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Li S, Li S, Chen D, Zhao S, Liu C, Zhang R, Chen Y, Guo X, Song X. Case report of a novel mutation in the TNC gene in Chinese patients with nonsyndromic hearing loss. Medicine (Baltimore) 2024; 103:e37702. [PMID: 38640279 PMCID: PMC11029965 DOI: 10.1097/md.0000000000037702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/04/2024] [Indexed: 04/21/2024] Open
Abstract
RATIONALE Hereditary hearing loss is known to exhibit a significant degree of genetic heterogeneity. Herein, we present a case report of a novel mutation in the tenascin-C (TNC) gene in Chinese patients with nonsyndromic hearing loss (NSHL). PATIENT CONCERNS This includes a young deaf couple and their 2-year-old baby. DIAGNOSES Based on the clinical information, hearing test, metagenomic next-generation sequencing (mNGS), Sanger sequencing, protein function and structure analysis, and model prediction, in our case, the study results revealed 2 heterozygous mutations in the TNC gene (c.2852C>T, p.Thr951Ile) and the TBC1 domain family member 24 (TBC1D24) gene (c.1570C>T, p.Arg524Trp). These mutations may be responsible for the hearing loss observed in this family. Notably, the heterozygous mutations in the TNC gene (c.2852C>T, p.Thr951Ile) have not been previously reported in the literature. INTERVENTIONS Avoid taking drugs that can cause deafness, wearing hearing AIDS, and cochlear implants. OUTCOMES Regular follow-up of family members is ongoing. LESSONS The genetic diagnosis of NSHL holds significant importance as it helps in making informed treatment decisions, providing prognostic information, and offering genetic counseling for the patient's family.
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Affiliation(s)
- Shouxia Li
- Department of Laboratory Medicine, Handan Central Hospital, Hebei Medical University, Handan, Hebei, China
| | - Shurui Li
- Department of Laboratory Medicine, Handan Central Hospital, Hebei Medical University, Handan, Hebei, China
| | - Dingli Chen
- Department of Laboratory Medicine, Handan Central Hospital, Hebei Medical University, Handan, Hebei, China
| | - Subin Zhao
- Department of General Surgery, Affiliated Hospital of Hebei University of Engineering, Handan, Hebei, China
| | - Cairu Liu
- Department of Obstetrics, Handan Central Hospital, Hebei Medical University, Handan, Hebei, China
| | - Ruimin Zhang
- Department of Neonatology, Handan Central Hospital, Hebei Medical University, Handan, Hebei, China
| | - Yongxue Chen
- Department of Anesthesiology, Handan Central Hospital, Hebei Medical University, Handan, Hebei, China
| | - Xiangrui Guo
- Department of Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Xuedong Song
- Department of Laboratory Medicine, Handan Central Hospital, Hebei Medical University, Handan, Hebei, China
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Chirasani VR, Elferdink M, Kral M, Carter JS, Heitmann S, Meissner G, Yamaguchi N. Structural and functional interactions between the EF hand domain and S2-S3 loop in the type-1 ryanodine receptor ion channel. J Biol Chem 2024; 300:105606. [PMID: 38159862 PMCID: PMC10832476 DOI: 10.1016/j.jbc.2023.105606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/04/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024] Open
Abstract
Previous cryo-electron micrographs suggested that the skeletal muscle Ca2+ release channel, ryanodine receptor (RyR)1, is regulated by intricate interactions between the EF hand Ca2+ binding domain and the cytosolic loop (S2-S3 loop). However, the precise molecular details of these interactions and functional consequences of the interactions remain elusive. Here, we used molecular dynamics simulations to explore the specific amino acid pairs involved in hydrogen bond interactions within the EF hand-S2-S3 loop interface. Our simulations unveiled two key interactions: (1) K4101 (EF hand) with D4730 (S2-S3 loop) and (2) E4075, Q4078, and D4079 (EF hand) with R4736 (S2-S3 loop). To probe the functional significance of these interactions, we constructed mutant RyR1 complementary DNAs and expressed them in HEK293 cells for [3H]ryanodine binding assays. Our results demonstrated that mutations in the EF hand, specifically K4101E and K4101M, resulted in reduced affinities for Ca2+/Mg2+-dependent inhibitions. Interestingly, the K4101E mutation increased the affinity for Ca2+-dependent activation. Conversely, mutations in the S2-S3 loop, D4730K and D4730N, did not significantly change the affinities for Ca2+/Mg2+-dependent inhibitions. Our previous finding that skeletal disease-associated RyR1 mutations, R4736Q and R4736W, impaired Ca2+-dependent inhibition, is consistent with the current results. In silico mutagenesis analysis aligned with our functional data, indicating altered hydrogen bonding patterns upon mutations. Taken together, our findings emphasize the critical role of the EF hand-S2-S3 loop interaction in Ca2+/Mg2+-dependent inhibition of RyR1 and provide insights into potential therapeutic strategies targeting this domain interaction for the treatment of skeletal myopathies.
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Affiliation(s)
- Venkat R Chirasani
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; R.L. Juliano Structural Bioinformatics Core, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Millar Elferdink
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, USA; Cardiac Signaling Center of University of South Carolina, Medical University of South Carolina and Clemson University, Charleston, South Carolina, USA; College of Charleston Honors College, Charleston, South Carolina, USA
| | - MacKenzie Kral
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, USA; Cardiac Signaling Center of University of South Carolina, Medical University of South Carolina and Clemson University, Charleston, South Carolina, USA; College of Charleston Honors College, Charleston, South Carolina, USA
| | - Jordan S Carter
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, USA; Cardiac Signaling Center of University of South Carolina, Medical University of South Carolina and Clemson University, Charleston, South Carolina, USA
| | - Savannah Heitmann
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, USA; Cardiac Signaling Center of University of South Carolina, Medical University of South Carolina and Clemson University, Charleston, South Carolina, USA
| | - Gerhard Meissner
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Naohiro Yamaguchi
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, USA; Cardiac Signaling Center of University of South Carolina, Medical University of South Carolina and Clemson University, Charleston, South Carolina, USA.
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Shah V, Singh JK, Srivastava SK, Konnur A, Gang S, Pandey SN. INF2 and ROBO2 gene mutation in an Indian family with end stage renal failure and follow-up of renal transplantation. Nephrology (Carlton) 2024; 29:48-54. [PMID: 37772439 DOI: 10.1111/nep.14244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/12/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023]
Abstract
BACKGROUND Accurate genetic diagnosis of end-stage renal disease patients with a family history of renal dysfunction is very essential. It not only helps in proper prognosis, but becomes crucial in designating donor for live related renal transplant. We here present a case of family with deleterious mutations in INF2 and ROBO2 and its importance of genetic testing before preparing for kidney transplantation. CASE PRESENTATION We report the case of a 29-year-female with end-stage renal disease and rapidly progressive renal failure. Mutational analysis revealed an Autosomal Dominant inheritance pattern and mutation in exon 4 of the INF2 gene (p. Thr215Ser) and exon 26 of the ROBO2 gene (p. Arg1371Cys). Her mother was diagnosed for CKD stage 4 with creatinine level of 4.3 mg/dL. Genetic variants (INF2 and ROBO2) identified in proband were tested in her sisters and mother. Her elder sister was positive for both heterozygous variants (INF2 and ROBO2). Her mother was positive for mutation in INF2 gene, and her donor elder sister did not showed mutation in INF2 gene and had mutation in ROBO2 gene without any clinical symptoms. CONCLUSION This case report emphasize that familial genetic screening has allowed us in allocating the donor selection in family where family member had history of genetic defect of Chronic Kidney Disease. Information of the causative renal disorder is extremely valuable for risk-assessment and planning of kidney transplantation.
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Affiliation(s)
- Vandit Shah
- Department of Pathology, Muljibhai Patel Urological Hospital, Nadiad, India
| | - Jaikee Kumar Singh
- Structural Biology and Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Jaipur, India
| | - Sandeep Kumar Srivastava
- Structural Biology and Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Jaipur, India
| | - Abhijit Konnur
- Department of Nephrology, Muljibhai Patel Urological Hospital, Nadiad, India
| | - Sishir Gang
- Department of Nephrology, Muljibhai Patel Urological Hospital, Nadiad, India
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Yan Z, Zhang W, Sun K. TREM1 is involved in the mechanism between asthma and lung cancer by regulating the Toll‑like receptor signaling pathway. Oncol Lett 2024; 27:16. [PMID: 38028174 PMCID: PMC10664071 DOI: 10.3892/ol.2023.14149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/09/2023] [Indexed: 12/01/2023] Open
Abstract
Lung cancer and asthma are both global health problems with significant economic consequences. Recent studies have demonstrated that asthma may be a risk factor for lung cancer. The present study aimed to explore the pathogenesis between these two diseases through a comprehensive analysis. Differentially expressed genes (DEGs) screened in the asthma-related GSE165934 dataset were analyzed to find relevant inflammatory pathways. Overlapping genes regulated by inflammatory pathways and lung cancer-DEGs from The Cancer Genome Atlas (TCGA) were obtained and subjected to survival and gene-wide mutation analyses, and nomogram construction to determine the hub gene. The hub gene was further analyzed through expression validation, immunoassays and functional experiments to investigate its role and mechanism in lung cancer. Functional enrichment analysis showed that 1,275 DEGs from GSE165934 were closely associated with the Toll-like receptor signaling pathway, and 8 overlapping genes were identified from 12 genes regulated by the Toll-like receptor signaling pathway and 3,134 TCGA-DEGs. After a series of bioinformatics analyses, it was found that triggering receptor expressed on myeloid cells 1 (TREM1) was the hub gene involved in the mechanism of asthma and lung cancer. TREM1 was also found to be a suppressor gene in lung cancer correlated with immune cells, immune checkpoint-related genes and tumor mutational burden score. Additionally, the results of Cell Counting Kit-8 and Transwell experiments demonstrated that overexpression of TREM1 could significantly inhibit the invasion, proliferation and migration of lung cancer cells. Reverse transcription-quantitative PCR and western blotting demonstrated that the overexpression of TREM1 could also significantly reduce the level of Toll-like receptor signaling pathway proteins. The present findings suggest that TREM1 is associated with the mechanism of asthma and lung cancer through its regulation of the Toll-like receptor signaling pathway. Furthermore, TREM1 may serve as a potential treatment target and prognostic indicator for patients with lung cancer.
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Affiliation(s)
- Zhulin Yan
- Department of Emergency Medicine, Minhang Hospital, Fudan University, Shanghai 201100, P.R. China
| | - Wei Zhang
- Department of Emergency Medicine, Minhang Hospital, Fudan University, Shanghai 201100, P.R. China
| | - Keyu Sun
- Department of Emergency Medicine, Minhang Hospital, Fudan University, Shanghai 201100, P.R. China
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Cacic AM, Schulz FI, Germing U, Dietrich S, Gattermann N. Molecular and clinical aspects relevant for counseling individuals with clonal hematopoiesis of indeterminate potential. Front Oncol 2023; 13:1303785. [PMID: 38162500 PMCID: PMC10754976 DOI: 10.3389/fonc.2023.1303785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) has fascinated the medical community for some time. Discovered about a decade ago, this phenomenon links age-related alterations in hematopoiesis not only to the later development of hematological malignancies but also to an increased risk of early-onset cardiovascular disease and some other disorders. CHIP is detected in the blood and is characterized by clonally expanded somatic mutations in cancer-associated genes, predisposing to the development of hematologic neoplasms such as MDS and AML. CHIP-associated mutations often involve DNA damage repair genes and are frequently observed following prior cytotoxic cancer therapy. Genetic predisposition seems to be a contributing factor. It came as a surprise that CHIP significantly elevates the risk of myocardial infarction and stroke, and also contributes to heart failure and pulmonary hypertension. Meanwhile, evidence of mutant clonal macrophages in vessel walls and organ parenchyma helps to explain the pathophysiology. Besides aging, there are some risk factors promoting the appearance of CHIP, such as smoking, chronic inflammation, chronic sleep deprivation, and high birth weight. This article describes fundamental aspects of CHIP and explains its association with hematologic malignancies, cardiovascular disorders, and other medical conditions, while also exploring potential progress in the clinical management of affected individuals. While it is important to diagnose conditions that can lead to adverse, but potentially preventable, effects, it is equally important not to stress patients by confronting them with disconcerting findings that cannot be remedied. Individuals with diagnosed or suspected CHIP should receive counseling in a specialized outpatient clinic, where professionals from relevant medical specialties may help them to avoid the development of CHIP-related health problems. Unfortunately, useful treatments and clinical guidelines for managing CHIP are still largely lacking. However, there are some promising approaches regarding the management of cardiovascular disease risk. In the future, strategies aimed at restoration of gene function or inhibition of inflammatory mediators may become an option.
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Affiliation(s)
- Anna Maria Cacic
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Felicitas Isabel Schulz
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Sascha Dietrich
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Norbert Gattermann
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
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Ren Y, Li S, Lei JJ, Li R, Dong BX, Yang J. Clinical feature and genetic analysis of HMBS gene in Chinese patients with acute intermittent porphyria: a systematic review. Front Genet 2023; 14:1291719. [PMID: 38148975 PMCID: PMC10750365 DOI: 10.3389/fgene.2023.1291719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/22/2023] [Indexed: 12/28/2023] Open
Abstract
Background: Early detection and diagnosis are important crucial to prevent life-threatening acute attacks in patients with acute intermittent porphyria (AIP). We aim to provide comprehensive data on the clinical and hydroxymethylbilane synthase (HMBS) gene variant characteristics and genotype-phenotype association of Chinese patients with AIP in order to improve clinicians' knowledge of AIP and reduce misdiagnosis and mistaken treatment. Methods: We searched the literature on Chinese patients with AIP in PubMed, Web of Science, Wiley Online Library, ScienceDirect and Chinese literature databases up to August 2023 in our analysis to explore the clinical and HMBS gene variant characteristics of Chinese patients with AIP. Results: A total of 41 original articles associated with Chinese AIP patients were included for analysis: 97 variants were detected in 160 unrelated families, including 35 missense, 29 frameshift, 24 splicing and 9 nonsense variants, with c.517C>T being the most common variant. Clinical data were reported in 77 of 160 patients: Most of them were female (67/77) and the age was 28.8 ± 9.9 years. The most common symptom was abdominal pain (73/77, 94.8%), followed by central nervous system symptoms (45/77, 58.4%). 13.0% (10/77) of patients experienced psychiatric symptoms. Hyponatremia was the most common electrolyte abnormality (42/77). 31 patients received carbohydrate loading therapy, and 30 of them were improved. 6 patients were treated with carbohydrate loading combined with hemin therapy and 5 eventually improved. All variants causing premature stop codons, frameshifts or enzyme activity center may experience more severe clinical phenotypes such as seizures, respiratory paralysis, intracranial hemorrhage disorder or respiratory failure. Conclusion: The most common presenting symptom in Chinese AIP patients was abdominal pain, followed by central nervous system symptoms. The HMBS gene analysis in Chinese AIP patients revealed that the heterogeneity is strong and the most common variant was missense mutation, with c.517C>T being the most common variant. The genotype-phenotype association helps guide clinical diagnosis and treatment. However, the treatment for AIP in China is limited and monolithic, and more attention needs to be paid to the treatment.
