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Ge J, Yue Y, Nie HY, Liu KG, Li H, Lin HG, Zhang T, Yan HF, Sun HW, Yang JW, Zhou JL, Cui Y. Simulated microgravity altered the gene expression profiles and inhibited the proliferation of Kupffer cells in the early phase by downregulating LMO2 and EZH2. LIFE SCIENCES IN SPACE RESEARCH 2024; 40:21-34. [PMID: 38245345 DOI: 10.1016/j.lssr.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/30/2023] [Accepted: 11/08/2023] [Indexed: 01/22/2024]
Abstract
Microgravity is a primary challenge that need to overcome, when human travel to space. Our study provided evidence that Kupffer cells (KCs) are sensitive to simulated microgravity (SMG), and no similar research report has been found in the literature. Using transcriptome sequencing technology, it was showed that 631 genes were upregulated and 801 genes were downregulated in KCs after treatment under SMG for 3 days. The GO analysis indicated that the proliferation of KCs was affected when exposed to SMG for 3 days. CCK-8 assay confirmed that the proliferation of KCs was inhibited in the third day under the environment of SMG. Furthermore, we identified 8 key genes that affect the proliferation of KCs and predicted 2 transcription factors (TFs) that regulate the 8 key genes. Significantly, we found that microgravity could affect the expression of LMO2 and EZH2 to reduce the transcription of Racgap1, Ccna2, Nek2, Aurka, Plk1, Haus4, Cdc20, Bub1b, which resulting in the reduction in KCs proliferation. These finding suggested that the inhibition of KCs proliferation under microgravity may influence the homeostasis of liver, and LMO2 and EZH2 can be the targets in management of KCs' disturbance in the future practice of space medicine.
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Affiliation(s)
- Jun Ge
- Department of General Surgery, The 306th Hospital of PLA-Peking University Teaching Hospital, Beijing, 100101, China
| | - Yuan Yue
- Department of General Surgery, The 306th Hospital of PLA-Peking University Teaching Hospital, Beijing, 100101, China
| | - Hong-Yun Nie
- Department of General Surgery, The 306th Hospital of PLA-Peking University Teaching Hospital, Beijing, 100101, China
| | - Kai-Ge Liu
- Department of General Surgery, Strategic Support Force Medical Center, Beijing, 100101, China
| | - Hao Li
- Department of General Surgery, Strategic Support Force Medical Center, Beijing, 100101, China.
| | - Hai-Guan Lin
- Department of General Surgery, Strategic Support Force Medical Center, Beijing, 100101, China
| | - Tao Zhang
- Department of General Surgery, Strategic Support Force Medical Center, Beijing, 100101, China
| | - Hong-Feng Yan
- Department of General Surgery, Strategic Support Force Medical Center, Beijing, 100101, China
| | - Hong-Wei Sun
- Department of General Surgery, Strategic Support Force Medical Center, Beijing, 100101, China
| | - Jian-Wu Yang
- Department of General Surgery, Strategic Support Force Medical Center, Beijing, 100101, China
| | - Jin-Lian Zhou
- Department of Pathology, Strategic Support Force Medical Center, Beijing, 100101, China
| | - Yan Cui
- Department of General Surgery, The 306th Hospital of PLA-Peking University Teaching Hospital, Beijing, 100101, China; Department of General Surgery, Strategic Support Force Medical Center, Beijing, 100101, China.
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Jia M, Liang J, Li Z, Qin Y, Li Q, Wang J, Lu X. Screening tumor stage-specific candidate neoantigens in thyroid adenocarcinoma using integrated exome and transcriptome sequencing. Front Immunol 2023; 14:1187160. [PMID: 37854594 PMCID: PMC10579579 DOI: 10.3389/fimmu.2023.1187160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023] Open
Abstract
Background The incidence of thyroid carcinoma (THCA), the most common endocrine tumor, is continuously increasing worldwide. Although the overall prognosis of THCA is good, patients with distant metastases exhibit a mortality rate of 5-20%. Methods To improve the diagnosis and overall prognosis of patients with thyroid cancer, we screened specific candidate neoantigen genes in early- and late-stage THCA by analyzing the transcriptome and somatic cell mutations in this study. Results The top five early-stage neoantigen-related genes (NRGs) were G protein-coupled receptor 4 [GPR4], chondroitin sulfate proteoglycan 4 [CSPG4], teneurin transmembrane protein 1 [TENM1], protein S 1 [PROS1], and thymidine kinase 1 [TK1], whereas the top five late-stage NRGs were cadherin 6 [CDH6], semaphorin 6B [SEMA6B], dysferlin [DYSF], xenotropic and polytropic retrovirus receptor 1 [XPR1], and ABR activator of RhoGEF and GTPase [ABR]. Subsequently, we used machine learning models to verify their ability to screen NRGs and analyze the correlations among NRGs, immune cell types, and immune checkpoint regulators. The use of candidate antigen genes resulted in a better diagnostic model (the area under the curve [AUC] value of the early-stage group [0.979] was higher than that of the late-stage group [0.959]). Then, a prognostic model was constructed to predict NRG survival, and the 1-, 3- and 5-year AUC values were 0.83, 0.87, and 0.86, respectively, which were closely related to different immune cell types. Comparison of the expression trends and mutation frequencies of NRGs in multiple tumors revealed their potential for the development of broad spectrum therapeutic drugs. Conclusion In conclusion, the candidate NRGs identified in this study could potentially be used as therapeutic targets and diagnostic biomarkers for the development of novel broad spectrum therapeutic agents.
