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Collinson RJ, Wilson L, Boey D, Ng ZY, Mirzai B, Chuah HS, Howman R, Grove CS, Malherbe JAJ, Leahy MF, Linden MD, Fuller KA, Erber WN, Guo BB. Transcription factor 3 is dysregulated in megakaryocytes in myelofibrosis. Platelets 2024; 35:2304173. [PMID: 38303515 DOI: 10.1080/09537104.2024.2304173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024]
Abstract
Transcription factor 3 (TCF3) is a DNA transcription factor that modulates megakaryocyte development. Although abnormal TCF3 expression has been identified in a range of hematological malignancies, to date, it has not been investigated in myelofibrosis (MF). MF is a Philadelphia-negative myeloproliferative neoplasm (MPN) that can arise de novo or progress from essential thrombocythemia [ET] and polycythemia vera [PV] and where dysfunctional megakaryocytes have a role in driving the fibrotic progression. We aimed to examine whether TCF3 is dysregulated in megakaryocytes in MPN, and specifically in MF. We first assessed TCF3 protein expression in megakaryocytes using an immunohistochemical approach analyses and showed that TCF3 was reduced in MF compared with ET and PV. Further, the TCF3-negative megakaryocytes were primarily located near trabecular bone and had the typical "MF-like" morphology as described by the WHO. Genomic analysis of isolated megakaryocytes showed three mutations, all predicted to result in a loss of function, in patients with MF; none were seen in megakaryocytes isolated from ET or PV marrow samples. We then progressed to transcriptomic sequencing of platelets which showed loss of TCF3 in MF. These proteomic, genomic and transcriptomic analyses appear to indicate that TCF3 is downregulated in megakaryocytes in MF. This infers aberrations in megakaryopoiesis occur in this progressive phase of MPN. Further exploration of this pathway could provide insights into TCF3 and the evolution of fibrosis and potentially lead to new preventative therapeutic targets.
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Affiliation(s)
- Ryan J Collinson
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Lynne Wilson
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Darren Boey
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Zi Yun Ng
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
| | - Bob Mirzai
- PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Hun S Chuah
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
- PathWest Laboratory Medicine, Nedlands, WA, Australia
- Department of Haematology, Rockingham General Hospital, Rockingham, WA, Australia
| | - Rebecca Howman
- Department of Haematology, Sir Charles Gairdner Hospital Nedlands Australia
| | - Carolyn S Grove
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
- Department of Haematology, Sir Charles Gairdner Hospital Nedlands Australia
| | | | - Michael F Leahy
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
- PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Matthew D Linden
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Kathryn A Fuller
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Wendy N Erber
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Belinda B Guo
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
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Wolf EB, Imperial R, Jiang L, Agarwal AK, Tun HW. Clinical and Genomic Profile of Primary Cranial Neurolymphomatosis. J Blood Med 2024; 15:291-303. [PMID: 38947230 PMCID: PMC11212808 DOI: 10.2147/jbm.s459123] [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: 02/11/2024] [Accepted: 06/12/2024] [Indexed: 07/02/2024] Open
Abstract
Primary cranial neurolymphomatosis (PCNL) is a rare subtype of primary CNS lymphoma (PCNSL) in which infiltrative lymphomatous involvement is confined to cranial nerves. Here, we report a case of PCNL with successful genomic profiling. A 57-year-old male had a lengthy prediagnostic phase spanning approximately 30 months, characterized by multiple episodes of cranial neuropathies managed by steroids. At the time of diagnosis, the patient had right-sided cranial neuropathies involving cranial nerves (CN) V, VI, and VII. Pathological findings of the right cavernous lesion biopsy were consistent with large B-cell lymphoma-infiltrating nerve fibers. The clinical course was aggressive and refractory, characterized by relentless progression with the development of cervical spinal neurolymphomatosis, cerebrospinal fluid involvement, and ependymal and intraparenchymal cerebral involvement, despite multiple lines of therapy, including chemoimmunotherapy, Bruton's tyrosine kinase inhibitor, radiation, autologous stem cell transplant, chimeric antigen receptor T-cell therapy (CAR-T), and whole-brain radiation. The patient survived for 22 months from the time of the initial diagnosis and 52 months after the first episode of cranial neuropathy. Next-generation sequencing identified mutations (MYD88, CD79b, and PIM1) that are frequently observed in PCNSL. The unusual findings included a total of 22 mutations involving PIM1, indicating a highly active aberrant somatic hypermutation and two missense CXCR4 mutations. CXCR4 mutations have never been described in PCNSL and may have implications for disease biology and therapeutic interventions. We provide a literature review to further elucidate PCNL.
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Affiliation(s)
- Emily B Wolf
- Division of Hematology and Medical Oncology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Robin Imperial
- Division of Hematology and Medical Oncology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Liuyan Jiang
- Department of Laboratory Medicine and Pathology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Amit K Agarwal
- Department of Radiology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Han W Tun
- Division of Hematology and Medical Oncology, Mayo Clinic Florida, Jacksonville, FL, USA
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AlSaeed MJ, Ramdhan P, Malave JG, Eljilany I, Langaee T, McDonough CW, Seabra G, Li C, Cavallari LH. Assessing the Performance of In silico Tools and Molecular Dynamics Simulations for Predicting Pharmacogenetic Variant Impact. Clin Pharmacol Ther 2024. [PMID: 38894625 DOI: 10.1002/cpt.3348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024]
Abstract
The ability of freely available in silico tools to predict the effect of non-synonymous single nucleotide polymorphisms (nsSNPs) in pharmacogenes on protein function is not well defined. We assessed the performance of seven sequence-based (SIFT, PolyPhen2, mutation accessor, FATHMM, PhD-SNP, MutPred2, and SNPs & Go) and five structure-based (mCSM, SDM, DDGun, CupSat, and MAESTROweb) tools in predicting the impact of 118 nsSNPs in the CYP2C19, CYP2C9, CYP2B6, CYP2D6, and DPYD genes with known function (24 normal, one increased, 42 decreased, and 51 no-function). Sequence-based tools had a higher median (IQR) positive predictive value (89% [89-94%] vs. 12% [10-15%], P < 0.001) and lower negative predictive value (30% [24-34%] vs. 90% [80-93%], P < 0.001) than structure-based tools. Accuracy did not significantly differ between sequence-based (59% [37-67%]) and structure-based (34% [23-44%]) tools (P = 0.070). Notably, the no-function CYP2C9*3 allele and decreased function CYP2C9*8 allele were predicted incorrectly as tolerated by 100% of sequenced-based tools and as stabilizing by 60% and 20% of structure-based tools, respectively. As a case study, we performed mutational analysis for the CYP2C9*1, *3 (I359L), and *8 (R150H) proteins through molecular dynamic (MD) simulations using S-warfarin as the substrate. The I359L variant increased the distance of the major metabolic site of S-warfarin to the oxy-ferryl center of CYP2C9, and I359L and R150H caused shifts in the conformation of S-warfarin to a position less favorable for metabolism. These data suggest that MD simulations may better capture the impact of nsSNPs in pharmacogenes than other tools.
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Affiliation(s)
- Maryam Jamal AlSaeed
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
- Department of Pharmacy Practice, College of Clinical Pharmacy, King Faisal University, Al Hofuf, Saudi Arabia
| | - Peter Ramdhan
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Jean Gabriel Malave
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Islam Eljilany
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Taimour Langaee
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Caitrin W McDonough
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Gustavo Seabra
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Chenglong Li
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
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Murciano-Goroff YR, Uppal M, Chen M, Harada G, Schram AM. Basket Trials: Past, Present, and Future. ANNUAL REVIEW OF CANCER BIOLOGY 2024; 8:59-80. [PMID: 38938274 PMCID: PMC11210107 DOI: 10.1146/annurev-cancerbio-061421-012927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Large-scale tumor molecular profiling has revealed that diverse cancer histologies are driven by common pathways with unifying biomarkers that can be exploited therapeutically. Disease-agnostic basket trials have been increasingly utilized to test biomarker-driven therapies across cancer types. These trials have led to drug approvals and improved the lives of patients while simultaneously advancing our understanding of cancer biology. This review focuses on the practicalities of implementing basket trials, with an emphasis on molecularly targeted trials. We examine the biologic subtleties of genomic biomarker and patient selection, discuss previous successes in drug development facilitated by basket trials, describe certain novel targets and drugs, and emphasize practical considerations for participant recruitment and study design. This review also highlights strategies for aiding patient access to basket trials. As basket trials become more common, steps to ensure equitable implementation of these studies will be critical for molecularly targeted drug development.
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Affiliation(s)
| | - Manik Uppal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Monica Chen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Guilherme Harada
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
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Cubuk J, Greenberg L, Greenberg AE, Emenecker RJ, Stuchell-Brereton MD, Holehouse AS, Soranno A, Greenberg MJ. Structural dynamics of the intrinsically disordered linker region of cardiac troponin T. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596451. [PMID: 38853835 PMCID: PMC11160775 DOI: 10.1101/2024.05.30.596451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The cardiac troponin complex, composed of troponins I, T, and C, plays a central role in regulating the calcium-dependent interactions between myosin and the thin filament. Mutations in troponin can cause cardiomyopathies; however, it is still a major challenge for the field to connect how changes in sequence affect troponin's function. Recent high-resolution structures of the thin filament revealed critical insights into the structure-function relationship of the troponin complex, but there remain large, unresolved segments of troponin, including the troponin-T linker region that is a hotspot for several cardiomyopathy mutations. This unresolved yet functionally-significant linker region has been proposed to be intrinsically disordered, with behaviors that are not well described by traditional structural approaches; however, this proposal has not been experimentally verified. Here, we used a combination of single-molecule Förster resonance energy transfer (FRET), molecular dynamics simulations, and functional reconstitution assays to investigate the troponin-T linker region. We experimentally and computationally show that in the context of both isolated troponin and the fully regulated troponin complex, the linker behaves as a dynamic, intrinsically disordered region. This region undergoes polyampholyte expansion in the presence of high salt and distinct conformational changes during the assembly of the troponin complex. We also examine the ΔE160 hypertrophic cardiomyopathy mutation in the linker, and we demonstrate that this mutation does not affect the conformational dynamics of the linker, rather it allosterically affects interactions with other subunits of the troponin complex, leading to increased molecular contractility. Taken together, our data clearly demonstrate the importance of disorder within the troponin-T linker and provide new insights into the molecular mechanisms controlling the pathogenesis of cardiomyopathies.
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Affiliation(s)
- Jasmine Cubuk
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130, Saint Louis, MO, USA
| | - Lina Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
| | - Akiva E. Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
| | - Ryan J. Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130, Saint Louis, MO, USA
| | - Melissa D. Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130, Saint Louis, MO, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130, Saint Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130, Saint Louis, MO, USA
| | - Michael J. Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
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Emanuelli G, Zhu J, Li W, Morrell NW, Marciniak SJ. Functional validation of EIF2AK4 (GCN2) missense variants associated with pulmonary arterial hypertension. Hum Mol Genet 2024:ddae082. [PMID: 38776952 DOI: 10.1093/hmg/ddae082] [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: 04/09/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Pulmonary arterial hypertension (PAH) is a disorder with a large genetic component. Biallelic mutations of EIF2AK4, which encodes the kinase GCN2, are causal in two ultra-rare subtypes of PAH, pulmonary veno-occlusive disease and pulmonary capillary haemangiomatosis. EIF2AK4 variants of unknown significance have also been identified in patients with classical PAH, though their relationship to disease remains unclear. To provide patients with diagnostic information and enable family testing, the functional consequences of such rare variants must be determined, but existing computational methods are imperfect. We applied a suite of bioinformatic and experimental approaches to sixteen EIF2AK4 variants that had been identified in patients. By experimentally testing the functional integrity of the integrated stress response (ISR) downstream of GCN2, we determined that existing computational tools have insufficient sensitivity to reliably predict impaired kinase function. We determined experimentally that several EIF2AK4 variants identified in patients with classical PAH had preserved function and are therefore likely to be non-pathogenic. The dysfunctional variants of GCN2 that we identified could be subclassified into three groups: misfolded, kinase-dead, and hypomorphic. Intriguingly, members of the hypomorphic group were amenable to paradoxical activation by a type-1½ GCN2 kinase inhibitor. This experiment approach may aid in the clinical stratification of EIF2AK4 variants and potentially identify hypomorophic alleles receptive to pharmacological activation.
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Affiliation(s)
- Giulia Emanuelli
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Keith Peters Building, Biomedical Campus, Hills Rd, Cambridge CB2 0XY, United Kingdom
| | - JiaYi Zhu
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Keith Peters Building, Biomedical Campus, Hills Rd, Cambridge CB2 0XY, United Kingdom
| | - Wei Li
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Papworth Road, Trumpington, Cambridge CB2 0BB, United Kingdom
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital (Box 157), Hills Road, Cambridge CB2 2QQ, United Kingdom
| | - Nicholas W Morrell
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Papworth Road, Trumpington, Cambridge CB2 0BB, United Kingdom
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital (Box 157), Hills Road, Cambridge CB2 2QQ, United Kingdom
- Royal Papworth Hospital NHS Foundation Trust, Papworth Rd, Trumpington, Cambridge CB2 0AY, United Kingdom
| | - Stefan J Marciniak
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Keith Peters Building, Biomedical Campus, Hills Rd, Cambridge CB2 0XY, United Kingdom
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital (Box 157), Hills Road, Cambridge CB2 2QQ, United Kingdom
- Royal Papworth Hospital NHS Foundation Trust, Papworth Rd, Trumpington, Cambridge CB2 0AY, United Kingdom
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Lv X, Gao J, Yang J, Zou Y, Chen J, Sun Y, Song J, Liu Y, Wang L, Xia L, Yu S, Wei Z, Chen L, Hou X. Clinical and functional characterization of a novel KCNJ11 (c.101G > A, p.R34H) mutation associated with maturity-onset diabetes mellitus of the young type 13. Endocrine 2024:10.1007/s12020-024-03873-6. [PMID: 38761346 DOI: 10.1007/s12020-024-03873-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/09/2024] [Indexed: 05/20/2024]
Abstract
PURPOSE This study aimed to describe the clinical features, diagnostic and therapeutic course of a patient with MODY13 caused by KCNJ11 (c.101G > A, p.R34H) and how it contributes to the pathogenesis of MODY13, and to explore new therapeutic targets. METHODS Whole-exome sequencing was used to screen prediagnosed individuals and family members with clinically suspected KCNJ11 mutations. Real-time fluorescence quantitative PCR, western blotting, thallium flux of potassium channels, glucose-stimulated insulin secretion (GSIS), and immunofluorescence assays were used to analyze the regulation of insulin secretion by the KCNJ11 mutant in MIN6 cells. Daily blood glucose levels were continuously monitored for 14 days in the proband using the ambulatory blood glucose meter (SIBIONICS). RESULTS Mutation screening of the entire exon of the gene identified a heterozygous KCNJ11 (c.101G > A, p.R34H) mutation in the proband and his mother. Cell-based GSIS assays after transfection of MIN6 using wild-type and mutant plasmids revealed that this mutation impaired insulin secretory function. Furthermore, we found that this impaired secretory function is associated with reduced functional activity of the mutant KCNJ11 protein and reduced expression of the insulin secretion-associated exocytosis proteins STXBP1 and SNAP25. CONCLUSION For the first time, we revealed the pathogenic mechanism of KCNJ11 (c.101G > A, p.R34H) associated with MODY13. This mutant can cause alterations in KATP channel activity, reduce sensitivity to glucose stimulation, and impair pancreatic β-cell secretory function by downregulating insulin secretion-associated exocytosis proteins. Therefore, oral sulfonylurea drugs can lower blood glucose levels through pro-insulinotropic effects and are more favorable for patients with this mutation.