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Affiliation(s)
- Yi Ren
- Department of Endocrinology, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Shuang Li
- Department of First Clinical Medical School, Shanxi Medical University, Taiyuan, China
| | - Jia-Jia Lei
- Department of First Clinical Medical School, Shanxi Medical University, Taiyuan, China
| | - Ru Li
- Department of First Clinical Medical School, Shanxi Medical University, Taiyuan, China
| | - Bai-Xue Dong
- Department of First Clinical Medical School, Shanxi Medical University, Taiyuan, China
| | - Jing Yang
- Department of Endocrinology, The First Hospital of Shanxi Medical University, Taiyuan, China
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Dwianingsih EK, Iskandar K, Hapsara S, Ping Liu C, Malueka RG, Gunadi, Matsuo M, Lai PS. Mutation spectrum analysis of DMD gene in Indonesian Duchenne and Becker muscular dystrophy patients. F1000Res 2023; 11:148. [PMID: 38009102 PMCID: PMC10668572 DOI: 10.12688/f1000research.73476.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/13/2023] [Indexed: 11/28/2023] Open
Abstract
Background Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are allelic disorders caused by mutations in the DMD gene. The full mutation spectrum of the DMD gene in Indonesian patients is currently unknown. Mutation-specific therapies are currently being developed, such as exon skipping or stop codon read-through therapy. This study was conducted with the aim of identifying the mutation spectrum of the DMD gene in Indonesia to guide future development and application of feasible therapeutic strategies. Methods This study is a cross sectional study that enrolled 43 male patients with a clinical suspicion of DMD or BMD. Multiplex ligation-dependent probe amplification (MLPA) reaction was performed to screen for the common mutations in the DMD gene. Results Out of 43 subjects, deletions accounted for 69.77% (n=30) cases, while duplications were found in 11.63% (n=5) cases. One novel duplication spanning exons 2 to 62 was identified. Deletion mutations clustered around the distal (66.67%) and proximal (26.67%) hot spot regions of the DMD gene while duplication mutations were observed solely at the proximal region. Two false positive cases of single exon deletion detected through MLPA were attributed to sequence mutations affecting primer ligation sites, confirming the need to validate all single exon deletions when using this screening method. Analysis of available maternal DNA samples showed that the rate of de novo mutations (48.15%) appears higher than expected in this population. Out of 31 patients who were classified as DMD based on clinical and genotype characterizations, 60.47% (n=26) of cases were suitable for exon skipping therapy. Conclusion This is the first comprehensive study showing the feasibility of implementing the MLPA method for routine screening of DMD patients in Indonesia. This is also the first study showing the potential applicability of exon skipping therapy in the majority of DMD cases in the country.
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Affiliation(s)
- Ery Kus Dwianingsih
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Dr. Sardjito General Hospital, Yogyakarta, 55281, Indonesia
- Department of Anatomical Pathology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Kristy Iskandar
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Academic Hospital, Universitas Gadjah Mada, Yogyakarta, 55291, Indonesia
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Sunartini Hapsara
- Academic Hospital, Universitas Gadjah Mada, Yogyakarta, 55291, Indonesia
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Chun Ping Liu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Rusdy Ghazali Malueka
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Dr. Sardjito General Hospital, Yogyakarta, 55281, Indonesia
- Department of Neurology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Gunadi
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Dr. Sardjito General Hospital, Yogyakarta, 55281, Indonesia
- Pediatric Surgery Division, Department of Surgery, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Masafumi Matsuo
- KNC Department of Nucleic Acid Drug Discovery, Faculty of Rehabilitation, Kobegakuin University, Kobe, 651-2180, Japan
| | - Poh San Lai
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
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Tian J, McFarland CD, Woodard J. Editorial: Structural understanding of the functional consequences of missense mutation. Front Genet 2023; 14:1325326. [PMID: 38028585 PMCID: PMC10661220 DOI: 10.3389/fgene.2023.1325326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Affiliation(s)
- Jian Tian
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Christopher D. McFarland
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, United States
| | - Jaie Woodard
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
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Lombardi M, Corrado L, Piola B, Comi C, Cantello R, D’Alfonso S, Mazzini L, De Marchi F. Variability in Clinical Phenotype in TARDBP Mutations: Amyotrophic Lateral Sclerosis Case Description and Literature Review. Genes (Basel) 2023; 14:2039. [PMID: 38002982 PMCID: PMC10671725 DOI: 10.3390/genes14112039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Mutations in the 43 kDa transactive-response (TAR)-DNA-binding protein (TARDBP) are associated with 2-5% of familial Amyotrophic Lateral Sclerosis (ALS) cases. TAR DNA-Binding Protein 43 (TDP-43) is an RNA/DNA-binding protein involved in several cellular mechanisms (e.g., transcription, pre-mRNA processing, and splicing). Many ALS-linked TARDBP mutations have been described in the literature, but few phenotypic data on monogenic TARDBP-mutated ALS are available. In this paper, (1) we describe the clinical features of ALS patients carrying mutations in the TARDBP gene evaluated at the Tertiary ALS Center at Maggiore della Carità University Hospital, Novara, Italy, from 2010 to 2020 and (2) present the results of our review of the literature on this topic, analyzing data obtained for 267 patients and highlighting their main clinical and demographic features.
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Affiliation(s)
- Michele Lombardi
- ALS Center, Neurology Unit, Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (M.L.); (R.C.); (L.M.)
| | - Lucia Corrado
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy; (L.C.); (B.P.); (S.D.)
| | - Beatrice Piola
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy; (L.C.); (B.P.); (S.D.)
| | - Cristoforo Comi
- Neurology Unit, S. Andrea Hospital, Department of Translational Medicine, University of Piemonte Orientale, 13100 Vercelli, Italy;
| | - Roberto Cantello
- ALS Center, Neurology Unit, Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (M.L.); (R.C.); (L.M.)
| | - Sandra D’Alfonso
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy; (L.C.); (B.P.); (S.D.)
| | - Letizia Mazzini
- ALS Center, Neurology Unit, Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (M.L.); (R.C.); (L.M.)
| | - Fabiola De Marchi
- ALS Center, Neurology Unit, Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (M.L.); (R.C.); (L.M.)
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Chen X, Leyendecker S, van den Bedem H. SARS-CoV-2 main protease mutation analysis via a kinematic method. Proteins 2023; 91:1496-1509. [PMID: 37408369 DOI: 10.1002/prot.26543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 05/23/2023] [Accepted: 06/08/2023] [Indexed: 07/07/2023]
Abstract
The Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is the virus responsible for the COVID-19 pandemic. COVID-19 continues to cause millions of deaths globally in part due to immune-evading mutations. SARS-CoV-2 main protease (Mpro) is an important enzyme for viral replication and potentially an effective drug target. Mutations affect the dynamics of enzymes and thereby their activity and ability to bind ligands. Here, we use kinematic flexibility analysis (KFA) to identify how mutations and ligand binding changes the conformational flexibility of Mpro. KFA decomposes macromolecules into regions of different flexibility near-instantly from a static structure, allowing conformational dynamics analysis at scale. Altogether, we analyzed 47 mutation sites across 69 Mpro-ligand complexes resulting in more than 3300 different structures which includes 69 mutated structures with all 47 sites mutated simultaneously and 3243 single residue mutated structures. We found that mutations generally increased the conformational flexibility of the protein. Understanding the impact of mutations on the flexibility of Mpro is essential for identifying potential drug targets in the treatment of SARS-CoV-2. Further studies in this area can offer valuable insights into the mechanisms of molecular recognition.
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Affiliation(s)
- Xiyu Chen
- Department of Mechanical Engineering, Institute of Applied Dynamics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sigrid Leyendecker
- Department of Mechanical Engineering, Institute of Applied Dynamics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Henry van den Bedem
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
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11
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Krasnov VP, Andronova VL, Belyavsky AV, Borisevich SS, Galegov GA, Kandarakov OF, Gruzdev DA, Vozdvizhenskaya OA, Levit GL. Large Subunit of the Human Herpes Simplex Virus Terminase as a Promising Target in Design of Anti-Herpesvirus Agents. Molecules 2023; 28:7375. [PMID: 37959793 PMCID: PMC10649544 DOI: 10.3390/molecules28217375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Herpes simplex virus type 1 (HSV-1) is an extremely widespread pathogen characterized by recurrent infections. HSV-1 most commonly causes painful blisters or sores around the mouth or on the genitals, but it can also cause keratitis or, rarely, encephalitis. First-line and second-line antiviral drugs used to treat HSV infections, acyclovir and related compounds, as well as foscarnet and cidofovir, selectively inhibit herpesvirus DNA polymerase (DNA-pol). It has been previously found that (S)-4-[6-(purin-6-yl)aminohexanoyl]-7,8-difluoro-3,4-dihydro-3-methyl-2H-[1,4]benzoxazine (compound 1) exhibits selective anti-herpesvirus activity against HSV-1 in cell culture, including acyclovir-resistant mutants, so we consider it as a lead compound. In this work, the selection of HSV-1 clones resistant to the lead compound was carried out. High-throughput sequencing of resistant clones and reference HSV-1/L2 parent strain was performed to identify the genetic determinants of the virus's resistance to the lead compound. We identified a candidate mutation presumably associated with resistance to the virus, namely the T321I mutation in the UL15 gene encoding the large terminase subunit. Molecular modeling was used to evaluate the affinity and dynamics of the lead compound binding to the putative terminase binding site. The results obtained suggest that the lead compound, by binding to pUL15, affects the terminase complex. pUL15, which is directly involved in the processing and packaging of viral DNA, is one of the crucial components of the HSV terminase complex. The loss of its functional activity leads to disruption of the formation of mature virions, so it represents a promising drug target. The discovery of anti-herpesvirus agents that affect biotargets other than DNA polymerase will expand our possibilities of targeting HSV infections, including those resistant to baseline drugs.
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Affiliation(s)
- Victor P. Krasnov
- Postovsky Institute of Organic Synthesis, Russian Academy of Sciences (Ural Branch), Ekaterinburg 620108, Russia; (D.A.G.); (O.A.V.); (G.L.L.)
| | - Valeriya L. Andronova
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow 123098, Russia; (V.L.A.); (G.A.G.)
| | - Alexander V. Belyavsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (A.V.B.); (O.F.K.)
| | | | - George A. Galegov
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow 123098, Russia; (V.L.A.); (G.A.G.)
| | - Oleg F. Kandarakov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (A.V.B.); (O.F.K.)
| | - Dmitry A. Gruzdev
- Postovsky Institute of Organic Synthesis, Russian Academy of Sciences (Ural Branch), Ekaterinburg 620108, Russia; (D.A.G.); (O.A.V.); (G.L.L.)
| | - Olga A. Vozdvizhenskaya
- Postovsky Institute of Organic Synthesis, Russian Academy of Sciences (Ural Branch), Ekaterinburg 620108, Russia; (D.A.G.); (O.A.V.); (G.L.L.)
| | - Galina L. Levit
- Postovsky Institute of Organic Synthesis, Russian Academy of Sciences (Ural Branch), Ekaterinburg 620108, Russia; (D.A.G.); (O.A.V.); (G.L.L.)
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12
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Bulus AD, Yasartekin Y, Ceylan AC, Dirican O, Husseini AA. Cases of hypogonadotropic hypogonadism: A single-center experience. Niger J Clin Pract 2023; 26:1552-1556. [PMID: 37929534 DOI: 10.4103/njcp.njcp_244_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Background Delayed puberty (DP) affects approximately 2% of adolescents. In most patients of both genders, delayed puberty is due to constitutional delay in growth and puberty (CDGP); it is a self-limiting condition starting later than usual during puberty but progressing normally. Other causes of DP include permanent hypogonadotropic hypogonadism, functional hypogonadotropic hypogonadism, and gonadal insufficiency. Methods Nine patients admitted to the Ankara Atatürk Sanatoryum Training and Research Hospital Pediatric Endocrinology Department with hypogonadotropic hypogonadism between January 2012 and December 2022 were analyzed. Results Nine patients who applied to our pediatric endocrinology clinic with delayed puberty were analyzed. These nine patients were diagnosed and reported as hypogonadotropic hypogonadism with molecular methods. We aimed to determine the status of these cases from a molecular point of view, to emphasize the importance of hypogonadotropic hypogonadism in patients with delayed puberty, and to reveal the rarely encountered delayed puberty together with the clinical and laboratory data set of the patients. Conclusions To emphasize the importance of hypogonadotropic hypogonadism, which is a rare cause of delayed puberty, the molecular predispositions of our patients followed in our clinic are reviewed, and the data we have provided will contribute to the accumulation of data in this area.
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Affiliation(s)
- A D Bulus
- Pediatric Endocrinology, Ankara Atatürk Sanatorium Training and Research Hospital, University of Health Sciences, Ankara, Türkiye
| | - Y Yasartekin
- Pediatric Endocrinology, Ankara Atatürk Sanatorium Training and Research Hospital, University of Health Sciences, Ankara, Türkiye
| | - A C Ceylan
- Medical Genetics, Ankara Bilkent City Hospital, Ankara, Türkiye
| | - O Dirican
- Department of Pathology, Istanbul Gelisim University, Istanbul, Türkiye
| | - A A Husseini
- Department of Biomedical Device Technology, Istanbul Gelişim University, Istanbul, Türkiye
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13
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Kaufmann L, Pilic J, Auinger L, Mayer AL, Blatterer J, Semmler-Bruckner J, Abbas S, Rehman K, Ayaz M, Graier WF, Malli R, Petek E, Wagner K, Al Kaissi A, Khan MA, Windpassinger C. Analysis of a non-lethal biallelic frameshift mutation in ZMPSTE24 reveals utilization of alternative translation initiation codons. Clin Genet 2023; 104:491-496. [PMID: 37270786 DOI: 10.1111/cge.14381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/06/2023]
Abstract
Restrictive dermopathy (RD) is a lethal condition caused by biallelic loss-of-function mutations in ZMPSTE24, whereas mutations preserving residual enzymatic activity of the ZMPSTE24 protein lead to the milder mandibuloacral dysplasia with type B lipodystrophy (MADB) phenotype. Remarkably, we identified a homozygous, presumably loss-of-function mutation in ZMPSTE24 [c.28_29insA, p.(Leu10Tyrfs*37)] in two consanguineous Pakistani families segregating MADB. To clarify how lethal consequences are prevented in affected individuals, functional analysis was performed. Expression experiments supported utilization of two alternative translation initiation sites, preventing complete loss of protein function consistent with the relatively mild phenotypic outcome in affected patients. One of these alternative start codons is newly formed at the insertion site. Our findings indicate that the creation of new potential start codons through N-terminal mutations in other disease-associated genes should generally be taken into consideration in the variant interpretation process.
