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Cai N, Cheng K, Ma Y, Liu S, Tao R, Li Y, Li D, Guo B, Jia W, Liang H, Zhao J, Xia L, Ding ZY, Chen J, Zhang W. Targeting MMP9 in CTNNB1 mutant hepatocellular carcinoma restores CD8 + T cell-mediated antitumour immunity and improves anti-PD-1 efficacy. Gut 2024; 73:985-999. [PMID: 38123979 DOI: 10.1136/gutjnl-2023-331342] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVE The gain of function (GOF) CTNNB1 mutations (CTNNB1 GOF ) in hepatocellular carcinoma (HCC) cause significant immune escape and resistance to anti-PD-1. Here, we aimed to investigate the mechanism of CTNNB1 GOF HCC-mediated immune escape and raise a new therapeutic strategy to enhance anti-PD-1 efficacy in HCC. DESIGN RNA sequencing was performed to identify the key downstream genes of CTNNB1 GOF associated with immune escape. An in vitro coculture system, murine subcutaneous or orthotopic models, spontaneously tumourigenic models in conditional gene-knock-out mice and flow cytometry were used to explore the biological function of matrix metallopeptidase 9 (MMP9) in tumour progression and immune escape. Single-cell RNA sequencing and proteomics were used to gain insight into the underlying mechanisms of MMP9. RESULTS MMP9 was significantly upregulated in CTNNB1 GOF HCC. MMP9 suppressed infiltration and cytotoxicity of CD8+ T cells, which was critical for CTNNB1 GOF to drive the suppressive tumour immune microenvironment (TIME) and anti-PD-1 resistance. Mechanistically, CTNNB1 GOF downregulated sirtuin 2 (SIRT2), resulting in promotion of β-catenin/lysine demethylase 4D (KDM4D) complex formation that fostered the transcriptional activation of MMP9. The secretion of MMP9 from HCC mediated slingshot protein phosphatase 1 (SSH1) shedding from CD8+ T cells, leading to the inhibition of C-X-C motif chemokine receptor 3 (CXCR3)-mediated intracellular of G protein-coupled receptors signalling. Additionally, MMP9 blockade remodelled the TIME and potentiated the sensitivity of anti-PD-1 therapy in HCC. CONCLUSIONS CTNNB1 GOF induces a suppressive TIME by activating secretion of MMP9. Targeting MMP9 reshapes TIME and potentiates anti-PD-1 efficacy in CTNNB1 GOF HCC.
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Affiliation(s)
- Ning Cai
- Hepatic Surgery Center, Clinical Medicine Research Center of Hepatic Surgery of Hubei Province, and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital,Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Kun Cheng
- Hepatic Surgery Center, Clinical Medicine Research Center of Hepatic Surgery of Hubei Province, and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital,Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Yue Ma
- Hepatobiliary Surgery, Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai, People's Republic of China
| | - Sha Liu
- Hepatic Surgery Center, Clinical Medicine Research Center of Hepatic Surgery of Hubei Province, and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital,Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Ran Tao
- Hepatic Surgery Center, Clinical Medicine Research Center of Hepatic Surgery of Hubei Province, and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital,Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Yani Li
- Hepatic Surgery Center, Clinical Medicine Research Center of Hepatic Surgery of Hubei Province, and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital,Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Danfeng Li
- Hepatic Surgery Center, Clinical Medicine Research Center of Hepatic Surgery of Hubei Province, and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital,Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Bin Guo
- Hepatic Surgery Center, Clinical Medicine Research Center of Hepatic Surgery of Hubei Province, and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital,Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Wenlong Jia
- Hepatic Surgery Center, Clinical Medicine Research Center of Hepatic Surgery of Hubei Province, and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital,Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Huifang Liang
- Hepatic Surgery Center, Clinical Medicine Research Center of Hepatic Surgery of Hubei Province, and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital,Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Jianping Zhao
- Hepatic Surgery Center, Clinical Medicine Research Center of Hepatic Surgery of Hubei Province, and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital,Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Limin Xia
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Ze-Yang Ding
- Hepatic Surgery Center, Clinical Medicine Research Center of Hepatic Surgery of Hubei Province, and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital,Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Jinhong Chen
- Hepatobiliary Surgery, Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai, People's Republic of China
| | - Wanguang Zhang
- Hepatic Surgery Center, Clinical Medicine Research Center of Hepatic Surgery of Hubei Province, and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital,Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
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Weinberg OK, Cantu MD, Gagan J, Madanat YF, Arber DA, Hasserjian RP. Presence but not number of secondary type mutations influences outcome in de novo AML without MDS-associated or recurring cytogenetic abnormalities. EJHaem 2023; 4:760-764. [PMID: 37601841 PMCID: PMC10435713 DOI: 10.1002/jha2.710] [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] [Received: 04/24/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 08/22/2023]
Abstract
A group of gene mutations has been identified to be strongly associated with secondary acute myeloid leukemias (AML) arising from prior myeloid neoplasms. The International Consensus Classification (ICC) and proposed 5th edition of the World Health Organization (WHO) classification differ by inclusion of RUNX1. A recent study suggested that having two or more secondary mutations is associated with a particularly poor prognosis. In a study of 294 de novo AML patients, we found that patients with at least one ICC-defined secondary mutation had shorter survival when compared to those without secondary mutations, and ICC/WHO groups of two or more mutations did not predict for worse outcomes.