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Affiliation(s)
- Xiaoyu Lv
- Department of Endocrinology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Jing Gao
- Department of Endocrinology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Jingwen Yang
- Department of Endocrinology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Ying Zou
- Department of Endocrinology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Jun Chen
- Department of Endocrinology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Yujing Sun
- Department of Endocrinology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Jia Song
- Department of Endocrinology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Yiran Liu
- Department of Endocrinology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Liming Wang
- Department of Endocrinology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Longqing Xia
- Department of Endocrinology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Shijia Yu
- Department of Endocrinology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Zichun Wei
- Department of Endocrinology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Li Chen
- Department of Endocrinology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
- Institute of Endocrine and Metabolic Diseases of Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Endocrine and Metabolic Diseases, Shandong Province Medicine & Health, Jinan, 250012, Shandong, China
- Jinan Clinical Research Center for Endocrine and Metabolic Disease, Jinan, 250012, Shandong, China
| | - Xinguo Hou
- Department of Endocrinology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.
- Institute of Endocrine and Metabolic Diseases of Shandong University, Jinan, 250012, Shandong, China.
- Key Laboratory of Endocrine and Metabolic Diseases, Shandong Province Medicine & Health, Jinan, 250012, Shandong, China.
- Jinan Clinical Research Center for Endocrine and Metabolic Disease, Jinan, 250012, Shandong, China.
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Zhong G, Zhao Y, Zhuang D, Chung WK, Shen Y. PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.20.581321. [PMID: 38746140 PMCID: PMC11092447 DOI: 10.1101/2024.02.20.581321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Accurate prediction of the functional impact of missense variants is important for disease gene discovery, clinical genetic diagnostics, therapeutic strategies, and protein engineering. Previous efforts have focused on predicting a binary pathogenicity classification, but the functional impact of missense variants is multi-dimensional. Pathogenic missense variants in the same gene may act through different modes of action (i.e., gain/loss-of-function) by affecting different aspects of protein function. They may result in distinct clinical conditions that require different treatments. We developed a new method, PreMode, to perform gene-specific mode-of-action predictions. PreMode models effects of coding sequence variants using SE(3)-equivariant graph neural networks on protein sequences and structures. Using the largest-to-date set of missense variants with known modes of action, we showed that PreMode reached state-of-the-art performance in multiple types of mode-of-action predictions by efficient transfer-learning. Additionally, PreMode's prediction of G/LoF variants in a kinase is consistent with inactive-active conformation transition energy changes. Finally, we show that PreMode enables efficient study design of deep mutational scans and optimization in protein engineering.
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Elangeeb ME, Elfaki I, Eleragi AMS, Ahmed EM, Mir R, Alzahrani SM, Bedaiwi RI, Alharbi ZM, Mir MM, Ajmal MR, Tayeb FJ, Barnawi J. Molecular Dynamics Simulation of Kir6.2 Variants Reveals Potential Association with Diabetes Mellitus. Molecules 2024; 29:1904. [PMID: 38675722 PMCID: PMC11054064 DOI: 10.3390/molecules29081904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/13/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Diabetes mellitus (DM) represents a problem for the healthcare system worldwide. DM has very serious complications such as blindness, kidney failure, and cardiovascular disease. In addition to the very bad socioeconomic impacts, it influences patients and their families and communities. The global costs of DM and its complications are huge and expected to rise by the year 2030. DM is caused by genetic and environmental risk factors. Genetic testing will aid in early diagnosis and identification of susceptible individuals or populations using ATP-sensitive potassium (KATP) channels present in different tissues such as the pancreas, myocardium, myocytes, and nervous tissues. The channels respond to different concentrations of blood sugar, stimulation by hormones, or ischemic conditions. In pancreatic cells, they regulate the secretion of insulin and glucagon. Mutations in the KCNJ11 gene that encodes the Kir6.2 protein (a major constituent of KATP channels) were reported to be associated with Type 2 DM, neonatal diabetes mellitus (NDM), and maturity-onset diabetes of the young (MODY). Kir6.2 harbors binding sites for ATP and phosphatidylinositol 4,5-diphosphate (PIP2). The ATP inhibits the KATP channel, while the (PIP2) activates it. A Kir6.2 mutation at tyrosine330 (Y330) was demonstrated to reduce ATP inhibition and predisposes to NDM. In this study, we examined the effect of mutations on the Kir6.2 structure using bioinformatics tools and molecular dynamic simulations (SIFT, PolyPhen, SNAP2, PANTHER, PhD&SNP, SNP&Go, I-Mutant, MuPro, MutPred, ConSurf, HOPE, and GROMACS). Our results indicated that M199R, R201H, R206H, and Y330H mutations influence Kir6.2 structure and function and therefore may cause DM. We conclude that MD simulations are useful techniques to predict the effects of mutations on protein structure. In addition, the M199R, R201H, R206H, and Y330H variant in the Kir6.2 protein may be associated with DM. These results require further verification in protein-protein interactions, Kir6.2 function, and case-control studies.
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Affiliation(s)
- Mohamed E. Elangeeb
- Department of Basic Medical Sciences, College of Applied Medical Sciences, University of Bisha, Bisha 61922, Saudi Arabia
| | - Imadeldin Elfaki
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia; (S.M.A.); (M.R.A.)
| | - Ali M. S. Eleragi
- Department of Microbiology, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia;
| | - Elsadig Mohamed Ahmed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha 61922, Saudi Arabia;
- Department of Clinical Chemistry, Faculty of Medical Laboratory Sciences, University of El Imam El Mahdi, Kosti 27711, Sudan
| | - Rashid Mir
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
| | - Salem M. Alzahrani
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia; (S.M.A.); (M.R.A.)
| | - Ruqaiah I. Bedaiwi
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
| | - Zeyad M. Alharbi
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
| | - Mohammad Muzaffar Mir
- Department of Clinical Biochemistry, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia;
| | - Mohammad Rehan Ajmal
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia; (S.M.A.); (M.R.A.)
| | - Faris Jamal Tayeb
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
| | - Jameel Barnawi
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
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Rajcsanyi LS, Zheng Y, Herpertz-Dahlmann B, Seitz J, de Zwaan M, Herzog W, Ehrlich S, Zipfel S, Giel K, Egberts K, Burghardt R, Föcker M, Antel J, Fischer-Posovszky P, Hebebrand J, Hinney A. Unexpected identification of obesity-associated mutations in LEP and MC4R genes in patients with anorexia nervosa. Sci Rep 2024; 14:7067. [PMID: 38528040 PMCID: PMC10963783 DOI: 10.1038/s41598-024-57517-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/19/2024] [Indexed: 03/27/2024] Open
Abstract
Mutations leading to a reduced or loss of function in genes of the leptin-melanocortin system confer a risk for monogenic forms of obesity. Yet, gain of function variants in the melanocortin-4-receptor (MC4R) gene predispose to a lower BMI. In individuals with reduced body weight, we thus expected mutations leading to an enhanced function in the respective genes, like leptin (LEP) and MC4R. Therefore, we have Sanger sequenced the coding regions of LEP and MC4R in 462 female patients with anorexia nervosa (AN), and 445 healthy-lean controls. In total, we have observed four and eight variants in LEP and MC4R, respectively. Previous studies showed different functional in vitro effects for the detected frameshift and non-synonymous variants: (1) LEP: reduced/loss of function (p.Val94Met), (2) MC4R: gain of function (p.Val103Ile, p.Ile251Leu), reduced or loss of function (p.Thr112Met, p.Ser127Leu, p.Leu211fsX) and without functional in vitro data (p.Val50Leut). In LEP, the variant p.Val94Met was detected in one patient with AN. For MC4R variants, one patient with AN carried the frameshift variant p.Leu211fsX. One patient with AN was heterozygous for two variants at the MC4R (p.Val103Ile and p.Ser127Leu). All other functionally relevant variants were detected in similar frequencies in patients with AN and lean individuals.
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Affiliation(s)
- Luisa Sophie Rajcsanyi
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstraße 174, 45147, Essen, Germany.
- Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany.
- Section for Molecular Genetics of Mental Disorders, University Hospital Essen, Essen, Germany.
- Institute of Sex- and Gender-Sensitive Medicine, University Hospital Essen, Essen, Germany.
| | - Yiran Zheng
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstraße 174, 45147, Essen, Germany
- Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany
| | - Beate Herpertz-Dahlmann
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Jochen Seitz
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstraße 174, 45147, Essen, Germany
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Martina de Zwaan
- Department of Psychosomatic Medicine and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Wolfgang Herzog
- Department of Internal Medicine II, General Internal and Psychosomatic Medicine, University of Heidelberg, Heidelberg, Germany
| | - Stefan Ehrlich
- Eating Disorders Research and Treatment Center, Department of Child and Adolescent Psychiatry, Faculty of Medicine, TU Dresden, Dresden, Germany
- Translational Developmental Neuroscience Section, Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Stephan Zipfel
- Department of Psychosomatic Medicine and Psychotherapy, Medical University Hospital Tübingen, Tübingen, Germany
- Center of Excellence in Eating Disorders KOMET, Tübingen, Germany
| | - Katrin Giel
- Department of Psychosomatic Medicine and Psychotherapy, Medical University Hospital Tübingen, Tübingen, Germany
- Center of Excellence in Eating Disorders KOMET, Tübingen, Germany
| | - Karin Egberts
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Würzburg, Würzburg, Germany
| | - Roland Burghardt
- Oberberg Clinic for Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Fasanenkiez, Berlin, Germany
| | - Manuel Föcker
- Department of Child and Adolescent Psychiatry, University Hospital Münster, Munster, Germany
- LWL-University Hospital Hamm for Child and Adolescent Psychiatry, Ruhr-University Bochum, Hamm, Germany
| | - Jochen Antel
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstraße 174, 45147, Essen, Germany
- Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany
| | | | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstraße 174, 45147, Essen, Germany
- Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstraße 174, 45147, Essen, Germany
- Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany
- Section for Molecular Genetics of Mental Disorders, University Hospital Essen, Essen, Germany
- Institute of Sex- and Gender-Sensitive Medicine, University Hospital Essen, Essen, Germany
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Liu Y, Dai S, Qin S, Zhou J, Wang Z, Yin G. The pathogenic mutations of APOA5 in Chinese patients with hyperlipidemic acute pancreatitis. Lipids Health Dis 2024; 23:44. [PMID: 38331899 PMCID: PMC10851583 DOI: 10.1186/s12944-024-02011-5] [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: 10/31/2023] [Accepted: 01/09/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND AND AIMS To study the role of gene mutations in the development of severe hypertriglyceridemia (HTG) in patients with hyperlipidemic acute pancreatitis (HLAP), especially different apolipoprotein A5 (APOA5) mutations. METHODS Whole-exome sequencing was performed on 163 patients with HLAP and 30 patients with biliary acute pancreatitis (BAP). The pathogenicity of mutations was then assessed by combining clinical information, predictions of bioinformatics programs, information from multiple gene databases, and residue location and conservation. The pathogenic mutations of APOA5 were visualized using the software. RESULTS 1. Compared with BAP patients, pathogenic mutations of APOA5 were frequent in HLAP patients; among them, the heterozygous mutation of p.G185C was the most common. 2. All six pathogenic mutations of APOA5 identified in this study (p.S35N, p.D167V, p.G185C, p.K188I, p.R223C, and p.H182fs) were positively correlated with severe HTG; they were all in the important domains of apolipoprotein A-V (apoA-V). Residue 223 is strictly conserved in multiple mammals and is located in the lipoprotein lipase (LPL)-binding domain (Pro215-Phe261). When Arg 223 is mutated to Cys 223, the positive charge of this residue is reduced, which is potentially destructive to the binding function of apoA-V to LPL. 3. Four new APOA5 mutations were identified, namely c.563A > T, c.667C > T, c.788G > A, and c.544_545 insGGTGC. CONCLUSIONS The pathogenic mutations of APOA5 were specific to the patients with HLAP and severe HTG in China, and identifying such mutations had clinical significance in elucidating the etiology and subsequent treatment.
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Affiliation(s)
- Yuxin Liu
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, District, No.1055, San-Xiang Road, Gu-Su, Suzhou, 215000, Jiangsu Province, China
| | - Si Dai
- Department of Gastroenterology, Songtao Miao Autonomous County People's Hospital, Tongren, 554199, Guizhou Province, China
| | - Shuqi Qin
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, District, No.1055, San-Xiang Road, Gu-Su, Suzhou, 215000, Jiangsu Province, China
| | - Jing Zhou
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, District, No.1055, San-Xiang Road, Gu-Su, Suzhou, 215000, Jiangsu Province, China
| | - Zhendan Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, District, No.1055, San-Xiang Road, Gu-Su, Suzhou, 215000, Jiangsu Province, China
| | - Guojian Yin
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, District, No.1055, San-Xiang Road, Gu-Su, Suzhou, 215000, Jiangsu Province, China.