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Affiliation(s)
- Meng Jia
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiawen Liang
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Zhuyao Li
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ye Qin
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qianqian Li
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianwei Wang
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou, China
| | - Xiubo Lu
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Ge M, Ji C, Li H, Huang H. De Novo Mutation in KRT1 Leads to Epidermolytic Palmoplantar Keratoderma: from Chinese Traditional Treatment to Prenatal Diagnosis Using Whole-Exome Sequencing-Plus. DNA Cell Biol 2023; 42:645-652. [PMID: 37566479 DOI: 10.1089/dna.2023.0154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023] Open
Abstract
Congenital skin disorders are a class of complex genetic diseases that are difficult to diagnose and treat. We developed trio whole-exome sequencing-plus (WES-plus) for detecting de novo mutations and evaluated the use of traditional Chinese medicine (TCM) for treating congenital skin disorders. In this study, we successively performed panel-based next-generation sequencing (NGS) and Trio WES-plus in a child with frequent large blisters. Panel-based NGS revealed no pathogenic mutations. Trio WES-plus for resequencing based on cutaneous keratosis of the palms and feet detected a missense mutation (c.1436T>A, p.Ile479Asn) in the coding region of KRT1 in the child but not in his parents. Following prenatal diagnosis, a healthy second baby without the mutation was born. The disease symptoms of epidermolytic palmoplantar keratoderma (EPPK) application were improved by TCM and Western medicine. Our study revealed the pathogenicity of a de novo mutation in human KRT1, which expands the mutation spectrum of EPPK. Trio WES-plus is useful for diagnosing genetic diseases and providing genetic guidance from prenatal diagnosis to treatment.
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Affiliation(s)
- Mengdi Ge
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chunmin Ji
- Department of Obstetrics and Gynecology, Air Force Hospital of Eastern Theater, Nanjing, China
| | - Huanzhen Li
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Huan Huang
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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O’Sullivan B, Seoighe C. Comprehensive and realistic simulation of tumour genomic sequencing data. NAR Cancer 2023; 5:zcad051. [PMID: 37746635 PMCID: PMC10516706 DOI: 10.1093/narcan/zcad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023] Open
Abstract
Accurate identification of somatic mutations and allele frequencies in cancer has critical research and clinical applications. Several computational tools have been developed for this purpose but, in the absence of comprehensive 'ground truth' data, assessing the accuracy of these methods is challenging. We created a computational framework to simulate tumour and matched normal sequencing data for which the source of all loci that contain non-reference bases is known, based on a phased, personalized genome. Unlike existing methods, we account for sampling errors inherent in the sequencing process. Using this framework, we assess accuracy and biases in inferred mutations and their frequencies in an established somatic mutation calling pipeline. We demonstrate bias in existing methods of mutant allele frequency estimation and show, for the first time, the observed mutation frequency spectrum corresponding to a theoretical model of tumour evolution. We highlight the impact of quality filters on detection sensitivity of clinically actionable variants and provide definitive assessment of false positive and false negative mutation calls. Our simulation framework provides an improved means to assess the accuracy of somatic mutation calling pipelines and a detailed picture of the effects of technical parameters and experimental factors on somatic mutation calling in cancer samples.
