty percent of patients with a diagnosis of tetralogy of Fallot (TOF) do not have a known genetic etiology or syndrome. We sought to identify key molecular pathways and biological processes that are enriched in non-syndromic TOF, the most common form of cyanotic congenital heart disease, rather than single driver genes to elucidate the pathogenesis of this disease. Methods We undertook exome sequencing of 362 probands with non-syndromic TOF and their parents within the Pediatric Cardiac Genomics Consortium (PCGC). We identified rare (minor allele frequency <1 × 10-4), de novo variants to ascertain pathways and processes affected in this population to better understand TOF pathogenesis. Pathways and biological processes enriched in the PCGC TOF cohort were compared to 317 controls without heart defects (and their parents) from the Simons Foundation Autism Research Initiative (SFARI). Results A total of 120 variants in 117 genes were identified as most likely to be deleterious, with CHD7, CLUH, UNC13C, and WASHC5 identified in two probands each. Gene ontology analyses of these variants using multiple bioinformatic tools demonstrated significant enrichment in processes including cell cycle progression, chromatin remodeling, myocyte contraction and calcium transport, and development of the ventricular septum and ventricle. There was also a significant enrichment of target genes of SOX9, which is critical in second heart field development and whose loss results in membranous ventricular septal defects related to disruption of the proximal outlet septum. None of these processes was significantly enriched in the SFARI control cohort. Conclusion Innate molecular defects in cardiac progenitor cells and genes related to their viability and contractile function appear central to non-syndromic TOF pathogenesis. Future research utilizing our results is likely to have significant implications in stratification of TOF patients and delivery of personalized clinical care.
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Affiliation(s)
- Drayton C. Harvey
- Departments of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Riya Verma
- Departments of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Brandon Sedaghat
- Department of Medicine, Rosalind Franklin University School of Medicine and Science, Chicago, IL, United States
| | - Brooke E. Hjelm
- Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Sarah U. Morton
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
| | - Jon G. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - S. Ram Kumar
- Departments of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Surgery, University of Nebraska Medical Center, Omaha, NE, United States
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Shah SB, Peddada TN, Song C, Mensah M, Sung H, Yavi M, Yuan P, Zarate CA, Mickey BJ, Burmeister M, Akula N, McMahon FJ. Exome-wide association study of treatment-resistant depression suggests novel treatment targets. Sci Rep 2023; 13:12467. [PMID: 37528149 PMCID: PMC10394052 DOI: 10.1038/s41598-023-38984-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/18/2023] [Indexed: 08/03/2023] Open
Abstract
Treatment-resistant depression (TRD) is a severe form of major depressive disorder (MDD) with substantial public health impact and poor treatment outcome. Treatment outcome in MDD is significantly heritable, but genome-wide association studies have failed to identify replicable common marker alleles, suggesting a potential role for uncommon variants. Here we investigated the hypothesis that uncommon, putatively functional genetic variants are associated with TRD. Whole-exome sequencing data was obtained from 182 TRD cases and 2021 psychiatrically healthy controls. After quality control, the remaining 149 TRD cases and 1976 controls were analyzed with tests designed to detect excess burdens of uncommon variants. At the gene level, 5 genes, ZNF248, PRKRA, PYHIN1, SLC7A8, and STK19 each carried exome-wide significant excess burdens of variants in TRD cases (q < 0.05). Analysis of 41 pre-selected gene sets suggested an excess of uncommon, functional variants among genes involved in lithium response. Among the genes identified in previous TRD studies, ZDHHC3 was also significant in this sample after multiple test correction. ZNF248 and STK19 are involved in transcriptional regulation, PHYIN1 and PRKRA are involved in immune response, SLC7A8 is associated with thyroid hormone transporter activity, and ZDHHC3 regulates synaptic clustering of GABA and glutamate receptors. These results implicate uncommon, functional alleles in TRD and suggest promising novel targets for future research.
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Affiliation(s)
- Shrey B Shah
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
- Rutgers New Jersey Medical School, Newark, NJ, USA.
| | - Teja N Peddada
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
- Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher Song
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Maame Mensah
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Heejong Sung
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Mani Yavi
- Experimental Therapeutics and Pathophysiology Branch and Section on the Neurobiology and Treatment of Mood Disorders, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Peixiong Yuan
- Experimental Therapeutics and Pathophysiology Branch and Section on the Neurobiology and Treatment of Mood Disorders, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Carlos A Zarate
- Experimental Therapeutics and Pathophysiology Branch and Section on the Neurobiology and Treatment of Mood Disorders, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Brian J Mickey
- Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Margit Burmeister
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
- Michigan Neuroscience Institute and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Nirmala Akula
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Francis J McMahon
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
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Pires SF, Barros JSD, Costa SSD, Carmo GBD, Scliar MDO, Lengert AVH, Boldrini É, Silva SRMD, Vidal DO, Maschietto M, Krepischi ACV. Analysis of the Mutational Landscape of Osteosarcomas Identifies Genes Related to Metastasis and Prognosis and Disrupted Biological Pathways of Immune Response and Bone Development. Int J Mol Sci 2023; 24:10463. [PMID: 37445641 DOI: 10.3390/ijms241310463] [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: 05/02/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 07/15/2023] Open
Abstract
Osteosarcoma (OS) is the most prevalent type of bone tumor, but slow progress has been achieved in disentangling the full set of genomic events involved in its initiation and progression. We assessed by NGS the mutational spectrum of 28 primary OSs from Brazilian patients, and identified 445 potentially deleterious SNVs/indels and 1176 copy number alterations (CNAs). TP53 was the most recurrently mutated gene, with an overall rate of ~60%, considering SNVs/indels and CNAs. The most frequent CNAs (~60%) were gains at 1q21.2q21.3, 6p21.1, and 8q13.3q24.22, and losses at 10q26 and 13q14.3q21.1. Seven cases presented CNA patterns reminiscent of complex events (chromothripsis and chromoanasynthesis). Putative RB1 and TP53 germline variants were found in five samples associated with metastasis at diagnosis along with complex genomic patterns of CNAs. PTPRQ, KNL1, ZFHX4, and DMD alterations were prevalent in metastatic or deceased patients, being potentially indicative of poor prognosis. TNFRSF11B, involved in skeletal system development and maintenance, emerged as a candidate for osteosarcomagenesis due to its biological function and a high frequency of copy number gains. A protein-protein network enrichment highlighted biological pathways involved in immunity and bone development. Our findings reinforced the high genomic OS instability and heterogeneity, and led to the identification of novel disrupted genes deserving further evaluation as biomarkers due to their association with poor outcomes.
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Affiliation(s)
- Sara Ferreira Pires
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | - Juliana Sobral de Barros
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | - Silvia Souza da Costa
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | - Gabriel Bandeira do Carmo
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | - Marília de Oliveira Scliar
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | | | - Érica Boldrini
- Barretos Children's Cancer Hospital, Barretos 14784-400, Brazil
| | | | - Daniel Onofre Vidal
- Molecular Oncology Research Center (CPOM), Barretos Cancer Hospital, Barretos 14784-384, Brazil
| | - Mariana Maschietto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-884, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
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9
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Lewis MA, Schulte J, Matthews L, Vaden KI, Steves CJ, Williams FMK, Schulte BA, Dubno JR, Steel KP. Accurate phenotypic classification and exome sequencing allow identification of novel genes and variants associated with adult-onset hearing loss. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.27.23289040. [PMID: 37163093 PMCID: PMC10168485 DOI: 10.1101/2023.04.27.23289040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Adult-onset progressive hearing loss is a common, complex disease with a strong genetic component. Although to date over 150 genes have been identified as contributing to human hearing loss, many more remain to be discovered, as does most of the underlying genetic diversity. Many different variants have been found to underlie adult-onset hearing loss, but they tend to be rare variants with a high impact upon the gene product. It is likely that combinations of more common, lower impact variants also play a role in the prevalence of the disease. Here we present our exome study of hearing loss in a cohort of 532 older adult volunteers with extensive phenotypic data, including 99 older adults with normal hearing, an important control set. Firstly, we carried out an outlier analysis to identify genes with a high variant load in older adults with hearing loss compared to those with normal hearing. Secondly, we used audiometric threshold data to identify individual variants which appear to contribute to different threshold values. We followed up these analyses in a second cohort. Using these approaches, we identified genes and variants linked to better hearing as well as those linked to worse hearing. These analyses identified some known deafness genes, demonstrating proof of principle of our approach. However, most of the candidate genes are novel associations with hearing loss. While the results support the suggestion that genes responsible for severe deafness may also be involved in milder hearing loss, they also suggest that there are many more genes involved in hearing which remain to be identified. Our candidate gene lists may provide useful starting points for improved diagnosis and drug development.
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Affiliation(s)
- Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, SE1 1UL, UK
- The Medical University of South Carolina, SC, USA
| | | | | | | | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, School of Life Course and Population Sciences, London, UK
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, King's College London, School of Life Course and Population Sciences, London, UK
| | | | - Judy R Dubno
- The Medical University of South Carolina, SC, USA
| | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, SE1 1UL, UK
- The Medical University of South Carolina, SC, USA
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10
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Pires SF, de Barros JS, da Costa SS, de Oliveira Scliar M, Van Helvoort Lengert A, Boldrini É, da Silva SRM, Tasic L, Vidal DO, Krepischi ACV, Maschietto M. DNA methylation patterns suggest the involvement of DNMT3B and TET1 in osteosarcoma development. Mol Genet Genomics 2023; 298:721-733. [PMID: 37020053 DOI: 10.1007/s00438-023-02010-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/24/2023] [Indexed: 04/07/2023]
Abstract
DNA methylation may be involved in the development of osteosarcomas. Osteosarcomas commonly arise during the bone growth and remodeling in puberty, making it plausible to infer the involvement of epigenetic alterations in their development. As a highly studied epigenetic mechanism, we investigated DNA methylation and related genetic variants in 28 primary osteosarcomas aiming to identify deregulated driver alterations. Methylation and genomic data were obtained using the Illumina HM450K beadchips and the TruSight One sequencing panel, respectively. Aberrant DNA methylation was spread throughout the osteosarcomas genomes. We identified 3146 differentially methylated CpGs comparing osteosarcomas and bone tissue samples, with high methylation heterogeneity, global hypomethylation and focal hypermethylation at CpG islands. Differentially methylated regions (DMR) were detected in 585 loci (319 hypomethylated and 266 hypermethylated), mapped to the promoter regions of 350 genes. These DMR genes were enriched for biological processes related to skeletal system morphogenesis, proliferation, inflammatory response, and signal transduction. Both methylation and expression data were validated in independent groups of cases. Six tumor suppressor genes harbored deletions or promoter hypermethylation (DLEC1, GJB2, HIC1, MIR149, PAX6, and WNT5A), and four oncogenes presented gains or hypomethylation (ASPSCR1, NOTCH4, PRDM16, and RUNX3). Our analysis also revealed hypomethylation at 6p22, a region that contains several histone genes. Copy-number changes in DNMT3B (gain) and TET1 (loss), as well as overexpression of DNMT3B in osteosarcomas provide a possible explanation for the observed phenotype of CpG island hypermethylation. While the detected open-sea hypomethylation likely contributes to the well-known osteosarcoma genomic instability, enriched CpG island hypermethylation suggests an underlying mechanism possibly driven by overexpression of DNMT3B likely resulting in silencing of tumor suppressors and DNA repair genes.
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Affiliation(s)
- Sara Ferreira Pires
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliana Sobral de Barros
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Marília de Oliveira Scliar
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | | | | | - Ljubica Tasic
- Laboratory of Biological Chemistry, Institute of Chemistry, University of Campinas, Campinas, Brazil
| | - Daniel Onofre Vidal
- Molecular Oncology Research Center (CPOM), Barretos Cancer Hospital, Barretos, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Mariana Maschietto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.
- Research Center, Boldrini Children's Hospital, Campinas, SP, Brazil.
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11
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Lewis MA, Schulte BA, Dubno JR, Steel KP. Investigating the characteristics of genes and variants associated with self-reported hearing difficulty in older adults in the UK Biobank. BMC Biol 2022; 20:150. [PMID: 35761239 PMCID: PMC9238072 DOI: 10.1186/s12915-022-01349-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/10/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Age-related hearing loss is a common, heterogeneous disease with a strong genetic component. More than 100 loci have been reported to be involved in human hearing impairment to date, but most of the genes underlying human adult-onset hearing loss remain unknown. Most genetic studies have focussed on very rare variants (such as family studies and patient cohort screens) or very common variants (genome-wide association studies). However, the contribution of variants present in the human population at intermediate frequencies is hard to quantify using these methods, and as a result, the landscape of variation associated with adult-onset hearing loss remains largely unknown. RESULTS Here we present a study based on exome sequencing and self-reported hearing difficulty in the UK Biobank, a large-scale biomedical database. We have carried out variant load analyses using different minor allele frequency and impact filters, and compared the resulting gene lists to a manually curated list of nearly 700 genes known to be involved in hearing in humans and/or mice. An allele frequency cutoff of 0.1, combined with a high predicted variant impact, was found to be the most effective filter setting for our analysis. We also found that separating the participants by sex produced markedly different gene lists. The gene lists obtained were investigated using gene ontology annotation, functional prioritisation and expression analysis, and this identified good candidates for further study. CONCLUSIONS Our results suggest that relatively common as well as rare variants with a high predicted impact contribute to age-related hearing impairment and that the genetic contributions to adult hearing difficulty may differ between the sexes. Our manually curated list of deafness genes is a useful resource for candidate gene prioritisation in hearing loss.