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12
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Nowicka Z, Kuna K, Stawiski K, Sołek J, Świderek M, Papis-Ubych A, Fijuth J, Fendler W, Tomasik B. Extreme acute radiation-induced toxicity in a patient with polymorphous low-grade adenocarcinoma of the nasopharynx and rare variants in DNA repair genes. Head Neck 2024; 46:E10-E17. [PMID: 37867397 DOI: 10.1002/hed.27555] [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: 05/30/2023] [Revised: 09/14/2023] [Accepted: 10/11/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Polymorphous low-grade adenocarcinoma (PLGA) is an extremely rare finding in the nasopharynx. There are no guidelines for the treatment of PLGA in this localization. Radiotherapy may be administered to treat this malignancy; however, in radiosensitive individuals, it is associated with a risk of severe radiotherapy-induced toxicity. METHODS We present a case of a 73-year-old woman with locally advanced polymorphous low-grade adenocarcinoma of the nasopharynx who developed a severe adverse acute reaction to radiotherapy leading to treatment discontinuation. Despite intensive treatment, the patient died 40 days after RT initiation. Whole genome sequencing was performed using DNA from peripheral blood mononuclear cells in the search for variants that could explain such extreme toxicity. RESULTS We identified a combination of pathogenic variants that may have contributed to the patient's reaction to radiation therapy, including predisposing variants in XRCC1, XRCC3, and LIG4. We also identified candidate variants, not previously described in this context, which could be associated with radiation toxicity based on plausible mechanisms. We discuss previous reports of this rare tumor from the literature and known contributors to radiation-induced toxicity. CONCLUSIONS Genetic causes should be considered in cases of extreme radiosensitivity, especially when is not explained by clinical factors.
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Affiliation(s)
- Zuzanna Nowicka
- Department of Biostatistics and Translational Medicine, Medical University of Łódź, Łódź, Poland
| | - Kasper Kuna
- Department of Biostatistics and Translational Medicine, Medical University of Łódź, Łódź, Poland
| | - Konrad Stawiski
- Department of Biostatistics and Translational Medicine, Medical University of Łódź, Łódź, Poland
- Department of Radiotherapy, Medical University of Łódź, Łódź, Poland
| | - Julia Sołek
- Department of Pathology, Chair of Oncology, Medical University of Łódź, Łódź, Poland
| | | | - Anna Papis-Ubych
- Department of Radiotherapy, Medical University of Łódź, Łódź, Poland
| | - Jacek Fijuth
- Department of Radiotherapy, Medical University of Łódź, Łódź, Poland
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Łódź, Łódź, Poland
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Bartłomiej Tomasik
- Department of Biostatistics and Translational Medicine, Medical University of Łódź, Łódź, Poland
- Department of Oncology and Radiotherapy, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
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Semjid D, Ahn H, Bayarmagnai S, Gantumur M, Kim S, Lee JH. Identification of novel candidate genes associated with non-syndromic tooth agenesis in Mongolian families. Clin Oral Investig 2023; 28:56. [PMID: 38157055 PMCID: PMC10756872 DOI: 10.1007/s00784-023-05415-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024]
Abstract
OBJECTIVES This study aimed to identify genetic variants associated with non-syndromic tooth agenesis (TA) in nine families from Mongolia using whole-exome sequencing (WES) and bioinformatics analysis. MATERIAL AND METHODS The study enrolled 41 participants, including three inherited and six non-inherited families. WES analysis was performed on 14 saliva samples from individuals with non-syndromic TA. The potential candidate genes were identified through variant filtering and segregation analysis. The filtered variants were then analyzed in silico mutation impact analysis. RESULTS WES analysis identified 21 variants associated with TA, and 5 of these variants met all filtering criteria. These variants were located in the exome region of MAST4, ITGA6, PITX2, CACNA1S, and CDON genes. The variant in PITX2 was found in eight participants from inherited and non-inherited families, while the MAST4 variant was identified in 6 participants from inherited families. CONCLUSIONS The study identified various genetic variant candidates associated with TA in different family groups, with PITX2 being the most commonly identified. Our findings suggest that MAST4 may also be a novel candidate gene for TA due to its association with the Wnt signaling pathway. Additionally, we found that five candidate genes related to focal adhesion and calcium channel complex were significant and essential in tooth development. CLINICAL RELEVANCE Identifying new pathogenic genes associated with TA can improve our understanding of the molecular mechanisms underlying the disease, leading to better diagnosis, prevention, and treatment. Early detection of TA based on biomarkers can improve dental management and facilitate orthodontic and prosthetic treatment.
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Affiliation(s)
- Dejidnorov Semjid
- Department of Prosthodontics, College of Dentistry at Yonsei University, 50-1 Yonsei-Ro, Seodaemoon-Gu, Seoul, 120-752, Republic of Korea
| | - Hyunsoo Ahn
- Department of Life Sciences, Pohang University of Science and Technology, 80 Jigok-Ro, Nam-Gu, Pohang, 790-784, Republic of Korea
| | - Sapaar Bayarmagnai
- Department of Prosthodontics, School of Dentistry, Mongolian National University of Medical Sciences, Chingeltei District, Nuuriin 2-21, Ulaanbaatar, Mongolia
| | - Munkhjargal Gantumur
- Department of Prosthodontics, School of Dentistry, Mongolian National University of Medical Sciences, Chingeltei District, Nuuriin 2-21, Ulaanbaatar, Mongolia
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology, 80 Jigok-Ro, Nam-Gu, Pohang, 790-784, Republic of Korea.
| | - Jae Hoon Lee
- Department of Prosthodontics, College of Dentistry at Yonsei University, 50-1 Yonsei-Ro, Seodaemoon-Gu, Seoul, 120-752, Republic of Korea.
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Eswaramoorthy V, Kandasamy T, Thiyagarajan K, Chockalingam V, Jegadeesan S, Natesan S, Adhimoolam K, Prabhakaran J, Singh R, Muthurajan R. Characterization of terminal flowering cowpea (Vigna unguiculata (L.) Walp.) mutants obtained by induced mutagenesis digs out the loss-of-function of phosphatidylethanolamine-binding protein. PLoS One 2023; 18:e0295509. [PMID: 38096151 PMCID: PMC10721064 DOI: 10.1371/journal.pone.0295509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 11/26/2023] [Indexed: 12/17/2023] Open
Abstract
Cowpea (Vigna unguiculata (L.) Walp) is one of the major food legume crops grown extensively in arid and semi-arid regions of the world. The determinate habit of cowpea has many advantages over the indeterminate and is well adapted to modern farming systems. Mutation breeding is an active research area to develop the determinate habit of cowpea. The present study aimed to develop new determinate habit mutants with terminal flowering (TFL) in locally well-adapted genetic backgrounds. Consequently, the seeds of popular cowpea cv P152 were irradiated with doses of gamma rays (200, 250, and, 300 Gy), and the M1 populations were grown. The M2 populations were produced from the M1 progenies and selected determinate mutants (TFLCM-1 and TFLCM-2) from the M2 generation (200 Gy) were forwarded up to the M5 generation to characterize the mutants and simultaneously they were crossed with P152 to develop a MutMap population. In the M5 generation, determinate mutants (80-81 days) were characterized by evaluating the TFL growth habit, longer peduncles (30.75-31.45 cm), erect pods (160°- 200°), number of pods per cluster (4-5 nos.), and early maturity. Further, sequencing analysis of the VuTFL1 gene in the determinate mutants and MutMap population revealed a single nucleotide transversion (A-T at 1196 bp) in the fourth exon and asparagine (N) to tyrosine (Y) amino acid change at the 143rd position of phosphatidylethanolamine-binding protein (PEBP). Notably, the loss of function PEPB with a higher confidence level modification of anti-parallel beta-sheets and destabilization of the protein secondary structure was observed in the mutant lines. Quantitative real-time PCR (qRT-PCR) analysis showed that the VuTFL1 gene was downregulated at the flowering stage in TFL mutants. Collectively, the insights garnered from this study affirm the effectiveness of induced mutation in modifying the plant's ideotype. The TFL mutants developed during this investigation have the potential to serve as a valuable resource for fostering determinate traits in future cowpea breeding programs and pave the way for mechanical harvesting.
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Affiliation(s)
- Vijayakumar Eswaramoorthy
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Thangaraj Kandasamy
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, Tamil Nadu, India
| | - Kalaimagal Thiyagarajan
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Vanniarajan Chockalingam
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, Tamil Nadu, India
| | - Souframanien Jegadeesan
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - Senthil Natesan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Karthikeyan Adhimoolam
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, South Korea
| | - Jeyakumar Prabhakaran
- Department of Crop Physiology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Ramji Singh
- Department of Plant Pathology, College of Agriculture, Sardar Vallabhbhai Patel University of Agricultural Sciences and Technology, Meerut, Uttar Pradesh, India
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
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Chirinskaite AV, Rotov AY, Ermolaeva ME, Tkachenko LA, Vaganova AN, Danilov LG, Fedoseeva KN, Kostin NA, Sopova JV, Firsov ML, Leonova EI. Does Background Matter? A Comparative Characterization of Mouse Models of Autosomal Retinitis Pigmentosa rd1 and Pde6b-KO. Int J Mol Sci 2023; 24:17180. [PMID: 38139011 PMCID: PMC10742838 DOI: 10.3390/ijms242417180] [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: 10/23/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Many retinal degenerative diseases result in vision impairment or permanent blindness due to photoreceptor loss or dysfunction. It has been observed that Pde6brd1 mice (rd1), which carry a spontaneous nonsense mutation in the pde6b gene, have a strong phenotypic similarity to patients suffering from autosomal recessive retinitis pigmentosa. In this study, we present a novel mouse model of retinitis pigmentosa generated through pde6b gene knockout using CRISPR/Cas9 technology. We compare this Pde6b-KO mouse model to the rd1 mouse model to gain insights into the progression of retinal degeneration. The functional assessment of the mouse retina and the tracking of degeneration dynamics were performed using electrophysiological methods, while retinal morphology was analyzed through histology techniques. Interestingly, the Pde6b-KO mouse model demonstrated a higher amplitude of photoresponse than the rd1 model of the same age. At postnatal day 12, the thickness of the photoreceptor layer in both mouse models did not significantly differ from that of control animals; however, by day 15, a substantial reduction was observed. Notably, the decline in the number of photoreceptors in the rd1 model occurred at a significantly faster rate. These findings suggest that the C3H background may play a significant role in the early stages of retinal degeneration.
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Affiliation(s)
- Angelina V. Chirinskaite
- Center of Transgenesis and Genome Editing, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia (J.V.S.)
| | - Alexander Yu. Rotov
- Laboratory of Evolution of Sense Organs, Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez Ave., 44, 194223 St. Petersburg, Russia (M.L.F.)
| | - Mariia E. Ermolaeva
- Laboratory of Evolution of Sense Organs, Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez Ave., 44, 194223 St. Petersburg, Russia (M.L.F.)
| | - Lyubov A. Tkachenko
- Department of Cytology and Histology, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia
| | - Anastasia N. Vaganova
- Institute of Translational Biomedicine, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia
| | - Lavrentii G. Danilov
- Department of Genetics and biotechnology, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia
| | - Ksenia N. Fedoseeva
- Resource Center “Molecular and Cell Technologies”, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia
| | - Nicolay A. Kostin
- Resource Center “Molecular and Cell Technologies”, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia
| | - Julia V. Sopova
- Center of Transgenesis and Genome Editing, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia (J.V.S.)
- Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia
| | - Michael L. Firsov
- Laboratory of Evolution of Sense Organs, Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez Ave., 44, 194223 St. Petersburg, Russia (M.L.F.)
| | - Elena I. Leonova
- Center of Transgenesis and Genome Editing, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia (J.V.S.)
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Pearce B, Jacobs C, Benjeddou M. Genetic preservation of SLC22A3 in the Admixed and Xhosa populations living in the Western Cape. Mol Biol Rep 2023; 50:10199-10206. [PMID: 37924453 PMCID: PMC10676312 DOI: 10.1007/s11033-023-08884-6] [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: 09/01/2023] [Accepted: 10/03/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Amphiphilic solute facilitator organic cation transporters mediate the movement of various endogenous and exogenous organic cations, including crucial drugs like metformin, oxaliplatin, and lamivudine. These transporters are now seen as a potential explanation for inter-individual differences in drug effectiveness, contributing to 15-30% of such variability due to genetic factors.The aim of this study was to determine the baseline minor allele frequency distribution of 18 known coding SNPs in the SLC22A3 gene of 278 Cape Admixed (130) and Xhosa (148) individuals residing in Cape Town, South Africa. METHODS A convenience sampling method was used for sample collection. DNA extraction and subsequent amplification of target sites was carried out according to standard established methodologies. All genotyping was performed using the SNaPshot™ mini-seuqencing platform. RESULTS This study found no genetic polymorphisms in the coding region of the SLC22A3 gene of both the Xhosa and Cape Admixed individuals investigated. CONCLUSION This study has shown that SLC22A3 coding SNPs observed in other populations are absent in the sample of both Cape Admixed and Xhosa individuals studied. The lack of protein sequence variation was consistent with other studies and may reflect the significant physiological role of human organic cation transporter 3 in maintaining cellular and organismal homeostasis.