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Affiliation(s)
- Olga K. Weinberg
- Department of PathologyUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Miguel D. Cantu
- Department of PathologyUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Jeffrey Gagan
- Department of PathologyUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Yazan F. Madanat
- Department of Internal MedicineUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Daniel A. Arber
- Department of PathologyUniversity of ChicagoChicagoIllinoisUSA
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Wei Z, Li S, Tao X, Zhu G, Sun Z, Wei Z, Jiao Q, Zhang H, Chen L, Li B, Zhang Z, Yue H. Mutations in Profilin 1 Cause Early-Onset Paget's Disease of Bone With Giant Cell Tumors. J Bone Miner Res 2021; 36:1088-1103. [PMID: 33599011 PMCID: PMC8251538 DOI: 10.1002/jbmr.4275] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/02/2021] [Accepted: 02/14/2021] [Indexed: 12/24/2022]
Abstract
Paget's disease of bone (PDB) is a late-onset chronic progressive bone disease characterized by abnormal activation of osteoclasts that results in bone pain, deformities, and fractures. PDB is very rare in Asia. A subset of PDB patients have early onset and can develop malignant giant cell tumors (GCTs) of the bone (PDB/GCTs), which arise within Paget bone lesions; the result is a significantly higher mortality rate. SQSTM1, TNFRSF11A, OPG, VCP, and HNRNPA2B1 have been identified as pathogenic genes of PDB, and ZNF687 is the only confirmed gene to date known to cause PDB/GCT. However, the molecular mechanism underlying PDB/GCT has not been fully elucidated. Here, we investigate an extended Chinese pedigree with eight individuals affected by early-onset and polyostotic PDB, two of whom developed GCTs. We identified a heterozygous 4-bp deletion in the Profilin 1 (PFN1) gene (c.318_321delTGAC) by genetic linkage analysis and exome sequencing for the family. Sanger sequencing revealed another heterozygous 1-bp deletion in PFN1 (c.324_324delG) in a sporadic early-onset PDB/GCT patient, further proving its causative role. Interestingly, a heterozygous missense mutation of PFN1 (c.335 T > C) was identified in another PDB/GCT family, revealing that not only deletion but also missense mutations in PFN1 can cause PDB/GCT. Furthermore, we established a Pfn1-mutated mouse model (C57BL/6J mice) and successfully obtained Pagetic phenotypes in heterozygous mice, verifying loss of function of PFN1 as the cause of PDB/GCT development. In conclusion, our findings reveal mutations in PFN1 as the pathological mechanism in PDB/GCT, and we successfully established Pfn1-mutated mice as a suitable animal model for studying PDB-associated pathological mechanisms. The identification of PFN1 mutations has great diagnostic value for identifying PDB individuals predisposed toward developing GCTs. © 2021 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Zhe Wei
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Shanshan Li
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xiaohui Tao
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Guoying Zhu
- Department of Radiation Health, Institute of Radiation Medicine, Fudan University, Shanghai, China
| | - Zhenkui Sun
- Department of Nuclear Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Zhanying Wei
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Qiong Jiao
- Department of Pathology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Huizhen Zhang
- Department of Pathology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Lin Chen
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, China
| | - Baojie Li
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Ministry of Education, Shanghai, China
| | - Zhenlin Zhang
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Hua Yue
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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Snanoudj S, Molin A, Colson C, Coudray N, Paulien S, Mittre H, Gérard M, Schaefer E, Goldenberg A, Bacchetta J, Odent S, Naudion S, Demeer B, Faivre L, Gruchy N, Kottler ML, Richard N. Maternal Transmission Ratio Distortion of GNAS Loss-of-Function Mutations. J Bone Miner Res 2020; 35:913-919. [PMID: 31886927 DOI: 10.1002/jbmr.3948] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 12/09/2019] [Accepted: 12/14/2019] [Indexed: 12/14/2022]
Abstract
