1
|
Li Y, Liu P, Wang W, Jia H, Bai Y, Yuan Z, Yang Z. A novel genotype-phenotype between persistent-cloaca-related VACTERL and mutations of 8p23 and 12q23.1. Pediatr Res 2024; 95:1246-1253. [PMID: 38135728 DOI: 10.1038/s41390-023-02928-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/02/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023]
Abstract
The mechanism underlying anorectal malformations (ARMs)-related VACTERL (vertebral defects, anal atresia, cardiac defects, tracheo-esophageal fistula, and renal and limb abnormalities) remains unclear. Copy number variation (CNV) contributed to VACTERL pathogenicity. Here, we report a novel CNV in 8p23 and 12q23.1 identified in a case of ARMs-related VACTERL association. This 12-year-old girl presented a cloaca (urethra, vagina, and rectum opening together and sharing a single tube length), an isolated kidney, and a perpetuation of the left superior vena cava at birth. Her intelligence, growth, and development were slightly lower than those of normal children of the same age. Array comparative genomic hybridization revealed a 9.6-Mb deletion in 8p23.1-23.3 and a 0.52-Mb duplication in 12q23.1 in her genome. Furthermore, we reviewed the cases involving CNVs in patients with VACTERL, 8p23 deletion, and 12q23.1 duplication, and our case was the first displaying ARMs-related VACTERL association with CNV in 8p23 and 12q23.1. These findings enriched our understanding between VACTERL association and the mutations of 8p23 deletion and 12q23.1 duplication. IMPACT: This is a novel case of a Chinese girl with anorectal malformations (ARMs)-related VACTERL with an 8p23.1-23.3 deletion and 12q23.1 duplication. Cloaca malformation is presented with novel copy number variation in 8p23.1-23.3 deletion and 12q23.1 duplication.
Collapse
Affiliation(s)
- Yue Li
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Peiqi Liu
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Weilin Wang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Huimin Jia
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yuzuo Bai
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Zhonghua Yang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| |
Collapse
|
2
|
O'Malley DE, Raspin K, Melton PE, Burdon KP, Dickinson JL, FitzGerald LM. Acquired copy number variation in prostate tumours: a review of common somatic copy number alterations, how they are formed and their clinical utility. Br J Cancer 2024; 130:347-357. [PMID: 37945750 PMCID: PMC10844642 DOI: 10.1038/s41416-023-02485-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
Prostate cancer is one of the most commonly diagnosed cancers in men and unfortunately, disease will progress in up to a third of patients despite primary treatment. Currently, there is a significant lack of prognostic tests that accurately predict disease course; however, the acquisition of somatic chromosomal variation in the form of DNA copy number variants may help understand disease progression. Notably, studies have found that a higher burden of somatic copy number alterations (SCNA) correlates with more aggressive disease, recurrence after surgery and metastasis. Here we will review the literature surrounding SCNA formation, including the roles of key tumour suppressors and oncogenes (PTEN, BRCA2, NKX3.1, ERG and AR), and their potential to inform diagnostic and prognostic clinical testing to improve predictive value. Ultimately, SCNAs, or inherited germline alterations that predispose to SCNAs, could have significant clinical utility in diagnostic and prognostic tests, in addition to guiding therapeutic selection.
Collapse
Affiliation(s)
- Dannielle E O'Malley
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Kelsie Raspin
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Phillip E Melton
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
- School of Population and Global Health, The University of Western Australia, Crawley, WA, Australia
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Liesel M FitzGerald
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia.