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Affiliation(s)
- Brian O’Sullivan
- School of Mathematical and Statistical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland
| | - Cathal Seoighe
- School of Mathematical and Statistical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland
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5
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Lin J, Su MF, Zheng JL, Gu L, Wu HC, Wu X, Lin HY, Wu ZX, Li DL. Fas/FasL and Complement Activation are Associated with Chronic Active Epstein-Barr Virus Hepatitis. J Clin Transl Hepatol 2023; 11:540-549. [PMID: 36969885 PMCID: PMC10037519 DOI: 10.14218/jcth.2022.00227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/12/2022] [Accepted: 07/26/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND AND AIMS Chronic active Epstein-Barr virus hepatitis (CAEBVH) is a rare and highly lethal disease characterized by hepatitis and hepatomegaly. This study aimed to investigate the clinicopathological features and pathogenic mechanisms of CAEBVH. METHODS Ten patients with confirmed Epstein-Barr virus hepatitis infection were enrolled. The clinicopathological characteristics of these patients were summarized and analyzed. Flow cytometry was utilized to detect peripheral blood immune cell phenotypes and whole exome sequencing was used to explore pathogenic genetic mechanisms. Lastly, immunohistochemical staining was employed to verify pathogenic mechanisms. RESULTS Clinical features observed in all Epstein-Barr virus hepatitis patients included fever (7/10), splenomegaly (10/10), hepatomegaly (9/10), abnormal liver function (8/10), and CD8+ T cell lymphopenia (6/7). Hematoxylin and eosin staining revealed lymphocytic infiltration in the liver. Positive Epstein-Barr virus-encoded small RNA in-situ hybridization (EBER-ISH) of lymphocytes of liver tissues was noted. Whole exome sequencing indicated that cytotoxic T lymphocytes and the complement system were involved. The expression of CD8, Fas, FasL, and Caspase-8 expression as well as apoptotic markers was enhanced in the Epstein-Barr virus hepatitis group relative to the controls (p<0.05). Lastly, Complement 1q and complement 3d expression, were higher in CAEBVH patients relative to controls (p<0.05). CONCLUSIONS CAEBVH patients developed fever, hepatosplenomegaly, and lymphadenopathy. Histopathological changes were a diffuse lymphocytic sinusoidal infiltrate with EBER-ISH positivity. Fas/FasL and complement activation were involved in CAEBVH patients.
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Affiliation(s)
- Jing Lin
- Department of Hepatobiliary Medicine, Fuzong Clinical Medical College of Fujian Medical University, 900TH Hospital of the Joint Logistic Support Force, PLA, Fuzhou, Fujian, China
| | - Miao-Fang Su
- Department of Hepatobiliary Medicine, Fuzong Clinical Medical College of Fujian Medical University, 900TH Hospital of the Joint Logistic Support Force, PLA, Fuzhou, Fujian, China
| | - Jiao-Long Zheng
- Department of Hepatobiliary Medicine, Fuzong Clinical Medical College of Fujian Medical University, 900TH Hospital of the Joint Logistic Support Force, PLA, Fuzhou, Fujian, China
| | - Lei Gu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hai-Cong Wu
- Department of Hepatobiliary Medicine, Fuzong Clinical Medical College of Fujian Medical University, 900TH Hospital of the Joint Logistic Support Force, PLA, Fuzhou, Fujian, China
| | - Xia Wu
- Department of Hepatobiliary Medicine, Fuzong Clinical Medical College of Fujian Medical University, 900TH Hospital of the Joint Logistic Support Force, PLA, Fuzhou, Fujian, China
| | - Hai-Yan Lin
- Department of Hepatobiliary Medicine, Fuzong Clinical Medical College of Fujian Medical University, 900TH Hospital of the Joint Logistic Support Force, PLA, Fuzhou, Fujian, China
| | - Zhi-Xian Wu
- Department of Hepatobiliary Medicine, Fuzong Clinical Medical College of Fujian Medical University, 900TH Hospital of the Joint Logistic Support Force, PLA, Fuzhou, Fujian, China
| | - Dong-Liang Li
- Department of Hepatobiliary Medicine, Fuzong Clinical Medical College of Fujian Medical University, 900TH Hospital of the Joint Logistic Support Force, PLA, Fuzhou, Fujian, China
- Correspondence to: Dong-Liang Li, Department of Hepatobiliary Medicine, Fuzong Clinical Medical College of Fujian Medical University, 900TH Hospital of the Joint Logistic Support Force, PLA, Fuzhou, Fujian 350025, China. ORCID: https://orcid.org/0000-0001-5536-8468. Tel/Fax: +86-591-2285-9128, E-mail:
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6