Pseudohypoparathyroidism type 1A (PHP1A) and pseudopseudohypoparathyroidism (PPHP) are two rare autosomal dominant disorders caused by loss-of-function mutations in the imprinted Guanine Nucleotide Binding Protein, Alpha Stimulating Activity (GNAS) gene, coding Gs α. PHP1A is caused by mutations in the maternal allele and results in Albright's hereditary osteodystrophy (AHO) and hormonal resistance, mainly to the parathormone (PTH), whereas PPHP, with AHO features and no hormonal resistance, is linked to mutations in the paternal allele. This study sought to investigate parental transmission of GNAS mutations. We conducted a retrospective study in a population of 204 families with 361 patients harboring GNAS mutations. To prevent ascertainment bias toward a higher proportion of affected children due to the way in which data were collected, we excluded from transmission analysis all probands in the ascertained sibships. After bias correction, the distribution ratio of the mutated alleles was calculated from the observed genotypes of the offspring of nuclear families and was compared to the expected ratio of 50% according to Mendelian inheritance (one-sample Z-test). Sex ratio, phenotype of the transmitting parent, and transmission depending on the severity of the mutation were also analyzed. Transmission analysis was performed in 114 nuclear families and included 250 descendants. The fertility rates were similar between male and female patients. We showed an excess of transmission from mother to offspring of mutated alleles (59%, p = .022), which was greater when the mutations were severe (61.7%, p = .023). Similarly, an excess of transmission was found when the mother had a PHP1A phenotype (64.7%, p = .036). By contrast, a Mendelian distribution was observed when the mutations were paternally inherited. Higher numbers of females within the carriers, but not in noncarriers, were also observed. The mother-specific transmission ratio distortion (TRD) and the sex-ratio imbalance associated to PHP1A point to a role of Gs α in oocyte biology or embryogenesis, with implications for genetic counseling. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
- Sarah Snanoudj
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Arnaud Molin
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Cindy Colson
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Nadia Coudray
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Sylvie Paulien
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Hervé Mittre
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Marion Gérard
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Elise Schaefer
- Department of Genetics, CHU de Strasbourg, Strasbourg, France
| | | | - Justine Bacchetta
- Department of Pediatric Nephrology, Rheumatology and Dermatology, CHU de Lyon, Bron, France
| | - Sylvie Odent
- Department of Genetics, CHU de Rennes, Rennes, France
| | - Sophie Naudion
- Department of Genetics, CHU de Bordeaux, Bordeaux, France
| | | | | | - Nicolas Gruchy
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Marie-Laure Kottler
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Nicolas Richard
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
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5
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Yu J, Sadakari Y, Shindo K, Suenaga M, Brant A, Almario JAN, Borges M, Barkley T, Fesharakizadeh S, Ford M, Hruban RH, Shin EJ, Lennon AM, Canto MI, Goggins M. Digital next-generation sequencing identifies low-abundance mutations in pancreatic juice samples collected from the duodenum of patients with pancreatic cancer and intraductal papillary mucinous neoplasms. Gut 2017; 66:1677-1687. [PMID: 27432539 PMCID: PMC5243915 DOI: 10.1136/gutjnl-2015-311166] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 04/27/2016] [Accepted: 05/19/2016] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Secretin-stimulated pancreatic juice contains DNA shed from cells lining the pancreatic ducts. Genetic analysis of this fluid may form a test to detect pancreatic ductal neoplasia. DESIGN We employed digital next-generation sequencing ('digital NGS') to detect low-abundance mutations in secretin-stimulated juice samples collected from the duodenum of subjects enrolled in Cancer of the Pancreas Screening studies at Johns Hopkins Hospital. For each juice sample, digital NGS necessitated 96 NGS reactions sequencing nine genes. The study population included 115 subjects (53 discovery, 62 validation) (1) with pancreatic ductal adenocarcinoma (PDAC), (2) intraductal papillary mucinous neoplasm (IPMN), (3) controls with non-suspicious pancreata. RESULTS Cases with PDAC and IPMN were more likely to have mutant DNA detected in pancreatic juice than controls (both p<0.0001); mutant DNA concentrations were higher in patients with PDAC than IPMN (p=0.003) or controls (p<0.001). TP53 and/or SMAD4 mutations were commonly detected in juice samples from patients with PDAC and were not detected in controls (p<0.0001); mutant TP53/SMAD4 concentrations could distinguish PDAC from IPMN cases with 32.4% sensitivity, 100% specificity (area under the curve, AUC 0.73, p=0.0002) and controls (AUC 0.82, p<0.0001). Two of four patients who developed pancreatic cancer despite close surveillance had SMAD4/TP53 mutations from their cancer detected in juice samples collected over 1 year prior to their pancreatic cancer diagnosis when no suspicious pancreatic lesions were detected by imaging. CONCLUSIONS The detection in pancreatic juice of mutations important for the progression of low-grade dysplasia to high-grade dysplasia and invasive pancreatic cancer may improve the management of patients undergoing pancreatic screening and surveillance.