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Affiliation(s)
- Lukas Kaufmann
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Johannes Pilic
- Gottfried Schatz Research Center, Department of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Lisa Auinger
- Division of Haematology, Medical University of Graz, Graz, Austria
| | - Anna-Lena Mayer
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jasmin Blatterer
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Johann Semmler-Bruckner
- Neurogenetics Laboratory, Department of Neurology, Medical University of Graz, Graz, Austria
| | - Safdar Abbas
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Khurram Rehman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gomal University, Dera Ismail Khan, Pakistan
| | - Muhammad Ayaz
- Department of Biological Sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Wolfgang F Graier
- Gottfried Schatz Research Center, Department of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Roland Malli
- Gottfried Schatz Research Center, Department of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Erwin Petek
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Klaus Wagner
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ali Al Kaissi
- Pediatric Orthopedic Department, Speising Hospital, Vienna, Austria
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Christian Windpassinger
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
- Neurogenetics Laboratory, Department of Neurology, Medical University of Graz, Graz, Austria
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14
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Ma S, Xiao G, Deng X, Tong M, Huang J, Li Q, Zhang Y. CovidShiny: An Integrated Web Tool for SARS-CoV-2 Mutation Profiling and Molecular Diagnosis Assay Evaluation In Silico. Viruses 2023; 15:2017. [PMID: 37896794 PMCID: PMC10611021 DOI: 10.3390/v15102017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is still ongoing, with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continuing to evolve and accumulate mutations. While various bioinformatics tools have been developed for SARS-CoV-2, a well-curated mutation-tracking database integrated with in silico evaluation for molecular diagnostic assays is currently unavailable. To address this, we introduce CovidShiny, a web tool that integrates mutation profiling, in silico evaluation, and data download capabilities for genomic sequence-based SARS-CoV-2 assays and data download. It offers a feasible framework for surveilling the mutation of SARS-CoV-2 and evaluating the coverage of the molecular diagnostic assay for SARS-CoV-2. With CovidShiny, we examined the dynamic mutation pattern of SARS-CoV-2 and evaluated the coverage of commonly used assays on a large scale. Based on our in silico analysis, we stress the importance of using multiple target molecular diagnostic assays for SARS-CoV-2 to avoid potential false-negative results caused by viral mutations. Overall, CovidShiny is a valuable tool for SARS-CoV-2 mutation surveillance and in silico assay design and evaluation.
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Affiliation(s)
- Shaoqian Ma
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Gezhi Xiao
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Xusheng Deng
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Mengsha Tong
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Jialiang Huang
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Qingge Li
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Yongyou Zhang
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
- Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361100, China
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15
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Khan H, Waqas M, Khurshid B, Ullah N, Khalid A, Abdalla AN, Alamri MA, Wadood A. Investigating the role of Sterol C24-Methyl transferase mutation on drug resistance in leishmaniasis and identifying potential inhibitors. J Biomol Struct Dyn 2023:1-14. [PMID: 37723868 DOI: 10.1080/07391102.2023.2256879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 09/02/2023] [Indexed: 09/20/2023]
Abstract
Leishmaniasis is a fatal disease caused by the leishmania parasite. For the survival of the leishmania parasite, Sterol C24-Methyl Transferase (SMT) is essential which is an enzyme of the ergosterol pathway. SMT protein mutation is responsible for Amphotericin-B drug resistance in Leishmania, which is the main treatment for visceral leishmaniasis. Amphotericin-B resistance is caused by three mutated residues V131I, V321I and F72C. The underlying mechanisms and structural changes in SMT enzymes responsible for resistance due to mutation are still not well understood. In the current study, the potential mechanism of resistance due to these mutations and the structure variation of wild and mutant SMT proteins were investigated through molecular dynamics simulations and molecular docking analysis. The results showed that AmB established strong bonding interaction with wild SMT as compare to mutants SMT. The binding energy calculation showed that binding energy of AmB with mutants SMT increases as compare to the wild SMT. Further structural based virtual screening was carried out to design potential inhibitors for the mutant SMT. On the basis of structural-based virtual screening four inhibitors (SANC01057, SANC00882, SANC00414, SANC01047) were computationally identified as potential mutant SMT (F72C) inhibitors. This work provides valuable information for improved management of drug resistant Leishmaniasis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Huma Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mouz Nizwa, Oman
| | - Beenish Khurshid
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Nazif Ullah
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, Jazan, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
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16
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Park J, Sim J, Ahn J, Kim YJ, Hwang S, Cho K, Chang DY, Jung JH, Moon JH, Sung K, Lim J. Molecular characteristics of incidental lower-grade glioma for treatment decision-making. J Neurosurg 2023; 138:629-638. [PMID: 35986732 DOI: 10.3171/2022.6.jns22967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/28/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Several limitations are associated with the early diagnosis and treatment of incidental lower-grade glioma (iLGG), and due to its unknown molecular features, its management is categorized as either the "wait-and-see" strategy or immediate treatment. Therefore, in this study the authors explored iLGG's clinical and molecular landscape to improve its management. METHODS The authors retrospectively assessed the differences between the molecular and clinical characteristics of iLGG and symptomatic lower-grade glioma (sLGG) samples filtered based on symptom data corresponding to The Cancer Genome Atlas cohort with mutations. Thereafter, genomic and transcriptomic analysis was performed. RESULTS There was no significant difference between iLGG and sLGG with respect to mutation status; however, there was an increase in the interaction between major mutations in sLGG, depending on the histological subtype and the IDH1 mutation status. Furthermore, the IDH1 mutation characteristics corresponding to wild-type glioma were much more obvious in sLGG than in iLGG. Additionally, in sLGG, genes associated with malignancy, including cell proliferation-related, cell migration-related, epithelial-to-mesenchymal transition-related, and negative regulation of cell death-related genes, were significantly upregulated, and groups showing higher expression levels of these genes were associated with worse prognosis. Also, 8 of the 75 identified upregulated genes showed positive correlation with resistance to the drugs that are normally used for glioma treatment, including procarbazine, carmustine, vincristine, and temozolomide. CONCLUSIONS The new insights regarding the different molecular features of iLGG and sLGG indicated that the immediate management of iLGG could result in better prognosis than the wait-and-see strategy.
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Affiliation(s)
- Jeongman Park
- 1Department of Neurosurgery, Bundang CHA Medical Center, CHA University, Seongnam
| | - Jeongmin Sim
- 1Department of Neurosurgery, Bundang CHA Medical Center, CHA University, Seongnam
| | - Juwon Ahn
- 1Department of Neurosurgery, Bundang CHA Medical Center, CHA University, Seongnam
| | - Yu Jin Kim
- 1Department of Neurosurgery, Bundang CHA Medical Center, CHA University, Seongnam
| | - Sojung Hwang
- 2Global Research Supporting Center, Bundang CHA Medical Center, CHA University, Seongnam
| | - Kyunggi Cho
- 1Department of Neurosurgery, Bundang CHA Medical Center, CHA University, Seongnam
| | | | | | - Ju Hyung Moon
- 4Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul; and
| | - KyoungSu Sung
- 5Department of Neurosurgery, Dong-A University Hospital, Dong-A University College of Medicine, Busan, Korea
| | - Jaejoon Lim
- 1Department of Neurosurgery, Bundang CHA Medical Center, CHA University, Seongnam
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17
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Shadrina MI, Slominsky PA. Genetic Architecture of Parkinson's Disease. Biochemistry (Mosc) 2023; 88:417-433. [PMID: 37076287 DOI: 10.1134/s0006297923030100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 03/28/2023]
Abstract
Year 2022 marks 25 years since the first mutation in familial autosomal dominant Parkinson's disease was identified. Over the years, our understanding of the role of genetic factors in the pathogenesis of familial and idiopathic forms of Parkinson's disease has expanded significantly - a number of genes for the familial form of the disease have been identified, and DNA markers for an increased risk of developing its sporadic form have been found. But, despite all the success achieved, we are far from an accurate assessment of the contribution of genetic and, even more so, epigenetic factors to the disease development. The review summarizes the information accumulated to date on the genetic architecture of Parkinson's disease and formulates issues that need to be addressed, which are primarily related to the assessment of epigenetic factors in the disease pathogenesis.
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Affiliation(s)
- Maria I Shadrina
- Institute of Molecular Genetics, Kurchatov Institute National Research Centre, Moscow, 123182, Russia.
| | - Petr A Slominsky
- Institute of Molecular Genetics, Kurchatov Institute National Research Centre, Moscow, 123182, Russia
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18
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Zhu Z, Kitano T, Morimatsu M, Ochiai K, Ishiguro-Oonuma T, Oosumi K, Lin X, Orino K, Yoshikawa Y. A Highly Conserved Region in BRCA2 Suppresses the RAD51-Interaction Activity of BRC Repeats. Vet Sci 2023; 10:vetsci10020145. [PMID: 36851449 PMCID: PMC9959916 DOI: 10.3390/vetsci10020145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Mammary tumors are the most prevalent type of tumors in female dogs. Breast cancer 2, early onset (BRCA2) malignant mutations are associated with tumorigenesis in humans and dogs. BRCA2 plays a pivotal role in homologous recombination repair by recruiting RAD51 recombinase to DNA damage sites to maintain genome stability. To recruit RAD51, BRCA2 must interact with RAD51 via BRC repeats, but the regulation of this interaction has been unclear. In this study, we focused on a highly conserved region (HCR) near BRC repeats. Using co-immunoprecipitation and mammalian two-hybrid assay, we found that HCR suppressed the RAD51-interaction activity of BRC repeats and that substitutions of HCR phosphorylation sites affected it. In canine tumor samples, we found ten mutations, including a novel HCR mutation (I1110M) from canine tumor samples. The effect of four HCR mutations, including I1110M, on the RAD51-interaction activity of BRC repeats was tested. One of the HCR mutations found in canine mammary tumors increased the interaction, but the two mutations found in human breast cancers decreased it. This study suggested that the HCR regulated the RAD51-interacting activity of BRC repeats through HCR phosphorylation and that mutations in HCR may be related to tumorigenesis in both dogs and humans.
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Affiliation(s)
- Zida Zhu
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada 034-8628, Japan
| | - Taisuke Kitano
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada 034-8628, Japan
| | - Masami Morimatsu
- Laboratory of Laboratory Animal Science and Medicine, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan
| | - Kazuhiko Ochiai
- Laboratory of Veterinary Hygiene, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Tokyo 180-8602, Japan
| | - Toshina Ishiguro-Oonuma
- Laboratory of Veterinary Physiology, Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka 020-8550, Japan
| | - Kosuke Oosumi
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada 034-8628, Japan
| | - Xianghui Lin
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada 034-8628, Japan
| | - Koichi Orino
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada 034-8628, Japan
| | - Yasunaga Yoshikawa
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada 034-8628, Japan
- Correspondence:
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Schrörs B, Hos BJ, Yildiz IG, Löwer M, Lang F, Holtsträter C, Becker J, Vormehr M, Sahin U, Ossendorp F, Diken M. MC38 colorectal tumor cell lines from two different sources display substantial differences in transcriptome, mutanome and neoantigen expression. Front Immunol 2023; 14:1102282. [PMID: 36969213 PMCID: PMC10030996 DOI: 10.3389/fimmu.2023.1102282] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/23/2023] [Indexed: 03/29/2023] Open
Abstract
Introduction The cell line MC38 is a commonly used murine model for colorectal carcinoma. It has a high mutational burden, is sensitive to immune checkpoint immunotherapy and endogenous CD8+ T cell responses against neoantigens have been reported. Methods Here, we re-sequenced exomes and transcriptomes of MC38 cells from two different sources, namely Kerafast (originating from NCI/NIH, MC38-K) and the Leiden University Medical Center cell line collection (MC38-L), comparing the cell lines on the genomic and transcriptomic level and analyzing their recognition by CD8+ T cells with known neo-epitope specificity. Results The data reveals a distinct structural composition of MC38-K and MC38-L cell line genomes and different ploidies. Further, the MC38-L cell line harbored about 1.3-fold more single nucleotide variations and small insertions and deletions than the MC38-K cell line. In addition, the observed mutational signatures differed; only 35.3% of the non-synonymous variants and 5.4% of the fusion gene events were shared. Transcript expression values of both cell lines correlated strongly (p = 0.919), but we found different pathways enriched in the genes that were differentially upregulated in the MC38-L or MC38-K cells, respectively. Our data show that previously described neoantigens in the MC38 model such as Rpl18mut and Adpgkmut were absent in the MC38-K cell line resulting that such neoantigen-specific CD8+ T cells recognizing and killing MC38-L cells did not recognize or kill MC38-K cells. Conclusion This strongly indicates that at least two sub-cell lines of MC38 exist in the field and underlines the importance of meticulous tracking of investigated cell lines to obtain reproducible results, and for correct interpretation of the immunological data without artifacts. We present our analyses as a reference for researchers to select the appropriate sub-cell line for their own studies.