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Wang A, Song Z, Zhang X, Xiao L, Feng Y, Qi C, Zhang G, Bai J, Liu Y, Sun T, Meng F, Wang F. MARS1 mutations linked to familial trigeminal neuralgia via the integrated stress response. J Headache Pain 2023; 24:4. [PMID: 36641423 PMCID: PMC9840295 DOI: 10.1186/s10194-022-01537-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND While new genetic analysis methods are widely used in the clinic, few researchers have focused on trigeminal neuralgia (TN) with familial clustering (≥ 2 TN patients in one kindred family). Previous literature suggests that familial trigeminal neuralgia (FTN) may be associated with inherited genetic factors. To date, few next-generation sequencing studies have been reported for FTN. This study investigated the pathogenic mechanism of FTN by using whole-exome sequencing (WES) technology, which may enhance our understanding of human TN pathophysiology. METHOD: We performed WES for 7 probands from families of FTN. Sanger sequencing was performed for two control groups (FTN family members group and nonfamilial TN subject group) to potentially identify new FTN-related gene mutations. In families where FTN probands carried potentially pathogenic gene mutations, the ribonucleic acid (RNA) of FTN probands and related family members, as well as nonfamilial TN patients were analysed by RNA sequencing (RNA-seq) to confirm differential gene expression. RESULTS Seven probands were derived from 3 Chinese families. WES and Sanger sequencing identified MARS1 mutation c.2398C > A p.(Pro800Thr) in Family 1. MARS1 mutation was confirmed in 14/26 [53.8%] members of Family 1 in FTN family member group, while none of nonfamilial TN subjects had this MARS1 mutation. RNA-seq showed that 3 probands in Family 1 had higher expression of Fosl1 (Fos-like antigen 1) and NFE2 (Nuclear factor, erythroid 2) than 3 subjects in the nonfamilial TN subject group. Fosl1 and NFE2 are genes related to integrated stress response (ISR). CONCLUSION MARS1 mutations may cause chronic activation of ISR, contribute to ISR pathophysiological changes in FTN, and cause/accelerate peripheral nerve degeneration. The findings of this study can enrich our knowledge of the role of molecular genetics in TN in humans.
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Affiliation(s)
- Anni Wang
- grid.411617.40000 0004 0642 1244Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, People’s Republic of China ,grid.411617.40000 0004 0642 1244Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, People’s Republic of China ,grid.413385.80000 0004 1799 1445Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia People’s Republic of China
| | - Zimu Song
- grid.413385.80000 0004 1799 1445Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia People’s Republic of China
| | - Xu Zhang
- grid.216938.70000 0000 9878 7032School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - LiFei Xiao
- grid.413385.80000 0004 1799 1445Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia People’s Republic of China ,grid.412194.b0000 0004 1761 9803China Ningxia Key Laboratory of Cerebrocranial Disease, The Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Yan Feng
- grid.413385.80000 0004 1799 1445Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia People’s Republic of China ,grid.412194.b0000 0004 1761 9803China Ningxia Key Laboratory of Cerebrocranial Disease, The Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Chong Qi
- grid.411617.40000 0004 0642 1244Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Guohuan Zhang
- grid.419052.b0000 0004 0467 2189State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, People’s Republic of China ,grid.410726.60000 0004 1797 8419Sino-Danish College, University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Jinbo Bai
- grid.413385.80000 0004 1799 1445Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia People’s Republic of China ,grid.412194.b0000 0004 1761 9803China Ningxia Key Laboratory of Cerebrocranial Disease, The Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Yang Liu
- grid.413385.80000 0004 1799 1445Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia People’s Republic of China ,grid.412194.b0000 0004 1761 9803China Ningxia Key Laboratory of Cerebrocranial Disease, The Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Tao Sun
- grid.413385.80000 0004 1799 1445Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia People’s Republic of China ,grid.412194.b0000 0004 1761 9803China Ningxia Key Laboratory of Cerebrocranial Disease, The Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Fangang Meng
- grid.411617.40000 0004 0642 1244Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, People’s Republic of China ,grid.411617.40000 0004 0642 1244Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, People’s Republic of China ,grid.413259.80000 0004 0632 3337Beijing Key Laboratory of Neurostimulation, Beijing, People’s Republic of China ,grid.510934.a0000 0005 0398 4153Chinese Institute for Brain Research, Beijing, People’s Republic of China
| | - Feng Wang