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Affiliation(s)
- Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, UK.
| | | | - Judy R Dubno
- The Medical University of South Carolina, Charleston, SC, USA
| | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, UK
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12
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Marciano DC, Wang C, Hsu TK, Bourquard T, Atri B, Nehring RB, Abel NS, Bowling EA, Chen TJ, Lurie PD, Katsonis P, Rosenberg SM, Herman C, Lichtarge O. Evolutionary action of mutations reveals antimicrobial resistance genes in Escherichia coli. Nat Commun 2022; 13:3189. [PMID: 35680894 PMCID: PMC9184624 DOI: 10.1038/s41467-022-30889-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/24/2022] [Indexed: 11/08/2022] Open
Abstract
Since antibiotic development lags, we search for potential drug targets through directed evolution experiments. A challenge is that many resistance genes hide in a noisy mutational background as mutator clones emerge in the adaptive population. Here, to overcome this noise, we quantify the impact of mutations through evolutionary action (EA). After sequencing ciprofloxacin or colistin resistance strains grown under different mutational regimes, we find that an elevated sum of the evolutionary action of mutations in a gene identifies known resistance drivers. This EA integration approach also suggests new antibiotic resistance genes which are then shown to provide a fitness advantage in competition experiments. Moreover, EA integration analysis of clinical and environmental isolates of antibiotic resistant of E. coli identifies gene drivers of resistance where a standard approach fails. Together these results inform the genetic basis of de novo colistin resistance and support the robust discovery of phenotype-driving genes via the evolutionary action of genetic perturbations in fitness landscapes.
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Affiliation(s)
- David C Marciano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Teng-Kuei Hsu
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Thomas Bourquard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Benu Atri
- Structural and Computational Biology & Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, 77030, USA
- Clara Analytics Inc., 451 El Camino Real #201, Santa Clara, CA, 95050, USA
| | - Ralf B Nehring
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicholas S Abel
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth A Bowling
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Taylor J Chen
- Integrative Molecular & Biomedical Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pamela D Lurie
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular & Biomedical Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Structural and Computational Biology & Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, 77030, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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13
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Aguiar T, Teixeira A, Scliar MO, Sobral de Barros J, Lemes RB, Souza S, Tolezano G, Santos F, Tojal I, Cypriano M, Caminada de Toledo SR, Valadares E, Borges Pinto R, Pinto Artigalas OA, Caetano de Aguirre Neto J, Novak E, Cristofani LM, Miura Sugayama SM, Odone V, Cunha IW, Lima da Costa CM, Rosenberg C, Krepischi A. Unraveling the Genetic Architecture of Hepatoblastoma Risk: Birth Defects and Increased Burden of Germline Damaging Variants in Gastrointestinal/Renal Cancer Predisposition and DNA Repair Genes. Front Genet 2022; 13:858396. [PMID: 35495172 PMCID: PMC9039399 DOI: 10.3389/fgene.2022.858396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/08/2022] [Indexed: 12/21/2022] Open
Abstract
The ultrarare hepatoblastoma (HB) is the most common pediatric liver cancer. HB risk is related to a few rare syndromes, and the molecular bases remain elusive for most cases. We investigated the burden of rare damaging germline variants in 30 Brazilian patients with HB and the presence of additional clinical signs. A high frequency of prematurity (20%) and birth defects (37%), especially craniofacial (17%, including craniosynostosis) and kidney (7%) anomalies, was observed. Putative pathogenic or likely pathogenic monoallelic germline variants mapped to 10 cancer predisposition genes (CPGs: APC, CHEK2, DROSHA, ERCC5, FAH, MSH2, MUTYH, RPS19, TGFBR2 and VHL) were detected in 33% of the patients, only 40% of them with a family history of cancer. These findings showed a predominance of CPGs with a known link to gastrointestinal/colorectal and renal cancer risk. A remarkable feature was an enrichment of rare damaging variants affecting different classes of DNA repair genes, particularly those known as Fanconi anemia genes. Moreover, several potentially deleterious variants mapped to genes impacting liver functions were disclosed. To our knowledge, this is the largest assessment of rare germline variants in HB patients to date, contributing to elucidate the genetic architecture of HB risk.
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Affiliation(s)
- Talita Aguiar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Columbia University Irving Medical Center, New York, NY, United States
| | - Anne Teixeira
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Marília O. Scliar
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliana Sobral de Barros
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Renan B. Lemes
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Silvia Souza
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Giovanna Tolezano
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Fernanda Santos
- Department of Pediatric Oncology, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Israel Tojal
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Monica Cypriano
- GRAACC—Grupo de Apoio Ao Adolescente e Criança Com Câncer, Federal University of São Paulo, São Paulo, Brazil
| | | | - Eugênia Valadares
- Benjamim Guimarães Foundation - Department of Pediatrics Hospital da Baleia, Belo Horizonte, Brazil
| | - Raquel Borges Pinto
- Department of Genetics, Hospital da Criança Conceição, Hospitalar Conceição Group, Porto Alegre, Brazil
| | | | | | - Estela Novak
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
- Molecular Genetics—Foundation Pro Sangue Blood Center of São Paulo, São Paulo, Brazil
| | - Lilian Maria Cristofani
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Sofia M. Miura Sugayama
- Department of Pediatric, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Vicente Odone
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | | | | | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- *Correspondence: Ana Krepischi,
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14
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Gorsi B, Hernandez E, Moore MB, Moriwaki M, Chow CY, Coelho E, Taylor E, Lu C, Walker A, Touraine P, Nelson LM, Cooper AR, Mardis ER, Rajkovic A, Yandell M, Welt CK. Causal and Candidate Gene Variants in a Large Cohort of Women With Primary Ovarian Insufficiency. J Clin Endocrinol Metab 2022; 107:685-714. [PMID: 34718612 PMCID: PMC9006976 DOI: 10.1210/clinem/dgab775] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT A genetic etiology likely accounts for the majority of unexplained primary ovarian insufficiency (POI). OBJECTIVE We hypothesized that heterozygous rare variants and variants in enhanced categories are associated with POI. DESIGN The study was an observational study. SETTING Subjects were recruited at academic institutions. PATIENTS Subjects from Boston (n = 98), the National Institutes of Health and Washington University (n = 98), Pittsburgh (n = 20), Italy (n = 43), and France (n = 32) were diagnosed with POI (amenorrhea with an elevated follicle-stimulating hormone level). Controls were recruited for health in old age or were from the 1000 Genomes Project (total n = 233). INTERVENTION We performed whole exome sequencing (WES), and data were analyzed using a rare variant scoring method and a Bayes factor-based framework for identifying genes harboring pathogenic variants. We performed functional studies on identified genes that were not previously implicated in POI in a D. melanogaster model. MAIN OUTCOME Genes with rare pathogenic variants and gene sets with increased burden of deleterious variants were identified. RESULTS Candidate heterozygous variants were identified in known genes and genes with functional evidence. Gene sets with increased burden of deleterious alleles included the categories transcription and translation, DNA damage and repair, meiosis and cell division. Variants were found in novel genes from the enhanced categories. Functional evidence supported 7 new risk genes for POI (USP36, VCP, WDR33, PIWIL3, NPM2, LLGL1, and BOD1L1). CONCLUSIONS Candidate causative variants were identified through WES in women with POI. Aggregating clinical data and genetic risk with a categorical approach may expand the genetic architecture of heterozygous rare gene variants causing risk for POI.
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Affiliation(s)
- Bushra Gorsi
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Edgar Hernandez
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Marvin Barry Moore
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Mika Moriwaki
- Division of Endocrinology, Metabolism and Diabetes, University of Utah, Salt Lake City, UT, USA
| | - Clement Y Chow
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Emily Coelho
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Elaine Taylor
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Claire Lu
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Amanda Walker
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Philippe Touraine
- Sorbonne Universite, Hôpital Universitaire Pitié Salpêtrière-Charles Foix, Service d’Endocrinologie et Médecine de la Reproduction, Centre de Maladies Endocriniennes Rares de la Croissance et du Développement, Centre de Pathologies Gynécologiques Rares, Paris, France
| | | | | | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Ohio State University College of Medicine, Columbus, OH, USA
| | - Aleksander Rajkovic
- Department of Pathology, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Mark Yandell
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Corrine K Welt
- Division of Endocrinology, Metabolism and Diabetes, University of Utah, Salt Lake City, UT, USA
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15
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Whole Genome Sequencing Unravels New Genetic Determinants of Early-Onset Familial Osteoporosis and Low BMD in Malta. Genes (Basel) 2022; 13:genes13020204. [PMID: 35205249 PMCID: PMC8871631 DOI: 10.3390/genes13020204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/19/2022] Open
Abstract
Background: Osteoporosis is a skeletal disease with a strong genetic background. The study aimed to identify the genetic determinants of early-onset familial osteoporosis and low bone mineral density (BMD) in a two-generation Maltese family. Methods: Fifteen relatives aged between 28–74 years were recruited. Whole genome sequencing was conducted on 12 relatives and shortlisted variants were genotyped in the Malta Osteoporotic Fracture Study (MOFS) for replication. Results: Sequential variant filtering following a dominant inheritance pattern identified rare missense variants within SELP, TGF-β2 and ADAMTS20, all of which were predicted to be likely pathogenic and participate in osteoimmunology. TGF-β2 c.1136C>T was identified in five individuals from the MOFS in heterozygosity, four of whom had osteopenia/osteoporosis at the lumbar spine and hip, and/or had sustained a low-trauma fracture. Heterozygosity for the ADAMTS20 c.4090A>T was accompanied by lower total hip BMD (p = 0.018) and lower total serum calcium levels in MOFS (p < 0.01), recapitulating the findings from the family. Women carrying at least one copy of the alternative allele (TC/CC) for SELP c.2177T>C exhibited a tendency for lower lumbar spine BMD and/or wrist fracture history relative to women with TT genotype. Conclusions: Our findings suggest that the identified variants, alone or in combination, could be causal factors of familial osteoporosis and low BMD, requiring replication in larger collections.
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16
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Moreira DDP, Suzuki AM, Silva ALTE, Varella-Branco E, Meneghetti MCZ, Kobayashi GS, Fogo M, Ferrari MDFR, Cardoso RR, Lourenço NCV, Griesi-Oliveira K, Zachi EC, Bertola DR, Weinmann KDS, de Lima MA, Nader HB, Sertié AL, Passos-Bueno MR. Neuroprogenitor Cells From Patients With TBCK Encephalopathy Suggest Deregulation of Early Secretory Vesicle Transport. Front Cell Neurosci 2022; 15:803302. [PMID: 35095425 PMCID: PMC8793280 DOI: 10.3389/fncel.2021.803302] [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: 10/27/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
Biallelic pathogenic variants in TBCK cause encephaloneuropathy, infantile hypotonia with psychomotor retardation, and characteristic facies 3 (IHPRF3). The molecular mechanisms underlying its neuronal phenotype are largely unexplored. In this study, we reported two sisters, who harbored biallelic variants in TBCK and met diagnostic criteria for IHPRF3. We provided evidence that TBCK may play an important role in the early secretory pathway in neuroprogenitor cells (iNPC) differentiated from induced pluripotent stem cells (iPSC). Lack of functional TBCK protein in iNPC is associated with impaired endoplasmic reticulum-to-Golgi vesicle transport and autophagosome biogenesis, as well as altered cell cycle progression and severe impairment in the capacity of migration. Alteration in these processes, which are crucial for neurogenesis, neuronal migration, and cytoarchitecture organization, may represent an important causative mechanism of both neurodevelopmental and neurodegenerative phenotypes observed in IHPRF3. Whether reduced mechanistic target of rapamycin (mTOR) signaling is secondary to impaired TBCK function over other secretory transport regulators still needs further investigation.