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Affiliation(s)
- Barbara Schrörs
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany
| | - Brett J. Hos
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Ikra G. Yildiz
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany
| | - Martin Löwer
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany
| | - Franziska Lang
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany
| | - Christoph Holtsträter
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany
| | - Julia Becker
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany
| | | | - Ugur Sahin
- BioNTech SE, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Ferry Ossendorp
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- *Correspondence: Ferry Ossendorp, ; Mustafa Diken,
| | - Mustafa Diken
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany
- BioNTech SE, Mainz, Germany
- *Correspondence: Ferry Ossendorp, ; Mustafa Diken,
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Wang J, Zhang M, Cui X, Gao X, Sun W, Ge X, Zhang Y, Guo X, Han J, Zhou L, Yang H. Attenuated Porcine Reproductive and Respiratory Syndrome Virus Regains Its Fatal Virulence by Serial Passaging in Pigs or Porcine Alveolar Macrophages To Increase Its Adaptation to Target Cells. Microbiol Spectr 2022; 10:e0308422. [PMID: 36219105 DOI: 10.1128/spectrum.03084-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is a globally important disease threatening the pork industry, and modified live-virus (MLV) vaccines are widely used for its prevention. However, PRRS MLV shows high potential for reversion to virulence, leading to a major concern about its safety. Yet the revertant mechanism is still poorly understood. Here, attenuated virus JXwn06-P80, derived from the highly pathogenic PRRS virus (PRRSV) strain JXwn06 by serial passaging in MARC-145 cells, was reversely passaged in pigs through intranasal inoculation to mimic natural infection for 13 rounds, and the pathogenicity of viruses at the 3rd, 5th, 9th, 10th, and 11th passages was evaluated in pigs. From the 9th passage, the viruses caused mortality, which was related to their increased adaptability and replication efficiency (100 times higher than those of JXwn06-P80) in porcine alveolar macrophage (PAM) target cells. Similarly, JXwn06-P80 could also regain fatal virulence through reverse passage in PAMs for 25 or more passages, indicating that the increased adaptability in PAMs directly contributes to its regained fatal virulence. Next, the full-genome sequences were analyzed to explore the genetic evolutionary processes during adaptation both in vivo and in vitro. Finally, by a reverse genetic operation, four reverse mutation sites, NSP12-W121R, ORF2b (open reading frame 2b)-H9D, ORF5-H15L, and ORF5-V189L, were finally identified to partially contribute to the ability of the virus to adapt to PAMs, which may be related to virulence reversion during reverse passage. These findings provided direct scientific evidence for the virulence reversion of PRRS MLV and provided valuable clues for exploring its molecular mechanism. IMPORTANCE Reversion to virulence of a live attenuated vaccine is a public concern; however, direct scientific evidence is limited, and the mechanism is still poorly understood. Here, we present direct evidence for the reversion to virulence of PRRS MLV after serial passaging in pigs or target cells and found a correlation between virulence reversion and increased replication fitness in primary PAMs. The genetic evolutionary process during adaptation will provide valuable clues for exploring the molecular mechanism of PRRS MLV virulence reversion and offer important implications for understanding the reversion mechanisms of other vaccines.
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Landsburg DJ, Morrissette JJD, Schuster SJ, Nasta SD, Gerson JN, Barta SK, Svoboda J, Chong EA, Lim MS. Mutation analysis performed on tumor biopsies from patients with newly-diagnosed germinal center aggressive B cell lymphomas. Oncotarget 2022; 13:1237-44. [PMID: 36441737 DOI: 10.18632/oncotarget.28309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comprehensive genomic analyses of tumor biopsies from patients with newly-diagnosed germinal center B cell (GCB) diffuse large B cell/high grade B cell lymphoma (DLBCL/HGBL) have identified molecular subtypes predictive of inferior survival, which are characterized by somatic mutations that can be detected through clinical laboratory mutation analysis (CLMA). To determine the frequency and predictive value of individual genetic mutations associated with these experimentally-defined poor-risk subgroups, we reviewed the findings from CLMA performed on tumors from patients with newly-diagnosed GCB DLBCL/HGBL who were previously treated at our institution. CLMA was successfully performed on 58/59 patient tumor biopsies with a median turnaround time of 16 days, and 51 on which CLMA was routinely performed with adequate clinical follow-up were analyzed. Patients whose tumors demonstrated CREBBP mutation experienced a lower estimated rate of 2-year disease free survival (DFS) as compared to those whose tumors did not (45% [95% CI 18-68%] vs. 67% [95% CI 44-83%], P = 0.045). CREBBP mutations may be frequent and predict for inferior DFS in patients with newly-diagnosed GCB DLBCL/HGBL. Furthermore, CLMA may be practically-applied to translate experimental findings into those with more direct application to risk stratification and clinical trial design in subsets of patients with DLBCL/HGBL.
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22
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Ravi V, Swaminathan A, Yadav S, Arya H, Pandey R. SARS-CoV-2 Variants of Concern and Variations within Their Genome Architecture: Does Nucleotide Distribution and Mutation Rate Alter the Functionality and Evolution of the Virus? Viruses 2022; 14:v14112499. [PMID: 36423107 PMCID: PMC9694950 DOI: 10.3390/v14112499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/02/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 virus pathogenicity and transmissibility are correlated with the mutations acquired over time, giving rise to variants of concern (VOCs). Mutations can significantly influence the genetic make-up of the virus. Herein, we analyzed the SARS-CoV-2 genomes and sub-genomic nucleotide composition in relation to the mutation rate. Nucleotide percentage distributions of 1397 in-house-sequenced SARS-CoV-2 genomes were enumerated, and comparative analyses (i) within the VOCs and of (ii) recovered and mortality patients were performed. Fisher's test was carried out to highlight the significant mutations, followed by RNA secondary structure prediction and protein modeling for their functional impacts. Subsequently, a uniform dinucleotide composition of AT and GC was found across study cohorts. Notably, the N gene was observed to have a high GC percentage coupled with a relatively higher mutation rate. Functional analysis demonstrated the N gene mutations, C29144T and G29332T, to induce structural changes at the RNA level. Protein secondary structure prediction with N gene missense mutations revealed a differential composition of alpha helices, beta sheets, and coils, whereas the tertiary structure displayed no significant changes. Additionally, the N gene CTD region displayed no mutations. The analysis highlighted the importance of N protein in viral evolution with CTD as a possible target for antiviral drugs.
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Affiliation(s)
- Varsha Ravi
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Aparna Swaminathan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Sunita Yadav
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Hemant Arya
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Correspondence: or ; Tel.: +91-9811029551
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23
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El Mazouri S, Bendani H, Boumajdi N, Aanniz T, Kandoussi I, Amzazi S, Belyamani L, Ibrahimi A, Ouadghiri M. Phylogeography and genomic analysis of SARS-CoV-2 delta variant in Morocco. J Infect Dev Ctries 2022; 16:1258-1268. [PMID: 36099368 DOI: 10.3855/jidc.16513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/09/2022] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION Since the COVID-19 pandemic began in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved with many variants of concern emerging across the world. METHODOLOGY In order to monitor the evolution of these variants in Morocco, we analyzed a total of 2130 genomes of the delta variant circulating around the world. We also included 164 Moroccan delta variant sequences in our analysis. RESULTS Our findings suggest at least four introductions from multiple international sources and a rise of a dominant delta sub-lineage AY.33 in Morocco. Moreover, we report three mutations in the N-terminal domain of the S protein specific to the Moroccan AY.33 isolates, T29A, T250I and T299I. The effect of these mutations on the secondary structure and the dynamic behavior of the S protein N-terminal domain was further determined. CONCLUSIONS We conclude that these mutations might have functional consequences on the S protein of SARS-CoV-2.
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Affiliation(s)
- Safae El Mazouri
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Houda Bendani
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Nasma Boumajdi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Tarik Aanniz
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Ilham Kandoussi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Saaïd Amzazi
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Mouna Ouadghiri
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco.
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24
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Zhang S, Zhou D, Li S, Bai Y, Huang B, Han J, Xu M, Wang S, Deng G. Performance of ImproGene cfDNA blood collection tubes for mutation analysis in cancer patients. Scand J Clin Lab Invest 2022; 82:378-384. [PMID: 35861435 DOI: 10.1080/00365513.2022.2100272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
With the widely application of liquid biopsy and the development of detection technology, the standardization of pre-analysis procedures is necessary. For controlling pre-analysis variation of circulating tumor DNA (ctDNA) in blood samples, the blood collection tubes for ctDNA preservation particularly contribute a lot. The objective of this study was to investigate whether ImproGene® Cell Free DNA Tube (ImproGene tube) can be used in sample collection, preservation and NGS based mutation detection for ctDNA. We investigated hemolysis and cell free DNA (cfDNA) concentration of blood samples stored in ImproGene tubes and detected β-actin, LINE1 and exogenous gene level by qPCR. We compared cfDNA and RNA quantity between samples in ImproGene tube and Streck Cell-Free DNA BCT® (Streck tube). And 10 gene mutations and three fusion mutations analysis were compared by sequencing. When stored at room temperature within 7 days in ImproGene tubes, blood samples had no visible hemolysis and the cfDNA concentration, levels of β-actin, LINE1 and exogenous gene remained stable which means no genomic DNA release and cfDNA was protected. There was no significant difference in cfDNA and RNA quantity between ImproGene tubes and Streck tubes. Furthermore, based on this limited data set, ImproGene tubes showed increased detection rates of low-level mutations. Therefore, ImproGene Cell Free DNA Tubes may have promising applications in sample collection, preservation and NGS based mutation detection for ctDNA by its good preservation performance.
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Affiliation(s)
- Shu Zhang
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Dongyao Zhou
- Department of Laboratory Medicine, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Siyun Li
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Yingming Bai
- Department of Laboratory Medicine, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Bo Huang
- Department of Laboratory Medicine, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Jianhong Han
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Mingfei Xu
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Sina Wang
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Guanhua Deng
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
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25
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Cui H, Mu X, Xu X, Ji J, Ma K, Leng C, Yao L, Kan Y, Bi Y, Xie Q. Extensive genetic heterogeneity and molecular characteristics of emerging astroviruses causing fatal gout in goslings. Poult Sci 2022; 101:101888. [PMID: 35550999 DOI: 10.1016/j.psj.2022.101888] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 11/22/2022] Open
Abstract
Since 2017, outbreaks of gosling astroviruses (GoAstV) causing the major symptoms related to gout in geese have posed a threat to China's poultry industry and caused huge economic losses. In this study, tissue samples from goslings with gout and urate deposition as the main symptoms were taken from 14 goose farms in different regions of China and screened for pathogen infection. The infection rate of GoAstV was 100%, whereas the infection rates of goose parvovirus, reovirus, Tembusu virus, and goose hemorrhagic polyomavirus were 2, 4, 0, and 0%, respectively. In total, 14 GoAstV strains were isolated and their complete genomes were sequenced. Based on the phylogenetic trees, the 14 isolated strains were classified as GoAstV (G-I) and were considered distant from strains belonging to GoAstV (G-II). The multiple sequence alignments indicated a tremendous amount of amino acid mutations in some parts of the encoding proteins of these strains; the main mutations were located in open reading frames (ORFs)—ORF1a and ORF2, such as M533V and F568S in ORF1a and A614T in ORF2. On the other hand, Further, 2 of the 14 GoAstV strains were possibly derived through inter-GoAstV-I recombination. Taken together, these findings indicate that GoAstVs are evolving in a more complex manner and have diverse transmission routes.
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26
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Tariq H, Barnea Slonim L, Coty Fattal Z, Alikhan MB, Segal J, Gurbuxani S, Helenowski IB, Zhang H, Sukhanova M, Lu X, Altman JK, Chen QC, Behdad A. Therapy-related myeloid neoplasms with normal karyotype show distinct genomic and clinical characteristics compared to their counterparts with abnormal karyotype. Br J Haematol 2022; 197:736-744. [PMID: 35304738 DOI: 10.1111/bjh.18154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 01/13/2023]
Abstract
Therapy-related myeloid neoplasms (t-MNs) are a complication of treatment with cytotoxic chemotherapy and/or radiation therapy. The majority of t-MNs show chromosomal abnormalities associated with myelodysplastic syndrome (MDS) or KMT2A rearrangements and are characterized by poor clinical outcomes. A small but substantial subset of patients have normal karyotype (NK) and their clinical characteristics and mutational profiles are not well studied. We retrospectively studied patients diagnosed with t-MN at three institutions and compared the mutational profile and survival data between t-MNs with NK and t-MNs with abnormal karyotype (AK). A total of 204 patients with t-MN were identified including 158 with AK and 46 with NK. NK t-MNs, compared to AK, were enriched for mutations in TET2 (p < 0.0001), NPM1 (p < 0.0001), ASXL1 (p = 0.0003), SRSF2 (p < 0.0001), RUNX1 (p = 0.0336) and STAG2 (p = 0.0099) and showed a significantly lower frequency of TP53 mutations (p < 0.0001). Overall survival (OS) was significantly lower in AK t-MNs as compared to NK cases (p = 0.0094). In our study, NK t-MNs showed a significantly better OS, a higher prevalence of MN-associated mutations and a lower frequency of TP53 mutations compared to their AK counterparts. The distinct clinical and mutational profile of NK t-MNs merits a separate classification.