- grid.452661.20000 0004 1803 6319Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang People’s Republic of China
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Sahajpal NS, Mondal AK, Tvrdik T, Hauenstein J, Shi H, Deeb KK, Saxe D, Hastie AR, Chaubey A, Savage NM, Kota V, Kolhe R. Clinical Validation and Diagnostic Utility of Optical Genome Mapping for Enhanced Cytogenomic Analysis of Hematological Neoplasms. J Mol Diagn 2022; 24:1279-1291. [PMID: 36265723 DOI: 10.1016/j.jmoldx.2022.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/29/2022] [Accepted: 09/12/2022] [Indexed: 11/07/2022] Open
Abstract
The current standard-of-care cytogenetic techniques for the analysis of hematological malignancies include karyotyping, fluorescence in situ hybridization, and chromosomal microarray, which are labor intensive and time and cost prohibitive, and they often do not reveal the genetic complexity of the tumor, demonstrating the need for alternative technology for better characterization of these tumors. Herein, we report the results from our clinical validation study and demonstrate the utility of optical genome mapping (OGM), evaluated using 92 sample runs (including replicates) that included 69 well-characterized unique samples (59 hematological neoplasms and 10 controls). The technical performance (quality control metrics) resulted in 100% first-pass rate, with analytical performance (concordance) showing a sensitivity of 98.7%, a specificity of 100%, and an accuracy of 99.2%. OGM demonstrated robust technical, analytical performance, and interrun, intrarun, and interinstrument reproducibility. The limit of detection was determined to be at 5% allele fraction for aneuploidy, translocation, interstitial deletion, and duplication. OGM identified several additional structural variations, revealing the genomic architecture in these neoplasms that provides an opportunity for better tumor classification, prognostication, risk stratification, and therapy selection. Overall, OGM has outperformed the standard-of-care tests in this study and demonstrated its potential as a first-tier cytogenomic test for hematologic malignancies.
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Affiliation(s)
- Nikhil S Sahajpal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Tatiana Tvrdik
- Department of Pathology, Emory University, Atlanta, Georgia
| | | | - Huidong Shi
- Georgia Cancer Center, Augusta University, Augusta, Georgia
| | - Kristin K Deeb
- Department of Pathology, Emory University, Atlanta, Georgia
| | - Debra Saxe
- Department of Pathology, Emory University, Atlanta, Georgia
| | | | | | - Natasha M Savage
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Vamsi Kota
- Department of Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia.
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8
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Zhong M, Huang LN, Zhang SJ, Yan SJ. Identification of a novel mutation in ALMS1 in a Chinese patient with monogenic diabetic syndrome by whole-exome sequencing. Niger J Clin Pract 2022; 25:2077-2080. [PMID: 36537469 DOI: 10.4103/njcp.njcp_544_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Alstrom syndrome (AS) is one type of monogenic diabetic syndromes caused by mutation in the ALMS1. Due to rare prevalence and overlaps of clinical symptoms, monogenic diabetes is often misdiagnosed. Here, we report a Chinese diabetes patient with poor blood glucose control and insulin resistance. With whole-exome sequencing (WES), this patient was classified into monogenic diabetes and diagnosed as AS with one novel gene mutation identified. This study highlights the clinical application of WES in the diagnosis of monogenic diabetes.
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Affiliation(s)
- Ming Zhong
- Department of Endocrinology; Fujian Diabetes Research Institute; Metabolic Diseases Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Ling-Ning Huang
- Department of Endocrinology; Fujian Diabetes Research Institute; Metabolic Diseases Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Song-Jing Zhang
- Department of Endocrinology; Fujian Diabetes Research Institute; Metabolic Diseases Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Sun-Jie Yan
- Department of Endocrinology; Fujian Diabetes Research Institute; Metabolic Diseases Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
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9
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Duncavage EJ, Bagg A, Hasserjian RP, DiNardo CD, Godley LA, Iacobucci I, Jaiswal S, Malcovati L, Vannucchi AM, Patel KP, Arber DA, Arcila ME, Bejar R, Berliner N, Borowitz MJ, Branford S, Brown AL, Cargo CA, Döhner H, Falini B, Garcia-Manero G, Haferlach T, Hellström-Lindberg E, Kim AS, Klco JM, Komrokji R, Lee-Cheun Loh M, Loghavi S, Mullighan CG, Ogawa S, Orazi A, Papaemmanuil E, Reiter A, Ross DM, Savona M, Shimamura A, Skoda RC, Solé F, Stone RM, Tefferi A, Walter MJ, Wu D, Ebert BL, Cazzola M. Genomic profiling for clinical decision making in myeloid neoplasms and acute leukemia. Blood 2022; 140:2228-2247. [PMID: 36130297 PMCID: PMC10488320 DOI: 10.1182/blood.2022015853] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/27/2022] [Indexed: 11/20/2022] Open