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Affiliation(s)
- Danielle de Paula Moreira
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Angela May Suzuki
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | - Elisa Varella-Branco
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | - Gerson Shigeru Kobayashi
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Mariana Fogo
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Instituto de Ensino e Pesquisa Albert Einstein, Albert Einstein Hospital, São Paulo, Brazil
| | | | - Rafaela Regina Cardoso
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Naila Cristina Vilaça Lourenço
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Karina Griesi-Oliveira
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Instituto de Ensino e Pesquisa Albert Einstein, Albert Einstein Hospital, São Paulo, Brazil
| | - Elaine Cristina Zachi
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Débora Romeo Bertola
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Instituto da Criança do Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Karina de Souza Weinmann
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Marcelo Andrade de Lima
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Helena Bonciani Nader
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Andrea Laurato Sertié
- Instituto de Ensino e Pesquisa Albert Einstein, Albert Einstein Hospital, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- *Correspondence: Maria Rita Passos-Bueno,
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Integrated Genomic Analysis Identifies ANKRD36 Gene as a Novel and Common Biomarker of Disease Progression in Chronic Myeloid Leukemia. BIOLOGY 2021; 10:biology10111182. [PMID: 34827175 PMCID: PMC8615070 DOI: 10.3390/biology10111182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 02/05/2023]
Abstract
Simple Summary Chronic myeloid leukemia is a type of blood cancer that is regarded as a success story in determining the exact biological origin, pathogenesis and development of a molecularly targeted (mutation-specific) therapy that has led to successful treatment of this fatal cancer. It is caused by the BCR-ABL fusion gene, which is formed from the translocation between chromosomes 9 and 22. Anti-BCR-ABL drugs, known as tyrosine kinase inhibitors (TKIs), have led to long-term remissions in more than 80% of CML patients and even cure in about one-third of patients. Nevertheless, many patients face drug resistance, and disease progression occurs in about 30% of CML patients, leading to morbidities and mortality. Unfortunately, no biomarkers of CML progression are available due to a poor understanding of the mechanism of progression. Therefore, finding reliable molecular biomarkers of CML progression is one of the most attractive research areas in 21st-century cancer research. In this study, we report novel genomic variants exclusively found in all our advanced-phase CML patients. This study will help in identifying CML patients at risk of disease progression and timely therapeutic interventions to avoid or at least delay fatal disease progression in this cancer. Abstract Background: Chronic myeloid leukemia (CML) is initiated in bone marrow due to chromosomal translocation t(9;22) leading to fusion oncogene BCR-ABL. Targeting BCR-ABL by tyrosine kinase inhibitors (TKIs) has changed fatal CML into an almost curable disease. Despite that, TKIs lose their effectiveness due to disease progression. Unfortunately, the mechanism of CML progression is poorly understood and common biomarkers for CML progression are unavailable. This study was conducted to find novel biomarkers of CML progression by employing whole-exome sequencing (WES). Materials and Methods: WES of accelerated phase (AP) and blast crisis (BC) CML patients was carried out, with chronic-phase CML (CP-CML) patients as control. After DNA library preparation and exome enrichment, clustering and sequencing were carried out using Illumina platforms. Statistical analysis was carried out using SAS/STAT software version 9.4, and R package was employed to find mutations shared exclusively by all AP-/BC-CML patients. Confirmation of mutations was carried out using Sanger sequencing and protein structure modeling using I-TASSER followed by mutant generation and visualization using PyMOL. Results: Three novel genes (ANKRD36, ANKRD36B and PRSS3) were mutated exclusively in all AP-/BC-CML patients. Only ANKRD36 gene mutations (c.1183_1184 delGC and c.1187_1185 dupTT) were confirmed by Sanger sequencing. Protein modeling studies showed that mutations induce structural changes in ANKRD36 protein. Conclusions: Our studies show that ANKRD36 is a potential common biomarker and drug target of early CML progression. ANKRD36 is yet uncharacterized in humans. It has the highest expression in bone marrow, specifically myeloid cells. We recommend carrying out further studies to explore the role of ANKRD36 in the biology and progression of CML.
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18
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Mutational patterns and their correlation to CHIP-related mutations and age in hematological malignancies. Blood Adv 2021; 5:4426-4434. [PMID: 34570179 PMCID: PMC8579257 DOI: 10.1182/bloodadvances.2021004668] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 08/03/2021] [Indexed: 01/17/2023] Open
Abstract
Comparison of the mutation frequencies and numbers of 122 genes in 3096 cases enables identification of “mutation-driven” entities. Differences in mutation patterns in cases with or without CHIP-associated mutations across entities suggest differences in pathophysiology.
Acquired somatic mutations are crucial for the development of most cancers. We performed a comprehensive comparative analysis of the mutational landscapes and their correlation with CHIP-related (clonal hematopoiesis of indeterminate potential) mutations and patient age of 122 genes in 3096 cases of 28 different hematological malignancies. Differences were observed regarding (1) the median number of mutations (highest, median n = 4; lowest, n = 0); (2) specificity of certain mutations (high frequencies in atypical chronic myeloid leukemia [aCML; ASXL1, 86%], follicular lymphoma [FL; KMT2D, 87%; CREBBP, 73%], hairy cell lymphoma [BRAF, 100%], lymphoplasmacytic lymphoma [MYD88, 98%; CXCR4, 51%], myeloproliferative neoplasm [MPN; AK2, 68%]); (3) distribution of mutations (broad distribution within/across the myeloid/lymphoid lineage for TET2, ASXL1, DNMT3A, TP53, BCOR, and ETV6); (4) correlation of mutations with patient’s age (correlated with older age across entities: TET2, DNMT3A, ASXL1, TP53, EZH2, BCOR, GATA2, and IDH2; younger age: KIT, POT1, RAD21, U2AF2, and WT1); (5) correlation of mutation number per patient with age. Moreover, we observed high frequencies of mutations in RUNX1, SRSF2, IDH2, NRAS, and EZH2 in cases comprising at least 1 DTA (DNMT3A, TET2, ASXL1) mutation, whereas in cases without DTA mutations, TP53, KRAS, WT1, and SF3B1 were more frequent across entities, suggesting differences in pathophysiology. These results give further insight into the complex genetic landscape and the role of DTA mutations in hematological neoplasms and define mutation-driven entities (myelodysplastic syndrome/MPN overlap; secondary acute myeloid) in comparison with entities defined by chromosomal fusions (chronic myeloid leukemia; myeloid/lymphoid neoplasm with eosinophilia).
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19
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Röcken C, Amallraja A, Halske C, Opasic L, Traulsen A, Behrens HM, Krüger S, Liu A, Haag J, Egberts JH, Rosenstiel P, Meißner T. Multiscale heterogeneity in gastric adenocarcinoma evolution is an obstacle to precision medicine. Genome Med 2021; 13:177. [PMID: 34749812 PMCID: PMC8576943 DOI: 10.1186/s13073-021-00975-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Cancer is a somatic evolutionary disease and adenocarcinomas of the stomach and gastroesophageal junction (GC) may serve as a two-dimensional model of cancer expansion, in which tumor subclones are not evenly mixed during tumor progression but rather spatially separated and diversified. We hypothesize that precision medicine efforts are compromised when clinical decisions are based on a single-sample analysis, which ignores the mechanisms of cancer evolution and resulting intratumoral heterogeneity. Using multiregional whole-exome sequencing, we investigated the effect of somatic evolution on intratumoral heterogeneity aiming to shed light on the evolutionary biology of GC. METHODS The study comprised a prospective discovery cohort of 9 and a validation cohort of 463 GCs. Multiregional whole-exome sequencing was performed using samples form 45 primary tumors and 3 lymph node metastases (range 3-10 tumor samples/patient) of the discovery cohort. RESULTS In total, the discovery cohort harbored 16,537 non-synonymous mutations. Intratumoral heterogeneity of somatic mutations and copy number variants were present in all tumors of the discovery cohort. Of the non-synonymous mutations, 53-91% were not present in each patient's sample; 399 genes harbored 2-4 different non-synonymous mutations in the same patient; 175 genes showed copy number variations, the majority being heterogeneous, including CD274 (PD-L1). Multi-sample tree-based analyses provided evidence for branched evolution being most complex in a microsatellite instable GC. The analysis of the mode of evolution showed a high degree of heterogeneity in deviation from neutrality within each tumor. We found evidence of parallel evolution and evolutionary trajectories: different mutations of SMAD4 aligned with different subclones and were found only in TP53 mutant GCs. CONCLUSIONS Neutral and non-neutral somatic evolution shape the mutational landscape in GC along its lateral expansions. It leads to complex spatial intratumoral heterogeneity, where lymph node metastases may stem from different areas of the primary tumor, synchronously. Our findings may have profound effects on future patient management. They illustrate the risk of mis-interpreting tumor genetics based on single-sample analysis and open new avenues for an evolutionary classification of GC, i.e., the discovery of distinct evolutionary trajectories which can be utilized for precision medicine.
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Affiliation(s)
- Christoph Röcken
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany.
- Institute for Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany.
| | - Anu Amallraja
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - Christine Halske
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Luka Opasic
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Hans-Michael Behrens
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Sandra Krüger
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Anne Liu
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Jochen Haag
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Jan-Hendrik Egberts
- Department of General Surgery, Visceral, Thoracic, Transplantation and Pediatric Surgery, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Department of General Surgery, Visceral, Thoracic, Transplantation and Pediatric Surgery, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Tobias Meißner
- Institute for Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
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20
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Magistri M, Happ LE, Ramdial J, Lu X, Stathias V, Kunkalla K, Agarwal N, Jiang X, Schürer SC, Dubovy SR, Chapman JR, Vega F, Dave S, Lossos IS. The Genetic Landscape of Ocular Adnexa MALT Lymphoma Reveals Frequent Aberrations in NFAT and MEF2B Signaling Pathways. CANCER RESEARCH COMMUNICATIONS 2021; 1:1-16. [PMID: 35528192 PMCID: PMC9075502 DOI: 10.1158/2767-9764.crc-21-0022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/03/2021] [Indexed: 12/31/2022]
Abstract
A comprehensive constellation of somatic non-silent mutations and copy number (CN) variations in ocular adnexa marginal zone lymphoma (OAMZL) is unknown. By utilizing whole-exome sequencing in 69 tumors we define the genetic landscape of OAMZL. Mutations and CN changes in CABIN1 (30%), RHOA (26%), TBL1XR1 (22%), and CREBBP (17%) and inactivation of TNFAIP3 (26%) were among the most common aberrations. Candidate cancer driver genes cluster in the B-cell receptor (BCR), NFkB, NOTCH and NFAT signaling pathways. One of the most commonly altered genes is CABIN1, a calcineurin inhibitor acting as a negative regulator of the NFAT and MEF2B transcriptional activity. CABIN1 deletions enhance BCR-stimulated NFAT and MEF2B transcriptional activity, while CABIN1 mutations enhance only MEF2B transcriptional activity by impairing binding of mSin3a to CABIN1. Our data provide an unbiased identification of genetically altered genes that may play a role in the molecular pathogenesis of OAMZL and serve as therapeutic targets.
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Affiliation(s)
- Marco Magistri
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Lanie E. Happ
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, North Carolina
| | - Jeremy Ramdial
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - XiaoQing Lu
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Vasileios Stathias
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida
- Center for Computational Science, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Kranthi Kunkalla
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Miami, Miami, Florida
| | - Nitin Agarwal
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Miami, Miami, Florida
| | - Xiaoyu Jiang
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Stephan C. Schürer
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida
- Center for Computational Science, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Sander R. Dubovy
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Jennifer R. Chapman
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Miami, Miami, Florida
| | - Francisco Vega
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Miami, Miami, Florida
| | - Sandeep Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, North Carolina
| | - Izidore S. Lossos
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida
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21
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Pemov A, Hansen NF, Sindiri S, Patidar R, Higham CS, Dombi E, Miettinen MM, Fetsch P, Brems H, Chandrasekharappa SC, Jones K, Zhu B, Wei JS, Mullikin JC, Wallace MR, Khan J, Legius E, Widemann BC, Stewart DR. Low mutation burden and frequent loss of CDKN2A/B and SMARCA2, but not PRC2, define premalignant neurofibromatosis type 1-associated atypical neurofibromas. Neuro Oncol 2021; 21:981-992. [PMID: 30722027 DOI: 10.1093/neuonc/noz028] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Neurofibromatosis type 1 (NF1) is a tumor-predisposition disorder caused by germline mutations in NF1. NF1 patients have an 8-16% lifetime risk of developing a malignant peripheral nerve sheath tumor (MPNST), a highly aggressive soft-tissue sarcoma, often arising from preexisting benign plexiform neurofibromas (PNs) and atypical neurofibromas (ANFs). ANFs are distinct from both PN and MPNST, representing an intermediate step in malignant transformation. METHODS In the first comprehensive genomic analysis of ANF originating from multiple patients, we performed tumor/normal whole-exome sequencing (WES) of 16 ANFs. In addition, we conducted WES of 3 MPNSTs, copy-number meta-analysis of 26 ANFs and 28 MPNSTs, and whole transcriptome sequencing analysis of 5 ANFs and 5 MPNSTs. RESULTS We identified a low number of mutations (median 1, range 0-5) in the exomes of ANFs (only NF1 somatic mutations were recurrent), and frequent deletions of CDKN2A/B (69%) and SMARCA2 (42%). We determined that polycomb repressor complex 2 (PRC2) genes EED and SUZ12 were frequently mutated, deleted, or downregulated in MPNSTs but not in ANFs. Our pilot gene expression study revealed upregulated NRAS, MDM2, CCND1/2/3, and CDK4/6 in ANFs and MPNSTs, and overexpression of EZH2 in MPNSTs only. CONCLUSIONS The PN-ANF transition is primarily driven by the deletion of CDKN2A/B. Further progression from ANF to MPNST likely involves broad chromosomal rearrangements and frequent inactivation of the PRC2 genes, loss of the DNA repair genes, and copy-number increase of signal transduction and cell-cycle and pluripotency self-renewal genes.