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Affiliation(s)
- Jun Yu
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yoshihiko Sadakari
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Koji Shindo
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Masaya Suenaga
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Aaron Brant
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jose Alejandro Navarro Almario
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Borges
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas Barkley
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shahriar Fesharakizadeh
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Madeline Ford
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eun Ji Shin
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anne Marie Lennon
- Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Marcia Irene Canto
- Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Goggins
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Affiliation(s)
- Alex Thompson
- Department of Gastroenterology, St. Vincent's Hospital, Melbourne, Victoria, Australia
| | - Stephen Locarnini
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute of Infection and Immunity, Melbourne, Victoria, Australia
| | - Peter Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute of Infection and Immunity, Melbourne, Victoria, Australia
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Jamal S, Goyal S, Shanker A, Grover A. Computational Screening and Exploration of Disease-Associated Genes in Alzheimer's Disease. J Cell Biochem 2017; 118:1471-1479. [PMID: 27883225 DOI: 10.1002/jcb.25806] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/22/2016] [Indexed: 02/05/2023]
Abstract
Alzheimer's is a neurodegenerative disease affecting large populations worldwide characterized mainly by progressive loss of memory along with various other symptoms. The foremost cause of the disease is still unclear, however various mechanisms have been proposed to cause the disease that include amyloid hypothesis, tau hypothesis, and cholinergic hypothesis in addition to genetic factors. Various genes have been known to be involved which are APOE, PSEN1, PSEN2, and APP among others. In the present study, we have used computational methods to examine the pathogenic effects of non-synonymous single nucleotide polymorphisms (SNPs) associated with ABCA7, CR1, MS4A6A, CD2AP, PSEN1, PSEN2, and APP genes. The SNPs were obtained from dbSNP database followed by identification of deleterious SNPs and prediction of their functional impact. Prediction of disease-associated mutations was performed and the impact of the mutations on the stability of the protein was carried out. To study the structural significance of the computationally prioritized mutations on the proteins, molecular dynamics simulation studies were carried out. On analysis, the SNPs with IDs rs76282929 ABCA7; CR1 rs55962594; MS4A6A rs601172; CD2AP rs61747098; PSEN1 rs63750231, rs63750265, rs63750526, rs63750577, rs63750687, rs63750815, rs63750900, rs63751037, rs63751163, rs63751399; PSEN2 rs63749851; and APP rs63749964, rs63750066, rs63750734, and rs63751039 were predicted to be deleterious and disease-associated having significant structural impact on the proteins. The current study proposes a precise computational methodology for the identification of disease-associated SNPs. J. Cell. Biochem. 118: 1471-1479, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Salma Jamal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan, India
| | - Sukriti Goyal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan, India
| | - Asheesh Shanker
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan, India.,Bioinformatics Programme, Centre for Biological Sciences, Central University of South Bihar, BIT Campus, Patna, Bihar, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Liu G, Wang Y, Anderson GJ, Camaschella C, Chang Y, Nie G. Functional Analysis of GLRX5 Mutants Reveals Distinct Functionalities of GLRX5 Protein. J Cell Biochem 2016; 117:207-17. [PMID: 26100117 DOI: 10.1002/jcb.25267] [Citation(s) in RCA: 28] [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: 05/21/2015] [Accepted: 06/17/2015] [Indexed: 11/10/2022]
