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Wang C, Li M, Liu Z, Guo Y, Liu H, Zhao P. Genetic evaluation in indeterminate acute liver failure: A post hoc analysis. Arab J Gastroenterol 2024; 25:125-128. [PMID: 38705812 DOI: 10.1016/j.ajg.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 01/28/2024] [Accepted: 03/20/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND AND STUDY AIMS There are limited data regarding indeterminate acute liver failure (ALF). The study aims to perform a post hoc analysis using genetic methods for the ALF cases with indeterminate etiology. PATIENTS AND METHODS Stored blood samples from these patients with indeterminate ALF were collected. Whole-exome sequencing (WES) was used to evaluate the pathogenesis of indeterminate ALF. RESULTS A total of 16 samples from 11 adult patients and 5 pediatric patients with indeterminate ALF were available. Among the adult patients, one female patient was identified with two heterozygous variants (c.2333G > T (p.Arg778Leu) and c.2310C > G (p.Leu770 = )) in the adenosine triphosphatase copper-transporting beta (ATP7B) gene, and two male patients were found to harbor heterozygous and homozygous variants (c.686C > A (p.Pro229Gln) plus homozygousvariantA(TA)6TAAinsTA (-), andc.1456 T > G (p.Tyr486Asp) plus c.211G > A (p.Gly71Arg)) in the uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) gene. For the pediatric patients, single heterozygous variant (c.2890C > T (p.Arg964Cys)) in the polymerase gamma (POLG) gene was found in 1 male child, and two heterozygous variants (c.1909A > G (p.Lys637Glu) and c.3646G > A (p.Val1216Ile)) in the tetratricopeptide repeat domain 37 (TTC37) gene were found in 1 female child. No variants clinically associated with known liver diseases were revealed in the remaining patients. CONCLUSION These results expand the knowledge of ALF with indeterminate etiology. WES is helpful to reveal possible candidate genes for indeterminate ALF, but incomplete consistency between the genotype and phenotype in some cases still challenge the accurate diagnosis.
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Affiliation(s)
- Chunya Wang
- Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China
| | - Meina Li
- Faculty of Military Health Services, Second Military Medical University, Shanghai 200433,China
| | - Zhenhua Liu
- Department of Pathology, Seventh Medical Center, Chinese PLA General Hospital, Beijing 100010, China
| | - Yupeng Guo
- College of Public Health, Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Huijuan Liu
- Fifth Medical Center (formerly Beijing 302 Hospital), Chinese PLA General Hospital, Beijing 100039, China
| | - Pan Zhao
- Fifth Medical Center (formerly Beijing 302 Hospital), Chinese PLA General Hospital, Beijing 100039, China.
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Konkwo C, Chowdhury S, Vilarinho S. Genetics of liver disease in adults. Hepatol Commun 2024; 8:e0408. [PMID: 38551385 PMCID: PMC10984672 DOI: 10.1097/hc9.0000000000000408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/30/2024] [Indexed: 04/02/2024] Open
Abstract
Chronic liver disease stands as a significant global health problem with an estimated 2 million annual deaths across the globe. Combining the use of next-generation sequencing technologies with evolving knowledge in the interpretation of genetic variation across the human genome is propelling our understanding, diagnosis, and management of both rare and common liver diseases. Here, we review the contribution of risk and protective alleles to common forms of liver disease, the rising number of monogenic diseases affecting the liver, and the role of somatic genetic variants in the onset and progression of oncological and non-oncological liver diseases. The incorporation of genomic information in the diagnosis and management of patients with liver disease is driving the beginning of a new era of genomics-informed clinical hepatology practice, facilitating personalized medicine, and improving patient care.