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Affiliation(s)
- Hamza Tariq
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | | | - Zachary Coty Fattal
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Mir B Alikhan
- Department of Pathology, NorthShore University Health System, Evanston, Illinois, USA
| | - Jeremy Segal
- Department of Pathology, The University of Chicago, Chicago, Illinois, USA
| | - Sandeep Gurbuxani
- Department of Pathology, The University of Chicago, Chicago, Illinois, USA
| | - Irene B Helenowski
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Hui Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Madina Sukhanova
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Xinyan Lu
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jessica K Altman
- Department of Medicine (Hematology and Oncology), Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Qing C Chen
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Amir Behdad
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.,Department of Medicine (Hematology and Oncology), Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Wang H, Zhu Y, Ye W, Hua J, Chen L, Ni Z, Yun T, Bao E, Zhang C. Genomic and Epidemiological Characteristics Provide Insights into the Phylogeographic Spread of Goose Astrovirus in China. Transbound Emerg Dis 2022; 69:e1865-e1876. [PMID: 35301812 DOI: 10.1111/tbed.14522] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/15/2022] [Accepted: 03/14/2022] [Indexed: 11/29/2022]
Abstract
Goose astrovirus (GAstV) is an emerging pathogen with a wide distribution in China that causes visceral gout and leads to significant economic losses in the goose industry. Here, 10 GAstV strains were isolated from different farms in southeast China. We performed an integrated analysis of the full-genome sequences of these new strains alongside comprehensive epidemiological surveillance information from the database. Interestingly, the results showed two distinct genotypes of GAstV, which were evolutionarily distant from each other. Group I GAstVs were closely related to DAstV IV, and group II strains were classified with duck astrovirus (DAstV) II and turkey astrovirus (TAstV) II. Further investigation showed that among the GAstV I strains, ZJC14 and AHDY differed from FLX. Comparative analysis of 58 available genomes clustered the GAstV II strains into two subgroups. We identified two major mutation sites, 456 (E/D) and 540 (L/Q), in the capsid protein, which were related to distinct subgroups according to evolution. GAstV II subgroup 1a strains are the predominant strains in the current prevalent epidemiology. Phylogeographic analysis based on 90 reported cases from 13 provinces revealed the complexity and severity of GAstV epidemics in China, within which Henan, Anhui and Jiangsu provinces have suffered great impacts. According to these phylogeographic investigations, following the initial introduction of GAstV from Hunan Province, the dispersal of GAstV with different subgenotypes on a nationwide scale may be explained by the live gosling trade. Our findings have important implications for the evolution and dispersal of GAstV and will contribute to understanding the potential risk of GAstV. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hongyu Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yinchu Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Weicheng Ye
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jionggang Hua
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Liu Chen
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Zheng Ni
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Tao Yun
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Endong Bao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cun Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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Matschos S, Bürtin F, Kdimati S, Radefeldt M, Krake S, Prall F, Engel N, Krohn M, Micheel B, Kreutzer M, Mullins CS, Linnebacher M. The HROC-Xenobank-A High Quality Assured PDX Biobank of >100 Individual Colorectal Cancer Models. Cancers (Basel) 2021; 13:5882. [PMID: 34884989 DOI: 10.3390/cancers13235882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 11/21/2022] Open
Abstract
Simple Summary Considering recent research, it was established that the best experimental models to conserve biological features of human tumors and to predict individual clinical treatment success are patient-derived xenografts (PDX). Their recognized and growing importance for translational research, especially for late-stage preclinical testing of novel therapeutics, necessitates a high number of well-defined PDX models from individual patients’ tumors. The starting platform for the Hansestadt Rostock colorectal cancer (HROC)-Xenobank was the assortment of colorectal tumor and normal tissue samples from patients stored in our university biobank. Abstract Based on our research group’s large biobank of colorectal cancers (CRC), we here describe the ongoing activity of establishing a high quality assured PDX biobank for more than 100 individual CRC cases. This includes sufficient numbers of vitally frozen (n > 30 aliquots) and snap frozen (n > 5) backups, “ready to use”. Additionally, PDX tumor pieces were paraffin embedded. At the current time, we have completed 125 cases. This resource allows histopathological examinations, molecular characterizations, and gene expression analysis. Due to its size, different issues of interest can be addressed. Most importantly, the application of low-passage, cryopreserved, and well-characterized PDX for in vivo studies guarantees the reliability of results due to the largely preserved tumor microenvironment. All cases described were molecularly subtyped and genetic identity, in comparison to the original tumor tissue, was confirmed by fingerprint analysis. The latter excludes ambiguity errors between the PDX and the original patient tumor. A cancer hot spot mutation analysis was performed for n = 113 of the 125 cases entities. All relevant CRC molecular subtypes identified so far are represented in the Hansestadt Rostock CRC (HROC)-Xenobank. Notably, all models are available for cooperative research approaches.
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Brune MM, Rau A, Overkamp M, Flaadt T, Bonzheim I, Schürch CM, Federmann B, Dirnhofer S, Fend F, Tzankov A. Molecular Progression of Myeloproliferative and Myelodysplastic/Myeloproliferative Neoplasms: A Study on Sequential Bone Marrow Biopsies. Cancers (Basel) 2021; 13:5605. [PMID: 34830756 PMCID: PMC8615857 DOI: 10.3390/cancers13225605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/26/2021] [Accepted: 11/03/2021] [Indexed: 11/16/2022] Open
Abstract
Myeloproliferative neoplasms (MPN) and myelodysplastic/myeloproliferative neoplasms (MDS/MPN) both harbor the potential to undergo myelodysplastic progression or acceleration and can transform into blast-phase MPN or MDS/MPN, a form of secondary acute myeloid leukemia (AML). Although the initiating transforming events are yet to be determined, current concepts suggest a stepwise acquisition of (additional) somatic mutations-apart from the initial driver mutations-that trigger disease evolution. In this study we molecularly analyzed paired bone marrow samples of MPN and MDS/MPN patients with known progression and compared them to a control cohort of patients with stable disease course. Cases with progression displayed from the very beginning a higher number of mutations compared to stable ones, of which mutations in five (ASXL1, DNMT3A, NRAS, SRSF2 and TP53) strongly correlated with progression and/or transformation, even if only one of these genes was mutated, and this particularly applied to MPN. TET2 mutations were found to have a higher allelic frequency than the putative driver mutation in three progressing cases ("TET2-first"), whereas two stable cases displayed a TET2-positive subclone ("TET2-second"), supporting the hypothesis that not only the sum of mutations but also their order of appearance matters in the course of disease. Our data emphasize the importance of genetic testing in MPN and MDS/MPN patients in terms of risk stratification and identification of imminent disease progression.
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Affiliation(s)
- Magdalena M. Brune
- Institute of Medical Genetics and Pathology, University Hospital Basel, Schönbeinstrasse 40, CH-4031 Basel, Switzerland; (M.M.B.); (S.D.)
| | - Achim Rau
- Institute of Pathology and Neuropathology, University Hospital Tübingen, 72076 Tübingen, Germany; (A.R.); (M.O.); (T.F.); (I.B.); (C.M.S.); (B.F.)
| | - Mathis Overkamp
- Institute of Pathology and Neuropathology, University Hospital Tübingen, 72076 Tübingen, Germany; (A.R.); (M.O.); (T.F.); (I.B.); (C.M.S.); (B.F.)
| | - Tim Flaadt
- Institute of Pathology and Neuropathology, University Hospital Tübingen, 72076 Tübingen, Germany; (A.R.); (M.O.); (T.F.); (I.B.); (C.M.S.); (B.F.)
| | - Irina Bonzheim
- Institute of Pathology and Neuropathology, University Hospital Tübingen, 72076 Tübingen, Germany; (A.R.); (M.O.); (T.F.); (I.B.); (C.M.S.); (B.F.)
| | - Christian M. Schürch
- Institute of Pathology and Neuropathology, University Hospital Tübingen, 72076 Tübingen, Germany; (A.R.); (M.O.); (T.F.); (I.B.); (C.M.S.); (B.F.)
- Institute of Pathology, University of Bern, Murtenstrasse 8, CH-3008 Bern, Switzerland
| | - Birgit Federmann
- Institute of Pathology and Neuropathology, University Hospital Tübingen, 72076 Tübingen, Germany; (A.R.); (M.O.); (T.F.); (I.B.); (C.M.S.); (B.F.)
| | - Stefan Dirnhofer
- Institute of Medical Genetics and Pathology, University Hospital Basel, Schönbeinstrasse 40, CH-4031 Basel, Switzerland; (M.M.B.); (S.D.)
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tübingen, 72076 Tübingen, Germany; (A.R.); (M.O.); (T.F.); (I.B.); (C.M.S.); (B.F.)
| | - Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital Basel, Schönbeinstrasse 40, CH-4031 Basel, Switzerland; (M.M.B.); (S.D.)
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Liu D, Liu Y, Zhang X, Wang Y, Zhang C, Zheng S. An Exploration of Mutagenesis in a Family with Cleidocranial Dysplasia without RUNX2 Mutation. Front Genet 2021; 12:748111. [PMID: 34737766 PMCID: PMC8560734 DOI: 10.3389/fgene.2021.748111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/29/2021] [Indexed: 11/22/2022] Open
Abstract
Cleidocranial dysplasia (CCD) is an autosomal dominant inheritable skeletal disorder characterized by cranial dysplasia, clavicle hypoplasia, and dental abnormalities. Mutations involving Runt-related transcription factor 2 (RUNX2) are currently the only known molecular etiology for CCD but are not identified in all CCD patients. No RUNX2 abnormality can be detected in about 20–30% of patients, and the molecular cause remains unknown. The present study includes a family case with typical features of CCD. RUNX2 mutation was first screened by sequencing analysis, and no mutation was detected. Copy number alterations of the RUNX2 gene were then measured by quantitative PCR and multiplex ligation-dependent probe amplification (MLPA). No copy number variation in RUNX2 could be detected. We performed whole-exome sequencing (WES) to identify the underlying genetic mutations. Unexpectedly, no abnormalities could be detected in genes related to the RUNX2 signaling pathway. Therefore, it was supposed that other new unknown gene variations might contribute to the CCD phenotype. We focused on Immunoglobulin superfamily member 10 (IGSF10), a gene related to bone development. An IGSF10 frameshift mutation (c.6001_6002delCT, p.Leu2001Valfs*24) was detected by WES. Sanger sequencing verified that this mutation was only detected in the patient and her affected mother but not in her unaffected father. Bioinformatics studies demonstrated that this mutation could change the 3D structure of the IGSF10 protein and severely damage its function. In addition, alkaline phosphatase (ALP) activity and the ability to form mineralized nodules were inhibited by IGSF10 knockdown compared with normal controls. The expression of bone sialoprotein (BSP) was significantly reduced by IGSF10 knockdown, but not that of other osteogenic markers. Our results provide new genetic evidence that IGSF10 mutation might contribute to CCD.
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Affiliation(s)
- Dandan Liu
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
| | - Yang Liu
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
| | - XianLi Zhang
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China.,Department of Stomatology, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Yixiang Wang
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Central Laboratory, Department of Oral and Maxillofacial Surgery, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
| | - Chenying Zhang
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
| | - Shuguo Zheng
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
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31
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Gimm O, Ivansson K, Beka E, Rossitti HM, Garvin S, Söderkvist P. Increased diagnostic sensitivity of palpation-guided thyroid nodule fine-needle aspiration cytology by BRAF V600E- mutation analysis. J Pathol Clin Res 2021; 7:556-564. [PMID: 34156770 PMCID: PMC8503891 DOI: 10.1002/cjp2.231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/22/2021] [Accepted: 05/27/2021] [Indexed: 12/16/2022]
Abstract
Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer and its incidence is increasing. Preoperative diagnosis is warranted in order to avoid 'two-stage' procedures that are associated with additional costs and higher radioactive iodine remnant uptake. In the setting of thyroid cancer, somatic BRAF V600E-mutations are highly specific for PTC and can be analyzed in aspirates from fine-needle aspiration cytology (FNAC). The 'gold standard' to perform FNAC is ultrasound guidance. Here, we analyze whether adding BRAF V600E-mutation analysis could be of value in palpation-guided FNACs. A total of 430 consecutive patients were included. Ultrasound-guided FNACs were performed in 251 patients and 179 patients underwent palpation-guided FNACs. BRAF V600E-mutation analysis was performed using two methods, an allele-specific polymerase chain reaction (PCR) analyzed by capillary gel electrophoresis (PCR/Qiaxcel), and a droplet digital PCR (ddPCR) assay. A total of 80 patients underwent surgery, and histology revealed 25 patients to have PTC. Of the 25 PTCs, 23 (92%) showed a BRAF V600E-mutation. Both mutation analysis methods (PCR/Qiaxcel and ddPCR) produced concordant results. In the ultrasound-guided group, the preoperative diagnostic sensitivity of FNAC using the Bethesda classification alone was very high and additional BRAF V600E-mutation analysis added little to the preoperative diagnostic sensitivity. By contrast, in the palpation-guided group, by adding BRAF V600E-mutation analysis, eight instead of four patients were diagnosed of having PTC. This increase in the diagnostic sensitivity was statistically significant (p < 0.05). The costs per sample were as low as 62 USD (PCR/Qiaxcel and ddPCR) and 35 USD (PCR/Qiaxcel only). Ultrasound-guided FNAC should be aimed for when dealing with thyroid nodules. However, if palpation-guided FNAC cannot be avoided or may be required due to resource utilization, adding BRAF V600E-mutation analysis using the methods described in this study might significantly increase the proportion of preoperatively diagnosed PTCs. The additional costs can be considered very reasonable.
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Affiliation(s)
- Oliver Gimm
- Department of Surgery and Department of Biomedical and Clinical SciencesLinköping UniversityLinköpingSweden
| | - Kristin Ivansson
- Department of Biomedical and Clinical SciencesLinköping UniversityLinköpingSweden
| | - Ervin Beka
- Department of Surgery and Department of Biomedical and Clinical SciencesLinköping UniversityLinköpingSweden
| | - Hugo M Rossitti
- Department of Biomedical and Clinical SciencesLinköping UniversityLinköpingSweden
| | - Stina Garvin
- Department of Clinical Pathology, and Department of Biomedical and Clinical SciencesLinköping UniversityLinköpingSweden
| | - Peter Söderkvist
- Department of Biomedical and Clinical SciencesLinköping UniversityLinköpingSweden
- Clinical Genomics Linköping, Science for Life LaboratoryLinköping UniversityLinköpingSweden
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32
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Hossain MS, Tonmoy MIQ, Fariha A, Islam MS, Roy AS, Islam MN, Kar K, Alam MR, Rahaman MM. Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. Bioinform Biol Insights 2021; 15:11779322211054684. [PMID: 34720581 PMCID: PMC8554545 DOI: 10.1177/11779322211054684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/02/2021] [Indexed: 12/15/2022] Open
Abstract
A new strain of the beta coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is solely responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic. Although several studies suggest that the spike protein of this virus interacts with the cell surface receptor, angiotensin-converting enzyme 2 (ACE2), and is subsequently cleaved by TMPRSS2 and FURIN to enter into the host cell, conclusive insight about the interaction pattern of the variants of these proteins is still lacking. Thus, in this study, we analyzed the functional conjugation among the spike protein, ACE2, TMPRSS2, and FURIN in viral pathogenesis as well as the effects of the mutations of the proteins through the implementation of several bioinformatics approaches. Analysis of the intermolecular interactions revealed that T27A (ACE2), G476S (receptor-binding domain [RBD] of the spike protein), C297T (TMPRSS2), and P812S (cleavage site for TMPRSS2) coding variants may render resistance in viral infection, whereas Q493L (RBD), S477I (RBD), P681R (cleavage site for FURIN), and P683W (cleavage site for FURIN) may lead to increase viral infection. Genotype-specific expression analysis predicted several genetic variants of ACE2 (rs2158082, rs2106806, rs4830971, and rs4830972), TMPRSS2 (rs458213, rs468444, rs4290734, and rs6517666), and FURIN (rs78164913 and rs79742014) that significantly alter their normal expression which might affect the viral spread. Furthermore, we also found that ACE2, TMPRSS2, and FURIN proteins are functionally co-related with each other, and several genes are highly co-expressed with them, which might be involved in viral pathogenesis. This study will thus help in future genomics and proteomics studies of SARS-CoV-2 and will provide an opportunity to understand the underlying molecular mechanism during SARS-CoV-2 pathogenesis.