Abstract
Myeloid neoplasms and acute leukemias derive from the clonal expansion of hematopoietic cells driven by somatic gene mutations. Although assessment of morphology plays a crucial role in the diagnostic evaluation of patients with these malignancies, genomic characterization has become increasingly important for accurate diagnosis, risk assessment, and therapeutic decision making. Conventional cytogenetics, a comprehensive and unbiased method for assessing chromosomal abnormalities, has been the mainstay of genomic testing over the past several decades and remains relevant today. However, more recent advances in sequencing technology have increased our ability to detect somatic mutations through the use of targeted gene panels, whole-exome sequencing, whole-genome sequencing, and whole-transcriptome sequencing or RNA sequencing. In patients with myeloid neoplasms, whole-genome sequencing represents a potential replacement for both conventional cytogenetic and sequencing approaches, providing rapid and accurate comprehensive genomic profiling. DNA sequencing methods are used not only for detecting somatically acquired gene mutations but also for identifying germline gene mutations associated with inherited predisposition to hematologic neoplasms. The 2022 International Consensus Classification of myeloid neoplasms and acute leukemias makes extensive use of genomic data. The aim of this report is to help physicians and laboratorians implement genomic testing for diagnosis, risk stratification, and clinical decision making and illustrates the potential of genomic profiling for enabling personalized medicine in patients with hematologic neoplasms.
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Affiliation(s)
- Eric J. Duncavage
- Department of Pathology and Immunology, Washington University, St. Louis, MO
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Courtney D. DiNardo
- Division of Cancer Medicine, Department of Leukemia, MD Anderson Cancer Center, Houston, TX
| | - Lucy A. Godley
- Section of Hematology and Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | | | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia & Fondazione IRCCS Policlinico S. Matteo, Pavia, Italy
| | - Alessandro M. Vannucchi
- Department of Hematology, Center Research and Innovation of Myeloproliferative Neoplasms, University of Florence and Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Keyur P. Patel
- Division of Pathology/Lab Medicine, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Lettering Cancer Center, New York, NY
| | - Rafael Bejar
- Division of Hematology and Oncology, University of California San Diego, La Jolla, CA
| | - Nancy Berliner
- Division of Hematology, Brigham and Women’s Hospital, Harvard University, Boston, MA
| | - Michael J. Borowitz
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Susan Branford
- Department of Genetics and Molecular Pathology, Center for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Anna L. Brown
- Department of Pathology, South Australia Heath Alliance, Adelaide, Australia
| | - Catherine A. Cargo
- Haematological Malignancy Diagnostic Service, St James’s University Hospital, Leeds, United Kingdom
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University Hospital, Ulm, Germany
| | - Brunangelo Falini
- Department of Hematology, CREO, University of Perugia, Perugia, Italy
| | | | | | - Eva Hellström-Lindberg
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital, Harvard University, Boston, MA
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Rami Komrokji
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL
| | - Mignon Lee-Cheun Loh
- Department of Pediatrics, Ben Towne Center for Childhood Cancer Research, Seattle Children’s Hospital, University of Washington, Seattle, WA
| | - Sanam Loghavi
- Division of Pathology/Lab Medicine, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Seishi Ogawa
- University of Kyoto School of Medicine, Kyoto, Japan
| | - Attilio Orazi
- Department of Pathology, Texas Tech University Health Sciences Center, El Paso, TX
| | | | - Andreas Reiter
- University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - David M. Ross
- Haematology Directorate, SA Pathology, Adelaide, Australia
| | - Michael Savona
- Department of Medicine, Vanderbilt University, Nashville, TN
| | - Akiko Shimamura
- Dana Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Radek C. Skoda