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Affiliation(s)
- Alexander Pemov
- Clinical Genetics Branch, DCEG, NCI, National Institutes of Health (NIH), Rockville, Maryland, USA
| | - Nancy F Hansen
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Rockville, Maryland, USA
| | - Sivasish Sindiri
- Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Rajesh Patidar
- Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA.,Molecular Characterization & Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Christine S Higham
- Children's National Medical Center, Washington, DC, USA.,Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Eva Dombi
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | | | | | - Hilde Brems
- Department of Human Genetics, Catholic University Leuven, Leuven, Belgium
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Rockville, Maryland, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, DCEG, NIH, Rockville, Maryland, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, DCEG, NIH, Rockville, Maryland, USA
| | - Jun S Wei
- Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | | | | | - James C Mullikin
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Rockville, Maryland, USA.,NISC, National Human Genome Research Institute, NIH, Rockville, Maryland, USA
| | - Margaret R Wallace
- Department of Molecular Genetics and Microbiology, UF Genetics Institute, UF Health Cancer Center, University of Florida, Gainesville, Florida, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Eric Legius
- Department of Human Genetics, Catholic University Leuven, Leuven, Belgium
| | - Brigitte C Widemann
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, DCEG, NCI, National Institutes of Health (NIH), Rockville, Maryland, USA
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22
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The OSMR Gene Is Involved in Hirschsprung Associated Enterocolitis Susceptibility through an Altered Downstream Signaling. Int J Mol Sci 2021; 22:ijms22083831. [PMID: 33917126 PMCID: PMC8067804 DOI: 10.3390/ijms22083831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 12/14/2022] Open
Abstract
Hirschsprung (HSCR) Associated Enterocolitis (HAEC) is a common life-threatening complication in HSCR. HAEC is suggested to be due to a loss of gut homeostasis caused by impairment of immune system, barrier defense, and microbiome, likely related to genetic causes. No gene has been claimed to contribute to HAEC occurrence, yet. Genetic investigation of HAEC by Whole-Exome Sequencing (WES) on 24 HSCR patients affected (HAEC) or not affected (HSCR-only) by enterocolitis and replication of results on a larger panel of patients allowed the identification of the HAEC susceptibility variant p.H187Q in the Oncostatin-M receptor (OSMR) gene (14.6% in HAEC and 5.1% in HSCR-only, p = 0.0024). Proteomic analysis on the lymphoblastoid cell lines from one HAEC patient homozygote for this variant and one HAEC patient not carrying the variant revealed two well distinct clusters of proteins significantly up or downregulated upon OSM stimulation. A marked enrichment in immune response pathways (q < 0.0001) was shown in the HAEC H187 cell line, while proteins upregulated in the HAEC Q187 lymphoblasts sustained pathways likely involved in pathogen infection and inflammation. In conclusion, OSMR p.H187Q is an HAEC susceptibility variant and perturbates the downstream signaling cascade necessary for the gut immune response and homeostasis maintenance.
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23
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Beversdorf DQ, Shah A, Jhin A, Noel-MacDonnell J, Hecht P, Ferguson BJ, Bruce D, Tilley M, Talebizadeh Z. microRNAs and Gene-Environment Interactions in Autism: Effects of Prenatal Maternal Stress and the SERT Gene on Maternal microRNA Expression. Front Psychiatry 2021; 12:668577. [PMID: 34290629 PMCID: PMC8288023 DOI: 10.3389/fpsyt.2021.668577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/24/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Genetics and environment both are critical in autism spectrum disorder (ASD), but their interaction (G × E) is less understood. Numerous studies have shown higher incidence of stress exposures during pregnancies with children later diagnosed with ASD. However, many stress-exposed mothers have unaffected children. The serotonin transporter (SERT) gene affects stress reactivity. Two independent samples have shown that the association between maternal stress exposure and ASD is greatest with maternal presence of the SERT short (S)-allele (deletion in the promoter region). MicroRNAs play a regulatory role in the serotonergic pathway and in prenatal stress and are therefore potential mechanistic targets in this setting. Design/methods: We profiled microRNA expression in blood from mothers of children with ASD, with known stress exposure during pregnancy. Samples were divided into groups based on SERT genotypes (LL/LS/SS) and prenatal stress level (high/low). Results: Two thousand five hundred mature microRNAs were examined. The ANOVA analysis showed differential expression (DE) of 119 microRNAs; 90 were DE in high- vs. low-stress groups (stress-dependent). Two (miR-1224-5p, miR-331-3p) were recently reported by our group to exhibit stress-dependent expression in rodent brain samples from embryos exposed to prenatal stress. Another, miR-145-5p, is associated with maternal stress. Across SERT genotypes, with high stress exposure, 20 significantly DE microRNAs were detected, five were stress-dependent. These microRNAs may be candidates for stress × SERT genotype interactions. This is remarkable as these changes were from mothers several years after stress-exposed pregnancies. Conclusions: Our study provides evidence for epigenetic alterations in relation to a G × E model (prenatal maternal stress × SERT gene) in ASD.
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Affiliation(s)
- David Q Beversdorf
- Departments of Radiology, Neurology, and Psychological Sciences, William and Nancy Thompson Endowed Chair in Radiology, University of Missouri, Columbia, MO, United States.,Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO, United States
| | - Ayten Shah
- Children's Mercy Hospital, Kansas City, MO, United States
| | - Allison Jhin
- Kansas City University, Kansas City, MO, United States
| | - Janelle Noel-MacDonnell
- Children's Mercy Hospital and University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
| | - Patrick Hecht
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO, United States
| | - Bradley J Ferguson
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO, United States.,Health Psychology, Radiology, and Thompson Center for Autism and Neurodevelopmental Disorders, University of Missouri, Columbia, MO, United States
| | - Danielle Bruce
- Department of Biology, Central Methodist University, Fayette, MO, United States
| | - Michael Tilley
- Department of Biology, Central Methodist University, Fayette, MO, United States
| | - Zohreh Talebizadeh
- Children's Mercy Hospital and University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
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24
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Borges MG, de Moraes HT, Rocha CDS, Lopes-Cendes I. The impact of post-alignment processing procedures on whole-exome sequencing data. Genet Mol Biol 2020; 43:e20200047. [PMID: 33306778 PMCID: PMC7783507 DOI: 10.1590/1678-4685-gmb-2020-0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 09/18/2020] [Indexed: 12/01/2022] Open
Abstract
The use of post-alignment procedures has been suggested to prevent the identification of false-positives in massive DNA sequencing data. Insertions and deletions are most likely to be misinterpreted by variant calling algorithms. Using known genetic variants as references for post-processing pipelines can minimize mismatches. They allow reads to be correctly realigned and recalibrated, resulting in more parsimonious variant calling. In this work, we aim to investigate the impact of using different sets of common variants as references to facilitate variant calling from whole-exome sequencing data. We selected reference variants from common insertions and deletions available within the 1K Genomes project data and from databases from the Latin American Database of Genetic Variation (LatinGen). We used the Genome Analysis Toolkit to perform post-processing procedures like local realignment, quality recalibration procedures, and variant calling in whole exome samples. We identified an increased number of variants from the call set for all groups when no post-processing procedure was performed. We found that there was a higher concordance rate between variants called using 1K Genomes and LatinGen. Therefore, we believe that the increased number of rare variants identified in the analysis without realignment or quality recalibration indicated that they were likely false-positives.
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Affiliation(s)
- Murilo Guimarães Borges
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências
Médicas, Departamento de Genética Médica e Medicina Genômica, Campinas, SP,
Brazil
- Instituto Brasileiro de Neurociência e Neurotecnologia (BRAINN),
Campinas, SP, Brazil
- Universidade Estadual de Campinas (UNICAMP), Centro de Engenharia
Biomédica. Campinas, SP, Brazil
| | - Helena Tadiello de Moraes
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências
Médicas, Departamento de Genética Médica e Medicina Genômica, Campinas, SP,
Brazil
- Instituto Brasileiro de Neurociência e Neurotecnologia (BRAINN),
Campinas, SP, Brazil
| | - Cristiane de Souza Rocha
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências
Médicas, Departamento de Genética Médica e Medicina Genômica, Campinas, SP,
Brazil
- Instituto Brasileiro de Neurociência e Neurotecnologia (BRAINN),
Campinas, SP, Brazil
| | - Iscia Lopes-Cendes
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências
Médicas, Departamento de Genética Médica e Medicina Genômica, Campinas, SP,
Brazil
- Instituto Brasileiro de Neurociência e Neurotecnologia (BRAINN),
Campinas, SP, Brazil
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25
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Geng Q, Lao J, Zuo X, Chen S, Bei JX, Xu D. Identification of the distinct genomic features in gastroesophageal junction adenocarcinoma and its Siewert subtypes. J Pathol 2020; 252:263-273. [PMID: 32715475 DOI: 10.1002/path.5516] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/15/2020] [Accepted: 07/21/2020] [Indexed: 12/21/2022]
Abstract
Rates of gastroesophageal junction adenocarcinomas (GEJAs) have shown an alarming increase; however, the genetic background of GEJA and its Siewert classification have yet to be uncovered. Here, 60 paired tumor and normal DNA samples from GEJA patients were analyzed by whole-exome sequencing. Among them, 13 were Siewert type I, 14 were type II, and 33 were type III. A predominance of C/G>T/A substitutions was discovered in GEJA, followed by C/G>A/T substitutions. Notably, Siewert type I and type II/III display distinct sets of driver genes, mutational spectrum, and recurrently disrupted pathways. Siewert type I showed similarity to esophageal adenocarcinomas (EACs) and the chromosomal instability subtype of stomach adenocarcinomas, while Siewert type II/III showed similarity to the genomic stable subtype of stomach adenocarcinoma. We also found that mutation of FBXW7, a driver gene of GEJA, was enriched in Siewert type I. Our data identify differences between GEJA and stomach/EACs at the genomic level and provide evidence for differential treatment based on Siewert classification of GEJA. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Qirong Geng
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Oncology, Shanghai Medical College, Fudan University, Dongan Road, Shanghai, PR China
| | - Jiawen Lao
- Department of Gastric Surgery, Sun Yat-sen University Cancer Center, Guangzhou, PR China.,Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Xiaoyu Zuo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Shangxiang Chen
- Department of Gastric Surgery, Sun Yat-sen University Cancer Center, Guangzhou, PR China.,Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Jin-Xin Bei
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Dazhi Xu
- Department of Oncology, Shanghai Medical College, Fudan University, Dongan Road, Shanghai, PR China.,Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, PR China
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26
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Robinson PN, Ravanmehr V, Jacobsen JOB, Danis D, Zhang XA, Carmody LC, Gargano MA, Thaxton CL, Karlebach G, Reese J, Holtgrewe M, Köhler S, McMurry JA, Haendel MA, Smedley D. Interpretable Clinical Genomics with a Likelihood Ratio Paradigm. Am J Hum Genet 2020; 107:403-417. [PMID: 32755546 PMCID: PMC7477017 DOI: 10.1016/j.ajhg.2020.06.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 06/26/2020] [Indexed: 10/23/2022] Open
Abstract
Human Phenotype Ontology (HPO)-based analysis has become standard for genomic diagnostics of rare diseases. Current algorithms use a variety of semantic and statistical approaches to prioritize the typically long lists of genes with candidate pathogenic variants. These algorithms do not provide robust estimates of the strength of the predictions beyond the placement in a ranked list, nor do they provide measures of how much any individual phenotypic observation has contributed to the prioritization result. However, given that the overall success rate of genomic diagnostics is only around 25%-50% or less in many cohorts, a good ranking cannot be taken to imply that the gene or disease at rank one is necessarily a good candidate. Here, we present an approach to genomic diagnostics that exploits the likelihood ratio (LR) framework to provide an estimate of (1) the posttest probability of candidate diagnoses, (2) the LR for each observed HPO phenotype, and (3) the predicted pathogenicity of observed genotypes. LIkelihood Ratio Interpretation of Clinical AbnormaLities (LIRICAL) placed the correct diagnosis within the first three ranks in 92.9% of 384 case reports comprising 262 Mendelian diseases, and the correct diagnosis had a mean posttest probability of 67.3%. Simulations show that LIRICAL is robust to many typically encountered forms of genomic and phenomic noise. In summary, LIRICAL provides accurate, clinically interpretable results for phenotype-driven genomic diagnostics.