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Affiliation(s)
- Brendon Pearce
- Genetics Department, Faculty of Agriscience, Stellenbosch University, Van Der Bijl Street, Stellenbosch, 7600, South Africa.
| | - Clifford Jacobs
- Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, 7535, South Africa
| | - Mongi Benjeddou
- Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, 7535, South Africa
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Pathira Kankanamge L, Mora A, Ondrechen MJ, Beuning PJ. Biochemical Activity of 17 Cancer-Associated Variants of DNA Polymerase Kappa Predicted by Electrostatic Properties. Chem Res Toxicol 2023; 36:1789-1803. [PMID: 37883788 PMCID: PMC10664756 DOI: 10.1021/acs.chemrestox.3c00233] [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: 08/06/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023]
Abstract
DNA damage and repair have been widely studied in relation to cancer and therapeutics. Y-family DNA polymerases can bypass DNA lesions, which may result from external or internal DNA damaging agents, including some chemotherapy agents. Overexpression of the Y-family polymerase human pol kappa can result in tumorigenesis and drug resistance in cancer. This report describes the use of computational tools to predict the effects of single nucleotide polymorphism variants on pol kappa activity. Partial Order Optimum Likelihood (POOL), a machine learning method that uses input features from Theoretical Microscopic Titration Curve Shapes (THEMATICS), was used to identify amino acid residues most likely involved in catalytic activity. The μ4 value, a metric obtained from POOL and THEMATICS that serves as a measure of the degree of coupling between one ionizable amino acid and its neighbors, was then used to identify which protein mutations are likely to impact the biochemical activity. Bioinformatic tools SIFT, PolyPhen-2, and FATHMM predicted most of these variants to be deleterious to function. Along with computational and bioinformatic predictions, we characterized the catalytic activity and stability of 17 cancer-associated DNA pol kappa variants. We identified pol kappa variants R48I, H105Y, G147D, G154E, V177L, R298C, E362V, and R470C as having lower activity relative to wild-type pol kappa; the pol kappa variants T102A, H142Y, R175Q, E210K, Y221C, N330D, N338S, K353T, and L383F were identified as being similar in catalytic efficiency to WT pol kappa. We observed that POOL predictions can be used to predict which variants have decreased activity. Predictions from bioinformatic tools like SIFT, PolyPhen-2, and FATHMM are based on sequence comparisons and therefore are complementary to POOL but are less capable of predicting biochemical activity. These bioinformatic and computational tools can be used to identify SNP variants with deleterious effects and altered biochemical activity from a large data set.
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Affiliation(s)
- Lakindu
S. Pathira Kankanamge
- Department
of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Alexandra Mora
- Department
of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Mary Jo Ondrechen
- Department
of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Penny J. Beuning
- Department
of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
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Larrea-Sebal A, Jebari-Benslaiman S, Galicia-Garcia U, Jose-Urteaga AS, Uribe KB, Benito-Vicente A, Martín C. Predictive Modeling and Structure Analysis of Genetic Variants in Familial Hypercholesterolemia: Implications for Diagnosis and Protein Interaction Studies. Curr Atheroscler Rep 2023; 25:839-859. [PMID: 37847331 PMCID: PMC10618353 DOI: 10.1007/s11883-023-01154-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2023] [Indexed: 10/18/2023]
Abstract
PURPOSE OF REVIEW Familial hypercholesterolemia (FH) is a hereditary condition characterized by elevated levels of low-density lipoprotein cholesterol (LDL-C), which increases the risk of cardiovascular disease if left untreated. This review aims to discuss the role of bioinformatics tools in evaluating the pathogenicity of missense variants associated with FH. Specifically, it highlights the use of predictive models based on protein sequence, structure, evolutionary conservation, and other relevant features in identifying genetic variants within LDLR, APOB, and PCSK9 genes that contribute to FH. RECENT FINDINGS In recent years, various bioinformatics tools have emerged as valuable resources for analyzing missense variants in FH-related genes. Tools such as REVEL, Varity, and CADD use diverse computational approaches to predict the impact of genetic variants on protein function. These tools consider factors such as sequence conservation, structural alterations, and receptor binding to aid in interpreting the pathogenicity of identified missense variants. While these predictive models offer valuable insights, the accuracy of predictions can vary, especially for proteins with unique characteristics that might not be well represented in the databases used for training. This review emphasizes the significance of utilizing bioinformatics tools for assessing the pathogenicity of FH-associated missense variants. Despite their contributions, a definitive diagnosis of a genetic variant necessitates functional validation through in vitro characterization or cascade screening. This step ensures the precise identification of FH-related variants, leading to more accurate diagnoses. Integrating genetic data with reliable bioinformatics predictions and functional validation can enhance our understanding of the genetic basis of FH, enabling improved diagnosis, risk stratification, and personalized treatment for affected individuals. The comprehensive approach outlined in this review promises to advance the management of this inherited disorder, potentially leading to better health outcomes for those affected by FH.
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Affiliation(s)
- Asier Larrea-Sebal
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080, Bilbao, Spain
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940, Leioa, Spain
- Fundación Biofisika Bizkaia, 48940, Leioa, Spain
| | - Shifa Jebari-Benslaiman
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080, Bilbao, Spain
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940, Leioa, Spain
| | - Unai Galicia-Garcia
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080, Bilbao, Spain
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940, Leioa, Spain
| | - Ane San Jose-Urteaga
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080, Bilbao, Spain
| | - Kepa B Uribe
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080, Bilbao, Spain
| | - Asier Benito-Vicente
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080, Bilbao, Spain
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940, Leioa, Spain
| | - César Martín
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080, Bilbao, Spain.
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940, Leioa, Spain.
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Liu W, Cao J, Shi X, Li Y, Qiao F, Wu Y. Genetic testing and diagnostic strategies of fetal skeletal dysplasia: a preliminary study in Wuhan, China. Orphanet J Rare Dis 2023; 18:336. [PMID: 37875969 PMCID: PMC10599061 DOI: 10.1186/s13023-023-02955-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 10/16/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Fetal skeletal dysplasia is a diverse group of degenerative diseases of bone and cartilage disorders that can lead to movement disorder and even death. This study aims to evaluate the diagnostic yield of sonographic examination and genetic testing for fetal skeletal dysplasia. METHODS From September 2015 to April 2021, the study investigated 24 cases with suspected short-limb fetuses, which were obtained from Tongji Hospital affiliated to Tongji Medical College of Huazhong University of Science and Technology. To identify the causative gene, multiple approaches (including karyotype analysis, copy number variations and whole exome sequencing) were performed on these fetuses. And further segregation analysis of the candidate variant was performed in parents by using Sanger sequencing. RESULTS ① Out of 24 cases, likely pathogenic variants in FGFR3, FBN2, COL1A2, CUL7 and DYNC2H1 were detected in 6 cases; pathogenic variants in FGFR3, IMPAD1 and GORAB were identified in other 6 cases; and variants in WNT1, FBN1, OBSL1, COL1A1, DYNC2H1 and NEK1, known as Variant of Undetermined Significance, were found in 4 cases. There were no variants detected in the rest 8 cases by the whole exome sequencing. ② Of 24 cases, 12 (50%) were found to carry variants (pathogenic or likely pathogenic) in seven genes with 12 variants. Four fetuses (16.7%) had variants of uncertain significance. CONCLUSION Genetic testing combining with ultrasound scanning enhances the accurate diagnosis of fatal skeletal dysplasia in utero, and then provides appropriate genetic counseling.
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Affiliation(s)
- Wanlu Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030 China
| | - Jing Cao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030 China
| | - Xinwei Shi
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030 China
| | - Yuqi Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030 China
| | - Fuyuan Qiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030 China
| | - Yuanyuan Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030 China
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20
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Ramzan A, Yousaf MA, Rashid MU, Basheera S, Malkani N. In-silico prediction of TGF-β1 non-synonymous variants and their impact on binding affinity to Fresolimumab. J Biomol Struct Dyn 2023:1-14. [PMID: 37817532 DOI: 10.1080/07391102.2023.2268198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/03/2023] [Indexed: 10/12/2023]
Abstract
TGF-β1 is a potent immunoregulatory cytokine that plays diverse roles in development, bone healing, fibrosis, and cancer. However, characterizing TGF-β1 gene variants is challenging because the structural and functional consequences of these variants are still undetermined. In this study, we aimed to perform an in-silico analysis of TGF-β1 non-synonymous variants and their pathogenic effects on the TGF-β1 protein. A total of 10,252 TGF-β1 SNPs were collected from the NCBI dbSNP database and in-silico tools (SIFT, PROVEAN, Mutation Taster, ClinVar, PolyPhen-2, CScape, MutPred, and ConSurf) were used. The in-silico predicted potential variants were further investigated for their binding to the TGF-β1 targeting drug "Fresolimumab". Molecular docking was performed using HADDOCK and confirmed by PRODIGY and PDBsum. The in-silico analysis predicted four potential TGF-β1 nsSNPs: E47G in the LAP domain of the propeptide and I22T, L28F, and E35D in the mature TGF-β1 peptide. HADDOCK and molecular dynamics simulations revealed that the I22T and E35D variants have higher binding affinity for Fresolimumab as compared to the wild type and L28F variants. Molecular dynamics simulations (100 ns) and principal component analysis showed that TGF-β1 variants influenced the protein structure and caused variations in the internal dynamics of protein complexes with the antibody. Among them, the E35D variant significantly destabilized the TGF-β1 protein structure, resulting in rearrangement in the binding site and affecting the interactions with the Fresolimumab. This study identified four variants that can affect the TGF-β1 protein structure and result in functional consequences such as impaired response to Fresolimumab.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ammara Ramzan
- Department of Zoology, GC University, Lahore, Pakistan
| | - Muhammad Abrar Yousaf
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Muhammad Usman Rashid
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, Pakistan
| | - Shefin Basheera
- Department of Biotechnology and Bioinformatics, Thiruvananthapuram, India
| | - Naila Malkani
- Department of Zoology, GC University, Lahore, Pakistan
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21
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Mallick I, Panchal P, Kadam S, Mohite P, Scheele J, Seiz W, Agarwal A, Sharma OP. In-silico identification and prioritization of therapeutic targets of asthma. Sci Rep 2023; 13:15706. [PMID: 37735578 PMCID: PMC10514284 DOI: 10.1038/s41598-023-42803-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
Asthma is a "common chronic disorder that affects the lungs causing variable and recurring symptoms like repeated episodes of wheezing, breathlessness, chest tightness and underlying inflammation. The interaction of these features of asthma determines the clinical manifestations and severity of asthma and the response to treatment" [cited from: National Heart, Lung, and Blood Institute. Expert Panel 3 Report. Guidelines for the Diagnosis and Management of Asthma 2007 (EPR-3). Available at: https://www.ncbi.nlm.nih.gov/books/NBK7232/ (accessed on January 3, 2023)]. As per the WHO, 262 million people were affected by asthma in 2019 that leads to 455,000 deaths ( https://www.who.int/news-room/fact-sheets/detail/asthma ). In this current study, our aim was to evaluate thousands of scientific documents and asthma associated omics datasets to identify the most crucial therapeutic target for experimental validation. We leveraged the proprietary tool Ontosight® Discover to annotate asthma associated genes and proteins. Additionally, we also collected and evaluated asthma related patient datasets through bioinformatics and machine learning based approaches to identify most suitable targets. Identified targets were further evaluated based on the various biological parameters to scrutinize their candidature for the ideal therapeutic target. We identified 7237 molecular targets from published scientific documents, 2932 targets from genomic structured databases and 7690 dysregulated genes from the transcriptomics and 560 targets from genomics mutational analysis. In total, 18,419 targets from all the desperate sources were analyzed and evaluated though our approach to identify most promising targets in asthma. Our study revealed IL-13 as one of the most important targets for asthma with approved drugs on the market currently. TNF, VEGFA and IL-18 were the other top targets identified to be explored for therapeutic benefit in asthma but need further clinical testing. HMOX1, ITGAM, DDX58, SFTPD and ADAM17 were the top novel targets identified for asthma which needs to be validated experimentally.
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Affiliation(s)
- Ishita Mallick
- Innoplexus Consulting Pvt. Ltd, 7th Floor, Midas Tower, Next to STPI Building, Phase 1, Hinjewadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Pradnya Panchal
- Innoplexus Consulting Pvt. Ltd, 7th Floor, Midas Tower, Next to STPI Building, Phase 1, Hinjewadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Smita Kadam
- Innoplexus Consulting Pvt. Ltd, 7th Floor, Midas Tower, Next to STPI Building, Phase 1, Hinjewadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Priyanka Mohite
- Innoplexus Consulting Pvt. Ltd, 7th Floor, Midas Tower, Next to STPI Building, Phase 1, Hinjewadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Jürgen Scheele
- Innoplexus AG, Frankfurter Str. 27, 65760, Eschborn, Germany
| | - Werner Seiz
- Innoplexus AG, Frankfurter Str. 27, 65760, Eschborn, Germany
| | - Amit Agarwal
- Innoplexus Consulting Pvt. Ltd, 7th Floor, Midas Tower, Next to STPI Building, Phase 1, Hinjewadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
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22
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Grunin M, de Jong S, Palmer EL, Jin B, Rinker D, Moth C, Capra A, Haines JL, Bush WS, den Hollander AI. Spatial Distribution of Missense Variants within Complement Proteins Associates with Age Related Macular Degeneration. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.28.23294686. [PMID: 37693462 PMCID: PMC10491280 DOI: 10.1101/2023.08.28.23294686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Purpose Genetic variants in complement genes are associated with age-related macular degeneration (AMD). However, many rare variants have been identified in these genes, but have an unknown significance, and their impact on protein function and structure is still unknown. We set out to address this issue by evaluating the spatial placement and impact on protein structureof these variants by developing an analytical pipeline and applying it to the International AMD Genomics Consortium (IAMDGC) dataset (16,144 AMD cases, 17,832 controls). Methods The IAMDGC dataset was imputed using the Haplotype Reference Consortium (HRC), leading to an improvement of over 30% more imputed variants, over the original 1000 Genomes imputation. Variants were extracted for the CFH , CFI , CFB , C9 , and C3 genes, and filtered for missense variants in solved protein structures. We evaluated these variants as to their placement in the three-dimensional structure of the protein (i.e. spatial proximity in the protein), as well as AMD association. We applied several pipelines to a) calculate spatial proximity to known AMD variants versus gnomAD variants, b) assess a variant's likelihood of causing protein destabilization via calculation of predicted free energy change (ddG) using Rosetta, and c) whole gene-based testing to test for statistical associations. Gene-based testing using seqMeta was performed using a) all variants b) variants near known AMD variants or c) with a ddG >|2|. Further, we applied a structural kernel adaptation of SKAT testing (POKEMON) to confirm the association of spatial distributions of missense variants to AMD. Finally, we used logistic regression on known AMD variants in CFI to identify variants leading to >50% reduction in protein expression from known AMD patient carriers of CFI variants compared to wild type (as determined by in vitro experiments) to determine the pipeline's robustness in identifying AMD-relevant variants. These results were compared to functional impact scores, ie CADD values > 10, which indicate if a variant may have a large functional impact genomewide, to determine if our metrics have better discriminative power than existing variant assessment methods. Once our pipeline had been validated, we then performed a priori selection of variants using this pipeline methodology, and tested AMD patient cell lines that carried those selected variants from the EUGENDA cohort (n=34). We investigated complement pathway protein expression in vitro , looking at multiple components of the complement factor pathway in patient carriers of bioinformatically identified variants. Results Multiple variants were found with a ddG>|2| in each complement gene investigated. Gene-based tests using known and novel missense variants identified significant associations of the C3 , C9 , CFB , and CFH genes with AMD risk after controlling for age and sex (P=3.22×10 -5 ;7.58×10 -6 ;2.1×10 -3 ;1.2×10 -31 ). ddG filtering and SKAT-O tests indicate that missense variants that are predicted to destabilize the protein, in both CFI and CFH, are associated with AMD (P=CFH:0.05, CFI:0.01, threshold of 0.05 significance). Our structural kernel approach identified spatial associations for AMD risk within the protein structures for C3, C9, CFB, CFH, and CFI at a nominal p-value of 0.05. Both ddG and CADD scores were predictive of reduced CFI protein expression, with ROC curve analyses indicating ddG is a better predictor (AUCs of 0.76 and 0.69, respectively). A priori in vitro analysis of variants in all complement factor genes indicated that several variants identified via bioinformatics programs PathProx/POKEMON in our pipeline via in vitro experiments caused significant change in complement protein expression (P=0.04) in actual patient carriers of those variants, via ELISA testing of proteins in the complement factor pathway, and were previously unknown to contribute to AMD pathogenesis. Conclusion We demonstrate for the first time that missense variants in complement genes cluster together spatially and are associated with AMD case/control status. Using this method, we can identify CFI and CFH variants of previously unknown significance that are predicted to destabilize the proteins. These variants, both in and outside spatial clusters, can predict in-vitro tested CFI protein expression changes, and we hypothesize the same is true for CFH . A priori identification of variants that impact gene expression allow for classification for previously classified as VUS. Further investigation is needed to validate the models for additional variants and to be applied to all AMD-associated genes.