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Francesc Solé
- MDS Group, Institut de Recerca contra la Leucèmia Josep Carreras, Barcelona, Spain
| | - Richard M. Stone
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | - David Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Mario Cazzola
- Division of Hematology, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
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Høy Hansen M, Steensboe Lang C, Abildgaard N, Nyvold CG. Comparative evaluation of the heterozygous variant standard deviation as a quality measure for next-generation sequencing. J Biomed Inform 2022; 135:104234. [DOI: 10.1016/j.jbi.2022.104234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/15/2022] [Accepted: 10/17/2022] [Indexed: 11/30/2022]
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11
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Genetic Polymorphisms Associated with Prothrombin Time and Activated Partial Thromboplastin Time in Chinese Healthy Population. Genes (Basel) 2022; 13:genes13101867. [PMID: 36292752 PMCID: PMC9602091 DOI: 10.3390/genes13101867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/30/2022] [Accepted: 10/12/2022] [Indexed: 11/04/2022] Open
Abstract
(1) Background: The purpose of this study was to evaluate the effect of gene polymorphisms on prothrombin time (PT) and activated partial thromboplastin time (APTT) in a healthy Chinese population. (2) Methods: A total of 403 healthy volunteers from a series of novel oral anticoagulants (NOACs) bioequivalence trials in China were included. Coagulation tests for PT and APTT were performed in the central lab at Peking University First Hospital. Whole-exome sequencing (WES) and genome-wide association analysis were performed. (3) Results: In the correlation analysis of PT, 105 SNPs from 84 genes reached the genome-wide significance threshold (p < 1 × 10−5). Zinc Finger Protein 594 (ZNF594) rs184838268 (p = 4.50 × 10−19) was most significantly related to PT, and Actinin Alpha 1 (ACTN1) was found to interact most with other candidate genes. Significant associations with previously reported candidate genes Aurora Kinase B (AURKB), Complement C5(C5), Clock Circadian Regulator (CLOCK), and Histone Deacetylase 9(HDAC9) were detected in our dataset (p < 1 × 10−5). PiggyBac Transposable Element Derived 2(PGBD2) rs75935520 (p = 4.49 × 10−6), Bromodomain Adjacent To Zinc Finger Domain 2A(BAZ2A) rs199970765 (p = 5.69 × 10−6) and Protogenin (PRTG) rs80064850 (p = 8.69 × 10−6) were significantly correlated with APTT (p < 1 × 10−5). The heritability values of PT and APTT were 0.83 and 0.64, respectively; (4) Conclusion: The PT and APTT of healthy populations are affected by genetic polymorphisms. ZNF594 and ACTN1 variants could be novel genetic markers of PT, while PRTG polymorphisms might be associated with APTT levels. The findings could be attributed to ethnic differences, and need further investigation.
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12
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Zhang Y, Zhang Y, Ge H, Li N, Liu C, Wang T, Fu R, Shao Z. Identification of potential pathogenic genes for severe aplastic anemia by whole-exome sequencing. J Clin Lab Anal 2022; 36:e24438. [PMID: 35435273 PMCID: PMC9102512 DOI: 10.1002/jcla.24438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/24/2022] [Accepted: 04/02/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Severe aplastic anemia (SAA) is a syndrome of severe bone marrow failure due to hyperfunction of CD8+ T cells. While, the genetic background of SAA is still unknown. In this study, we tried to explore the possible genetic variants in CD8+ T cells of SAA patients. METHODS We performed whole-exome sequencing (WES) in CD8+ T cells of 4 SAA patients and 7 normal controls. The mutations that existed in SAA but not in NCs were identified as candidate genes. Then, we compared them with genes in the enriched KEGG pathway of differently expressed genes (DEGs) from previous RNA-seq. After analyzing the types of mutations, we identified possible pathogenic genes and validated them by RT-PCR. Finally, we compared them with the autoimmune disease-related genes in DisGeNET database to select the most possible pathogenic genes. RESULTS We found 95 candidate mutant genes in which, 4 possible pathogenic genes were identified: PRSS1, KCNJ18, PRSS2, and DGKK. RT-PCR results showed that compared with NCs, PRSS1 and KCNJ18 mRNA expression was significantly increased in SAA patients (p < 0.05), PRSS2 was also increased in SAA patients but without statistical difference, and DGKK gene could not be detected by RT-PCR in SAA patients. In addition, PRSS1 was associated with autoimmune diseases from the DisGeNET database. CONCLUSION The mutations of PRSS1, KCNJ18, PRSS2, and DGKK, especially PRSS1 in CD8+T cells, may be involved in the immune pathogenesis of SAA.