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Affiliation(s)
- Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA.
| | - Vida Ravanmehr
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Julius O B Jacobsen
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Daniel Danis
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Leigh C Carmody
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Michael A Gargano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Courtney L Thaxton
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Guy Karlebach
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Justin Reese
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Manuel Holtgrewe
- Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Sebastian Köhler
- Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | | | | | - Damian Smedley
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
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27
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Pemov A, Dewan R, Hansen NF, Chandrasekharappa SC, Ray-Chaudhury A, Jones K, Luo W, Heiss JD, Mullikin JC, Chittiboina P, Stewart DR, Asthagiri AR. Comparative clinical and genomic analysis of neurofibromatosis type 2-associated cranial and spinal meningiomas. Sci Rep 2020; 10:12563. [PMID: 32724039 PMCID: PMC7387487 DOI: 10.1038/s41598-020-69074-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/19/2020] [Indexed: 12/31/2022] Open
Abstract
Neurofibromatosis type 2 (NF2) is an autosomal dominant Mendelian tumor predisposition disorder caused by germline pathogenic variants in the tumor suppressor NF2. Meningiomas are the second most common neoplasm in NF2, often occurring in multiple intracranial and spinal locations within the same patient. In this prospective longitudinal study, we assessed volumes and growth rates of ten spinal and ten cranial benign meningiomas in seven NF2 patients that concluded with surgical resection and performed whole-exome sequencing and copy-number variant (CNV) analysis of the tumors. Our comparison of the volume and the growth rate of NF2-associated spinal and cranial meningiomas point to the differences in timing of tumor initiation and/or to the differences in tumor progression (e.g., non-linear, saltatory growth) at these two anatomical locations. Genomic investigation of these tumors revealed that somatic inactivation of NF2 is the principal and perhaps the only driver of tumor initiation; and that tumor progression likely occurs via accumulation of CNVs, rather than point mutations. Results of this study contribute to a better understanding of NF2-associated meningiomas clinical behavior and their genetic underpinnings.
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Affiliation(s)
- Alexander Pemov
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Ramita Dewan
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA.,Neuromuscular Disease Research Section, National Institute On Aging, NIH, Bethesda, MD, USA
| | - Nancy F Hansen
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Abhik Ray-Chaudhury
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Kristine Jones
- Frederick National Laboratory for Cancer Research, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Wen Luo
- Frederick National Laboratory for Cancer Research, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - John D Heiss
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - James C Mullikin
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA.,NIH Intramural Sequencing Center, National Human Genome Research Institute, NIH, Rockville, MD, USA
| | - Prashant Chittiboina
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA.
| | - Ashok R Asthagiri
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA. .,Department of Neurological Surgery, University of Virginia School of Medicine, Charlottesville, VA, USA.
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28
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Whole-exome sequencing in multiplex preeclampsia families identifies novel candidate susceptibility genes. J Hypertens 2020; 37:997-1011. [PMID: 30633125 DOI: 10.1097/hjh.0000000000002023] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Preeclampsia is a common and serious heritable disorder of human pregnancy. Although there have been notable successes in identification of maternal susceptibility genes a large proportion of the heritability of preeclampsia remains unaccounted for. It is has been postulated that rare variation may account for some of this missing heritability. In this study, we performed whole-exome sequencing (WES) in multiplex families to identify rare exonic risk variants. METHODS We conducted WES in 244 individuals from 34 Australian/New Zealand multiplex preeclampsia families. Variants were tested for association with preeclampsia using a threshold model and logistic regression. RESULTS We found significant association for two moderately rare missense variants, rs145743393 (Padj = 0.0032, minor allele frequency = 0.016) in the chromosome 1 open reading frame 35 (C1orf35) gene, and rs34270076 (Padj = 0.0128, minor allele frequency = 0.024) in the pyroglutamylated RFamide peptide receptor (QRFPR) gene. To replicate these associations we performed imputation in our Australian genome wide association scan for preeclampsia and found no significant exonic variants in either C1orf35 or QRFPR. However, 11 variants demonstrating nominal significance (P < 0.05) in the genomic region between QRFPR and annexin A5 (ANXA5) were identified. We further leveraged publicly available genome-wide available summary data from the UK Biobank to investigate association of these two variants with the underlying clinical phenotypes of preeclampsia and detected nominal association of the QRFPR variant (rs34270076, P = 0.03) with protein levels in females. CONCLUSION The study represents the first to use WES in multiplex families for preeclampsia and identifies two novel genes (QRFPR and C1orf35) not previously associated with preeclampsia and find nominal association of rs34270076 with protein levels, a key clinical feature of preeclampsia. We find further support for ANXA5 previously associated with pregnancy complications, including preeclampsia.
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29
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Yang L, Zhang X, MacKay M, Foox J, Hou Q, Zheng X, Zhou R, Huang M, Jing Z, Mason CE, Wu S. Identification of Radioresponsive Genes in Esophageal Cancer from Longitudinal and Single Cell Exome Sequencing. Int J Radiat Oncol Biol Phys 2020; 108:1103-1114. [PMID: 32561500 DOI: 10.1016/j.ijrobp.2020.06.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 05/02/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE The majority (70%) of the esophageal squamous cell carcinoma (ESCC) cases in the world occur in China, where radiation therapy is the most common treatment. Yet the majority of ESCC patients still relapse. METHODS AND MATERIALS To better understand the genetic basis of radiation therapy resistance for ESCC, we performed longitudinal, whole-exome sequencing throughout radiation therapy on 42 patient tumor samples, including single-cell whole-exome sequencing for 147 cells for 2 patients. RESULTS Significant allelic changes were observed during clinical irradiation, with 42 recurrent radioresponsive genes (sensitive and resistant) identified in multiple patients, including NOTCH1, MAML3, CDKN2A, NFE2L2, GAS2L2, OBSCN and TP53, with the last 3 genes implicated as radioresponsive in both bulk and single-cell whole-exome sequencing. Most (37/42) radioresponsive genes showed regional variegation in both radioresistant and radiosensitive mutations, with a paucity of resistant-only mutations (2.5%). A subset of sensitive mutations in 10 genes and resistant mutations in 18 genes defined a significantly improved prognosis and the shortest time for locoregional recurrence, respectively, indicating possible clinical utility. We also confirmed these significant mutational signatures in orthogonal Cancer Genome Atlas ESCC cohorts. CONCLUSIONS Overall, our results quantify the allelic shifts underlying radioresponse in bulk and single-cell ESCC exomes for the first time, provide a temporal resolution to such mutational dynamics, and offer new therapeutic target genes and loci for esophageal and potentially other cancers.
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Affiliation(s)
- Ling Yang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Xiaoyan Zhang
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Qiang Hou
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
| | - Xiaoli Zheng
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
| | - Rongjing Zhou
- Department of Pathology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Ming Huang
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
| | - Zhao Jing
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China; Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York; The Feil Family Brain and Mind Research Institute (BMRI), New York, New York
| | - Shixiu Wu
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.
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30
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Muyas F, Zapata L, Guigó R, Ossowski S. The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues. Genome Med 2020; 12:49. [PMID: 32460841 PMCID: PMC7254727 DOI: 10.1186/s13073-020-00746-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/08/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Mosaic mutations acquired during early embryogenesis can lead to severe early-onset genetic disorders and cancer predisposition, but are often undetectable in blood samples. The rate and mutational spectrum of embryonic mosaic mutations (EMMs) have only been studied in few tissues, and their contribution to genetic disorders is unknown. Therefore, we investigated how frequent mosaic mutations occur during embryogenesis across all germ layers and tissues. METHODS Mosaic mutation detection in 49 normal tissues from 570 individuals (Genotype-Tissue Expression (GTEx) cohort) was performed using a newly developed multi-tissue, multi-individual variant calling approach for RNA-seq data. Our method allows for reliable identification of EMMs and the developmental stage during which they appeared. RESULTS The analysis of EMMs in 570 individuals revealed that newborns on average harbor 0.5-1 EMMs in the exome affecting multiple organs (1.3230 × 10-8 per nucleotide per individual), a similar frequency as reported for germline de novo mutations. Our multi-tissue, multi-individual study design allowed us to distinguish mosaic mutations acquired during different stages of embryogenesis and adult life, as well as to provide insights into the rate and spectrum of mosaic mutations. We observed that EMMs are dominated by a mutational signature associated with spontaneous deamination of methylated cytosines and the number of cell divisions. After birth, cells continue to accumulate somatic mutations, which can lead to the development of cancer. Investigation of the mutational spectrum of the gastrointestinal tract revealed a mutational pattern associated with the food-borne carcinogen aflatoxin, a signature that has so far only been reported in liver cancer. CONCLUSIONS In summary, our multi-tissue, multi-individual study reveals a surprisingly high number of embryonic mosaic mutations in coding regions, implying novel hypotheses and diagnostic procedures for investigating genetic causes of disease and cancer predisposition.
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Affiliation(s)
- Francesc Muyas
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Luis Zapata
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Roderic Guigó
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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31
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Macnamara EF, D’Souza P, Tifft CJ. The undiagnosed diseases program: Approach to diagnosis. TRANSLATIONAL SCIENCE OF RARE DISEASES 2020; 4:179-188. [PMID: 32477883 PMCID: PMC7250153 DOI: 10.3233/trd-190045] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Undiagnosed and rare conditions are collectively common and affect millions of people worldwide. The NIH Undiagnosed Diseases Program (UDP) strives to achieve both a comprehensive diagnosis and a better understanding of the mechanisms of disease for many of these individuals. Through the careful review of records, a well-orchestrated inpatient evaluation, genomic sequencing and testing, and with the use of emerging strategies such as matchmaking programs, the UDP succeeds nearly 30 percent of the time for these highly selective cases. Although the UDP process is built on a unique set of resources, case examples demonstrate steps genetic professionals can take, in both clinical and research settings, to arrive at a diagnosis for their most challenging cases.
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Affiliation(s)
- Ellen F. Macnamara
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
| | - Precilla D’Souza
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
| | - Undiagnosed Diseases Network
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J. Tifft
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Neuropathology-driven Whole-genome Sequencing Study Points to Novel Candidate Genes for Healthy Brain Aging. Alzheimer Dis Assoc Disord 2020; 33:7-14. [PMID: 30681437 DOI: 10.1097/wad.0000000000000294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE Understanding the healthy brain aging process is key to uncover the mechanisms that lead to pathologic age-related neurodegeneration, including progression to Alzheimer disease (AD). We aimed to address the issue of pathologic heterogeneity that often underlies a clinical AD diagnosis. METHODS We performed a deep whole-genome sequencing study aiming to identify variants that are associated specifically with healthy brain aging. PATIENTS We examined samples from the community-based longitudinal Vienna Transdanubian Aging study comparing neuropathologically "healthy" aging in individuals above 80 years of age with pure AD patients of the same age. RESULTS Focusing on potentially functional variants, we discovered a single variant (rs10149146) that lies on the autophagy-associated TECPR2 gene and was carried by 53.6% of the "healthy" brain elderly individuals (15/28). An additional nonsynonymous variant on the CINP gene (encoding a cell cycle checkpoint protein) was also found in 46% of healthy controls. Both variants are absent from all AD cases. TECPR2 and CINP appear to be "partner" genes in terms of regulation and their associated transcription factors have been previously implicated in AD and neurodegeneration. CONCLUSIONS Our study underlines the strength of neuropathology-driven definitions in genetic association studies and points to a potentially neuroprotective effect of key molecules of autophagy and cell cycle control.
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Genetic diagnosis of autoinflammatory disease patients using clinical exome sequencing. Eur J Med Genet 2020; 63:103920. [PMID: 32222431 DOI: 10.1016/j.ejmg.2020.103920] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/13/2020] [Accepted: 03/21/2020] [Indexed: 11/22/2022]
Abstract
Autoinflammatory diseases comprise a wide range of syndromes caused by dysregulation of the innate immune response. They are difficult to diagnose due to their phenotypic heterogeneity and variable expressivity. Thus, the genetic origin of the disease remains undetermined for an important proportion of patients. We aim to identify causal genetic variants in patients with suspected autoinflammatory disease and to test the advantages and limitations of the clinical exome gene panels for molecular diagnosis. Twenty-two unrelated patients with clinical features of autoinflammatory diseases were analyzed using clinical exome sequencing (~4800 genes), followed by bioinformatic analyses to detect likely pathogenic variants. By integrating genetic and clinical information, we found a likely causative heterozygous genetic variant in NFKBIA (p.D31N) in a North-African patient with a clinical picture resembling the deficiency of interleukin-1 receptor antagonist, and a heterozygous variant in DNASE2 (p.G322D) in a Spanish patient with a suspected lupus-like monogenic disorder. We also found variants likely to increase the susceptibility to autoinflammatory diseases in three additional Spanish patients: one with an initial diagnosis of juvenile idiopathic arthritis who carries two heterozygous UNC13D variants (p.R727Q and p.A59T), and two with early-onset inflammatory bowel disease harbouring NOD2 variants (p.L221R and p.A728V respectively). Our results show a similar proportion of molecular diagnosis to other studies using whole exome or targeted resequencing in primary immunodeficiencies. Thus, despite its main limitation of not including all candidate genes, clinical exome targeted sequencing can be an appropriate approach to detect likely causative variants in autoinflammatory diseases.