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23
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Guo JH, Ma YS, Lin JW, Jiang GX, He J, Lu HM, Wu W, Diao X, Fan QY, Wu CY, Liu JB, Fu D, Hou LK. Whole-exome and targeted gene sequencing of large-cell lung carcinoma reveals recurrent mutations in the PI3K pathway. Br J Cancer 2023; 129:366-373. [PMID: 37179440 PMCID: PMC10338432 DOI: 10.1038/s41416-023-02301-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Large cell lung carcinoma (LCLC) is an exceptionally aggressive disease with a poor prognosis. At present, little is known about the molecular pathology of LCLC. METHODS Ultra-deep sequencing of cancer-related genes and exome sequencing were used to detect the LCLC mutational in 118 tumor-normal pairs. The cell function test was employed to confirm the potential carcinogenic mutation of PI3K pathway. RESULTS The mutation pattern is determined by the predominance of A > C mutations. Genes with a significant non-silent mutation frequency (FDR) < 0.05) include TP53 (47.5%), EGFR (13.6%) and PTEN (12.1%). Moreover, PI3K signaling (including EGFR, FGRG4, ITGA1, ITGA5, and ITGA2B) is the most mutated pathway, influencing 61.9% (73/118) of the LCLC samples. The cell function test confirmed that the potential carcinogenic mutation of PI3K pathway had a more malignant cell function phenotype. Multivariate analysis further revealed that patients with the PI3K signaling pathway mutations have a poor prognosis (P = 0.007). CONCLUSIONS These results initially identified frequent mutation of PI3K signaling pathways in LCLC and indicate potential targets for the treatment of this fatal type of LCLC.
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Affiliation(s)
- Jun-Hong Guo
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Yu-Shui Ma
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China
| | - Jie-Wei Lin
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Geng-Xi Jiang
- Department of Thoracic Surgery, Navy Military Medical University Affiliated Changhai Hospital, Shanghai, 200433, China
| | - Juan He
- Pharmacy Department, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Hai-Min Lu
- Department of Thoracic Surgery, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China
| | - Wei Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Xun Diao
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China
| | - Qi-Yu Fan
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China
| | - Chun-Yan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China.
| | - Ji-Bin Liu
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China.
| | - Da Fu
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China.
| | - Li-Kun Hou
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China.
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Saccuzzo EG, Youngblood HA, Lieberman RL. Myocilin misfolding and glaucoma: A 20-year update. Prog Retin Eye Res 2023; 95:101188. [PMID: 37217093 PMCID: PMC10330797 DOI: 10.1016/j.preteyeres.2023.101188] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
Mutations in the gene MYOC account for approximately 5% of cases of primary open angle glaucoma (POAG). MYOC encodes for the protein myocilin, a multimeric secreted glycoprotein composed of N-terminal coiled-coil (CC) and leucine zipper (LZ) domains that are connected via a disordered linker to a 30 kDa olfactomedin (OLF) domain. More than 90% of glaucoma-causing mutations are localized to the OLF domain. While myocilin is expressed in numerous tissues, mutant myocilin is only associated with disease in the anterior segment of the eye, in the trabecular meshwork. The prevailing pathogenic mechanism involves a gain of toxic function whereby mutant myocilin aggregates intracellularly instead of being secreted, which causes cell stress and an early timeline for TM cell death, elevated intraocular pressure, and subsequent glaucoma-associated retinal degeneration. In this review, we focus on the work our lab has conducted over the past ∼15 years to enhance our molecular understanding of myocilin-associated glaucoma, which includes details of the molecular structure and the nature of the aggregates formed by mutant myocilin. We conclude by discussing open questions, such as predicting phenotype from genotype alone, the elusive native function of myocilin, and translational directions enabled by our work.
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Affiliation(s)
- Emily G Saccuzzo
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr. NW, Atlanta, GA, 30332-0400, USA
| | - Hannah A Youngblood
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr. NW, Atlanta, GA, 30332-0400, USA
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr. NW, Atlanta, GA, 30332-0400, USA.
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Geraghty RM, Orr S, Olinger E, Neatu R, Barroso-Gil M, Mabillard H, Consortium GER, Wilson I, Sayer JA. Use of whole genome sequencing to determine the genetic basis of visceral myopathies including Prune Belly syndrome. JOURNAL OF RARE DISEASES (BERLIN, GERMANY) 2023; 2:9. [PMID: 37288276 PMCID: PMC10241726 DOI: 10.1007/s44162-023-00012-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/21/2023] [Indexed: 06/09/2023]
Abstract
Objectives/aims The visceral myopathies (VM) are a group of disorders characterised by poorly contractile or acontractile smooth muscle. They manifest in both the GI and GU tracts, ranging from megacystis to Prune Belly syndrome. We aimed to apply a bespoke virtual genetic panel and describe novel variants associated with this condition using whole genome sequencing data within the Genomics England 100,000 Genomes Project. Methods We screened the Genomics England 100,000 Genomes Project rare diseases database for patients with VM-related phenotypes. These patients were screened for sequence variants and copy number variants (CNV) in ACTG2, ACTA2, MYH11, MYLK, LMOD1, CHRM3, MYL9, FLNA and KNCMA1 by analysing whole genome sequencing data. The identified variants were analysed using variant effect predictor online tool, and any possible segregation in other family members and novel missense mutations was modelled using in silico tools. The VM cohort was also used to perform a genome-wide variant burden test in order to identify confirm gene associations in this cohort. Results We identified 76 patients with phenotypes consistent with a diagnosis of VM. The range of presentations included megacystis/microcolon hypoperistalsis syndrome, Prune Belly syndrome and chronic intestinal pseudo-obstruction. Of the patients in whom we identified heterozygous ACTG2 variants, 7 had likely pathogenic variants including 1 novel likely pathogenic allele. There were 4 patients in whom we identified a heterozygous MYH11 variant of uncertain significance which leads to a frameshift and a predicted protein elongation. We identified one family in whom we found a heterozygous variant of uncertain significance in KCNMA1 which in silico models predicted to be disease causing and may explain the VM phenotype seen. We did not find any CNV changes in known genes leading to VM-related disease phenotypes. In this phenotype selected cohort, ACTG2 is the largest monogenic cause of VM-related disease accounting for 9% of the cohort, supported by a variant burden test approach, which identified ACTG2 variants as the largest contributor to VM-related phenotypes. Conclusions VM are a group of disorders that are not easily classified and may be given different diagnostic labels depending on their phenotype. Molecular genetic analysis of these patients is valuable as it allows precise diagnosis and aids understanding of the underlying disease manifestations. We identified ACTG2 as the most frequent genetic cause of VM. We recommend a nomenclature change to 'autosomal dominant ACTG2 visceral myopathy' for patients with pathogenic variants in ACTG2 and associated VM phenotypes. Supplementary Information The online version contains supplementary material available at 10.1007/s44162-023-00012-z.
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Affiliation(s)
- Robert M. Geraghty
- Renal Services, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Freeman Road, Newcastle Upon Tyne, NE7 7DN UK
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Sarah Orr
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Eric Olinger
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Ruxandra Neatu
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Miguel Barroso-Gil
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Holly Mabillard
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Genomics England Research Consortium
- Renal Services, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Freeman Road, Newcastle Upon Tyne, NE7 7DN UK
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
- National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle Upon Tyne, NE4 5PL UK
| | - Ian Wilson
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - John A. Sayer
- Renal Services, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Freeman Road, Newcastle Upon Tyne, NE7 7DN UK
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
- National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle Upon Tyne, NE4 5PL UK
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26
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Tan WX, Sim X, Khoo CM, Teo AKK. Prioritization of genes associated with type 2 diabetes mellitus for functional studies. Nat Rev Endocrinol 2023:10.1038/s41574-023-00836-1. [PMID: 37169822 DOI: 10.1038/s41574-023-00836-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/28/2023] [Indexed: 05/13/2023]
Abstract
Existing therapies for type 2 diabetes mellitus (T2DM) show limited efficacy or have adverse effects. Numerous genetic variants associated with T2DM have been identified, but progress in translating these findings into potential drug targets has been limited. Here, we describe the tools and platforms available to identify effector genes from T2DM-associated coding and non-coding variants and prioritize them for functional studies. We discuss QSER1 and SLC12A8 as examples of genes that have been identified as possible T2DM candidate genes using these tools and platforms. We suggest further approaches, including the use of sequencing data with increased sample size and ethnic diversity, single-cell omics data for analyses, glycaemic trait associations to predict gene function and, potentially, human induced pluripotent stem cell 'village' cultures, to strengthen current gene functionalization workflows. Effective prioritization of T2DM-associated genes for experimental validation could expedite our understanding of the genetic mechanisms responsible for T2DM to facilitate the use of precision medicine in its treatment.
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Affiliation(s)
- Wei Xuan Tan
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Chin Meng Khoo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Adrian K K Teo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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27
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Pratim Das P, Jyoti Kalita M, Jyoti Talukdar A, Mohd Khan F, Dutta K, Kalita S, Goswami N, Hazarika G, Samudrala G, Ghaznavi Idris M, Dutta S, Medhi S. Evaluation and analysis of novel germline variants in ethanol metabolism pathway genes predisposition to liver disease. Gene 2023; 873:147451. [PMID: 37150234 DOI: 10.1016/j.gene.2023.147451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 05/09/2023]
Abstract
The pathogenetic events of liver disease are seemingly determined by factors linked to ethanol metabolism. The variations in genes encoding enzymes of the ethanol metabolic pathway can influence exposure to alcohol and thus may act as risk factors for the development of liver disease. The present study aimed to understand the genetic aspect of germline variations in ethanol metabolic pathway genes in two major categories of liver disease i.e. ALD and NAFLD. Targeted Re-sequencing was performed in the two disease categories along with healthy control followed by an assessment and evaluation of the variants in a case vs control manner. The pathogenicity prediction was evaluated using SIFT, PolyPhen, PROVEN, LRT, CADD, FATHMM, EIGEN, REVEL and VarSome, while MD simulation of a novel significant variant was performed using the GROMACS 5.1.4 package. The annotation of targeted re-sequencing results revealed 2172 variants in different locations of the genes. Upon recurrent assessment predominantly focusing on exonic missense variants from these genes of the alcohol metabolism pathway, the ALDH1L2 [c.337C>G, p.Pro113Ala, (rs199841702)] variant was found highly significant with comprehensive results. The amino acid substitution tool that predicted protein stability due to a point mutation showed a decrease in stability. The genotyping distribution of the identified novel variant in the population revealed that heterozygosity is significantly distributed in ALD patients. However, the predominant association between the inherited variant and the cause of developing disease needs further robust study.
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Affiliation(s)
- Partha Pratim Das
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Manash Jyoti Kalita
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Anjan Jyoti Talukdar
- Department of Medicine, Gauhati Medical College & Hospital, Guwahati, Assam-781032
| | - Faraz Mohd Khan
- School of Life sciences, Jawaharlal Nehru University, New Delhi, 110067
| | - Kalpajit Dutta
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Simanta Kalita
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Nabajyoti Goswami
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Gautam Hazarika
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | | | | | - Sangit Dutta
- Department of Medicine, Gauhati Medical College & Hospital, Guwahati, Assam-781032
| | - Subhash Medhi
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014.
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Tam B, Qin Z, Zhao B, Wang SM, Lei CL. Integration of deep learning with Ramachandran plot molecular dynamics simulation for genetic variant classification. iScience 2023; 26:106122. [PMID: 36879825 PMCID: PMC9984559 DOI: 10.1016/j.isci.2023.106122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/07/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Functional classification of genetic variants is a key for their clinical applications in patient care. However, abundant variant data generated by the next-generation DNA sequencing technologies limit the use of experimental methods for their classification. Here, we developed a protein structure and deep learning (DL)-based system for genetic variant classification, DL-RP-MDS, which comprises two principles: 1) Extracting protein structural and thermodynamics information using the Ramachandran plot-molecular dynamics simulation (RP-MDS) method, 2) combining those data with an unsupervised learning model of auto-encoder and a neural network classifier to identify the statistical significance patterns of the structural changes. We observed that DL-RP-MDS provided higher specificity than over 20 widely used in silico methods in classifying the variants of three DNA damage repair genes: TP53, MLH1, and MSH2. DL-RP-MDS offers a powerful platform for high-throughput genetic variant classification. The software and online application are available at https://genemutation.fhs.um.edu.mo/DL-RP-MDS/.