| |
Collapse
|
3
|
Ma Y, Chen X, Wang A, Zhao H, Lin Q, Bao H, Zhang Y, Hong S, Tang W, Huang Y, Yang Y, Wu X, Shao Y, Fang W, Zhang L. Copy number loss in granzyme genes confers resistance to immune checkpoint inhibitor in nasopharyngeal carcinoma. J Immunother Cancer 2021; 9:jitc-2020-002014. [PMID: 33737344 PMCID: PMC7978327 DOI: 10.1136/jitc-2020-002014] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2021] [Indexed: 12/21/2022] Open
Abstract
Background Anti-programmed death (PD)-1 therapy has recently been used in recurrent or metastatic (R/M) nasopharyngeal carcinoma (NPC). The long-term survival and its biomarkers responding to anti-PD-1 treatment in patients with R/M NPC remain unclear. Methods Patients with R/M NPC were enrolled between March 2016 and January 2018 from two phase I clinical trials. The median follow-up period was 24.7 months. Eligible patients progressed on standard chemotherapy had measurable disease by Response Evaluation Criteria in Solid Tumor V.1.1. Non-obligatory contemporaneous tumor samples were collected for whole-exome sequencing. The primary outcome was objective response rate (ORR). Duration of response (DOR), progression-free survival (PFS), and overall survival (OS) were secondary outcomes assessed in all patients. Results Among 124 evaluable patients, anti-PD-1 therapy achieved an ORR of 29.8% and a durable clinical benefit rate of 60.5%. The median OS (mOS) was 17.1 months (95% CI 14.2 to 24.7), median PFS (mPFS) was 3.8 months (95% CI 3.4 to 6.0), and median DOR was 9.5 months. Significant OS benefit from treatment was observed in patients without liver metastasis (23.8 vs 13.3 months, p=0.006). Copy number deletion in genes encoding granzyme B or granzyme H (GZMB/H) was associated with poor treatment outcome (mPFS altered vs wildtype: 1.7 vs 3.6 months, p=0.03; mOS altered vs wildtype: 10.1 vs 18 months, p=0.012). Conclusions Anti-PD-1 treatment provided promising clinical benefit in pretreated patients with R/M NPC. Copy number loss in either GZMB or GZMH genes was associated with reduced survival.
Collapse
Affiliation(s)
- Yuxiang Ma
- Department of Clinical Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xi Chen
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ao Wang
- Medical Department, Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Hongyun Zhao
- Department of Clinical Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Qingguang Lin
- Department of Ultrasonography, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Hua Bao
- Medical Department, Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Yang Zhang
- Department of Clinical Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shaodong Hong
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Wanxiangfu Tang
- Medical Department, Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Yan Huang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yunpeng Yang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xue Wu
- Medical Department, Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Yang Shao
- Medical Department, Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China .,School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wenfeng Fang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Li Zhang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| |
Collapse
|
4
|
Copy number variant analysis and expression profiling of the olfactory receptor-rich 11q11 region in obesity predisposition. Mol Genet Metab Rep 2020; 25:100656. [PMID: 33145169 PMCID: PMC7596328 DOI: 10.1016/j.ymgmr.2020.100656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 11/22/2022] Open
Abstract
Genome-wide copy number surveys associated chromosome 11q11 with obesity. As this is an olfactory receptor-rich region, we hypothesize that genetic variation in olfactory receptor genes might be implicated in the pathogenesis of obesity. Multiplex Amplicon Quantification analysis was applied to screen for copy number variants at chromosome 11q11 in 627 patients with obesity and 330 healthy-weight individuals. A ± 80 kb deletion with an internally 1.3 kb retained segment was identified, covering the three olfactory receptor genes OR4C11, OR4P4, and OR4S2. A significant increase in copy number loss(es) was perceived in our patient cohort (MAF = 27%; p = 0.02). Gene expression profiling in metabolic relevant tissues was performed to evaluate the functional impact of the obesity susceptible locus. All three 11q11 genes were present in visceral and subcutaneous adipose tissue while no expression was perceived in the liver. These results support the 'metabolic system' hypothesis and imply that gene disruption of OR4C11, OR4P4, and OR4S2 will negatively influence energy metabolism, ultimately leading to fat accumulation and obesity. Our study thus demonstrates a role for structural variation within olfactory receptor-rich regions in complex diseases and defines the 11q11 deletion as a risk factor for obesity.