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Affiliation(s)
- Yang Zhang
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yu Zhang
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Hongyu Ge
- Department of Infectious Disease, Tianjin Medical University General Hospital, Tianjin, China
| | - Nianbin Li
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Chunyan Liu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Ting Wang
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Rong Fu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Zonghong Shao
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
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13
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Rausch C, Rothenberg-Thurley M, Buerger SA, Tschuri S, Dufour A, Neusser M, Schneider S, Spiekermann K, Metzeler KH, Ziemann F. Double Drop-Off Droplet Digital PCR: A Novel, Versatile Tool for Mutation Screening and Residual Disease Monitoring in Acute Myeloid Leukemia Using Cellular or Cell-Free DNA. J Mol Diagn 2021; 23:975-985. [PMID: 34020042 DOI: 10.1016/j.jmoldx.2021.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022] Open
Abstract
In acute myeloid leukemia (AML), somatic gene mutations are important prognostic markers and increasingly constitute therapeutic targets. Therefore, robust, sensitive, and fast diagnostic assays are needed. Current techniques for mutation screening and quantification, including next-generation sequencing and quantitative PCR, each have weaknesses that leave a need for novel diagnostic tools. We established double drop-off digital droplet PCR (DDO-ddPCR) assays for gene mutations in NPM1, IDH2, and NRAS, which can detect and quantify diverse alterations at two nearby hotspot regions present in these genes. These assays can be used for mutation screening as well as quantification and sequential monitoring. The assays were validated against next-generation sequencing and existing ddPCR assays and achieved high concordance with an overall sensitivity comparable to conventional digital PCR. In addition, the feasibility of detecting and monitoring genetic alterations in peripheral blood cell-free DNA (cfDNA) of patients with AML by DDO-ddPCR was studied. cfDNA analysis was found to have similar sensitivity compared to quantitative PCR-based analysis of peripheral blood. Finally, the cfDNA-based digital PCR in several clinical scenarios was found to be useful in long-term monitoring of target-specific therapy, early response assessment during induction chemotherapy, and identification of mutations in patients with extramedullary disease. Thus, DDO-ddPCR-based cfDNA analysis may complement existing genetic tools for diagnosis and disease monitoring in AML.
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Affiliation(s)
- Christian Rausch
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Maja Rothenberg-Thurley
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Simon A Buerger
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Sebastian Tschuri
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Annika Dufour
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Michaela Neusser
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany; Institute of Human Genetics, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Stephanie Schneider
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany; Institute of Human Genetics, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Karsten Spiekermann
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Klaus H Metzeler
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany; Department of Hematology, Cellular Therapy, and Hemostaseology, University of Leipzig, Leipzig, Germany.
| | - Frank Ziemann
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
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14
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Yahia A, Stevanin G. The History of Gene Hunting in Hereditary Spinocerebellar Degeneration: Lessons From the Past and Future Perspectives. Front Genet 2021; 12:638730. [PMID: 33833777 PMCID: PMC8021710 DOI: 10.3389/fgene.2021.638730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/02/2021] [Indexed: 01/02/2023] Open
Abstract
Hereditary spinocerebellar degeneration (SCD) encompasses an expanding list of rare diseases with a broad clinical and genetic heterogeneity, complicating their diagnosis and management in daily clinical practice. Correct diagnosis is a pillar for precision medicine, a branch of medicine that promises to flourish with the progressive improvements in studying the human genome. Discovering the genes causing novel Mendelian phenotypes contributes to precision medicine by diagnosing subsets of patients with previously undiagnosed conditions, guiding the management of these patients and their families, and enabling the discovery of more causes of Mendelian diseases. This new knowledge provides insight into the biological processes involved in health and disease, including the more common complex disorders. This review discusses the evolution of the clinical and genetic approaches used to diagnose hereditary SCD and the potential of new tools for future discoveries.
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Affiliation(s)
- Ashraf Yahia
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
- Department of Biochemistry, Faculty of Medicine, National University, Khartoum, Sudan
- Institut du Cerveau, INSERM U1127, CNRS UMR7225, Sorbonne Université, Paris, France
- Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Giovanni Stevanin
- Institut du Cerveau, INSERM U1127, CNRS UMR7225, Sorbonne Université, Paris, France
- Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
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15
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Manor J, Lalani SR. Overgrowth Syndromes-Evaluation, Diagnosis, and Management. Front Pediatr 2020; 8:574857. [PMID: 33194904 PMCID: PMC7661798 DOI: 10.3389/fped.2020.574857] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 09/29/2020] [Indexed: 12/14/2022] Open
Abstract
Abnormally excessive growth results from perturbation of a complex interplay of genetic, epigenetic, and hormonal factors that orchestrate human growth. Overgrowth syndromes generally present with inherent health concerns and, in some instances, an increased risk of tumor predisposition that necessitate prompt diagnosis and appropriate referral. In this review, we introduce some of the more common overgrowth syndromes, along with their molecular mechanisms, diagnostics, and medical complications for improved recognition and management of patients affected with these disorders.
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Affiliation(s)
- Joshua Manor
- Department of Molecular Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Seema R Lalani
- Department of Molecular Genetics, Baylor College of Medicine, Houston, TX, United States
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