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Affiliation(s)
- Benjamin Tam
- Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Zixin Qin
- Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chon Lok Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau SAR, China
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29
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Variant Landscape of 15 Genes Involved in Corneal Dystrophies: Report of 30 Families and Comprehensive Analysis of the Literature. Int J Mol Sci 2023; 24:ijms24055012. [PMID: 36902444 PMCID: PMC10003302 DOI: 10.3390/ijms24055012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Corneal dystrophies (CDs) represent a group of inherited diseases characterized by the progressive deposit of abnormal materials in the cornea. This study aimed to describe the variant landscape of 15 genes responsible for CDs based on a cohort of Chinese families and a comparative analysis of literature reports. Families with CDs were recruited from our eye clinic. Their genomic DNA was analyzed using exome sequencing. The detected variants were filtered using multi-step bioinformatics and confirmed using Sanger sequencing. Previously reported variants in the literature were summarized and evaluated based on the gnomAD database and in-house exome data. In 30 of 37 families with CDs, 17 pathogenic or likely pathogenic variants were detected in 4 of the 15 genes, including TGFBI, CHST6, SLC4A11, and ZEB1. A comparative analysis of large datasets revealed that 12 of the 586 reported variants are unlikely causative of CDs in monogenic mode, accounting for 61 of 2933 families in the literature. Of the 15 genes, the gene most frequently implicated in CDs was TGFBI (1823/2902, 62.82% of families), followed by CHST6 (483/2902, 16.64%) and SLC4A11 (201/2902, 6.93%). This study presents, for the first time, the landscape of pathogenic and likely pathogenic variants in the 15 genes responsible for CDs. Awareness of frequently misinterpreted variants, such as c.1501C>A, p.(Pro501Thr) in TGFBI, is crucial in the era of genomic medicine.
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30
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Scelsi HF, Hill KR, Barlow BM, Martin MD, Lieberman RL. Quantitative differentiation of benign and misfolded glaucoma-causing myocilin variants on the basis of protein thermal stability. Dis Model Mech 2023; 16:286212. [PMID: 36579626 PMCID: PMC9844228 DOI: 10.1242/dmm.049816] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/28/2022] [Indexed: 12/30/2022] Open
Abstract
Accurate predictions of the pathogenicity of mutations associated with genetic diseases are key to the success of precision medicine. Inherited missense mutations in the myocilin (MYOC) gene, within its olfactomedin (OLF) domain, constitute the strongest genetic link to primary open-angle glaucoma via a toxic gain of function, and thus MYOC is an attractive precision-medicine target. However, not all mutations in MYOC cause glaucoma, and common variants are expected to be neutral polymorphisms. The Genome Aggregation Database (gnomAD) lists ∼100 missense variants documented within OLF, all of which are relatively rare (allele frequency <0.001%) and nearly all are of unknown pathogenicity. To distinguish disease-causing OLF variants from benign OLF variants, we first characterized the most prevalent population-based variants using a suite of cellular and biophysical assays, and identified two variants with features of aggregation-prone familial disease variants. Next, we considered all available biochemical and clinical data to demonstrate that pathogenic and benign variants can be differentiated statistically based on a single metric: the thermal stability of OLF. Our results motivate genotyping MYOC in patients for clinical monitoring of this widespread, painless and irreversible ocular disease.
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Affiliation(s)
- Hailee F. Scelsi
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr. NW, Atlanta, GA 30332-0400, USA
| | - Kamisha R. Hill
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr. NW, Atlanta, GA 30332-0400, USA
| | - Brett M. Barlow
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr. NW, Atlanta, GA 30332-0400, USA
| | - Mackenzie D. Martin
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr. NW, Atlanta, GA 30332-0400, USA
| | - Raquel L. Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr. NW, Atlanta, GA 30332-0400, USA,Author for correspondence ()
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31
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Boudeau S, Ramakodi MP, Zhou Y, Liu JC, Ragin C, Kulathinal RJ. Extensive set of African ancestry-informative markers (AIMs) to study ancestry and population health. Front Genet 2023; 14:1061781. [PMID: 36911410 PMCID: PMC9997643 DOI: 10.3389/fgene.2023.1061781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/20/2023] [Indexed: 02/16/2023] Open
Abstract
Introduction: Human populations are often highly structured due to differences in genetic ancestry among groups, posing difficulties in associating genes with diseases. Ancestry-informative markers (AIMs) aid in the detection of population stratification and provide an alternative approach to map population-specific alleles to disease. Here, we identify and characterize a novel set of African AIMs that separate populations of African ancestry from other global populations including those of European ancestry. Methods: Using data from the 1000 Genomes Project, highly informative SNP markers from five African subpopulations were selected based on estimates of informativeness (In) and compared against the European population to generate a final set of 46,737 African ancestry-informative markers (AIMs). The AIMs identified were validated using an independent set and functionally annotated using tools like SIFT, PolyPhen. They were also investigated for representation of commonly used SNP arrays. Results: This set of African AIMs effectively separates populations of African ancestry from other global populations and further identifies substructure between populations of African ancestry. When a subset of these AIMs was studied in an independent dataset, they differentiated people who self-identify as African American or Black from those who identify their ancestry as primarily European. Most of the AIMs were found to be in their intergenic and intronic regions with only 0.6% in the coding regions of the genome. Most of the commonly used SNP array investigated contained less than 10% of the AIMs. Discussion: While several functional annotations of both coding and non-coding African AIMs are supported by the literature and linked these high-frequency African alleles to diseases in African populations, more effort is needed to map genes to diseases in these genetically diverse subpopulations. The relative dearth of these African AIMs on current genotyping platforms (the array with the highest fraction, llumina's Omni 5, harbors less than a quarter of AIMs), further demonstrates a greater need to better represent historically understudied populations.
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Affiliation(s)
- Samantha Boudeau
- Department of Biology, Temple University, Philadelphia, PA, United States.,Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,African Caribbean Cancer Consortium, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Meganathan P Ramakodi
- Department of Biology, Temple University, Philadelphia, PA, United States.,Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,African Caribbean Cancer Consortium, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Yan Zhou
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Jeffrey C Liu
- Department of Otolaryngology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States.,Department of Surgical Oncology, Fox chase Cancer center, Philadelphia, PA, United States
| | - Camille Ragin
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,African Caribbean Cancer Consortium, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Rob J Kulathinal
- Department of Biology, Temple University, Philadelphia, PA, United States.,African Caribbean Cancer Consortium, Fox Chase Cancer Center, Philadelphia, PA, United States
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32
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Valverde-Hernández JC, Flores-Cruz A, Chavarría-Soley G, Silva de la Fuente S, Campos-Sánchez R. Frequencies of variants in genes associated with dyslipidemias identified in Costa Rican genomes. Front Genet 2023; 14:1114774. [PMID: 37065472 PMCID: PMC10098023 DOI: 10.3389/fgene.2023.1114774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/14/2023] [Indexed: 04/18/2023] Open
Abstract
Dyslipidemias are risk factors in diseases of significant importance to public health, such as atherosclerosis, a condition that contributes to the development of cardiovascular disease. Unhealthy lifestyles, the pre-existence of diseases, and the accumulation of genetic variants in some loci contribute to the development of dyslipidemia. The genetic causality behind these diseases has been studied primarily on populations with extensive European ancestry. Only some studies have explored this topic in Costa Rica, and none have focused on identifying variants that can alter blood lipid levels and quantifying their frequency. To fill this gap, this study focused on identifying variants in 69 genes involved in lipid metabolism using genomes from two studies in Costa Rica. We contrasted the allelic frequencies with those of groups reported in the 1000 Genomes Project and gnomAD and identified potential variants that could influence the development of dyslipidemias. In total, we detected 2,600 variants in the evaluated regions. However, after various filtering steps, we obtained 18 variants that have the potential to alter the function of 16 genes, nine variants have pharmacogenomic or protective implications, eight have high risk in Variant Effect Predictor, and eight were found in other Latin American genetic studies of lipid alterations and the development of dyslipidemia. Some of these variants have been linked to changes in blood lipid levels in other global studies and databases. In future studies, we propose to confirm at least 40 variants of interest from 23 genes in a larger cohort from Costa Rica and Latin American populations to determine their relevance regarding the genetic burden for dyslipidemia. Additionally, more complex studies should arise that include diverse clinical, environmental, and genetic data from patients and controls and functional validation of the variants.
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Affiliation(s)
| | - Andrés Flores-Cruz
- Centro de Investigación en Biología Celular y Molecular, University of Costa Rica, San José, Costa Rica
| | - Gabriela Chavarría-Soley
- Centro de Investigación en Biología Celular y Molecular, University of Costa Rica, San José, Costa Rica
- Escuela de Biología, University of Costa Rica, San José, Costa Rica
| | - Sandra Silva de la Fuente
- Centro de Investigación en Biología Celular y Molecular, University of Costa Rica, San José, Costa Rica
| | - Rebeca Campos-Sánchez
- Centro de Investigación en Biología Celular y Molecular, University of Costa Rica, San José, Costa Rica
- *Correspondence: Rebeca Campos-Sánchez,
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Lopes TJS, Rios RA, Rios TN, Alencar BM, Ferreira MV, Morishita E. Computational analyses reveal fundamental properties of the AT structure related to thrombosis. BIOINFORMATICS ADVANCES 2022; 3:vbac098. [PMID: 36698764 PMCID: PMC9838315 DOI: 10.1093/bioadv/vbac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/28/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
Summary Blood coagulation is a vital process for humans and other species. Following an injury to a blood vessel, a cascade of molecular signals is transmitted, inhibiting and activating more than a dozen coagulation factors and resulting in the formation of a fibrin clot that ceases the bleeding. In this process, antithrombin (AT), encoded by the SERPINC1 gene is a key player regulating the clotting activity and ensuring that it stops at the right time. In this sense, mutations to this factor often result in thrombosis-the excessive coagulation that leads to the potentially fatal formation of blood clots that obstruct veins. Although this process is well known, it is still unclear why even single residue substitutions to AT lead to drastically different phenotypes. In this study, to understand the effect of mutations throughout the AT structure, we created a detailed network map of this protein, where each node is an amino acid, and two amino acids are connected if they are in close proximity in the three-dimensional structure. With this simple and intuitive representation and a machine-learning framework trained using genetic information from more than 130 patients, we found that different types of thrombosis have emerging patterns that are readily identifiable. Together, these results demonstrate how clinical features, genetic data and in silico analysis are converging to enhance the diagnosis and treatment of coagulation disorders. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | - Ricardo A Rios
- Institute of Computing, Federal University of Bahia, Salvador 40170-110, Brazil
| | - Tatiane N Rios
- Institute of Computing, Federal University of Bahia, Salvador 40170-110, Brazil
| | - Brenno M Alencar
- Institute of Computing, Federal University of Bahia, Salvador 40170-110, Brazil
| | - Marcos V Ferreira
- Institute of Computing, Federal University of Bahia, Salvador 40170-110, Brazil
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Yi Z, Li S, Wang S, Xiao X, Sun W, Zhang Q. Clinical features and genetic spectrum of NMNAT1-associated retinal degeneration. Eye (Lond) 2022; 36:2279-2285. [PMID: 34837036 PMCID: PMC9674661 DOI: 10.1038/s41433-021-01853-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/14/2021] [Accepted: 11/10/2021] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES To systematically analyse the NMNAT1 variant spectrum and frequency, the associated phenotypic characteristics, and potential genotype-phenotype correlations based on our data and literature review. METHODS Biallelic potential pathogenic variants (PPV) in NMNAT1 were collected from our in-house exome sequencing data. Whole-genome sequencing was conducted subsequently for patients with only one heterozygous PPV detected in NMNAT1. The clinical data were reviewed and evaluated in detail. Furthermore, the literature was reviewed for reports of NMNAT1 variants and their associated phenotypes. RESULTS Eleven NMNAT1 variants, including two novel variants, were detected in 8 families from our cohort. All of the 9 available patients showed generalized tapetoretinal dystrophy at an early age (88.9% in the first decade), and disciform macular atrophy was identified in six patients from five unrelated families. Among a total of 125 patients from 8 families of our cohort and 91 families reported by the available literature, 92.9% patients showed onset of disease in the first year after birth, and 89.0% patients showed visual acuity of 0.05 or lower. All of the 39 patients with fundus photos available presented disciform macular atrophy with generalized tapetoretinal dystrophy. Most (54/80, 67.5%) of causative NMNAT1 variants were missense. The most frequent variants in Caucasian and Asian population are p.E257K and p.R237C, respectively. CONCLUSIONS Early-onset age, disciform macular atrophy with generalized tapetoretinal dystrophy, and poor visual acuity are the typical features of NMNAT1-associated retinal degeneration. Different variant hot spots of NMNAT1 were observed in different populations.
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Affiliation(s)
- Zhen Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Siyu Wang
- Department of Ophthalmology, Li Chuan People's Hospital, Enshi, HuBei, 445400, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China.
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Caswell RC, Gunning AC, Owens MM, Ellard S, Wright CF. Assessing the clinical utility of protein structural analysis in genomic variant classification: experiences from a diagnostic laboratory. Genome Med 2022; 14:77. [PMID: 35869530 PMCID: PMC9308257 DOI: 10.1186/s13073-022-01082-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/04/2022] [Indexed: 12/21/2022] Open
Abstract
Background The widespread clinical application of genome-wide sequencing has resulted in many new diagnoses for rare genetic conditions, but testing regularly identifies variants of uncertain significance (VUS). The remarkable rise in the amount of genomic data has been paralleled by a rise in the number of protein structures that are now publicly available, which may have clinical utility for the interpretation of missense and in-frame insertions or deletions. Methods Within a UK National Health Service genomic medicine diagnostic laboratory, we investigated the number of VUS over a 5-year period that were evaluated using protein structural analysis and how often this analysis aided variant classification. Results We found 99 novel missense and in-frame variants across 67 genes that were initially classified as VUS by our diagnostic laboratory using standard variant classification guidelines and for which further analysis of protein structure was requested. Evidence from protein structural analysis was used in the re-assessment of 64 variants, of which 47 were subsequently reclassified as pathogenic or likely pathogenic and 17 remained as VUS. We identified several case studies where protein structural analysis aided variant interpretation by predicting disease mechanisms that were consistent with the observed phenotypes, including loss-of-function through thermodynamic destabilisation or disruption of ligand binding, and gain-of-function through de-repression or escape from proteasomal degradation. Conclusions We have shown that using in silico protein structural analysis can aid classification of VUS and give insights into the mechanisms of pathogenicity. Based on our experience, we propose a generic evidence-based workflow for incorporating protein structural information into diagnostic practice to facilitate variant classification. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01082-2.