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Affiliation(s)
- Chigoziri Konkwo
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - Shanin Chowdhury
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Silvia Vilarinho
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
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Wiethoff H, Mohr I, Fichtner A, Merle U, Schirmacher P, Weiss KH, Longerich T. Metallothionein: a game changer in histopathological diagnosis of Wilson disease. Histopathology 2023; 83:936-948. [PMID: 37661783 DOI: 10.1111/his.15041] [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: 04/12/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023]
Abstract
AIMS Wilson disease (WD) is a genetic disorder of copper metabolism caused by mutations in the ATP7B gene. Toxic copper accumulation leads to hepatic, neurologic, and psychiatric disorders with variable presentation. Metallothionein (MT) immunohistochemistry was proposed as a diagnostic marker. METHODS MT immunohistochemistry was performed on liver specimens of WD patients (n = 64) and control cases (n = 160) including acute liver failure, steatotic liver disease, autoimmune hepatitis, normal liver, primary biliary cholangitis, primary and secondary sclerosing cholangitis, and progressive familial intrahepatic cholestasis. The optimal cutoff for detection of WD was determined by receiver operating characteristic (ROC) analysis. RESULTS At least moderate staining in >50% of hepatocytes was observed in 81% of analysed liver specimens (n = 56/69) of WD patients, while only five control cases showed this staining pattern. The sensitivity, specificity, and accuracy for a new diagnosis of WD were 85.7%, 96.9%, and 94.9%, respectively. Sensitivity in nonfibrotic patients was 70.6% and this MT pattern was robust in small biopsies. The hepatic copper concentration was similar between MT-positive and MT-negative liver samples (P > 0.05). Zinc treatment may induce hepatocellular MT expression. Kayser-Fleischer rings (50% versus 15%) and neurologic disorders (50% versus 13%) were significantly more prevalent in MT-negative compared to MT-positive WD patients, respectively. CONCLUSION MT immunostaining is an excellent biomarker for histological diagnosis of WD, should be incorporated in the diagnostic work-up of patients with potential WD, and is useful in a modified Leipzig score.
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Affiliation(s)
- Hendrik Wiethoff
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Isabelle Mohr
- Department of Gastroenterology, Infectious Diseases and Intoxication, Internal Medicine IV, Heidelberg University Hospital, Heidelberg, Germany
| | - Alexander Fichtner
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
| | - Uta Merle
- Department of Gastroenterology, Infectious Diseases and Intoxication, Internal Medicine IV, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Karl H Weiss
- Department of Internal Medicine, Salem Medical Center, Heidelberg, Germany
| | - Thomas Longerich
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
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Monfrini E, Pelucchi S, Hollmén M, Viitala M, Mariani R, Bertola F, Majore S, Di Fonzo A, Piperno A. A form of inherited hyperferritinemia associated with bi-allelic pathogenic variants of STAB1. Am J Hum Genet 2023; 110:1436-1443. [PMID: 37490907 PMCID: PMC10432174 DOI: 10.1016/j.ajhg.2023.07.004] [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: 02/14/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/27/2023] Open
Abstract
Hyperferritinemia is a frequent finding in several conditions, both genetic and acquired. We previously studied eleven healthy subjects from eight different families presenting with unexplained hyperferritinemia. Their findings suggested the existence of an autosomal-recessive disorder. We carried out whole-exome sequencing to detect the genetic cause of hyperferritinemia. Immunohistochemistry and flow cytometry assays were performed on liver biopsies and monocyte-macrophages to confirm the pathogenic role of the identified candidate variants. Through a combined approach of whole-exome sequencing and homozygosity mapping, we found bi-allelic STAB1 variants in ten subjects from seven families. STAB1 encodes the multifunctional scavenger receptor stabilin-1. Immunohistochemistry and flow cytometry analyses showed absent or markedly reduced stabilin-1 in liver samples, monocytes, and monocyte-derived macrophages. Our findings show a strong association between otherwise unexplained hyperferritinemia and bi-allelic STAB1 mutations suggesting the existence of another genetic cause of hyperferritinemia without iron overload and an unexpected function of stabilin-1 in ferritin metabolism.