Abstract
Glutaredoxin 5 (GLRX5) is a 156 amino acid mitochondrial protein that plays an essential role in mitochondrial iron-sulfur cluster transfer. Mutations in this protein were reported to result in sideroblastic anemia and variant nonketotic hyperglycinemia in human. Recently, we have characterized a Chinese congenital sideroblastic anemia patient who has two compound heterozygous missense mutations (c. 301 A>C and c. 443 T>C) in his GLRX5 gene. Herein, we developed a GLRX5 knockout K562 cell line and studied the biochemical functions of the identified pathogenic mutations and other conserved amino acids with predicted essential functions. We observed that the K101Q mutation (due to c. 301 A>C mutation) may prevent the binding of [Fe-S] to GLRX5 protein, while L148S (due to c. 443 T>C mutation) may interfere with [Fe-S] transfer from GLRX5 to iron regulatory protein 1 (IRP1), mitochondrial aconitase (m-aconitase) and ferrochelatase. We also demonstrated that L148S is functionally complementary to the K51del mutant with respect to Fe/S-ferrochelatase, Fe/S-IRP1, Fe/S-succinate dehydrogenase, and Fe/S-m-aconitase biosynthesis and lipoylation of pyruvate dehydrogenase complex and α-ketoglutarate dehydrogenase complex. Furthermore, we demonstrated that the mutations of highly conserved amino acid residues in GLRX5 protein can have different effects on downstream Fe/S proteins. Collectively, our current work demonstrates that GLRX5 protein is multifunctional in [Fe-S] protein synthesis and maturation and defects of the different amino acids of the protein will lead to distinct effects on downstream Fe/S biosynthesis.
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Affiliation(s)
- Gang Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, No.11 Zhongguancun Beiyitiao, Beijing, 100190, China
| | - Yongwei Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, No.11 Zhongguancun Beiyitiao, Beijing, 100190, China.,Laboratory of Molecular Iron Metabolism, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, Hebei Province, China
| | - Gregory J Anderson
- Iron Metabolism Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Clara Camaschella
- Vita-Salute University, and IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Yanzhong Chang
- Laboratory of Molecular Iron Metabolism, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, Hebei Province, China
| | - Guangjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, No.11 Zhongguancun Beiyitiao, Beijing, 100190, China
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Kamaraj B, Purohit R. Mutational Analysis on Membrane Associated Transporter Protein (MATP) and Their Structural Consequences in Oculocutaeous Albinism Type 4 (OCA4)-A Molecular Dynamics Approach. J Cell Biochem 2016; 117:2608-19. [PMID: 27019209 DOI: 10.1002/jcb.25555] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [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: 01/08/2016] [Accepted: 03/24/2016] [Indexed: 12/11/2022]
Abstract
Oculocutaneous albinism type IV (OCA4) is an autosomal recessive inherited disorder which is characterized by reduced biosynthesis of melanin pigmentation in skin, hair, and eyes and caused by the genetic mutations in the membrane-associated transporter protein (MATP) encoded by SLC45A2 gene. The MATP protein consists of 530 amino acids which contains 12 putative transmembrane domains and plays an important role in pigmentation and probably functions as a membrane transporter in melanosomes. We scrutinized the most OCA4 disease-associated mutation and their structural consequences on SLC45A2 gene. To understand the atomic arrangement in 3D space, the native and mutant structures were modeled. Further the structural behavior of native and mutant MATP protein was investigated by molecular dynamics simulation (MDS) approach in explicit lipid and water background. We found Y317C as the most deleterious and disease-associated SNP on SLC45A2 gene. In MDS, mutations in MATP protein showed loss of stability and became more flexible, which alter its structural conformation and function. This phenomenon has indicated a significant role in inducing OCA4. Our study explored the understanding of molecular mechanism of MATP protein upon mutation at atomic level and further helps in the field of pharmacogenomics to develop a personalized medicine for OCA4 disorder. J. Cell. Biochem. 117: 2608-2619, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Balu Kamaraj
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk-Antwerp, Belgium
| | - Rituraj Purohit
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India.