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Multiple rare inherited variants in a four generation schizophrenia family offer leads for complex mode of disease inheritance. Schizophr Res 2020; 216:288-294. [PMID: 31813803 PMCID: PMC8958857 DOI: 10.1016/j.schres.2019.11.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/23/2019] [Accepted: 11/24/2019] [Indexed: 02/01/2023]
Abstract
Schizophrenia is a clinically and genetically heterogeneous neuropsychiatric disorder, with a polygenic basis but identification of the specific determinants is a continuing challenge. In this study, we analyzed a multigenerational family, with all healthy individuals in the first two generations, and four progeny affected with schizophrenia in the subsequent two generations, using whole exome sequencing. We identified five rare protein sequence altering heterozygous variants, in five different genes namely SMARCA5, PDE1B, TNIK, SMARCA2 and FLRT shared among all affected members and predicted to be damaging. Variants in SMARCA5 and PDE1B were inherited from the unaffected father whereas variants in TNIK, SMARCA2 and FLRT1 were inherited from the unaffected mother in all the three affected individuals in the third generation; and notably all these five variants were transmitted by an affected mother to her affected son. Microsatellite based analysis lent a modest linkage support (LOD score of 1.2; θ=0.0 at each variant). Of note, analysis of exome data of an ancestry matched unrelated schizophrenia cohort (n = 350), revealed a total of 16 rare variants (MAF < 0.01) in these five genes. Interestingly, these five genes involved in neurodevelopmental and/or neurotransmitter signaling processes are implicated in the etiology of schizophrenia previously. This study provides good evidence for a likely cumulative contribution of multiple rare variants from disease relevant genes with a threshold effect in disease development and seems to explain the unusual disease transmission pattern generally witnessed in such conditions, but warrants extensive replication efforts in families with similar complex disease inheritance profiles.
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Genome-wide significant regions in 43 Utah high-risk families implicate multiple genes involved in risk for completed suicide. Mol Psychiatry 2020; 25:3077-3090. [PMID: 30353169 PMCID: PMC6478563 DOI: 10.1038/s41380-018-0282-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/31/2018] [Accepted: 09/26/2018] [Indexed: 12/31/2022]
Abstract
Suicide is the 10th leading cause of death in the United States. Although environment has undeniable impact, evidence suggests that genetic factors play a significant role in completed suicide. We linked a resource of ~ 4500 DNA samples from completed suicides obtained from the Utah Medical Examiner to genealogical records and medical records data available on over eight million individuals. This linking has resulted in the identification of high-risk extended families (7-9 generations) with significant familial risk of completed suicide. Familial aggregation across distant relatives minimizes effects of shared environment, provides more genetically homogeneous risk groups, and magnifies genetic risks through familial repetition. We analyzed Illumina PsychArray genotypes from suicide cases in 43 high-risk families, identifying 30 distinct shared genomic segments with genome-wide evidence (p = 2.02E-07-1.30E-18) of segregation with completed suicide. The 207 genes implicated by the shared regions provide a focused set of genes for further study; 18 have been previously associated with suicide risk. Although PsychArray variants do not represent exhaustive variation within the 207 genes, we investigated these for specific segregation within the high-risk families, and for association of variants with predicted functional impact in ~ 1300 additional Utah suicides unrelated to the discovery families. None of the limited PsychArray variants explained the high-risk family segregation; sequencing of these regions will be needed to discover segregating risk variants, which may be rarer or regulatory. However, additional association tests yielded four significant PsychArray variants (SP110, rs181058279; AGBL2, rs76215382; SUCLA2, rs121908538; APH1B, rs745918508), raising the likelihood that these genes confer risk of completed suicide.
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36
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George JW, Fan H, Johnson B, Carpenter TJ, Foy KK, Chatterjee A, Patterson AL, Koeman J, Adams M, Madaj ZB, Chesla D, Marsh EE, Triche TJ, Shen H, Teixeira JM. Integrated Epigenome, Exome, and Transcriptome Analyses Reveal Molecular Subtypes and Homeotic Transformation in Uterine Fibroids. Cell Rep 2019; 29:4069-4085.e6. [PMID: 31851934 PMCID: PMC6956710 DOI: 10.1016/j.celrep.2019.11.077] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 09/20/2019] [Accepted: 11/19/2019] [Indexed: 11/29/2022] Open
Abstract
Uterine fibroids are benign myometrial smooth muscle tumors of unknown etiology that, when symptomatic, are the most common indication for hysterectomy in the United States. Unsupervised clustering of results from DNA methylation analyses segregates normal myometrium from fibroids and further segregates the fibroids into subtypes characterized by MED12 mutation or activation of either HMGA2 or HMGA1 expression. Upregulation of HMGA2 expression does not always appear to be dependent on translocation but is associated with hypomethylation in the HMGA2 gene body. HOXA13 expression is upregulated in fibroids and correlates with expression of typical uterine fibroid genes. Significant overlap of differentially expressed genes is observed between cervical stroma and uterine fibroids compared with normal myometrium. These analyses show a possible role of DNA methylation in fibroid biology and suggest that homeotic transformation of myometrial cells to a more cervical stroma phenotype could be an important mechanism for etiology of the disease.
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Affiliation(s)
- Jitu Wilson George
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Huihui Fan
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Benjamin Johnson
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Tyler James Carpenter
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | | | - Anindita Chatterjee
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Amanda Lynn Patterson
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA; Division of Animal Sciences, Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO, USA
| | - Julie Koeman
- Genomics Core, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Marie Adams
- Genomics Core, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Zachary Brian Madaj
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, MI, USA
| | - David Chesla
- Spectrum Health Universal Biorepository, Spectrum Health System, Grand Rapids, MI, USA
| | - Erica Elizabeth Marsh
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA.
| | - Jose Manuel Teixeira
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA.
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Hartmann L, Nadarajah N, Meggendorfer M, Höllein A, Vetro C, Kern W, Haferlach T, Haferlach C, Stengel A. Molecular characterization of a second myeloid neoplasm developing after treatment for acute myeloid leukemia. Leukemia 2019; 34:811-820. [PMID: 31719678 DOI: 10.1038/s41375-019-0633-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/28/2019] [Indexed: 11/09/2022]
Abstract
Therapy-related myeloid neoplasms (tMN) following successful treatment of acute myeloid leukemia (AML) are rare and poorly characterized. To evaluate the presence of a common ancestral clone, we performed whole-exome sequencing of 25 patients at AML diagnosis, tMN diagnosis (tMDS: 13; tAML: 12), and matched remission samples, identifying 607 mutations affecting 504 different genes (46 recurrently mutated). Number of mutations was higher in tAML vs. tMDS cases (median 19 vs 13 mutations, p = 0.05). Focusing on 24 genes commonly mutated in hematological malignancies, 19/25 (76%) patients were found to share mutations between AML and tMN, mostly affecting epigenetic modifiers (21/32; 66%), splicing factors (6/32; 19%), and chromatin modifiers (3/32; 9%). Analysis of remission samples identified 13 persisting mutations in 10/22 patients, affecting DNMT3A (n = 6), TET2 (n = 5), IDH1 and SRSF2 (n = 1, each). Comparison of cytogenetics revealed that 9/12 patients with a normal karyotype (NK) in AML harbored aberrations in tMN, four aberrant AML cases presented with NK in tMN, four other patients showed unrelated cytogenetic aberrations. Our study provides novel insights into the pathogenesis of tMN, hypothesizing the presence of a common ancestral clone in AML and tMN. Mutations mostly affected epigenetic modifiers, which have previously been linked to clonal hematopoiesis.
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Affiliation(s)
- Luise Hartmann
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Niroshan Nadarajah
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Alexander Höllein
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Calogero Vetro
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Anna Stengel
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
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38
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Wang M, Chun J, Genovese G, Knob AU, Benjamin A, Wilkins MS, Friedman DJ, Appel GB, Lifton RP, Mane S, Pollak MR. Contributions of Rare Gene Variants to Familial and Sporadic FSGS. J Am Soc Nephrol 2019; 30:1625-1640. [PMID: 31308072 PMCID: PMC6727251 DOI: 10.1681/asn.2019020152] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/25/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Over the past two decades, the importance of genetic factors in the development of FSGS has become increasingly clear. However, despite many known monogenic causes of FSGS, single gene defects explain only 30% of cases. METHODS To investigate mutations underlying FSGS, we sequenced 662 whole exomes from individuals with sporadic or familial FSGS. After quality control, we analyzed the exome data from 363 unrelated family units with sporadic or familial FSGS and compared this to data from 363 ancestry-matched controls. We used rare variant burden tests to evaluate known disease-associated genes and potential new genes. RESULTS We validated several FSGS-associated genes that show a marked enrichment of deleterious rare variants among the cases. However, for some genes previously reported as FSGS related, we identified rare variants at similar or higher frequencies in controls. After excluding such genes, 122 of 363 cases (33.6%) had rare variants in known disease-associated genes, but 30 of 363 controls (8.3%) also harbored rare variants that would be classified as "causal" if detected in cases; applying American College of Medical Genetics filtering guidelines (to reduce the rate of false-positive claims that a variant is disease related) yielded rates of 24.2% in cases and 5.5% in controls. Highly ranked new genes include SCAF1, SETD2, and LY9. Network analysis showed that top-ranked new genes were located closer than a random set of genes to known FSGS genes. CONCLUSIONS Although our analysis validated many known FSGS-causing genes, we detected a nontrivial number of purported "disease-causing" variants in controls, implying that filtering is inadequate to allow clinical diagnosis and decision making. Genetic diagnosis in patients with FSGS is complicated by the nontrivial rate of variants in known FSGS genes among people without kidney disease.
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Affiliation(s)
- Minxian Wang
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Justin Chun
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Division of Nephrology, Department of Medicine, University of Calgary, Cumming School of Medicine, Calgary, Alberta, Canada
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Andrea U Knob
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Ava Benjamin
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Maris S Wilkins
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - David J Friedman
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Gerald B Appel
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York; and
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | - Martin R Pollak
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts;
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
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39
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Golyan FF, Druley TE, Abbaszadegan MR. Whole-exome sequencing of familial esophageal squamous cell carcinoma identified rare pathogenic variants in new predisposition genes. Clin Transl Oncol 2019; 22:681-693. [PMID: 31321674 DOI: 10.1007/s12094-019-02174-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/28/2019] [Indexed: 11/26/2022]
Abstract
PURPOSE Esophageal squamous cell carcinoma (ESCC) is one of the most important causes of mortality in the developing world. Although hereditary forms arise from germ-line mutations in TP53, Rb, and the mismatch repair genes, many familial cases present with an unknown inherited cause. The new theory of rare, high-penetrance mutations in less known genes is a likely explanation for the underlying predisposition in some of these familial cases. METHODS Exome sequencing was performed in 9 patients with esophageal squamous cancer from 9 families with strong disease aggregation without mutations in known hereditary esophageal cancer genes. Data analysis was limited to only really rare variants (0-0.01%), producing a putative loss of function and located in genes with a role compatible with carcinogenesis. RESULTS Twenty-two final candidate variants were selected and validated by Sanger sequencing. Correct family segregation and somatic studies were used to categorize the most interesting variants in CDK11A, ARID1A, JMJD6, MAML3, CDKN2AIP, and PHLDA1. CONCLUSION Together, we identified new potential esophageal squamous cancer predisposition variants in genes which may have a role in cancer and are involved in chromatin remodeling and cell-cycle pathway, which could increase the risk of ESCC.
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Affiliation(s)
- F F Golyan
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - T E Druley
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - M R Abbaszadegan
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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40
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Field MA, Burgio G, Chuah A, Al Shekaili J, Hassan B, Al Sukaiti N, Foote SJ, Cook MC, Andrews TD. Recurrent miscalling of missense variation from short-read genome sequence data. BMC Genomics 2019; 20:546. [PMID: 31307400 PMCID: PMC6631443 DOI: 10.1186/s12864-019-5863-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Short-read resequencing of genomes produces abundant information of the genetic variation of individuals. Due to their numerous nature, these variants are rarely exhaustively validated. Furthermore, low levels of undetected variant miscalling will have a systematic and disproportionate impact on the interpretation of individual genome sequence information, especially should these also be carried through into in reference databases of genomic variation. RESULTS We find that sequence variation from short-read sequence data is subject to recurrent-yet-intermittent miscalling that occurs in a sequence intrinsic manner and is very sensitive to sequence read length. The miscalls arise from difficulties aligning short reads to redundant genomic regions, where the rate of sequencing error approaches the sequence diversity between redundant regions. We find the resultant miscalled variants to be sensitive to small sequence variations between genomes, and thereby are often intrinsic to an individual, pedigree, strain or human ethnic group. In human exome sequences, we identify 2-300 recurrent false positive variants per individual, almost all of which are present in public databases of human genomic variation. From the exomes of non-reference strains of inbred mice, we identify 3-5000 recurrent false positive variants per mouse - the number of which increasing with greater distance between an individual mouse strain and the reference C57BL6 mouse genome. We show that recurrently miscalled variants may be reproduced for a given genome from repeated simulation rounds of read resampling, realignment and recalling. As such, it is possible to identify more than two-thirds of false positive variation from only ten rounds of simulation. CONCLUSION Identification and removal of recurrent false positive variants from specific individual variant sets will improve overall data quality. Variant miscalls arising are highly sequence intrinsic and are often specific to an individual, pedigree or ethnicity. Further, read length is a strong determinant of whether given false variants will be called for any given genome - which has profound significance for cohort studies that pool datasets collected and sequenced at different points in time.