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Affiliation(s)
- Edoardo Monfrini
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milano, Milano, Italy; Foundation IRCCS Cà Granda Ospedale Maggiore Policlinico, Neurology Unit, Milano, Italy
| | - Sara Pelucchi
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Maija Hollmén
- MediCity Research Laboratory and InFLAMES flagship, University of Turku, Turku, Finland
| | - Miro Viitala
- MediCity Research Laboratory and InFLAMES flagship, University of Turku, Turku, Finland
| | - Raffaella Mariani
- Centre for Rare Disease - Disorders of Iron Metabolism, Fondazione IRCCS, San Gerardo dei Tintori, European Reference Network - EuroBloodNet, Monza, Italy
| | - Francesca Bertola
- Cytogenetics and Medical Genetics, Fondazione IRCCS, San Gerardo dei Tintori, Monza, Italy
| | - Silvia Majore
- Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Roma, Italy
| | - Alessio Di Fonzo
- Foundation IRCCS Cà Granda Ospedale Maggiore Policlinico, Neurology Unit, Milano, Italy
| | - Alberto Piperno
- Centre for Rare Disease - Disorders of Iron Metabolism, Fondazione IRCCS, San Gerardo dei Tintori, European Reference Network - EuroBloodNet, Monza, Italy; Centro Ricerca Tettamanti, Monza, Italy.
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Xu WQ, Wang RM, Dong Y, Wu ZY. Pathogenicity of Intronic and Synonymous Variants of ATP7B in Wilson Disease. J Mol Diagn 2023; 25:57-67. [PMID: 36343861 DOI: 10.1016/j.jmoldx.2022.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/30/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Wilson disease (WD) is a hereditary disorder of copper metabolism, resulting from mutations within ATP7B. Early diagnosis is essential for affected individuals. However, there are still patients with clinically suspected WD who do not have detectable pathogenic variants, which makes diagnosis difficult and delays treatment. This study included such patients from the authors' center and screened for the full-length sequence of ATP7B by next-generation sequencing. Newly identified synonymous and intronic variants were then analyzed with in silico tools. A minigene system was constructed to determine the pathogenicity of these variants in terms of splicing and blood RNA extraction, and RT-PCR experiments were performed on several patients to verify the splicing alterations. The phenotypes of the patients were also analyzed. Fourteen suspected pathogenic variants, including nine synonymous and five intronic variants, were detected in 12 patients with clinically suspected WD. Among them, four synonymous variants (c.1050G>A, c.1122C>G, c.3243G>A, and c.4014T>A) and four intronic variants (c.1543 +40G>A, c.1707+6_1707+16del, c.1870-49A>G, and c.2731-67A>G) resulted in splicing changes in ATP7B. After the above analysis, the diagnosis of WD could be confirmed in eight clinically suspected patients with WD who showed a late age of onset.
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Affiliation(s)
- Wan-Qing Xu
- Departments of Neurology and Medical Genetics, Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Rou-Min Wang
- Departments of Neurology and Medical Genetics, Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Dong
- Departments of Neurology and Medical Genetics, Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhi-Ying Wu
- Departments of Neurology and Medical Genetics, Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China.