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Ressler AK, Goldstein DB. Using reported pathogenic variants to identify therapeutic opportunities for genetic diseases. Mol Genet Genomic Med 2022; 11:e2097. [PMID: 36374045 PMCID: PMC9834146 DOI: 10.1002/mgg3.2097] [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: 09/08/2020] [Accepted: 11/03/2022] [Indexed: 11/16/2022] Open
Abstract
PURPOSE Drug development strategies for genetic diseases depend critically on accurate knowledge of how pathogenic variants cause disease. For some well-studied genes, the direct effects of pathogenic variants are well documented as loss-of-function, gain-of-function or hypermorphic, or a combination of the two. For many genes, however, even the direction of effect of variants remains unclear. Classification of Mendelian disease genes in terms of whether pathogenic variants are loss- or gain-of-function would directly inform drug development strategies. METHODS We leveraged the recent dramatic increase in reported pathogenic variants to provide a novel approach to inferring the direction of effect of pathogenic variants. Specifically, we quantify the ratio of reported pathogenic variants that are missense compared to loss-of-function. RESULTS We first show that for many genes that cause dominant Mendelian disease, the ratio of reported pathogenic missense variants is diagnostic of whether the gene causes disease through loss- or gain-of-function, or a combination. Second, we identify a set of genes that appear to cause disease largely or entirely through gain-of-function or hypermorphic pathogenic variants. CONCLUSIONS We suggest a set of 16 genes suitable for drug developmental efforts utilizing direct inhibition.
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Affiliation(s)
- Andrew K. Ressler
- Institute for Genomic MedicineColumbia UniversityNew YorkNew YorkUSA
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Toh H, Yang C, Formenti G, Raja K, Yan L, Tracey A, Chow W, Howe K, Bergeron LA, Zhang G, Haase B, Mountcastle J, Fedrigo O, Fogg J, Kirilenko B, Munegowda C, Hiller M, Jain A, Kihara D, Rhie A, Phillippy AM, Swanson SA, Jiang P, Clegg DO, Jarvis ED, Thomson JA, Stewart R, Chaisson MJP, Bukhman YV. A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes. BMC Biol 2022; 20:245. [DOI: 10.1186/s12915-022-01427-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022] Open
Abstract
Abstract
Background
The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic.
Results
We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse.
Conclusions
Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.
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Lai A, Soucy A, El Achkar CM, Barkovich AJ, Cao Y, DiStefano M, Evenson M, Guerrini R, Knight D, Lee YS, Mefford HC, Miller DT, Mirzaa G, Mochida G, Rodan LH, Patel M, Smith L, Spencer S, Walsh CA, Yang E, Yuskaitis CJ, Yu T, Poduri A. The ClinGen Brain Malformation Variant Curation Expert Panel: Rules for somatic variants in AKT3, MTOR, PIK3CA, and PIK3R2. Genet Med 2022; 24:2240-2248. [PMID: 35997716 PMCID: PMC9883838 DOI: 10.1016/j.gim.2022.07.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 01/30/2023] Open
Abstract
PURPOSE Postzygotic (somatic) variants in the mTOR pathway genes cause a spectrum of distinct developmental abnormalities. Accurate classification of somatic variants in this group of disorders is crucial for affected individuals and their families. METHODS The ClinGen Brain Malformation Variant Curation Expert Panel was formed to curate somatic variants associated with developmental brain malformations. We selected the genes AKT3, MTOR, PIK3CA, and PIK3R2 as the first set of genes to provide additional specifications to the 2015 American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) sequence variant interpretation guidelines, which currently focus solely on germline variants. RESULTS A total of 24 of the original 28 ACMG/AMP criteria required modification. Several modifications used could be applied to other genes and disorders in which somatic variants play a role: 1) using variant allele fraction differences as evidence that somatic mutagenesis occurred as a proxy for de novo variation, 2) incorporating both somatic and germline evidence, and 3) delineating phenotype on the basis of variable tissue expression. CONCLUSION We have established a framework for rigorous interpretation of somatic mosaic variants, addressing issues unique to somatic variants that will be applicable to many genes and conditions.
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Affiliation(s)
- Abbe Lai
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA; Epilepsy Genetics Program, Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Aubrie Soucy
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Christelle Moufawad El Achkar
- Epilepsy Genetics Program, Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA; Department of Neurology, Harvard Medical School, Boston, MA
| | | | - Yang Cao
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Marina DiStefano
- Broad Institute of MIT and Harvard, Cambridge, MA; Precision Health Program, Geisinger, Danville, PA
| | - Michael Evenson
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Department of Neuroscience, Meyer Children's University Hospital, University of Florence, Florence, Italy
| | - Devon Knight
- Epilepsy Genetics Program, Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA
| | - Yi-Shan Lee
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Heather C Mefford
- Center for Pediatric Neurological Disease Research, St. Jude Hospital, Memphis, TN
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Ghayda Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA; Department of Pediatrics, University of Washington, Seattle, WA
| | - Ganesh Mochida
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA; Department of Neurology, Harvard Medical School, Boston, MA
| | - Mayher Patel
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Lacey Smith
- Epilepsy Genetics Program, Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA
| | - Sara Spencer
- Division of Reproductive Genetics, Northwestern Medicine, Chicago, IL
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA; Department of Neurology, Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA
| | - Edward Yang
- Department of Radiology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Christopher J Yuskaitis
- Epilepsy Genetics Program, Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA; Department of Neurology, Harvard Medical School, Boston, MA
| | - Timothy Yu
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA; Department of Neurology, Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA.
| | - Annapurna Poduri
- Epilepsy Genetics Program, Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA; Department of Neurology, Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA.
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Li Z, Li K, Sun Y, Jiang X, Liu J, Li J, Fang L, Li G, Guan Q, Xu C. Mutations in GCK May Lead to MODY2 by Reducing Glycogen Synthesis. Adv Biol (Weinh) 2022; 6:e2200097. [PMID: 35770790 DOI: 10.1002/adbi.202200097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/18/2022] [Indexed: 01/28/2023]
Abstract
Dysfunction of glucokinase (GCK) caused by mutations in the GCK gene is the main cause of maturity-onset diabetes of the young type-2 (MODY2, also known as GCK-MODY), which is usually present in adolescence or young adulthood. MODY2 is characterized by mild, stable fasting hyperglycemia that presents at birth, usually 5.4-8.3 mmol L-1 , and rarely develops complications from diabetes. The treatment of MODY2 prefers a manageable diet rather than the use of insulin. Previous studies have identified GCK mutations only by online software prediction or enzyme kinetic analysis and thermolability assays which are complicated to be conducted. In this study, six mutations in the GCK gene, including four novel mutations and two mutations that are previously reported, are identified. All the six locations are highly conserved according to the sequencing alignment. Moreover, missense mutations are strongly predicted to be pathogenic using online programs. Functional studies show that mutations in GCK mutation do not affect insulin secretion but affect glycogen synthesis. These findings demonstrate that GCK mutations decrease glycogen synthesis, which leads to hyperglycemia in MODY2. Meanwhile, this study provides a new perspective and methods for identifying pathogenic mutations in GCK.
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Affiliation(s)
- Zongyue Li
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.,Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, Shandong, 250021, China.,Shandong Institute of Endocrine and Metabolic Disease, Jinan, Shandong, 250021, China
| | - Kunxia Li
- Department of Pediatric, Yantai Yuhuangding Hospital affiliated to Qingdao University, Qingdao, Shandong, 266000, China
| | - Yan Sun
- Department of Pediatrics, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Xiuyun Jiang
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Jia Liu
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Jingyi Li
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.,Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, Shandong, 250021, China.,Shandong Institute of Endocrine and Metabolic Disease, Jinan, Shandong, 250021, China
| | - Li Fang
- Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, Shandong, 250021, China.,Shandong Institute of Endocrine and Metabolic Disease, Jinan, Shandong, 250021, China.,Department of Endocrinology, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Guimei Li
- Department of Pediatrics, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Qingbo Guan
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Chao Xu
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.,Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, Shandong, 250021, China.,Shandong Institute of Endocrine and Metabolic Disease, Jinan, Shandong, 250021, China.,Department of Endocrinology, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
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Jawad Ul Hasnain M, Amin F, Ghani A, Ahmad S, Rahman Z, Aslam T, Pervez MT. Structural and Functional Impact of Damaging Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs) on Human VPS35 Protein Using Computational Approaches. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3715-3724. [PMID: 34613918 DOI: 10.1109/tcbb.2021.3118054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Parkinson's disease is the second most common progressive neurodegenerative movement disorder. Mutations in retromer complex subunit and VPS35 represent the second most common cause of late-onset familial Parkinson's disease. The mutation in VPS35 can disrupt the normal protein functions resulting in Parkinson's disease. The aim of this study was the identification of deleterious missense Single Nucleotide Polymorphisms (nsSNPs) and their structural and functional impact on the VPS35 protein. In this study, several insilico tools were used to identify deleterious and disease-associated nsSNPs. 3D structure of VPS35 protein was constructed through MODELLER 9.2, normalized using FOLDX, and evaluated through RAMPAGE and ERRAT whereas, FOLDX was used for mutagenesis. 25 ligands were obtained from literature and docked using PyRx 0.8 software. Based on the binding affinity, five ligands i.e., PG4, MSE, GOL, EDO, and CAF were further analyzed. Molecular Dynamic simulation analysis was performed using GROMACS 5.1.4, where temperature, pressure, density, RMSD, RMSF, Rg, and SASA graphs were analyzed. The results showed that the mutations Y67H, R524W, and D620N had a structural and functional impact on the VPS35 protein. The current findings will help in appropriate drug design against the disease caused by these mutations in a large population using in-vitro study.
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Anterior Umbilication of Lens in a Family with Congenital Cataracts Associated with a Missense Mutation of MIP Gene. Genes (Basel) 2022; 13:genes13111987. [DOI: 10.3390/genes13111987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/04/2022] Open
Abstract
Congenital cataracts (CCs) have significant genotypic and phenotypic heterogeneity. The major intrinsic protein (MIP) gene, one of the causative genes of CCs, plays a vital role in maintaining the homeostasis and transparency of the lens. In this study, we identified a unique phenotype of anterior umbilication of the lens in a four-generation pedigree with CCs. All patients in the observed family had nystagmus, nuclear cataracts, and elongated axial lengths compared with their healthy counterparts except for patient I:2, whose axial length was unavailable, and patientII:4, who had total cataracts. We confirmed, using Sanger sequencing based on whole-exon sequencing (WES) data, that all patients carried a heterozygous variant NM_012064.4:c.97C > T (NP_036196.1:p.R33C) in their MIP gene. To our knowledge, 29 variants of the human MIP gene and the relative phenotypes associated with CCs have been identified. Nevertheless, this is the first report on the anterior umbilication of the lens with nuclear or total opacity caused by the c.97C > T (p.R33C) variant in the MIP gene. These results also provide evidence that the elongated axial length might be associated with this variant. This study further confirms the phenotypic heterogeneity of CCs.
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McCarthy-Leo C, Darwiche F, Tainsky MA. DNA Repair Mechanisms, Protein Interactions and Therapeutic Targeting of the MRN Complex. Cancers (Basel) 2022; 14:5278. [PMID: 36358700 PMCID: PMC9656488 DOI: 10.3390/cancers14215278] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 08/27/2023] Open
Abstract
Repair of a DNA double-strand break relies upon a pathway of proteins to identify damage, regulate cell cycle checkpoints, and repair the damage. This process is initiated by a sensor protein complex, the MRN complex, comprised of three proteins-MRE11, RAD50, and NBS1. After a double-stranded break, the MRN complex recruits and activates ATM, in-turn activating other proteins such as BRCA1/2, ATR, CHEK1/2, PALB2 and RAD51. These proteins have been the focus of many studies for their individual roles in hereditary cancer syndromes and are included on several genetic testing panels. These panels have enabled us to acquire large amounts of genetic data, much of which remains a challenge to interpret due to the presence of variants of uncertain significance (VUS). While the primary aim of clinical testing is to accurately and confidently classify variants in order to inform medical management, the presence of VUSs has led to ambiguity in genetic counseling. Pathogenic variants within MRN complex genes have been implicated in breast, ovarian, prostate, colon cancers and gliomas; however, the hundreds of VUSs within MRE11, RAD50, and NBS1 precludes the application of these data in genetic guidance of carriers. In this review, we discuss the MRN complex's role in DNA double-strand break repair, its interactions with other cancer predisposing genes, the variants that can be found within the three MRN complex genes, and the MRN complex's potential as an anti-cancer therapeutic target.
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Affiliation(s)
- Claire McCarthy-Leo
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Fatima Darwiche
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Michael A. Tainsky
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Molecular Therapeutics Program, Karmanos Cancer Institute at Wayne State University School of Medicine, Detroit, MI 48201, USA
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Zhang Y, Wang Z, Hu G, Li J, Chen Y, Jiang Y, Zhong H, Liu X, Hu C, Peng H, Xu Y, Cheng Z, Zhang G. A novel germline HAVCR2 (TIM-3) compound heterozygous mutation is related to hemophagocytic lymphohistiocytic syndrome in EBV-positive peripheral T-cell lymphoma (NOS) with down-regulated TIM-3 signaling. Front Oncol 2022; 12:870676. [PMID: 36212426 PMCID: PMC9539911 DOI: 10.3389/fonc.2022.870676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
Recently, it have been reported that Hepatitis A Virus-Cellular Receptor 2(HAVCR2,encoding T-cell immunoglobulin and Mucin-Containing Protein 3[TIM3]) mutations are associated with severe hemophagocytic syndrome(HLH) in subcutaneous panniculitis-like T-cell lymphoma(SPTCL),and there are also frequent mutations in sporadic SPTCL, suggesting the individuals harboring HAVCR2(TIM-3) germline mutations are highly susceptible to familial or sporadic SPTCL. Here, we identify a novel germline compound heterozygous mutation of TIM-3 gene,c.245A>G (p.Tyr82Cys) and c.265C>T(p.Arg89Cys) variations in a single familial case with EBV-positive peripheral T-cell lymphoma(NOS),accompanied HLH;we also detected Tyr82Cys germline mutation in TIM-3 gene in one sporadic patient with cutaneous T cell lymphoma. We screened the distributive frequencies for TIM-3 mutations in healthy controls(n=87), B-(n=79) or T-cell lymphoma(n=25) not SPTCL, and the results showed that the mutation was found in two out of 25 patients with T-cell lymphoma but was not detected in 79 patients with B-cell lymphoma nor in a group of 87 controls. The mRNA expression of TIM-3 on primary cells and transfected HEK293 cells reduced significantly, indicating Tyr82Cys and Arg89Cys mutations is a loss-of function mutations on TIM-3,resulting in a weakened TIM-3 signaling. Our results suggest Tyr82Cys TIM-3 germline mutations are not only limited in SPTCL, and also occurred in other types of T-cell lymphoma, especially complicated HLH. TIM-3 mutations may be an predisposing factor for T-cell lymphoma and molecular marker for auxiliary diagnosis in T cell lymphoma,especially complicated with HLH.