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Affiliation(s)
- Md. Shahadat Hossain
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Atqiya Fariha
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md. Sajedul Islam
- Department of Biochemistry & Biotechnology, University of Barishal, Barishal, Bangladesh
| | - Arpita Singha Roy
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md. Nur Islam
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Kumkum Kar
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Mohammad Rahanur Alam
- Department of Food Technology & Nutrition Science, Noakhali Science and Technology University, Noakhali, Bangladesh
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33
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Chen Q, Yu Z, Xu X, Ji J, Yao L, Kan Y, Bi Y, Xie Q. First report of a novel goose astrovirus outbreak in Muscovy ducklings in China. Poult Sci 2021; 100:101407. [PMID: 34438326 PMCID: PMC8383103 DOI: 10.1016/j.psj.2021.101407] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 02/07/2023] Open
Abstract
A highly acute disease characterized as visceral gout broke out in Muscovy ducklings in Henan province (China) in June 2020, with a mortality rate of up to 61%. In this study, common pathogenic agents were screened using reverse-transcription polymerase chain reaction or polymerase chain reaction. The results found the novel goose astrovirus (GoAstV) to be the pathogenic agent. We isolated the GoAstV, which has been designated as HNNY0620, using the Leghorn male chicken hepatocellular carcinoma (LMH) cell line and sequenced the complete genome. The phylogenetic tree showed that the amino acid (aa) sequences of ORF1a and ORF2 and the completed nucleotide sequences of the HNNY0620 strain were clustered in the GoAstV-I clade. ORF1a aa and whole-genome sequences were genetically close to TAstV-2 and DHV-3, whereas the ORF2 aa sequences were clustered with TAstV-2 and DHV2. Both the duck-origin GoAstVs and HNNY0620 harbored some special mutations, but ORF1a in 700 (I/T), ORF1b in 288 (F/L), and ORF2 in 306 (A/T) were only found in HNNY0620. These results suggest that the host range of GoAstV is diffusing, which can potentially affect other waterfowl.
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Affiliation(s)
- Qinxi Chen
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, 473061, PR China
| | - Zhengli Yu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, 473061, PR China
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, 473061, PR China
| | - Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, 473061, PR China.
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, 473061, PR China
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, 473061, PR China
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou 510642, PR China
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34
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Sahin E, Bozdayi G, Yigit S, Muftah H, Dizbay M, Tunccan OG, Fidan I, Caglar K. Genomic characterization of SARS-CoV-2 isolates from patients in Turkey reveals the presence of novel mutations in spike and nsp12 proteins. J Med Virol 2021; 93:6016-6026. [PMID: 34241906 PMCID: PMC8426744 DOI: 10.1002/jmv.27188] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/06/2021] [Indexed: 12/29/2022]
Abstract
Novel mutations have been emerging in the genome of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2); consequently, the evolving of more virulent and treatment resistance strains have the potential to increase transmissibility and mortality rates. The characterization of full-length SARS-CoV-2 genomes is critical for understanding the origin and transmission pathways of the virus, as well as identifying mutations that affect the transmissibility and pathogenicity of the virus. We present an analysis of the mutation pattern and clade distribution of full-length SARS-CoV-2 genome sequences obtained from specimens tested at Gazi University Medical Virology Laboratory. Viral RNA was extracted from nasopharyngeal specimens. Next-generation sequencing libraries were prepared and sequenced on Illumina iSeq 100 platform. Raw sequencing data were processed to obtain full-length genome sequences and variant calling was performed to analyze amino acid changes. Clade distribution was determined to understand the phylogenetic background in relation to global data. A total of 293 distinct mutations were identified, of which 152 missense, 124 synonymous, 12 noncoding, and 5 deletions. The most frequent mutations were P323L (nsp12), D614G (ORF2/S), and 2421C>T (5'-untranslated region) found simultaneously in all sequences. Novel mutations were found in nsp12 (V111A, H133R, Y453C, M626K) and ORF2/S (R995G, V1068L). Nine different Pangolin lineages were detected. The most frequently assigned lineage was B.1.1 (17 sequences), followed by B.1 (7 sequences) and B.1.1.36 (3 sequences). Sequence information is essential for revealing genomic diversity. Mutations might have significant functional implications and analysis of these mutations provides valuable information for therapeutic and vaccine development studies. Our findings point to the introduction of the virus into Turkey through various sources and the subsequent spread of several key variants.
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Affiliation(s)
- Erdem Sahin
- Division of Medical Virology, Department of Medical Microbiology, Faculty of MedicineGazi UniversityAnkaraTurkey
| | - Gulendam Bozdayi
- Division of Medical Virology, Department of Medical Microbiology, Faculty of MedicineGazi UniversityAnkaraTurkey
| | - Selin Yigit
- Division of Medical Virology, Department of Medical Microbiology, Faculty of MedicineGazi UniversityAnkaraTurkey
| | - Hager Muftah
- Division of Medical Virology, Department of Medical Microbiology, Faculty of MedicineGazi UniversityAnkaraTurkey
| | - Murat Dizbay
- Department of Infectious Diseases and Medical Microbiology, Faculty of MedicineGazi UniversityAnkaraTurkey
| | - Ozlem G. Tunccan
- Department of Infectious Diseases and Medical Microbiology, Faculty of MedicineGazi UniversityAnkaraTurkey
| | - Isil Fidan
- Division of Medical Virology, Department of Medical Microbiology, Faculty of MedicineGazi UniversityAnkaraTurkey
| | - Kayhan Caglar
- Division of Medical Virology, Department of Medical Microbiology, Faculty of MedicineGazi UniversityAnkaraTurkey
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35
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Häberle J, Moore MB, Haskins N, Rüfenacht V, Rokicki D, Rubio-Gozalbo E, Tuchman M, Longo N, Yandell M, Andrews A, AhMew N, Caldovic L. Noncoding sequence variants define a novel regulatory element in the first intron of the N-acetylglutamate synthase gene. Hum Mutat 2021; 42:1624-1636. [PMID: 34510628 DOI: 10.1002/humu.24281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/19/2021] [Accepted: 09/08/2021] [Indexed: 11/10/2022]
Abstract
N-acetylglutamate synthase deficiency is an autosomal recessive urea cycle disorder caused either by decreased expression of the NAGS gene or defective NAGS enzyme resulting in decreased production of N-acetylglutamate (NAG), an allosteric activator of carbamylphosphate synthetase 1 (CPS1). NAGSD is the only urea cycle disorder that can be effectively treated with a single drug, N-carbamylglutamate (NCG), a stable NAG analog, which activates CPS1 to restore ureagenesis. We describe three patients with NAGSD due to four novel noncoding sequence variants in the NAGS regulatory regions. All three patients had hyperammonemia that resolved upon treatment with NCG. Sequence variants NM_153006.2:c.427-222G>A and NM_153006.2:c.427-218A>C reside in the 547 bp-long first intron of NAGS and define a novel NAGS regulatory element that binds retinoic X receptor α. Sequence variants NC_000017.10:g.42078967A>T (NM_153006.2:c.-3065A>T) and NC_000017.10:g.42078934C>T (NM_153006.2:c.-3098C>T) reside in the NAGS enhancer, within known HNF1 and predicted glucocorticoid receptor binding sites, respectively. Reporter gene assays in HepG2 and HuH-7 cells demonstrated that all four substitutions could result in reduced expression of NAGS. These findings show that analyzing noncoding regions of NAGS and other urea cycle genes can reveal molecular causes of disease and identify novel regulators of ureagenesis.
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Affiliation(s)
- Johannes Häberle
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Marvin B Moore
- Department of Human Genetics, University of Utah Health Science Center, Salt Lake City, Utah, USA
| | - Nantaporn Haskins
- Center for Genetic Medicine Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Véronique Rüfenacht
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Dariusz Rokicki
- Department of Pediatrics, Nutrition and Metabolic Diseases, The Children's Memorial Health Institute, Warsaw, Poland
| | - Estela Rubio-Gozalbo
- Department of Pediatrics and Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Mendel Tuchman
- Center for Genetic Medicine Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Nicola Longo
- Division of Medical Genetics, Department of Pediatrics, University of Utah Health Science Center, Salt Lake City, Utah, USA
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah Health Science Center, Salt Lake City, Utah, USA.,8USTAR Center for Genetic Discovery, University of Utah Health Science Center, Salt Lake City, Utah, USA
| | - Ashley Andrews
- Division of Medical Genetics, Pediatrics, University of Utah Health Science Center, Salt Lake City, Utah, USA
| | - Nicholas AhMew
- Center for Genetic Medicine Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Ljubica Caldovic
- Center for Genetic Medicine Research, Children's National Hospital, Washington, District of Columbia, USA.,Department of Genomics and Precision Medicine, School of Medical and Health Sciences, The George Washington University, Washington, District of Columbia, USA
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36
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Bernal S, Pelaez I, Alias L, Baena M, De Pablo-Moreno JA, Serrano LJ, Camero MD, Tizzano EF, Berrueco R, Liras A. High Mutational Heterogeneity, and New Mutations in the Human Coagulation Factor V Gene. Future Perspectives for Factor V Deficiency Using Recombinant and Advanced Therapies. Int J Mol Sci 2021; 22:9705. [PMID: 34575869 DOI: 10.3390/ijms22189705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 02/07/2023] Open
Abstract
Factor V is an essential clotting factor that plays a key role in the blood coagulation cascade on account of its procoagulant and anticoagulant activity. Eighty percent of circulating factor V is produced in the liver and the remaining 20% originates in the α-granules of platelets. In humans, the factor V gene is about 80 kb in size; it is located on chromosome 1q24.2, and its cDNA is 6914 bp in length. Furthermore, nearly 190 mutations have been reported in the gene. Factor V deficiency is an autosomal recessive coagulation disorder associated with mutations in the factor V gene. This hereditary coagulation disorder is clinically characterized by a heterogeneous spectrum of hemorrhagic manifestations ranging from mucosal or soft-tissue bleeds to potentially fatal hemorrhages. Current treatment of this condition consists in the administration of fresh frozen plasma and platelet concentrates. This article describes the cases of two patients with severe factor V deficiency, and of their parents. A high level of mutational heterogeneity of factor V gene was identified, nonsense mutations, frameshift mutations, missense changes, synonymous sequence variants and intronic changes. These findings prompted the identification of a new mutation in the human factor V gene, designated as Jaén-1, which is capable of altering the procoagulant function of factor V. In addition, an update is provided on the prospects for the treatment of factor V deficiency on the basis of yet-to-be-developed recombinant products or advanced gene and cell therapies that could potentially correct this hereditary disorder.
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37
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Arakawa F, Miyoshi H, Yoshida N, Nakashima K, Watatani Y, Furuta T, Yamada K, Moritsubo M, Takeuchi M, Yanagida E, Shimasaki Y, Kohno K, Kataoka K, Ohshima K. Expression of telomerase reverse transcriptase in peripheral T-cell lymphoma. Cancer Med 2021; 10:6786-6794. [PMID: 34477310 PMCID: PMC8495278 DOI: 10.1002/cam4.4200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/17/2021] [Accepted: 07/31/2021] [Indexed: 12/15/2022] Open
Abstract
Telomere length is maintained by the activation of telomerase, which causes continuous cell division and proliferation in many carcinomas. A catalytic reverse transcriptase protein (TERT) encoded by the TERT gene plays a critical role in the activation of telomerase. We performed a molecular and pathological analysis of the TERT against three different peripheral T‐cell lymphoma (PTCL) subtypes: PTCL, not otherwise specified (PTCL‐NOS), angioimmunoblastic T‐cell lymphoma (AITL), and adult T‐cell leukemia/lymphoma (ATLL). Immunohistochemical analysis demonstrated TERT expression in 31% of AITL, 11% of PTCL‐NOS, and 5% of ATLL. Among them, AITL frequently showed high TERT expression with statistical significance. TERT promoter mutation analysis and genomic copy number evaluation were performed. TERT promoter mutation was observed in two cases of PTCL‐NOS (2/40) and not in other PTCLs. Genome copy number amplification was detected in 33% of PTCL‐NOS, 33% of AITL, and 50% of ATLL cases. We evaluated the relationship between the analyzed TERT genomic abnormalities and protein expression; however, no apparent relationship was observed. Furthermore, immunostaining showed TERT expression in the PTCL cytoplasm, suggesting the existence of mechanisms other than the maintenance of telomere length. Statistical analysis of the effect of TERT expression on the prognosis in PTCL cases revealed that TERT expression tended to have a poor prognosis in PTCL‐NOS. Since TERT expression was not an independent factor in multivariate analysis, further research will be needed to clarify the poor prognosis of PTCL‐NOS in TERT expression.
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Affiliation(s)
- Fumiko Arakawa
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Hiroaki Miyoshi
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Noriaki Yoshida
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan.,Department of Clinical Studies, Radiation Effects Research Foundation Hiroshima Laboratory, Hiroshima, Japan
| | - Kazutaka Nakashima
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Yosaku Watatani
- Departments of Hematology and Rheumatology, Faculty of Medicine, Kindai University Hospital, Osaka, Japan
| | - Takuya Furuta
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Kyohei Yamada
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Mayuko Moritsubo
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Mai Takeuchi
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Eriko Yanagida
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Yasumasa Shimasaki
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Kei Kohno
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Keisuke Kataoka
- Division of Hematology Department of Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Koichi Ohshima
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
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38
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Abstract
The term diffuse large B-cell lymphoma (DLBCL) includes a heterogeneous collection of biologically distinct tumours. This heterogeneity currently presents a barrier to the successful deployment of novel, biologically targeted therapies. Molecular profiling studies have recently proposed new molecular classification systems. These have the potential to resolve the biological heterogeneity of DLBCL into manageable subgroups of tumours that rely on shared oncogenic programmes. In many cases these biological programmes straddle the boundaries of our existing systems for classifying B-cell lymphomas. Here we review the findings from these major molecular profiling studies with a specific focus on those that propose new genetic subgroups of DLBCL. We highlight the areas of consensus and discordance between these studies and discuss the implications for current clinical practice and for clinical trials. Finally, we address the outstanding challenges and solutions to the introduction of genomic subtyping and precision medicine in DLBCL.