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Rodrigues KF, Yong WTL, Bhuiyan MSA, Siddiquee S, Shah MD, Venmathi Maran BA. Current Understanding on the Genetic Basis of Key Metabolic Disorders: A Review. BIOLOGY 2022; 11:biology11091308. [PMID: 36138787 PMCID: PMC9495729 DOI: 10.3390/biology11091308] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 12/02/2022]
Abstract
Simple Summary Metabolic disorders (MD) are a challenge to healthcare systems; the emergence of the modern socio-economic system has led to a profound change in lifestyles in terms of dietary habits, exercise regimens, and behavior, all of which complement the genetic factors associated with MD. Diabetes Mellitus and Familial hypercholesterolemia are two of the 14 most widely researched MD, as they pose the greatest challenge to the public healthcare system and have an impact on productivity and the economy. Research findings have led to the development of new therapeutic molecules for the mitigation of MD as well as the invention of experimental strategies, which target the genes themselves via gene editing and RNA interference. Although these approaches may herald the emergence of a new toolbox to treat MD, the current therapeutic approaches still heavily depend on substrate reduction, dietary restrictions based on genetic factors, exercise, and the maintenance of good mental health. The development of orphan drugs for the less common MD such as Krabbe, Farber, Fabry, and Gaucher diseases, remains in its infancy, owing to the lack of investment in research and development, and this has driven the development of personalized therapeutics based on gene silencing and related technologies. Abstract Advances in data acquisition via high resolution genomic, transcriptomic, proteomic and metabolomic platforms have driven the discovery of the underlying factors associated with metabolic disorders (MD) and led to interventions that target the underlying genetic causes as well as lifestyle changes and dietary regulation. The review focuses on fourteen of the most widely studied inherited MD, which are familial hypercholesterolemia, Gaucher disease, Hunter syndrome, Krabbe disease, Maple syrup urine disease, Metachromatic leukodystrophy, Mitochondrial encephalopathy lactic acidosis stroke-like episodes (MELAS), Niemann-Pick disease, Phenylketonuria (PKU), Porphyria, Tay-Sachs disease, Wilson’s disease, Familial hypertriglyceridemia (F-HTG) and Galactosemia based on genome wide association studies, epigenetic factors, transcript regulation, post-translational genetic modifications and biomarker discovery through metabolomic studies. We will delve into the current approaches being undertaken to analyze metadata using bioinformatic approaches and the emerging interventions using genome editing platforms as applied to animal models.
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Affiliation(s)
- Kenneth Francis Rodrigues
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia
- Correspondence: (K.F.R.); (B.A.V.M.); Tel.: +60-16-2096905 (B.A.V.M.)
| | - Wilson Thau Lym Yong
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia
| | | | | | - Muhammad Dawood Shah
- Borneo Marine Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia
| | - Balu Alagar Venmathi Maran
- Borneo Marine Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia
- Correspondence: (K.F.R.); (B.A.V.M.); Tel.: +60-16-2096905 (B.A.V.M.)
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Sarkar A, Panati K, Narala VR. Code inside the codon: The role of synonymous mutations in regulating splicing machinery and its impact on disease. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108444. [PMID: 36307006 DOI: 10.1016/j.mrrev.2022.108444] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
In eukaryotes, precise pre-mRNA processing, including alternative splicing, is essential to carry out the intricate protein translation process. Both point mutations (that alter the translated protein sequence) and synonymous mutations (that do not alter the translated protein sequence) are capable of affecting the splicing process. Synonymous mutations are known to affect gene expression via altering mRNA stability, mRNA secondary structure, splicing processes, and translational kinetics. In higher eukaryotes, precise splicing is regulated by three weakly conserved cis-elements, 5' and 3' splice sites and the branch site. Many other cis-acting elements (exonic/intronic splicing enhancers and silencers) and trans-acting splicing factors (serine and arginine-rich proteins and heterogeneous nuclear ribonucleoproteins) have also been found to enhance or suppress the splicing process. The appearance of synonymous mutations in cis-acting elements can alter the splicing process by changing the binding pattern of splicing factors to exonic splicing enhancers or silencer motifs. This results in exon skipping, intron retention, and various other forms of alternative splicing, eventually leading to the emergence of a wide range of diseases. The focus of this review is to elucidate the role of synonymous mutations and their impact on abnormal splicing mechanisms. Further, this study highlights the function of synonymous mutation in mediating abnormal splicing in cancer and development of X-linked, and autosomal inherited diseases.
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Affiliation(s)
- Avik Sarkar
- Department of Zoology, Vidyasagar University, Midnapore, West Bengal 721102, India
| | - Kalpana Panati
- Department of Biotechnology, Government College for Men, Kadapa 516004, India
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