Collapse
|
5
|
Chen G, Cai ZD, Lin ZY, Wang C, Liang YX, Han ZD, He HC, Mo RJ, Lu JM, Pan B, Wu CL, Wang F, Zhong WD. ARNT-dependent CCR8 reprogrammed LDH isoform expression correlates with poor clinical outcomes of prostate cancer. Mol Carcinog 2020; 59:897-907. [PMID: 32319143 DOI: 10.1002/mc.23201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 01/09/2023]
Abstract
Lactate dehydrogenase isozyme (LDH) is a tetramer constituted of two isoforms, LDHA and LDHB, the expression of which is associated with cell metabolism and cancer progression. Our previous study reveals that CC-chemokine ligand-18 (CCL18) is involved in progression of prostate cancer (PCa).This study aims to investigate how CCL18 regulates LDH isoform expression, and therefore, contributes to PCa progression. The data revealed that the expression of LDHA was upregulated and LDHB was downregulated in PCa cells by CCL18 at both messenger RNA and protein levels. The depletion of CCR8 reduced the ability of CCL18 to promote the proliferation, migration, and lactate production of PCa cells. Depletion of a CCR8 regulated transcription factor, ARNT, significantly reduced the expression of LDHA. In addition, The Cancer Genome Atlas dataset analyses revealed a positive correlation between CCR8 and ARNT expression. Two dimension difference gel electrophoresis revealed that the LDHA/LDHB ratio was increased in the prostatic fluid of patients with PCa and PCa tissues. Furthermore, increased LDHA/LDHB ratio was associated with poor clinical outcomes of patients with PCa. Together, our results indicate that the CCR8 pathway programs LDH isoform expression in an ARNT dependent manner and that the ratio of LDHA/LDHB has the potential to serve as biomarkers for PCa diagnosis and prognosis.
Collapse
Affiliation(s)
- Guo Chen
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Zhi-Duan Cai
- Guangdong Provincial Institute of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhuo-Yuan Lin
- Department of Urology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Cong Wang
- School of pharmaceutical sciences, Wenzhou Medical University, Wenzhou, China
| | - Yu-Xiang Liang
- Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Department of Urology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Zhao-Dong Han
- Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Department of Urology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Hui-Chan He
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital, Guangzhou Institute of Urology, Guangzhou, Guangdong, China
| | - Ru-Jun Mo
- Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Department of Urology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Jian-Ming Lu
- Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Department of Urology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Bin Pan
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Chin-Lee Wu
- Department of Pathology and Urology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Fen Wang
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas
| | - Wei-de Zhong
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China.,Guangdong Provincial Institute of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Department of Urology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| |
Collapse
|
6
|
Kilaru V, Knight AK, Katrinli S, Cobb D, Lori A, Gillespie CF, Maihofer AX, Nievergelt CM, Dunlop AL, Conneely KN, Smith AK. Critical evaluation of copy number variant calling methods using DNA methylation. Genet Epidemiol 2019; 44:148-158. [PMID: 31737926 PMCID: PMC7028453 DOI: 10.1002/gepi.22269] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/24/2019] [Accepted: 10/12/2019] [Indexed: 12/21/2022]
Abstract
Recent technological and methodological developments have enabled the use of array-based DNA methylation data to call copy number variants (CNVs). ChAMP, Conumee, and cnAnalysis450k are popular methods currently used to call CNVs using methylation data. However, so far, no studies have analyzed the reliability of these methods using real samples. Data from a cohort of individuals with genotype and DNA methylation data generated using the HumanMethylation450 and MethylationEPIC BeadChips were used to assess the consistency between the CNV calls generated by methylation and genotype data. We also took advantage of repeated measures of methylation data collected from the same individuals to compare the reliability of CNVs called by ChAMP, Conumee, and cnAnalysis450k for both the methylation arrays. ChAMP identified more CNVs than Conumee and cnAnalysis450k for both the arrays and, as a consequence, had a higher overlap (~62%) with the calls from the genotype data. However, all methods had relatively low reliability. For the MethylationEPIC array, Conumee had the highest reliability (57.6%), whereas for the HumanMethylation450 array, cnAnalysis450k had the highest reliability (43.0%). Overall, the MethylationEPIC array provided significant gains in reliability for CNV calling over the HumanMethylation450 array but not for overlap with CNVs called using genotype data.