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Affiliation(s)
- Yang Zhang
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhihua Wang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Guoyu Hu
- Department of Hematology, The Affiliated Zhuzhou Hospital of Xiangya Medical College, Central South University, Zhuzhou, China
| | - Jieping Li
- Department of Hematology, The Central Hospital of Changsha City, Changsha, China
| | - Yongheng Chen
- Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
| | - Yi Jiang
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Haiying Zhong
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xianling Liu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Chunhong Hu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Honglin Peng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yunxiao Xu
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhao Cheng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Guangsen Zhang, ; Zhao Cheng,
| | - Guangsen Zhang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Guangsen Zhang, ; Zhao Cheng,
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Rajcsanyi LS, Zheng Y, Fischer-Posovszky P, Wabitsch M, Hebebrand J, Hinney A. Prevalence estimates of putatively pathogenic leptin variants in the gnomAD database. PLoS One 2022; 17:e0266642. [PMID: 36121795 PMCID: PMC9484668 DOI: 10.1371/journal.pone.0266642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/26/2022] [Indexed: 11/18/2022] Open
Abstract
Homozygosity for pathogenic variants in the leptin gene leads to congenital leptin deficiency causing severe early-onset obesity. This monogenic form of obesity has mainly been detected in patients from consanguineous families. Prevalence estimates for the general population using the Exome Aggregation Consortium (ExAC) database reported a low frequency of leptin mutations. One in approximately 15 million individuals will be homozygous for a deleterious leptin variant. With the present study, we aimed to extend these findings utilizing the augmented Genome Aggregation Database (gnomAD) v2.1.1 including more than 140,000 samples. In total, 68 non-synonymous and 7 loss-of-function leptin variants were deposited in gnomAD. By predicting functional implications with the help of in silico tools, like SIFT, PolyPhen2 and MutationTaster2021, the prevalence of hetero- and homozygosity for putatively pathogenic variants (n = 32; pathogenic prediction by at least two tools) in the leptin gene were calculated. Across all populations, the estimated prevalence for heterozygosity for functionally relevant variants was approximately 1:2,100 and 1:17,830,000 for homozygosity. This prevalence deviated between the individual populations. Accordingly, people from East Asia and individuals of mixed ethnicities (‘Others’) were at greater risk to carry a possibly damaging leptin variant. Generally, this study emphasises the scarcity of pathogenic leptin variants in the general population with varying prevalence for distinct study groups.
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Affiliation(s)
- Luisa Sophie Rajcsanyi
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany
| | - Yiran Zheng
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany
| | | | - Martin Wabitsch
- Department of Paediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany
- * E-mail:
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Adadey SM, Wonkam-Tingang E, Alves de Souza Rios L, Aboagye ET, Esoh K, Manyisa N, De Kock C, Awandare GA, Mowla S, Wonkam A. Cell-based analysis of CLIC5A and SLC12A2 variants associated with hearing impairment in two African families. Front Genet 2022; 13:924904. [PMID: 36035115 PMCID: PMC9403182 DOI: 10.3389/fgene.2022.924904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/18/2022] [Indexed: 01/18/2023] Open
Abstract
We have previously reported CLIC5A and SLC12A2 variants in two families from Cameroon and Ghana, segregating non-syndromic hearing impairment (NSHI). In this study, biological assays were performed to further functionally investigate the pathogenicity of CLIC5 [c.224T>C; p.(L75P)] and SCL12A2 [c.2935G>A: p.(E979K)] variants. Ectopic expression of the proteins in a cell model shows that compared to wild-type, both the CLIC5A and SLC12A2 variants were overexpressed. The mutant CLIC5A protein appears as aggregated perinuclear bodies while the wild-type protein was evenly distributed in the cytoplasm. Furthermore, cells transfected with the wild-type CLIC5A formed thin membrane filopodia-like protrusions which were absent in the CLIC5A mutant expressing and control cells. On the other hand, the wild-type SLC12A2 expressing cells had an axon-like morphology which was not observed in the mutant expressing and control cells. A network analysis revealed that CLIC5A can interact with at least eight proteins at the base of the stereocilia. This study has generated novel biological data associated with the pathogenicity of targeted variants in CLIC5A and SLC12A2, found in two African families, and therefore expands our understanding of their pathobiology in hearing impairment.
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Affiliation(s)
- Samuel Mawuli Adadey
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Biochemistry, Cell, and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Edmond Wonkam-Tingang
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Leonardo Alves de Souza Rios
- Department of Pathology, Division of Haematology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Elvis Twumasi Aboagye
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Biochemistry, Cell, and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Kevin Esoh
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Noluthando Manyisa
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Carmen De Kock
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gordon A. Awandare
- Department of Biochemistry, Cell, and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Shaheen Mowla
- Department of Pathology, Division of Haematology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Ambroise Wonkam
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- McKusick-Nathans Institute and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure. Nat Commun 2022; 13:3895. [PMID: 35794153 PMCID: PMC9259657 DOI: 10.1038/s41467-022-31686-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 06/29/2022] [Indexed: 12/12/2022] Open
Abstract
Most known pathogenic mutations occur in protein-coding regions of DNA and change the way proteins are made. Taking protein structure into account has therefore provided great insight into the molecular mechanisms underlying human genetic disease. While there has been much focus on how mutations can disrupt protein structure and thus cause a loss of function (LOF), alternative mechanisms, specifically dominant-negative (DN) and gain-of-function (GOF) effects, are less understood. Here, we investigate the protein-level effects of pathogenic missense mutations associated with different molecular mechanisms. We observe striking differences between recessive vs dominant, and LOF vs non-LOF mutations, with dominant, non-LOF disease mutations having much milder effects on protein structure, and DN mutations being highly enriched at protein interfaces. We also find that nearly all computational variant effect predictors, even those based solely on sequence conservation, underperform on non-LOF mutations. However, we do show that non-LOF mutations could potentially be identified by their tendency to cluster in three-dimensional space. Overall, our work suggests that many pathogenic mutations that act via DN and GOF mechanisms are likely being missed by current variant prioritisation strategies, but that there is considerable scope to improve computational predictions through consideration of molecular disease mechanisms. Most known pathogenic mutations occur in protein-coding regions of DNA and change the way proteins are made. Here the authors analyse the locations of thousands of human disease mutations and their predicted effects on protein structure and show that,while loss-of-function mutations tend to be highly disruptive, non-loss-of-function mutations are in general much milder at a protein structural level.
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Zhai Q, van der Lee M, van Gelder T, Swen JJ. Why We Need to Take a Closer Look at Genetic Contributions to CYP3A Activity. Front Pharmacol 2022; 13:912618. [PMID: 35784699 PMCID: PMC9243486 DOI: 10.3389/fphar.2022.912618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Cytochrome P450 3A (CYP3A) subfamily enzymes are involved in the metabolism of 40% of drugs in clinical use. Twin studies have indicated that 66% of the variability in CYP3A4 activity is hereditary. Yet, the complexity of the CYP3A locus and the lack of distinct drug metabolizer phenotypes has limited the identification and clinical application of CYP3A genetic variants compared to other Cytochrome P450 enzymes. In recent years evidence has emerged indicating that a substantial part of the missing heritability is caused by low frequency genetic variation. In this review, we outline the current pharmacogenomics knowledge of CYP3A activity and discuss potential future directions to improve our genetic knowledge and ability to explain CYP3A variability.
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Gao Y, Wu D, Chen B, Chen Y, Zhang Q, Zhao P. Rare Variants in Novel Candidate Genes Associated With Nonsyndromic Patent Ductus Arteriosus Identified With Whole-Exome Sequencing. Front Genet 2022; 13:921925. [PMID: 35734438 PMCID: PMC9207465 DOI: 10.3389/fgene.2022.921925] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/09/2022] [Indexed: 11/18/2022] Open
Abstract
Background: Patent ductus arteriosus (PDA) is one of the most common congenital heart defects causing pulmonary hypertension, infective endocarditis, and even death. The important role of genetics in determining spontaneous ductal closure has been well-established. However, as many of the identified variants are rare, thorough identification of the associated genetic factors is necessary to further explore the genetic etiology of PDA. Methods: We performed whole-exome sequencing (WES) on 39 isolated nonsyndromic PDA patients and 100 healthy controls. Rare variants and novel genes were identified through bioinformatic filtering strategies. The expression patterns of candidate genes were explored in human embryo heart samples. Results: Eighteen rare damaging variants of six novel PDA-associated genes (SOX8, NES, CDH2, ANK3, EIF4G1, and HIPK1) were newly identified, which were highly expressed in human embryo hearts. Conclusions: WES is an efficient diagnostic tool for exploring the genetic pathogenesis of PDA. These findings contribute new insights into the molecular basis of PDA and may inform further studies on genetic risk factors for congenital heart defects.
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Affiliation(s)
- Ying Gao
- Department of Pediatric, Shidong Hospital, Shanghai, China
| | - Dan Wu
- Department of Pediatric, Shidong Hospital, Shanghai, China
| | - Bo Chen
- Department of Cardiothoracic Surgery, School of Medicine, Heart Center, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yinghui Chen
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qi Zhang
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pengjun Zhao
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Pengjun Zhao,
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van den Berg FF, Issa Y, Vreijling JP, Lerch MM, Weiss FU, Besselink MG, Baas F, Boermeester MA, van Santvoort HC. Whole-exome Sequencing Identifies SLC52A1 and ZNF106 Variants as Novel Genetic Risk Factors for (Early) Multiple-organ Failure in Acute Pancreatitis. Ann Surg 2022; 275:e781-e788. [PMID: 33427755 DOI: 10.1097/sla.0000000000004312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
OBJECTIVE The aim of this study was to identify genetic variants associated with early multiple organ failure (MOF) in acute pancreatitis. SUMMARY BACKGROUND DATA MOF is a life-threatening complication of acute pancreatitis, and risk factors are largely unknown, especially in early persistent MOF. Genetic risk factors are thought to enhance severity in complex diseases such as acute pancreatitis. METHODS A 2-phase study design was conducted. First, we exome sequenced 9 acute pancreatitis patients with early persistent MOF and 9 case-matched patients with mild edematous pancreatitis (phenotypic extremes) from our initial Dutch cohort of 387 patients. Secondly, 48 candidate variants that were overrepresented in MOF patients and 10 additional variants known from literature were genotyped in a replication cohort of 286 Dutch and German patients. RESULTS Exome sequencing resulted in 161,696 genetic variants, of which the 38,333 non-synonymous variants were selected for downstream analyses. Of these, 153 variants were overrepresented in patients with multiple-organ failure, as compared with patients with mild acute pancreatitis. In total, 58 candidate variants were genotyped in the joined Dutch and German replication cohort. We found the rs12440118 variant of ZNF106 to be overrepresented in patients with MOF (minor allele frequency 20.4% vs 11.6%, Padj=0.026). Additionally, SLC52A1 rs346821 was found to be overrepresented (minor allele frequency 48.0% vs 42.4%, Padj= 0.003) in early MOF. None of the variants known from literature were associated.Conclusions: This study indicates that SLC52A1, a riboflavin plasma membrane transporter, and ZNF106, a zinc finger protein, may be involved in disease progression toward (early) MOF in acute pancreatitis.
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Affiliation(s)
- Fons F van den Berg
- Department of Surgery, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yama Issa
- Department of Surgery, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen P Vreijling
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Markus M Lerch
- Departments of Clinical Chemistry, Genetics and Pediatrics, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Frank Ulrich Weiss
- Departments of Clinical Chemistry, Genetics and Pediatrics, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Marc G Besselink
- Department of Surgery, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Frank Baas
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Marja A Boermeester
- Department of Surgery, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hjalmar C van Santvoort
- Department of Surgery, University Medical Center, Utrecht, The Netherlands; Department of Surgery, St. Antonius Hospital, Nieuwegein, The Netherlands
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Livesey BJ, Marsh JA. Interpreting protein variant effects with computational predictors and deep mutational scanning. Dis Model Mech 2022; 15:275742. [PMID: 35736673 PMCID: PMC9235876 DOI: 10.1242/dmm.049510] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Computational predictors of genetic variant effect have advanced rapidly in recent years. These programs provide clinical and research laboratories with a rapid and scalable method to assess the likely impacts of novel variants. However, it can be difficult to know to what extent we can trust their results. To benchmark their performance, predictors are often tested against large datasets of known pathogenic and benign variants. These benchmarking data may overlap with the data used to train some supervised predictors, which leads to data re-use or circularity, resulting in inflated performance estimates for those predictors. Furthermore, new predictors are usually found by their authors to be superior to all previous predictors, which suggests some degree of computational bias in their benchmarking. Large-scale functional assays known as deep mutational scans provide one possible solution to this problem, providing independent datasets of variant effect measurements. In this Review, we discuss some of the key advances in predictor methodology, current benchmarking strategies and how data derived from deep mutational scans can be used to overcome the issue of data circularity. We also discuss the ability of such functional assays to directly predict clinical impacts of mutations and how this might affect the future need for variant effect predictors.
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Affiliation(s)
- Benjamin J Livesey
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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