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Affiliation(s)
- Matthew A Field
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
- Australian Institute of Tropical Health and Medicine, Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia
| | - Gaetan Burgio
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Aaron Chuah
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jalila Al Shekaili
- Department of Microbiology and Immunology, Sultan Qaboos University Hospital, Seeb, Oman
| | - Batool Hassan
- Department of Medicine, Sultan Qaboos University Hospital, Muscat, Oman
| | - Nashat Al Sukaiti
- Department of Paediatrics, Allergy, and Clinical Immunology Unit, Royal Hospital, Muscat, Oman
| | - Simon J Foote
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Matthew C Cook
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
- Department of Immunology, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - T Daniel Andrews
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.
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41
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John J, Kukshal P, Sharma A, Bhatia T, Nimgaonkar VL, Deshpande SN, Thelma BK. Rare variants in Protein tyrosine phosphatase, receptor type A (PTPRA) in schizophrenia: Evidence from a family based study. Schizophr Res 2019; 206:75-81. [PMID: 30594456 PMCID: PMC7321970 DOI: 10.1016/j.schres.2018.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/25/2018] [Accepted: 12/08/2018] [Indexed: 12/23/2022]
Abstract
The contribution of both common and rare risk variants to the genetic architecture of schizophrenia (SZ) has been documented in genome-wide association studies, whole exome and whole genome sequencing approaches. As SZ is highly heritable and segregates in families, highly penetrant rare variants are more likely to be identified through analyses of multiply affected families. Further, much of the gene mapping studies in SZ have utilized individuals of Caucasian ancestry. Analysis of other ethnic groups may be informative. In this study, we aimed at identification of rare, penetrant risk variants utilizing whole exome sequencing (WES) in a three-generation Indian family with multiple members affected. Filtered data from WES, combined with in silico analyses revealed a novel heterozygous missense variant (NM_080841:c.1730C>G:p.T577R; exon18) in Protein tyrosine phosphatase, receptor type A (PTPRA 20p13). The variant was located in an evolutionarily conserved position and predicted to be damaging. Screening for variants in this gene in the WES data of an independent SZ cohort (n = 350) of matched ethnicity, identified five additional rare missense variants with MAF < 0.003, which were also predicted to be damaging. In conclusion, the rare missense variants in PTPRA identified in this study could confer risk for SZ. This has also derived support from concordant data from prior linkage and association, as well as animal studies which indicated a role for PTPRA in glutamate function.
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Affiliation(s)
- Jibin John
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Prachi Kukshal
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Aditya Sharma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Triptish Bhatia
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - V L Nimgaonkar
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, 3811 O'Hara Street, Pittsburgh, PA 15213, USA; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, DeSoto St, Pittsburgh, PA 15213, USA
| | - S N Deshpande
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India.
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42
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Integrated Somatic and Germline Whole-Exome Sequencing Analysis in Women with Lung Cancer after a Previous Breast Cancer. Cancers (Basel) 2019; 11:cancers11040441. [PMID: 30925779 PMCID: PMC6520745 DOI: 10.3390/cancers11040441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/12/2019] [Accepted: 03/25/2019] [Indexed: 12/11/2022] Open
Abstract
Women treated for breast cancer (BC) are at risk of developing secondary tumors, such as lung cancer (LC). Since rare germline variants have been linked to multiple cancer development, we hypothesized that BC survivors might be prone to develop LC as a result of harboring rare variants. Sixty patients with LC with previous BC (the study population; SP) and 53 women with either BC or LC and no secondary cancer (control population; CP) were enrolled. Whole exome sequencing was performed in both tumors and unaffected tissues from 28/60 SP patients, and in germline DNA from 32/53 CP. Candidate genes were validated in the remaining individuals from both populations. We found two main mutational signature profiles: S1 (C>T) in all BCs and 16/28 LCs, and S2 (C>A) which is strongly associated with smoking, in 12/28 LCs. The burden test over rare germline variants in S1-LC vs CP identified 248 genes. Validation confirmed GSN as significantly associated with LC in never-smokers. In conclusion, our data suggest two signatures involved in LC onset in women with previous BC. One of these signatures is linked to smoking. Conversely, regardless of smoking habit, in a subgroup of BC survivors genetic susceptibility may contribute to LC risk.
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43
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Asgari S, Chaturvedi N, Scepanovic P, Hammer C, Semmo N, Giostra E, Müllhaupt B, Angus P, Thompson AJ, Moradpour D, Fellay J. Human genomics of acute liver failure due to hepatitis B virus infection: An exome sequencing study in liver transplant recipients. J Viral Hepat 2019; 26:271-277. [PMID: 30315682 DOI: 10.1111/jvh.13019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 09/05/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022]
Abstract
Acute liver failure (ALF) or fulminant hepatitis is a rare, yet severe outcome of infection with hepatitis B virus (HBV) that carries a high mortality rate. The occurrence of a life-threatening condition upon infection with a prevalent virus in individuals without known risk factors is suggestive of pathogen-specific immune dysregulation. In the absence of established differences in HBV virulence, we hypothesized that ALF upon primary infection with HBV could be due to rare deleterious variants in the human genome. To search for such variants, we performed exome sequencing in 21 previously healthy adults who required liver transplantation upon fulminant HBV infection and 172 controls that were positive for anti-HBc and anti-HBs but had no clinical history of jaundice or liver disease. After a series of hypothesis-driven filtering steps, we searched for putatively pathogenic variants that were significantly associated with case-control status. We did not find any causal variant or gene, a result that does not support the hypothesis of a shared monogenic basis for human susceptibility to HBV-related ALF in adults. This study represents a first attempt at deciphering the human genetic contribution to the most severe clinical presentation of acute HBV infection in previously healthy individuals.
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Affiliation(s)
- Samira Asgari
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nimisha Chaturvedi
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Petar Scepanovic
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christian Hammer
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nasser Semmo
- Department for BioMedical Research, Hepatology, University of Bern, Bern, Switzerland
| | - Emiliano Giostra
- Department of Gastroenterology and Hepatology, Geneva University Hospital, Geneva, Switzerland
| | - Beat Müllhaupt
- Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland
| | - Peter Angus
- Gastroenterology and Hepatology Department, Austin Health and the University of Melbourne, Melbourne, Victoria, Australia
| | - Alexander J Thompson
- Department of Gastroenterology, St Vincent's Hospital, University of Melbourne, Melbourne, Australia
| | - Darius Moradpour
- Service of Gastroenterology and Hepatology, Lausanne University Hospital, Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital, Lausanne, Switzerland
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44
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Geier EG, Bourdenx M, Storm NJ, Cochran JN, Sirkis DW, Hwang JH, Bonham LW, Ramos EM, Diaz A, Van Berlo V, Dokuru D, Nana AL, Karydas A, Balestra ME, Huang Y, Russo SP, Spina S, Grinberg LT, Seeley WW, Myers RM, Miller BL, Coppola G, Lee SE, Cuervo AM, Yokoyama JS. Rare variants in the neuronal ceroid lipofuscinosis gene MFSD8 are candidate risk factors for frontotemporal dementia. Acta Neuropathol 2019; 137:71-88. [PMID: 30382371 PMCID: PMC6371791 DOI: 10.1007/s00401-018-1925-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022]
Abstract
Pathogenic variation in MAPT, GRN, and C9ORF72 accounts for at most only half of frontotemporal lobar degeneration (FTLD) cases with a family history of neurological disease. This suggests additional variants and genes that remain to be identified as risk factors for FTLD. We conducted a case-control genetic association study comparing pathologically diagnosed FTLD patients (n = 94) to cognitively normal older adults (n = 3541), and found suggestive evidence that gene-wide aggregate rare variant burden in MFSD8 is associated with FTLD risk. Because homozygous mutations in MFSD8 cause neuronal ceroid lipofuscinosis (NCL), similar to homozygous mutations in GRN, we assessed rare variants in MFSD8 for relevance to FTLD through experimental follow-up studies. Using post-mortem tissue from middle frontal gyrus of patients with FTLD and controls, we identified increased MFSD8 protein levels in MFSD8 rare variant carriers relative to non-variant carrier patients with sporadic FTLD and healthy controls. We also observed an increase in lysosomal and autophagy-related proteins in MFSD8 rare variant carrier and sporadic FTLD patients relative to controls. Immunohistochemical analysis revealed that MFSD8 was expressed in neurons and astrocytes across subjects, without clear evidence of abnormal localization in patients. Finally, in vitro studies identified marked disruption of lysosomal function in cells from MFSD8 rare variant carriers, and identified one rare variant that significantly increased the cell surface levels of MFSD8. Considering the growing evidence for altered autophagy in the pathogenesis of neurodegenerative disorders, our findings support a role of NCL genes in FTLD risk and suggest that MFSD8-associated lysosomal dysfunction may contribute to FTLD pathology.
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Affiliation(s)
- Ethan G Geier
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
| | - Mathieu Bourdenx
- Department of Development and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Nadia J Storm
- Department of Development and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | | | - Daniel W Sirkis
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Ji-Hye Hwang
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Luke W Bonham
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
| | - Eliana Marisa Ramos
- Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, The David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Antonio Diaz
- Department of Development and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Victoria Van Berlo
- Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, The David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Deepika Dokuru
- Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, The David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Alissa L Nana
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
| | - Anna Karydas
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
| | | | - Yadong Huang
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Silvia P Russo
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
| | - Salvatore Spina
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Lea T Grinberg
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - William W Seeley
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Bruce L Miller
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
| | - Giovanni Coppola
- Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, The David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Suzee E Lee
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
| | - Ana Maria Cuervo
- Department of Development and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Jennifer S Yokoyama
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA.
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Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis. Proc Natl Acad Sci U S A 2018; 116:950-959. [PMID: 30591557 DOI: 10.1073/pnas.1808403116] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Computational analyses of human patient exomes aim to filter out as many nonpathogenic genetic variants (NPVs) as possible, without removing the true disease-causing mutations. This involves comparing the patient's exome with public databases to remove reported variants inconsistent with disease prevalence, mode of inheritance, or clinical penetrance. However, variants frequent in a given exome cohort, but absent or rare in public databases, have also been reported and treated as NPVs, without rigorous exploration. We report the generation of a blacklist of variants frequent within an in-house cohort of 3,104 exomes. This blacklist did not remove known pathogenic mutations from the exomes of 129 patients and decreased the number of NPVs remaining in the 3,104 individual exomes by a median of 62%. We validated this approach by testing three other independent cohorts of 400, 902, and 3,869 exomes. The blacklist generated from any given cohort removed a substantial proportion of NPVs (11-65%). We analyzed the blacklisted variants computationally and experimentally. Most of the blacklisted variants corresponded to false signals generated by incomplete reference genome assembly, location in low-complexity regions, bioinformatic misprocessing, or limitations inherent to cohort-specific private alleles (e.g., due to sequencing kits, and genetic ancestries). Finally, we provide our precalculated blacklists, together with ReFiNE, a program for generating customized blacklists from any medium-sized or large in-house cohort of exome (or other next-generation sequencing) data via a user-friendly public web server. This work demonstrates the power of extracting variant blacklists from private databases as a specific in-house but broadly applicable tool for optimizing exome analysis.