Collapse
Affiliation(s)
- Varun Kilaru
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia
| | - Anna K Knight
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia
| | - Seyma Katrinli
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia
| | - Dawayland Cobb
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia
| | - Adriana Lori
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia
| | - Charles F Gillespie
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia
| | - Adam X Maihofer
- Department of Psychiatry, University of California San Diego, San Diego, California
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, San Diego, California.,Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, California.,Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Anne L Dunlop
- Nell Hodgson Woodruff School of Nursing, Emory University School of Medicine, Atlanta, Georgia.,Department of Family and Preventive Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia.,Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia
| |
Collapse
|
7
|
Heidegger I, Tsaur I, Borgmann H, Surcel C, Kretschmer A, Mathieu R, Visschere PD, Valerio M, van den Bergh RCN, Ost P, Tilki D, Gandaglia G, Ploussard G. Hereditary prostate cancer - Primetime for genetic testing? Cancer Treat Rev 2019; 81:101927. [PMID: 31783313 DOI: 10.1016/j.ctrv.2019.101927] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 12/11/2022]
Abstract
Prostate cancer (PCa) remains the most common cancer in men. The proportion of all PCa attributable to high-risk hereditary factors has been estimated to 5-15%. Recent landmark discoveries in PCa genetics led to the identification of germline mutations/alterations (eg. BRCA1, BRCA2, ATM or HOXB13), single nucleotide polymorphisms or copy number variations associated with PCa incidence and progression. However, offering germline testing to men with an assumed hereditary component is currently controversial. In the present review article, we provide an overview about the epidemiology and the genetic basis of PCa predisposition and critically discuss the significance and consequence in the clinical routine. In addition, we give an overview about genetic tests and report latest findings from ongoing clinical studies. Lastly, we discuss the impact of genetic testing in personalized therapy in advanced stages of the disease.
Collapse
Affiliation(s)
- Isabel Heidegger
- Department of Urology, Medical University Innsbruck, Innsbruck, Austria.
| | - Igor Tsaur
- Department of Urology and Pediatric Urology, Mainz University Medicine, Mainz, Germany
| | - Hendrik Borgmann
- Department of Urology and Pediatric Urology, Mainz University Medicine, Mainz, Germany
| | - Christian Surcel
- Department of Urology, Fundeni Clinical Institute, University of Medicine and Pharmacy, Carol Davila Bucharest, Bucharest, Romania
| | | | | | - Pieter De Visschere
- Department of Radiology and Nuclear Medicine, Ghent University Hospital, Ghent, Belgium
| | | | | | - Piet Ost
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Derya Tilki
- Martini Klinik Prostate Cancer Center, University Hospital Hamburg-Eppendorf, Hamburg, Germany; Department of Urology, University Hospital-Hamburg Eppendorf, Hamburg, Germany
| | - Giorgio Gandaglia
- Department of Urology, Urological Research Institute, Vita-Salute University and San Raffaele Hospital, Milan, Italy
| | - Guillaume Ploussard
- Department of Urology, La Croix du Sud Hospital, Toulouse, France; Institut Universitaire du Cancer Toulouse - Oncopole, Toulouse, France
| | | |
Collapse
|
8
|
Yu B, Ding Y, Liao X, Wang C, Wang B, Chen X. Overexpression of PARPBP Correlates with Tumor Progression and Poor Prognosis in Hepatocellular Carcinoma. Dig Dis Sci 2019; 64:2878-2892. [PMID: 30949905 DOI: 10.1007/s10620-019-05608-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 03/27/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND PARP1-binding protein (PARPBP/PARI/C12orf48), a negative regulator of homologous recombination (HR), has been suggested to function as an oncogene in cervical, lung, and pancreatic cancer. OBJECTIVE To investigate the expression profile of PARPBP and its role in hepatocellular carcinoma (HCC). METHODS Using data from the Cancer Genome Atlas and Human Protein Atlas databases, PARPBP expression level and its clinical implication in HCC were identified by t test and Chi-square test. The prognostic value of PARPBP in HCC was evaluated by Kaplan-Meier method, Cox regression analysis, and nomogram. Gene set enrichment analysis (GSEA) was used to screen biological pathways correlated with PARPBP expression in HCC. RESULTS PARPBP was significantly upregulated in HCC tissues compared with normal liver tissues (P < 0.05). High PARPBP expression was significantly associated with elevated serum AFP level, vascular invasion, poor tumor differentiation, and advanced TNM stage (all P < 0.05). Kaplan-Meier analyses suggested that upregulation of PARPBP was correlated with worse overall survival (OS) and recurrence-free survival (RFS) in HCC. Multivariate analyses further confirmed that PARPBP upregulation was an independent indicator of poor OS and RFS (all P < 0.05). The prognostic nomograms based on PARPBP mRNA expression and TNM stage were superior to those based on the TNM staging system alone (all P < 0.05). Besides, PARPBP DNA copy gain and miR-139-5p downregulation were associated with PARPBP upregulation in HCC. GSEA revealed that "cell cycle," "HR," "DNA replication," and "p53 signaling" pathways were enriched in high PARPBP expression group. CONCLUSION PARPBP may be a promising prognostic biomarker and candidate therapeutic target in HCC.