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Affiliation(s)
- Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
| | - Sarah E Arthur
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
| | - Daniel J Hodson
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK.,Department of Haematology, University of Cambridge, Cambridge, UK
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Hosoguchi T, Uchiyama Y, Komazawa H, Yahata M, Shimokawa T, Tominaga A. Effect of Three Types of Ion Beam Irradiation on Gerbera ( Gerbera hybrida) In Vitro Shoots with Mutagenesis Efficiency. Plants (Basel) 2021; 10:plants10071480. [PMID: 34371682 PMCID: PMC8309275 DOI: 10.3390/plants10071480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/01/2021] [Accepted: 07/14/2021] [Indexed: 11/28/2022]
Abstract
Gerbera in vitro shoots were irradiated using three types of ion beams with different line energy transfers (LETs) to investigate the effective LET and absorbed doses for mutagenesis. Furthermore, genomic mutation analyses were conducted on the obtained mutants. Survival rate analysis showed a lower lethal dose 50% (LD50) with ion beams with higher LETs. Trait/morphological mutations exhibited changes in the color and shape of petals and male sterility. Irradiation conditions with the highest growth change and trait/morphological mutation rates in each ion were C irradiation at 10 Gy, Ar irradiation at 5 Gy, and Fe irradiation at 5 Gy, with a range of absorbed dose of around LD50 to about 10 Gy lower. The highest trait/morphological mutation rate was 14.1% with Ar irradiation at 5 Gy, which was one of the criteria for ion beam irradiation of gerbera in vitro shoots. Furthermore, the genomic mutation in the flower color, petal shape, and male sterile mutants were confirmed by genotype analysis using Genotyping by Random Amplicon Sequencing-Direct technology. This is the first study to report the efficient production of gerbera mutants that could be analyzed. Our findings may lead to more efficient gerbera mutant production and analysis technology.
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Affiliation(s)
- Tomoya Hosoguchi
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan; (T.H.); (Y.U.); (M.Y.)
| | - Yuna Uchiyama
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan; (T.H.); (Y.U.); (M.Y.)
| | - Hinata Komazawa
- Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan;
| | - Masaki Yahata
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan; (T.H.); (Y.U.); (M.Y.)
- Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan;
| | - Takashi Shimokawa
- Department of Accelerator and Medical Physics, National Institutes of Quantum and Radiological Science and Technology, Chiba 263-8555, Japan;
| | - Akiyoshi Tominaga
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan; (T.H.); (Y.U.); (M.Y.)
- Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan;
- Correspondence:
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Chapman JR, Bouska AC, Zhang W, Alderuccio JP, Lossos IS, Rimsza LM, Maguire A, Yi S, Chan WC, Vega F, Song JY. EBV-positive HIV-associated diffuse large B cell lymphomas are characterized by JAK/STAT (STAT3) pathway mutations and unique clinicopathologic features. Br J Haematol 2021; 194:870-878. [PMID: 34272731 DOI: 10.1111/bjh.17708] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 12/20/2022]
Abstract
Even in the era of highly active combination antiretroviral therapy (cART), patients with HIV have a disproportionate risk of developing aggressive lymphomas that are frequently Epstein-Barr virus (EBV)-related. Here, we investigate HIV-associated diffuse large B-cell lymphoma (HIV-DLBCL) and compare EBV-positive and EBV-negative cases. HIV-DLBCL were identified from two academic medical centres and characterised by immunohistochemistry, EBV status, fluorescence in situ hybridisation, cell of origin determination by gene expression profiling, and targeted deep sequencing using a custom mutation panel of 334 genes. We also applied the Lymphgen tool to determine the genetic subtype of each case. Thirty HIV-DLBCL were identified, with a median patient age of 46 years and male predominance (5:1). Thirteen cases (48%) were EBV-positive and 14 (52%) EBV-negative. Nine of the 16 tested cases (56%) had MYC rearrangement, three (19%) had BCL6 (two of which were double hit MYC/BCL6) and none had BCL2 rearrangements. Using the Lymphgen tool, half of the cases (15) were classified as other. All HIV-DLBCL showed mutational abnormalities, the most frequent being TP53 (37%), MYC (30%), STAT3 (27%), HIST1H1E (23%), EP300 (20%), TET2 (20%), SOCS1 (17%) and SGK1 (17%). EBV-negative cases were mostly of germinal centre B-cell (GCB) origin (62%), showed more frequent mutations per case (a median of 13·5/case) and significant enrichment of TP53 (57% vs. 15%; P = 0·046), SGK1 (36% vs. 0%; P = 0·04), EP300 (43% vs. 0%; P = 0·02) and histone-modifying gene (e.g. HIST1H1E, HIST1H1D, 79% vs. 31%; P = 0·02) mutations. EBV-positive cases were mostly of non-GCB origin (70%), with fewer mutations per case (median 8/case; P = 0·007), and these tumours were enriched for STAT3 mutations (P = 0·10). EBV-positive cases had a higher frequency of MYC mutations but the difference was not significant (36% vs. 15%; P = 0·38). EBV-association was more frequent in HIV-DLBCLs, arising in patients with lower CD4 counts at diagnosis (median 46·5 vs. 101, P = 0·018). In the era of cART, approximately half of HIV-DLBCL are EBV-related. HIV-DLBCL are enriched for MYC rearrangements, MYC mutations and generally lack BCL2 rearrangements, regardless of EBV status. Among HIV-DLBCL, tumours that are EBV-negative and EBV-positive appear to have important differences, the latter arising in context of lower CD4 count, showing frequent non-GCB origin, lower mutation burden and recurrent STAT3 mutations.
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Affiliation(s)
- Jennifer R Chapman
- Division of Hematopathology, Department of Pathology, University of Miami and Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Alyssa C Bouska
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Weiwei Zhang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Juan Pablo Alderuccio
- Division of Hematology, Department of Medicine, University of Miami and Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Izidore S Lossos
- Division of Hematology, Department of Medicine, University of Miami and Sylvester Comprehensive Cancer Center, Miami, FL, USA.,Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL, USA
| | - Lisa M Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ, USA
| | - Alanna Maguire
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ, USA
| | - Shuhua Yi
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Wing C Chan
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Francisco Vega
- Department of Hematopathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Joo Y Song
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
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Nurden A. Profiling the Genetic and Molecular Characteristics of Glanzmann Thrombasthenia: Can It Guide Current and Future Therapies? J Blood Med 2021; 12:581-599. [PMID: 34267570 PMCID: PMC8275161 DOI: 10.2147/jbm.s273053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/16/2021] [Indexed: 12/15/2022] Open
Abstract
Glanzmann thrombasthenia (GT) is the most widely studied inherited disease of platelet function. Platelets fail to aggregate due to a defect in platelet-to-platelet attachment. The hemostatic plug fails to form and a moderate to severe bleeding diathesis results. Classically of autosomal recessive inheritance, GT is caused by defects within the ITGA2B and ITGB3 genes that encode the αIIbβ3 integrin expressed at high density on the platelet surface and also in intracellular pools. Activated αIIbβ3 acts as a receptor for fibrinogen and other adhesive proteins that hold platelets together in a thrombus. Over 50 years of careful clinical and biological investigation have provided important advances that have improved not only the quality of life of the patients but which have also contributed to an understanding of how αIIbβ3 functions. Despite major improvements in our knowledge of GT and its genetic causes, extensive biological and clinical variability with respect to the severity and intensity of bleeding remains poorly understood. I now scan the repertoire of ITGA2B and ITGB3 gene defects and highlight the wide genetic and biological heterogeneity within the type II and variant subgroups especially with regard to bleeding, clot retraction, the internal platelet Fg storage pool and the nature of the mutations causing the disease. I underline the continued importance of gene profiling and biological studies and emphasize the multifactorial etiology of the clinical expression of the disease. This is done in a manner to provide guidelines for future studies and future treatments of a disease that has not only aided research on rare diseases but also contributed to advances in antithrombotic therapy.
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Affiliation(s)
- Alan Nurden
- Institut Hospitalo-Universitaire LIRYC, Pessac, France
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Mokánszki A, Bicskó R, Gergely L, Méhes G. Cell-Free Total Nucleic Acid-Based Genotyping of Aggressive Lymphoma: Comprehensive Analysis of Gene Fusions and Nucleotide Variants by Next-Generation Sequencing. Cancers (Basel) 2021; 13:3032. [PMID: 34204385 DOI: 10.3390/cancers13123032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary This study aimed to simultaneously demonstrate pathogenic chromosomal translocations and point mutations from both tissue biopsy and peripheral blood (PB) liquid biopsy (LB) samples of aggressive lymphoma patients. Matched samples were analyzed by next-generation sequencing for the same 125 genes. Eight different gene fusions, including the classical BCL2, BCL6, and MYC genes were detected in the corresponding samples with generally good agreement. Besides, mutations of 29 commonly affected genes, such as BCL2, MYD88, NOTCH2, EZH2, and CD79B could be identified in the matched samples at a rate of 16/24 (66.7%). Our prospective study demonstrates a non-invasive approach to identify frequent gene fusions and variants in aggressive lymphomas. In conclusion, PB LB sampling substantially supports the oncogenetic diagnostics of lymphomas, especially at anatomically critical sites (such as the central nervous system). Abstract Chromosomal translocations and pathogenic nucleotide variants both gained special clinical importance in lymphoma diagnostics. Non-invasive genotyping from peripheral blood (PB) circulating free nucleic acid has been effectively used to demonstrate cancer-related nucleotide variants, while gene fusions were not covered in the past. Our prospective study aimed to isolate and quantify PB cell-free total nucleic acid (cfTNA) from patients diagnosed with aggressive lymphoma and to compare with tumor-derived RNA (tdRNA) from the tissue sample of the same patients for both gene fusion and nucleotide variant testing. Matched samples from 24 patients were analyzed by next-generation sequencing following anchored multiplexed polymerase chain reaction (AMP) for 125 gene regions. Eight different gene fusions, including the classical BCL2, BCL6, and MYC genes, were detected in the corresponding tissue biopsy and cfTNA specimens with generally good agreement. Synchronous BCL2 and MYC translocations in double-hit high-grade B-cell lymphomas were obvious from cfTNA. Besides, mutations of 29 commonly affected genes, such as BCL2, MYD88, NOTCH2, EZH2, and CD79B, could be identified in matched cfTNA, and previously described pathogenic variants were detected in 16/24 cases (66.7%). In 3/24 cases (12.5%), only the PB sample was informative. Our prospective study demonstrates a non-invasive approach to identify frequent gene fusions and variants in aggressive lymphomas. cfTNA was found to be a high-value representative reflecting the complexity of the lymphoma aberration landscape.
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Sabatini PJB, Tremblay-LeMay R, Ahmadi Moghaddam P, Delabie JMA, Sakhdari A. Marginal zone lymphoma transdifferentiated to histiocytic sarcoma. Br J Haematol 2021; 194:1090-1094. [PMID: 34096049 DOI: 10.1111/bjh.17582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Peter J B Sabatini
- Laboratory Medicine and Pathobiology, University Health Network, Toronto, Canada
| | | | | | - Jan M A Delabie
- Laboratory Medicine and Pathobiology, University Health Network, Toronto, Canada
| | - Ali Sakhdari
- Laboratory Medicine and Pathobiology, University Health Network, Toronto, Canada
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Rudnik-Schöneborn S, Messner M, Vockel M, Wirleitner B, Pinggera GM, Witsch-Baumgartner M, Murtinger M, Kliesch S, Swoboda M, Sänger N, Zschocke J, Tüttelmann F. Andrological findings in infertile men with two (biallelic) CFTR mutations: results of a multicentre study in Germany and Austria comprising 71 patients. Hum Reprod 2021; 36:551-559. [PMID: 33374015 DOI: 10.1093/humrep/deaa348] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
STUDY QUESTION When should cystic fibrosis transmembrane conductance regulator (CFTR) mutation analysis be recommended in infertile men based on andrological findings? SUMMARY ANSWER CFTR mutation analysis is recommended in all men with unexplained azoospermia in the presence of normal gonadotropin levels. WHAT IS KNOWN ALREADY While 80-97% of men with congenital bilateral absence of the vas deferens (CBAVD) are thought to carry CFTR mutations, there is uncertainty about the spectrum of clinical and andrological abnormalities in infertile men with bilallelic CFTR mutations. This information is relevant for evidence-based recommendations to couples requesting assisted reproduction. STUDY DESIGN, SIZE, DURATION We studied the andrological findings of patients with two CFTR mutations who were examined in one of the cooperating fertility centres in Germany and Austria. In the period of January till July 2019, the completed and anonymized data sheets of 78 adult male patients were returned to and analysed by the project leader at the Institute of Human Genetics in Innsbruck, Austria. PARTICIPANTS/MATERIALS, SETTING, METHODS Minimum study entry criteria were the presence of two (biallelic) CFTR mutations and results of at least one semen analysis. Andrological assessments were undertaken by standardized data sheets and compared with normal reference values. Seventy-one patients were eligible for the study (n = 30, 42% from Germany, n = 26, 37% from Austria, n = 15, 21% other nations). MAIN RESULTS AND THE ROLE OF CHANCE Gonadotropin levels (FSH, LH) were normal, 22% of patients had reduced testosterone values. Mean right testis volume was 23.38 ml (SD 8.77), mean left testis volume was 22.59 ml (SD 8.68) and thereby statistically increased compared to normal (P < 0.01). although the means remained in the reference range of 12-25 ml. Semen analysis revealed azoospermia in 70 of 71 (99%) patients and severe oligozoospermia <0.1 × 106/ml in one patient. Four semen parameters, i.e. ejaculate volume, pH, α-glucosidase and fructose values, were significantly reduced (P < 0.01). Only 18% of patients had a palpatory and sonographically diagnosed CBAVD, while in 31% the diagnosis of CBAVD was uncertain, in 12% patients, the vas deferens was present but hypoplastic, and in 39% the vas deferens was normally present bilaterally. Seminal vesicles were not detectable in 37% and only unilaterally present in 37% of patients. Apart from total testes volume, clinical findings were similar in patients with two confirmed pathogenic CFTR mutations (Group I) compared with patients who carried one pathogenic mutation and one CFTR variant of unknown significance (Group II). LIMITATIONS, REASONS FOR CAUTION We could not formally confirm the in trans position of genetic variants in most patients as no family members were available for segregation studies. Nonetheless, considering that most mutations in our study have been previously described without other rare variants in cis, and in view of the compatible andrological phenotype, it is reasonable to assume that the biallelic genotypes are correct. WIDER IMPLICATIONS OF THE FINDINGS Our study reveals that CFTR mutation analysis has a broader indication than just the absence of the vas deferens. We recommend to completely sequence the CFTR gene if there is a suspicion of obstructive azoospermia, and to extend this analysis to all patients with unexplained azoospermia in the presence of normal gonadotropin levels. STUDY FUNDING/COMPETING INTEREST(S) German Research Foundation Clinical Research Unit 'Male Germ Cells: from Genes to Function' (DFG CRU326, grants to F.T.). There are no conflicts of interest to declare. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- S Rudnik-Schöneborn
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - M Messner
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - M Vockel
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - B Wirleitner
- NEXTCLINIC, IVF Centres Prof. Zech, Bregenz, Bregenz, Austria
| | - G-M Pinggera
- Department of Urology, Medical University Innsbruck, Innsbruck, Austria
| | | | - M Murtinger
- NEXTCLINIC, IVF Centres Prof. Zech, Bregenz, Bregenz, Austria
| | - S Kliesch
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - M Swoboda
- VivaNeo Kinderwunschzentrum Dr. Loimer GmbH, Wels-Thalheim, Austria
| | - N Sänger
- Clinic of Gynecological Endocrinology, University of Bonn, Bonn, Germany
| | - J Zschocke
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - F Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
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Liu Y, Liu Y, Huang Y, Wen H, Zhao L, Song Y, Wang Z. The effect of the HRB linker of Newcastle disease virus fusion protein on the fusogenic activity. J Microbiol 2021; 59:513-521. [PMID: 33779959 DOI: 10.1007/s12275-021-0539-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 10/21/2022]
Abstract
Newcastle disease, designated a class A disease of poultry by the Office international des epizooties (OIE), is an acute infection caused by Newcastle disease virus (NDV). The merging of the envelope of NDV with the membrane of a target host cell is the key step in the infection pathway, which is driven by the concerted action of two glycoproteins: haemagglutinin-neuraminidase (HN) and fusion (F) protein. When the HN protein binds to the host cell surface receptor, the F protein is activated to mediate fusion. The three-dimensional structure of the F protein has been reported to have low electron density between the DIII domain and the HRB domain, and this electron-poor region is defined as the HRB linker. To clarify the contributing role of the HRB linker in the NDV F protein-mediated fusion process, 6 single amino acid mutants were obtained by site-directed mutagenesis of the HRB linker. The expression of the mutants and their abilities to mediate fusion were analysed, and the key amino acids in the HRB linker were identified as L436, E439, I450, and S453, as they can modulate the fusion ability or expression of the active form to a certain extent. The data shed light on the crucial role of the F protein HRB linker in the acquisition of a normal fusogenic phenotype.