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Indraccolo S, Lombardi G, Fassan M, Pasqualini L, Giunco S, Marcato R, Gasparini A, Candiotto C, Nalio S, Fiduccia P, Fanelli GN, Pambuku A, Della Puppa A, D'Avella D, Bonaldi L, Gardiman MP, Bertorelle R, De Rossi A, Zagonel V. Genetic, Epigenetic, and Immunologic Profiling of MMR-Deficient Relapsed Glioblastoma. Clin Cancer Res 2018; 25:1828-1837. [PMID: 30514778 DOI: 10.1158/1078-0432.ccr-18-1892] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/25/2018] [Accepted: 11/28/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE In-depth characterization of recurrent glioblastoma (rGBM) might contribute to a better understanding of the mechanisms behind tumor progression and enable rGBM treatment with targeted drugs.Experimental Design: In this study, GBM samples were collected at diagnosis and recurrence from adult patients treated with Stupp protocol. Expression of mismatch repair (MMR) proteins was evaluated by IHC, followed by whole exome sequencing (WES) of tumor samples showing loss of MSH6 reactivity. Established genetic, epigenetic, and immunologic markers were assessed by standard methods and correlated with loss of MMR proteins and patient survival. RESULTS Expression of MMR proteins was partially or completely lost in 25.9% rGBM samples. Specifically, 12 samples showed partial or total MSH6 expression reduction. Conversely, 96.4% of GBM samples at diagnosis expressed MMR markers. WES disclosed lack of variants in MMR genes in primary samples, whereas two MSH6-negative rGBM samples shared a c.3438+1G>A* splicing MSH6 variant with a potential loss of function effect. MSH6-negative rGBM specimens had high tumor mutational burden (TMB), but no microsatellite instability. In contrast, GBM samples with partial loss of MMR proteins disclosed low TMB. MMR-deficient rGBM showed significant telomere shortening and MGMT methylation and are characterized by highly heterogeneous MHC class I expression. CONCLUSIONS Multilevel profiling of MMR-deficient rGBM uncovered hypermutated genotype uncoupled from enriched expression of immune-related markers. Assessment of MHC class I expression and TMB should be included in protocols aiming to identify rGBM patients potentially eligible for treatment with drugs targeting immune-checkpoint inhibitors.
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Affiliation(s)
- Stefano Indraccolo
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy.
| | - Giuseppe Lombardi
- Department of Oncology, Oncology 1, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padova, Padova, Italy
| | - Lorenza Pasqualini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Silvia Giunco
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Raffaella Marcato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Alessandra Gasparini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Cinzia Candiotto
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Silvia Nalio
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Pasquale Fiduccia
- Clinical Trials and Biostatistics Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Giuseppe Nicolò Fanelli
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padova, Padova, Italy
| | - Ardi Pambuku
- Department of Oncology, Oncology 1, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | | | - Domenico D'Avella
- Neurosurgery, Department of Neurosciences DNS, University Hospital of Padova, Padova, Italy
| | - Laura Bonaldi
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Marina Paola Gardiman
- Surgical Pathology and Cytopathology Unit, University Hospital of Padova, Padova, Italy
| | - Roberta Bertorelle
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Anita De Rossi
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy.,Department of Surgery, Oncology and Gastroenterology (DISCOG), University of Padova, Padova, Italy
| | - Vittorina Zagonel
- Department of Oncology, Oncology 1, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
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Lewis MA, Nolan LS, Cadge BA, Matthews LJ, Schulte BA, Dubno JR, Steel KP, Dawson SJ. Whole exome sequencing in adult-onset hearing loss reveals a high load of predicted pathogenic variants in known deafness-associated genes and identifies new candidate genes. BMC Med Genomics 2018; 11:77. [PMID: 30180840 PMCID: PMC6123954 DOI: 10.1186/s12920-018-0395-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/21/2018] [Indexed: 12/22/2022] Open
Abstract
Background Deafness is a highly heterogenous disorder with over 100 genes known to underlie human non-syndromic hearing impairment. However, many more remain undiscovered, particularly those involved in the most common form of deafness: adult-onset progressive hearing loss. Despite several genome-wide association studies of adult hearing status, it remains unclear whether the genetic architecture of this common sensory loss consists of multiple rare variants each with large effect size or many common susceptibility variants each with small to medium effects. As next generation sequencing is now being utilised in clinical diagnosis, our aim was to explore the viability of diagnosing the genetic cause of hearing loss using whole exome sequencing in individual subjects as in a clinical setting. Methods We performed exome sequencing of thirty patients selected for distinct phenotypic sub-types from well-characterised cohorts of 1479 people with adult-onset hearing loss. Results Every individual carried predicted pathogenic variants in at least ten deafness-associated genes; similar findings were obtained from an analysis of the 1000 Genomes Project data unselected for hearing status. We have identified putative causal variants in known deafness genes and several novel candidate genes, including NEDD4 and NEFH that were mutated in multiple individuals. Conclusions The high frequency of predicted-pathogenic variants detected in known deafness-associated genes was unexpected and has significant implications for current diagnostic sequencing in deafness. Our findings suggest that in a clinic setting, efforts should be made to a) confirm key sequence results by Sanger sequencing, b) assess segregations of variants and phenotypes within the family if at all possible, and c) use caution in applying current pathogenicity prediction algorithms for diagnostic purposes. We conclude that there may be a high number of pathogenic variants affecting hearing in the ageing population, including many in known deafness-associated genes. Our findings of frequent predicted-pathogenic variants in both our hearing-impaired sample and in the larger 1000 Genomes Project sample unselected for auditory function suggests that the reference population for interpreting variants for this very common disorder should be a population of people with good hearing for their age rather than an unselected population. Electronic supplementary material The online version of this article (10.1186/s12920-018-0395-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, WC2R 2LS, London, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Lisa S Nolan
- UCL Ear Institute, University College London, WC1X 8EE, London, UK
| | - Barbara A Cadge
- UCL Ear Institute, University College London, WC1X 8EE, London, UK
| | - Lois J Matthews
- Medical University of South Carolina, Charleston, SC, 29425, USA
| | | | - Judy R Dubno
- Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, WC2R 2LS, London, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Sally J Dawson
- UCL Ear Institute, University College London, WC1X 8EE, London, UK.
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Wong TH, van der Lee SJ, van Rooij JGJ, Meeter LHH, Frick P, Melhem S, Seelaar H, Ikram MA, Rozemuller AJ, Holstege H, Hulsman M, Uitterlinden A, Neumann M, Hoozemans JJM, van Duijn CM, Rademakers R, van Swieten JC. EIF2AK3 variants in Dutch patients with Alzheimer's disease. Neurobiol Aging 2018; 73:229.e11-229.e18. [PMID: 30314817 DOI: 10.1016/j.neurobiolaging.2018.08.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/17/2018] [Accepted: 08/15/2018] [Indexed: 10/28/2022]
Abstract
Next-generation sequencing has contributed to our understanding of the genetics of Alzheimer's disease (AD) and has explained a substantial part of the missing heritability of familial AD. We sequenced 19 exomes from 8 Dutch families with a high AD burden and identified EIF2AK3, encoding for protein kinase RNA-like endoplasmic reticulum kinase (PERK), as a candidate gene. Gene-based burden analysis in a Dutch AD exome cohort containing 547 cases and 1070 controls showed a significant association of EIF2AK3 with AD (OR 1.84 [95% CI 1.07-3.17], p-value 0.03), mainly driven by the variant p.R240H. Genotyping of this variant in an additional cohort from the Rotterdam Study showed a trend toward association with AD (p-value 0.1). Immunohistochemical staining with pPERK and peIF2α of 3 EIF2AK3 AD carriers showed an increase in hippocampal neuronal cells expressing these proteins compared with nondemented controls, but no difference was observed in AD noncarriers. This study suggests that rare variants in EIF2AK3 may be associated with disease risk in AD.
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Affiliation(s)
- Tsz Hang Wong
- Alzheimer Center and Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sven J van der Lee
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jeroen G J van Rooij
- Alzheimer Center and Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lieke H H Meeter
- Alzheimer Center and Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Petra Frick
- DZNE, German Centre for Neurodegenerative Disease, Tübingen, Germany
| | - Shamiram Melhem
- Alzheimer Center and Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Harro Seelaar
- Alzheimer Center and Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Henne Holstege
- Alzheimer Center, Department of Neurology, VU University Medical Center, Amsterdam, The Netherlands; Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Marc Hulsman
- Alzheimer Center, Department of Neurology, VU University Medical Center, Amsterdam, The Netherlands; Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands; Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Andre Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Manuela Neumann
- DZNE, German Centre for Neurodegenerative Disease, Tübingen, Germany; Department of Neuropathology, University of Tübingen, Tübingen, Germany
| | - Jeroen J M Hoozemans
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - John C van Swieten
- Alzheimer Center and Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands; Alzheimer Center, Department of Neurology, VU University Medical Center, Amsterdam, The Netherlands.
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Nandakumar P, Morrison AC, Grove ML, Boerwinkle E, Chakravarti A. Contributions of rare coding variants in hypotension syndrome genes to population blood pressure variation. Medicine (Baltimore) 2018; 97:e11865. [PMID: 30113482 PMCID: PMC6113003 DOI: 10.1097/md.0000000000011865] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Rare variants, in particular renal salt handling genes, contribute to monogenic forms of hypertension and hypotension syndromes with electrolyte abnormalities. A study by Ji et al (2008) demonstrated this effect for rare loss-of-function coding variants in SLC12A3 (NCCT), SLC12A1 (NKCC2), and KCNJ1 (ROMK) that led to reduction of ∼6 mm Hg for SBP and ∼3 mm Hg for DBP among carriers in 2492 European ancestry Framingham Heart Study (FHS) subjects. These findings support a potentially large role for these variants in interindividual variation in systolic and diastolic blood pressure (SBP, DBP) in the population. The present study focuses on replicating the analyses completed by Ji et al to identify effects of rare variants in the population-based Atherosclerosis Risk in Communities (ARIC) study.We attempted to replicate the findings by Ji et al by applying their criteria to identify putative loss-of-function variants with allele frequency <0.001 and complete conservation across a set of orthologs, to exome sequencing data from 7444 European ancestry participants of the ARIC study.Although we failed to replicate the previous findings when applying their methods to the ARIC study data, we observed a similar effect when we restricted analyses to the subset of variants they observed.These results simultaneously support the utility of exome sequencing data for studying extremely rare coding variants in hypertension and underscore the need for improved filtering methods for identifying functional variants in human sequences.
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Affiliation(s)
- Priyanka Nandakumar
- Center for Complex Disease Genomics Predoctoral Training Program in Human Genetics and Molecular Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD Human Genome Sequencing Center, Baylor College of Medicine Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX. Center for Human Genetics and Genomics, NYU School of Medicine, New York, NY
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50
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Wu IC, Liu WC, Chang TT. Applications of next-generation sequencing analysis for the detection of hepatocellular carcinoma-associated hepatitis B virus mutations. J Biomed Sci 2018; 25:51. [PMID: 29859540 PMCID: PMC5984823 DOI: 10.1186/s12929-018-0442-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/30/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is a powerful and high-throughput method for the detection of viral mutations. This article provides a brief overview about optimization of NGS analysis for hepatocellular carcinoma (HCC)-associated hepatitis B virus (HBV) mutations, and hepatocarcinogenesis of relevant mutations. MAIN BODY For the application of NGS analysis in the genome of HBV, four noteworthy steps were discovered in testing. First, a sample-specific reference sequence was the most effective mapping reference for NGS. Second, elongating the end of reference sequence improved mapping performance at the end of the genome. Third, resetting the origin of mapping reference sequence could probed deletion mutations and variants at a certain location with common mutations. Fourth, using a platform-specific cut-off value to distinguish authentic minority variants from technical artifacts was found to be highly effective. One hundred and sixty-seven HBV single nucleotide variants (SNVs) were found to be studied previously through a systematic literature review, and 12 SNVs were determined to be associated with HCC by meta-analysis. From comprehensive research using a HBV genome-wide NGS analysis, 60 NGS-defined HCC-associated SNVs with their pathogenic frequencies were identified, with 19 reported previously. All the 12 HCC-associated SNVs proved by meta-analysis were confirmed by NGS analysis, except for C1766T and T1768A which were mainly expressed in genotypes A and D, but including the subgroup analysis of A1762T. In the 41 novel NGS-defined HCC-associated SNVs, 31.7% (13/41) had cut-off values of SNV frequency lower than 20%. This showed that NGS could be used to detect HCC-associated SNVs with low SNV frequency. Most SNV II (the minor strains in the majority of non-HCC patients) had either low (< 20%) or high (> 80%) SNV frequencies in HCC patients, a characteristic U-shaped distribution pattern. The cut-off values of SNV frequency for HCC-associated SNVs represent their pathogenic frequencies. The pathogenic frequencies of HCC-associated SNV II also showed a U-shaped distribution. Hepatocarcinogenesis induced by HBV mutated proteins through cellular pathways was reviewed. CONCLUSION NGS analysis is useful to discover novel HCC-associated HBV SNVs, especially those with low SNV frequency. The hepatocarcinogenetic mechanisms of novel HCC-associated HBV SNVs defined by NGS analysis deserve further investigation.
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Affiliation(s)
- I-Chin Wu
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, 138 Sheng-Li Road, Tainan, 70403, Taiwan, Republic of China.,Infectious Disease and Signaling Research Center, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - Wen-Chun Liu
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, 138 Sheng-Li Road, Tainan, 70403, Taiwan, Republic of China.,Infectious Disease and Signaling Research Center, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - Ting-Tsung Chang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, 138 Sheng-Li Road, Tainan, 70403, Taiwan, Republic of China.
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