Collapse
Affiliation(s)
- Bin Yu
- Department of Hepatobiliary and Laparoscopic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| | - Youming Ding
- Department of Hepatobiliary and Laparoscopic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China.
| | - Xiaofeng Liao
- Department of General Surgery, Xiangyang Central Hospital, Xiangyang, 441021, Hubei Province, People's Republic of China
| | - Changhua Wang
- Department of Pathology and Pathophysiology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Bin Wang
- Department of Hepatobiliary and Laparoscopic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| | - Xiaoyan Chen
- Department of Hepatobiliary and Laparoscopic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| |
Collapse
|
9
|
Scarano WR, Bedrat A, Alonso-Costa LG, Aquino AM, Fantinatti B, Justulin LA, Barbisan LF, Freire PP, Flaws JA, Bernardo L. Exposure to an environmentally relevant phthalate mixture during prostate development induces microRNA upregulation and transcriptome modulation in rats. Toxicol Sci 2019; 171:84-97. [PMID: 31199487 PMCID: PMC6736208 DOI: 10.1093/toxsci/kfz141] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/14/2019] [Accepted: 06/02/2019] [Indexed: 12/14/2022] Open
Abstract
Environmental exposure to phthalates during intrauterine development might increase susceptibility to neoplasms in reproductive organs such as the prostate. Although studies have suggested an increase in prostatic lesions in adult animals submitted to perinatal exposure to phthalates, the molecular pathways underlying these alterations remain unclear. Genome-wide levels of mRNAs and miRNAs were monitored with RNA-seq to determine if perinatal exposure to a phthalate mixture in pregnant rats is capable of modifying gene expression expression during prostate development of the filial generation. The mixture contains diethyl-phthalate, di-(2-ethylhexyl)-phthalate, dibutyl-phthalate, di-isononyl-phthalate, di-isobutyl-phthalate, and benzylbutyl-phthalate. Pregnant females were divided into 4 groups and orally dosed daily from GD10 to PND21 with corn oil (Control:C) or the phthalate mixture at three doses (20 μg/kg/d:T1; 200 μg/kg/d:T2; 200 mg/kg/d:T3). The phthalate mixture decreased anogenital distance, prostate weight and decreased testosterone level at the lowest exposure dose at PND22. The mixture also increased inflammatory foci and focal hyperplasia incidence at PND120. miR-184 was upregulated in all treated groups in relation to control and miR-141-3p was only upregulated at the lowest dose. In addition, 120 genes were deregulated at the lowest dose with several of these genes related to developmental, differentiation and oncogenesis. The data indicate that phthalate exposure at lower doses can cause greater gene expression modulation as well as other downstream phenotypes than exposure at higher doses. A significant fraction of the downregulated genes were predicted to be targets of miR-141-3p and miR-184, both of which were induced at the lower exposure doses.