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Affiliation(s)
- Yaqing Liu
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250014, China
| | - Ying Liu
- Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250014, China
| | - Yanan Huang
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250014, China
| | - Hongling Wen
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250014, China
| | - Li Zhao
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250014, China
| | - Yanyan Song
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250014, China
| | - Zhiyu Wang
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250014, China.
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Mokánszki A, Bádon ES, Mónus A, Tóth L, Bittner N, Méhes G. Cell-free DNA From Pleural Effusion Samples: Is It Right for Molecular Testing in Lung Adenocarcinoma? Pathol Oncol Res 2021; 27:613071. [PMID: 34257581 PMCID: PMC8262152 DOI: 10.3389/pore.2021.613071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/19/2021] [Indexed: 12/03/2022]
Abstract
Pathogenic molecular features gained specific significance in therapeutic decisions in lung carcinoma in the past decade. Initial and follow up genetic testing requres appropriate amounts and quality of tumor derived DNA, but tumor sampling, especially for disease monitoring is generally limited. Further to the peripheral blood (PB), samples from pleural fluid, accumulating in diverse lung processes might serve as an alternative source for cell-free DNA (cfDNA) for genetic profiling. In our study, cfDNA isolated from the pleural effusion and from the PB, and genomic DNA (gDNA) obtained from tissue/cellular samples were analyzed and compared from altogether 65 patients with pulmonary disease, including 36 lung adenocarcinomas. The quantity of effusion cfDNA yield appeared to be significantly higher compared to that from simultaneously collected PB plasma (23.2 vs. 4.8 ng/μl, p < 0.05). Gene mutations could be safely demonstrated from the effusion cfDNA fraction obtained from adenocarcinoma patients, 3/36 EGFR, 9/36 KRAS and 1/36 BRAF gene variants were detected. In this series, 9/13 samples showed an effusion+/plasma-mutational status, while only 1/13 samples presented with the opposite findings (effusion-/plasma+). gDNA analysis from sediment cell blocks from the identical effusion sample was surprisingly ineffective for lung adenocarcinoma profiling due to the low DNA yield. In conclusion, the cell free supernatant of pleural effusions appears to concentrate cancer derived cfDNA and seems to be particularly suitable for serial genotyping of pulmonary adenocarcinoma.
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Affiliation(s)
- Attila Mokánszki
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Emese Sarolta Bádon
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Anikó Mónus
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Tóth
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Nóra Bittner
- Department of Pulmonology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Joshi M, Puvar A, Kumar D, Ansari A, Pandya M, Raval J, Patel Z, Trivedi P, Gandhi M, Pandya L, Patel K, Savaliya N, Bagatharia S, Kumar S, Joshi C. Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. Front Genet 2021; 12:586569. [PMID: 33815459 PMCID: PMC8017293 DOI: 10.3389/fgene.2021.586569] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/15/2021] [Indexed: 12/19/2022] Open
Abstract
Humanity has seen numerous pandemics during its course of evolution. The list includes several incidents from the past, such as measles, Ebola, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS), etc. The latest edition to this is coronavirus disease 2019 (COVID-19), caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of August 18, 2020, COVID-19 has affected over 21 million people from 180 + countries with 0.7 million deaths across the globe. Genomic technologies have enabled us to understand the genomic constitution of pathogens, their virulence, evolution, and rate of mutation, etc. To date, more than 83,000 viral genomes have been deposited in public repositories, such as GISAID and NCBI. While we are writing this, India is the third most affected country by COVID-19, with 2.7 million cases and > 53,000 deaths. Gujarat is the 11th highest affected state with a 3.48% death rate compared to the national average of 1.91%. In this study, a total of 502 SARS-CoV-2 genomes from Gujarat were sequenced and analyzed to understand its phylogenetic distribution and variants against global and national sequences. Further variants were analyzed from diseased and recovered patients from Gujarat and the world to understand its role in pathogenesis. Among the missense mutations present in the Gujarat SARS-CoV-2 genomes, C28854T (Ser194Leu) had an allele frequency of 47.62 and 7.25% in deceased patients from the Gujarat and global datasets, respectively. In contrast, the allele frequency of 35.16 and 3.20% was observed in recovered patients from the Gujarat and global datasets, respectively. It is a deleterious mutation present in the nucleocapsid (N) gene and is significantly associated with mortality in Gujarat patients with a p-value of 0.067 and in the global dataset with a p-value of 0.000924. The other deleterious variant identified in deceased patients from Gujarat (p-value of 0.355) and the world (p-value of 2.43E-06) is G25563T, which is located in Orf3a and plays a potential role in viral pathogenesis. SARS-CoV-2 genomes from Gujarat are forming distinct clusters under the GH clade of GISAID. This study will shed light on the viral haplotype in SARS-CoV-2 samples from Gujarat, India.
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Affiliation(s)
- Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology (DST), Gandhinagar, India
| | - Apurvasinh Puvar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology (DST), Gandhinagar, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology (DST), Gandhinagar, India
| | - Afzal Ansari
- Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology (DST), Gandhinagar, India
| | - Maharshi Pandya
- Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology (DST), Gandhinagar, India
| | - Janvi Raval
- Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology (DST), Gandhinagar, India
| | - Zarna Patel
- Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology (DST), Gandhinagar, India
| | - Pinal Trivedi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology (DST), Gandhinagar, India
| | - Monika Gandhi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology (DST), Gandhinagar, India
| | - Labdhi Pandya
- Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology (DST), Gandhinagar, India
| | - Komal Patel
- Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology (DST), Gandhinagar, India
| | - Nitin Savaliya
- Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology (DST), Gandhinagar, India
| | | | - Sachin Kumar
- Indian Institute of Technology Guwahati, Guwahati, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science & Technology (DST), Gandhinagar, India
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Tschirka J, Bach M, Kisis I, Lemmen J, Gnoth MJ, Gründemann D. Transporter tandems: precise tools for normalizing active transporter in the plasma membrane. Biochem J 2020; 477:4191-206. [PMID: 33073844 DOI: 10.1042/BCJ20200666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/12/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022]
Abstract
The transport efficiency (TE) describes the performance of a transport protein for a specific substrate. To compare the TE of different transporters, the number of active transporters in the plasma membrane must be monitored, as it may vary for each transporter and experiment. Available methods, like LC-MS quantification of tryptic peptides, fail to discriminate inactive intracellular transporters or, like cell-surface biotinylation followed by affinity chromatography and Western blotting, are imprecise and very laborious. We wanted to normalize active transporters by the activity of a second transporter. A transporter tandem, generated by joining two transporter cDNAs into a single open reading frame, should guarantee a 1 : 1 stoichiometry. Here we created a series of tandems with different linkers between the human ergothioneine (ET) transporter ETT (gene symbol SLC22A4) and organic cation transporter OCT2 (SLC22A2). The linker sequence strongly affected the expression strength. The stoichiometry was validated by absolute peptide quantification and untargeted peptide analysis. Compared with wild-type ETT, the normalized ET clearance of the natural variant L503F was higher (f = 1.34); G462E was completely inactive. The general usefulness of the tandem strategy was demonstrated by linking several transporters with ETT; every construct was active in both parts. Transporter tandems can be used - without membrane isolation or protein quantification - as precise tools for transporter number normalization, to identify, for example, relevant transporters for a drug. It is necessary, however, to find suitable linkers, to check the order of transporters, and to verify the absence of functional interference by saturation kinetics.
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Stergiopoulou D, Markou A, Tzanikou E, Ladas I, Makrigiorgos GM, Georgoulias V, Lianidou E. ESR1 NAPA Assay: Development and Analytical Validation of a Highly Sensitive and Specific Blood-Based Assay for the Detection of ESR1 Mutations in Liquid Biopsies. Cancers (Basel) 2021; 13:556. [PMID: 33535614 DOI: 10.3390/cancers13030556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/15/2021] [Accepted: 01/26/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary A considerable number of estrogen-receptor–positive (ER+) breast cancer patients develop resistance to endocrine treatment. One of the most important resistance mechanisms is the presence of ESR1 mutations. In the present study, we developed and analytically validated a novel, highly sensitive and specific nuclease-assisted minor-allele enrichment with probe-overlap (NaME-PrO)-assisted Amplification refractory mutation system (ARMS) (NAPA) assay for the detection of four ESR1 mutations (Y537S, Y537C, Y537N and D538G). The assay was further applied in 13 ER+ breast cancer (BrCa) primary tumour tissues (FFPEs), 13 non-cancerous breast tissues (mammoplasties), and 32 pairs of liquid biopsy samples [circulating tumour cells (CTCs) and paired plasma circulating tumour DNA (ctDNA)] obtained at different time points from 8 ER+ metastatic breast cancer patients. In the plasma ctDNA, the ESR1 mutations were not identified at the baseline, whereas the D538G mutation was detected during the follow-up period at five consecutive time points in one patient. In the CTCs, only the Y537C mutation was detected in one patient sample at the baseline. A direct comparison of the ESR1 NAPA assay with the drop-off ddPCR using 32 identical plasma ctDNA samples gave a concordance of 90.6%. We present a low-cost, highly specific, sensitive and robust assay for blood-based ESR1 profiling. Abstract A considerable number of estrogen receptor-positive breast cancer (ER+ BrCa) patients develop resistance to endocrine treatment. One of the most important resistance mechanisms is the presence of ESR1 mutations. We developed and analytically validated a highly sensitive and specific NaME-PrO-assisted ARMS (NAPA) assay for the detection of four ESR1 mutations (Y537S, Y537C, Y537N and D538G) in circulating tumour cells (CTCs) and paired plasma circulating tumour DNA (ctDNA) in patients with ER+ BrCa. The analytical specificity, analytical sensitivity and reproducibility of the assay were validated using synthetic oligos standards. We further applied the developed ESR1 NAPA assay in 13 ER+ BrCa primary tumour tissues, 13 non-cancerous breast tissues (mammoplasties) and 64 liquid biopsy samples: 32 EpCAM-positive cell fractions and 32 paired plasma ctDNA samples obtained at different time points from 8 ER+ metastatic breast cancer patients, during a 5-year follow-up period. Peripheral blood from 11 healthy donors (HD) was used as a control. The developed assay is highly sensitive (a detection of mutation-allelic-frequency (MAF) of 0.5% for D538G and 0.1% for Y537S, Y537C, Y537N), and highly specific (0/13 mammoplasties and 0/11 HD for all mutations). In the plasma ctDNA, ESR1 mutations were not identified at the baseline, whereas the D538G mutation was detected in five sequential ctDNA samples during the follow-up period in the same patient. In the EpCAM-isolated cell fractions, only the Y537C mutation was detected in one patient sample at the baseline. A direct comparison of the ESR1 NAPA assay with the drop-off ddPCR using 32 identical plasma ctDNA samples gave a concordance of 90.6%. We present a low cost, highly specific, sensitive and robust assay for blood-based ESR1 profiling. The clinical performance of the ESR1 NAPA assay will be prospectively evaluated in a large number of well-characterized patient cohorts.
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Sadeh TT, Black GC, Manson F. A Review of Genetic and Physiological Disease Mechanisms Associated With Cav1 Channels: Implications for Incomplete Congenital Stationary Night Blindness Treatment. Front Genet 2021; 12:637780. [PMID: 33584831 PMCID: PMC7876387 DOI: 10.3389/fgene.2021.637780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/12/2021] [Indexed: 11/13/2022] Open
Abstract
Calcium channels are crucial to a number of cellular functions. The high voltage-gated calcium channel family comprise four heteromeric channels (Cav1.1-1.4) that function in a similar manner, but that have distinct expression profiles. Three of the pore-forming α1 subunits are located on autosomes and the forth on the X chromosome, which has consequences for the type of pathogenic mutation and the disease mechanism associated with each gene. Mutations in this family of channels are associated with malignant hyperthermia (Cav1.1), various QT syndromes (Cav1.2), deafness (Cav1.3), and incomplete congenital stationary night blindness (iCSNB; Cav1.4). In this study we performed a bioinformatic analysis on reported mutations in all four Cav α1 subunits and correlated these with variant frequency in the general population, phenotype and the effect on channel conductance to produce a comprehensive composite Cav1 mutation analysis. We describe regions of mutation clustering, identify conserved residues that are mutated in multiple family members and regions likely to cause a loss- or gain-of-function in Cav1.4. Our research highlights that therapeutic treatments for each of the Cav1 channels will have to consider channel-specific mechanisms, especially for the treatment of X-linked iCSNB.
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Affiliation(s)
- Tal T Sadeh
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Graeme C Black
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, Manchester University NHS Foundation Trust, St Mary's Hospital, Manchester, United Kingdom
| | - Forbes Manson
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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