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Zou WB, Masson E, Boulling A, Cooper DN, Li ZS, Liao Z, Férec C, Chen JM. Digging deeper into the intronic sequences of the SPINK1 gene. Gut 2016; 65:1055-6. [PMID: 26884424 DOI: 10.1136/gutjnl-2016-311428] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 01/21/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Wen-Bin Zou
- Department of Gastroenterology, Changhai Hospital, the Second Military Medical University, Shanghai, China Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Etablissement Français du Sang (EFS)-Bretagne, Brest, France Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Emmanuelle Masson
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Universitaire (CHU) Brest, Hôpital Morvan, Brest, France
| | - Arnaud Boulling
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Etablissement Français du Sang (EFS)-Bretagne, Brest, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Zhao-Shen Li
- Department of Gastroenterology, Changhai Hospital, the Second Military Medical University, Shanghai, China Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, the Second Military Medical University, Shanghai, China Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Claude Férec
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Etablissement Français du Sang (EFS)-Bretagne, Brest, France Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Universitaire (CHU) Brest, Hôpital Morvan, Brest, France Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France
| | - Jian-Min Chen
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Etablissement Français du Sang (EFS)-Bretagne, Brest, France Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France
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11
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Swetha RG, Ramaiah S, Anbarasu A. Molecular Dynamics Studies on D835N Mutation in FLT3-Its Impact on FLT3 Protein Structure. J Cell Biochem 2015; 117:1439-45. [PMID: 26566084 DOI: 10.1002/jcb.25434] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 07/22/2015] [Accepted: 11/10/2015] [Indexed: 01/08/2023]
Abstract
Mutations in Fetal Liver Tyrosine Kinase 3 (FLT3) genes are implicated in the constitutive activation and development of Acute Myeloid Leukaemia (AML). They are involved in signalling pathway of autonomous proliferation and block differentiation in leukaemia cells. FLT3 is considered as a promising target for the therapeutic intervention of AML. There are a few missense mutations associated with FLT3 that are found in AML patients. The D835N mutation is the most frequently observed and the aspartic acid in this position acts as a key residue for the receptor activation. The present study aims to understand the structural effect of D835N mutation in FLT3. We carried out the molecular dynamics (MD) simulation for a period of 120 ns at 300 K. Root-mean square deviation, root-mean square fluctuations, surface accessibility, radius of gyration, hydrogen bond, eigenvector projection analysis, trace of covariance matrix, and density analysis revealed the instability of mutant (D835N) protein. Our study provides new insights on the conformational changes in the mutant (D835N) structure of FLT3 protein. Our observations will be useful for researchers exploring AML and for the development of FLT3 inhibitors.
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Affiliation(s)
- Rayapadi G Swetha
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, 632014, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, 632014, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, 632014, India
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14
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STRONG LC, DEMEREC N. Virus- and carcinogen-induced mutations. Lancet 1948; 2:56. [PMID: 18939251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
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15
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MULLER HJ. Mutational prophylaxis. Bull N Y Acad Med 1948; 24:447-470. [PMID: 18864210 PMCID: PMC1871399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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IVES PT, ANDREWS MB. Analysis of the sex-linked mutation rate in the Florida high stock. Genetics 1946; 31:220. [PMID: 21021053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
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CHILD GP. The effect of delaying time of development on mutation rate. Genetics 1946; 31:214. [PMID: 21021049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
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MULLER HJ. Physiological effects on spontaneous mutation rate in Drosophila. Genetics 1946; 31:225. [PMID: 21021056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
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BLARINGHEM L. [Double flowers by variation of buds; reversible mutation of Cardamine pratensis L. var. pleno flora]. C R Hebd Seances Acad Sci 1945; 221:322-325. [PMID: 21016835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
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