Collapse
Affiliation(s)
- Wellerson R Scarano
- São Paulo State University (UNESP), Institute of Biosciences, Department of Morphology, Botucatu, SP, Brazil.,Harvard T. H. Chan School of Public Health, Department of Environmental Health & Molecular and Integrative Physiological Sciences Program, Boston, MA, USA
| | - Amina Bedrat
- Harvard T. H. Chan School of Public Health, Department of Environmental Health & Molecular and Integrative Physiological Sciences Program, Boston, MA, USA
| | - Luiz G Alonso-Costa
- São Paulo State University (UNESP), Institute of Biosciences, Department of Morphology, Botucatu, SP, Brazil
| | - Ariana M Aquino
- São Paulo State University (UNESP), Institute of Biosciences, Department of Morphology, Botucatu, SP, Brazil
| | - Bruno Fantinatti
- São Paulo State University (UNESP), Institute of Biosciences, Department of Morphology, Botucatu, SP, Brazil
| | - Luis A Justulin
- São Paulo State University (UNESP), Institute of Biosciences, Department of Morphology, Botucatu, SP, Brazil
| | - Luis F Barbisan
- São Paulo State University (UNESP), Institute of Biosciences, Department of Morphology, Botucatu, SP, Brazil
| | - Paula P Freire
- São Paulo State University (UNESP), Institute of Biosciences, Department of Morphology, Botucatu, SP, Brazil
| | - Jodi A Flaws
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, IL
| | - Lemos Bernardo
- Harvard T. H. Chan School of Public Health, Department of Environmental Health & Molecular and Integrative Physiological Sciences Program, Boston, MA, USA
| |
Collapse
|
10
|
Kobayashi PE, Fonseca-Alves CE, Rivera-Calderón LG, Carvalho M, Kuasne H, Rogatto SR, Laufer-Amorim R. Deregulation of E-cadherin, β-catenin, APC and Caveolin-1 expression occurs in canine prostate cancer and metastatic processes. Res Vet Sci 2018. [PMID: 29529534 DOI: 10.1016/j.rvsc.2018.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Prostate cancer is a heterogeneous disease with high levels of clinical and gene heterogeneity, consequently offering several targets for therapy. Dogs with naturally occurring prostate cancer are useful models for molecular investigations and studying new treatment efficacy. Three genes and proteins associated with the WNT pathway (β-catenin, APC and E-cadherin) and Caveolin-1 (CAV-1) were evaluated in canine pre-neoplastic proliferative inflammatory atrophy (PIA), prostate cancer and metastatic disease. The APC gene methylation status was also investigated. As in human prostate cancer, cytoplasmic and nuclear β-catenin, which are fundamental for activating the canonical WNT pathway, were found in canine prostate cancer and metastasis. Membranous E-cadherin was also lost in these lesions, allowing cellular migration to the stroma and nuclear localization of β-catenin. In contrast to human prostate tumours, no APC downregulation or hypermethylation was found in canine prostate cancer. The CAV-1 gene and protein overexpression were found in canine prostate cancer, and as in humans, the highest levels were found in Gleason scores ≥8. In conclusion, as with human prostate cancer, β-catenin and E-cadherin in the WNT pathway, as well as Caveolin-1, are molecular drivers in canine prostate cancer. These findings provide additional evidence that dogs are useful models for studying new therapeutic targets in prostate cancer.
Collapse
Affiliation(s)
- Priscila E Kobayashi
- São Paulo State University (UNESP), Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, Botucatu, SP, Brazil
| | - Carlos E Fonseca-Alves
- São Paulo State University (UNESP), Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, Botucatu, SP, Brazil
| | - Luis G Rivera-Calderón
- São Paulo State University (UNESP), Department of Veterinary Pathology, School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, Brazil
| | - Márcio Carvalho
- São Paulo State University (UNESP), Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, Botucatu, SP, Brazil
| | - Hellen Kuasne
- International Center for Research (CIPE), AC Camargo Hospital, Liberdade, São Paulo, Brazil
| | - Silvia R Rogatto
- Department of Clinical Genetics, Vejle Hospital and Institute of Regional Health, University of Southern Denmark, Denmark
| | - Renée Laufer-Amorim
- São Paulo State University (UNESP), Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, Botucatu, SP, Brazil.
| |
Collapse
|