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Abstract
Neuroblastoma (NB) is a pediatric tumor of embryonic origin. About 1-2% of all NBs are familial cases, and genetic predisposition is suspected for the remaining cases. During the last decade, genome-wide association studies (GWAS) and high-throughput sequencing approaches have been used to identify associations among common and rare genetic variants and NB risk. Substantial data has been produced by large patient cohorts that implicate various genes in NB tumorigenesis, such as CASC15, BARD1, CHEK2, LMO1, LIN28B, AXIN2, BRCA1, TP53, SMARCA4, and CDK1NB. NB, as well as other pediatric cancers, has few recurrent mutations but several copy number variations (CNVs). Almost all NBs show both numerical and structural CNVs. The proportion between numerical and structural CNVs differs between localized and metastatic tumors, with a greater prevalence of structural CNVs in metastatic NB. This genomic chaos frequently identified in NBs suggests that chromosome instability (CIN) could be one of the major actors in NB oncogenesis. Interestingly, many NB-predisposing variants occur in genes involved in the control of genome stability, mitosis, and normal chromosome separation. Here, we discuss the relationship between genetic predisposition and CIN in NB.
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Affiliation(s)
- Gian Paolo Tonini
- Neuroblastoma Laboratory, Pediatric Research Institute, Città della Speranza, Corso Stati Uniti 4, 35127, Padova, Italy.
| | - Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Univeristà degli Studi di Napoli Federico II, Naples, Italy. .,CEINGE Biotecnologie Avanzate, Naples, Italy.
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Wang L, Guo J, Xi Y, Ma S, Li Y, He H, Wang J, Han C, Bai L, Mustafa A, Liu H, Li L. Understanding the Genetic Domestication History of the Jianchang Duck by Genotyping and Sequencing of Genomic Genes Under Selection. G3 (BETHESDA, MD.) 2020; 10:1469-1476. [PMID: 32165372 PMCID: PMC7202016 DOI: 10.1534/g3.119.400893] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/01/2020] [Indexed: 12/11/2022]
Abstract
The Jianchang duck is mainly distributed in Southwest China, and has the characteristics of fast growth rate and strong abilities in lipid deposition in the liver. In order to investigate the effects of domestication process on formation of the unique characteristics of Jianchang duck, the whole genome of sixteen individuals and three pooling of Jianchang duck were re-sequenced, and genome data of 70 mallards and 83 domestic ducks from thirteen different places in China were obtained from NCBI. The population stratification and evolution analysis showed gene exchanges existed between the Jianchang and other domestic duck populations, as well as Jianchang ducks and mallards. Genomic comparison between mallards and Jianchang ducks showed genes, including CNTN1, CHRNA9, and SHANK2, which is involved in brain and nerve development, experienced strong positive selection in the process of Jianchang duck domestication. The genomic comparison between Jianchang and domestic duck populations showed that HSD17B12 and ESM1, which affect lipid metabolism, experienced strong positive selection during the domestication process. FST analysis among populations of Jianchang duck with different plumage colors indicated that MITF was related to the phenotype of a white feather, while MC1R was related to the phenotype of hemp feather. Our results provided a base for the domestication process of Jianchang duck and the genomic genes for unique traits.
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Affiliation(s)
- Lei Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Yang Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Shengchao Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Yanying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Hua He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Chunchun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Lili Bai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Ahsan Mustafa
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, P.R. China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
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Single nucleotide polymorphisms in piRNA-pathway genes: an insight into genetic determinants of human diseases. Mol Genet Genomics 2019; 295:1-12. [DOI: 10.1007/s00438-019-01612-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/22/2019] [Indexed: 12/23/2022]
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Ritenour LE, Randall MP, Bosse KR, Diskin SJ. Genetic susceptibility to neuroblastoma: current knowledge and future directions. Cell Tissue Res 2018; 372:287-307. [PMID: 29589100 DOI: 10.1007/s00441-018-2820-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 02/27/2018] [Indexed: 12/16/2022]
Abstract
Neuroblastoma, a malignancy of the developing peripheral nervous system that affects infants and young children, is a complex genetic disease. Over the past two decades, significant progress has been made toward understanding the genetic determinants that predispose to this often lethal childhood cancer. Approximately 1-2% of neuroblastomas are inherited in an autosomal dominant fashion and a combination of co-morbidity and linkage studies has led to the identification of germline mutations in PHOX2B and ALK as the major genetic contributors to this familial neuroblastoma subset. The genetic basis of "sporadic" neuroblastoma is being studied through a large genome-wide association study (GWAS). These efforts have led to the discovery of many common susceptibility alleles, each with modest effect size, associated with the development and progression of sporadic neuroblastoma. More recently, next-generation sequencing efforts have expanded the list of potential neuroblastoma-predisposing mutations to include rare germline variants with a predicted larger effect size. The evolving characterization of neuroblastoma's genetic basis has led to a deeper understanding of the molecular events driving tumorigenesis, more precise risk stratification and prognostics and novel therapeutic strategies. This review details the contemporary understanding of neuroblastoma's genetic predisposition, including recent advances and discusses ongoing efforts to address gaps in our knowledge regarding this malignancy's complex genetic underpinnings.
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Affiliation(s)
- Laura E Ritenour
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael P Randall
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristopher R Bosse
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sharon J Diskin
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Wu Q, Zhuo ZJ, Zeng J, Zhang J, Zhu J, Zou Y, Zhang R, Yang T, Zhu D, He J, Xia H. Association between NEFL Gene Polymorphisms and Neuroblastoma Risk in Chinese Children: A Two-Center Case-Control Study. J Cancer 2018; 9:535-539. [PMID: 29483959 PMCID: PMC5820921 DOI: 10.7150/jca.22681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/26/2017] [Indexed: 02/07/2023] Open
Abstract
Neuroblastoma is a lethal tumor that mainly occurs in children. To date, the genetic etiology of sporadic neuroblastoma remains obscure. A previous study identified three neuroblastoma susceptibility loci (rs11994014 G>A, rs2979704 T>C, rs1059111 A>T) in neurofilament light (NEFL) gene. Here, we attempted to evaluate the contributions of these three single nucleotide polymorphisms to neuroblastoma susceptibility in Chinese children. We genotyped these three polymorphisms using subjects from Guangdong province (256 cases and 531 controls) and Henan province (118 cases and 281 controls). Logistic regression models were performed to generate odds ratios and 95% confidence intervals to access the association of these three polymorphisms with neuroblastoma risk. Overall, we failed to provide any evidence supporting the association between these three polymorphisms and neuroblastoma susceptibility, either in single center population or in the combined population. Moreover, such null association was also observed when the samples were stratified by age, gender, tumor sites, and clinical stages. In the future, larger samples from different ethnicities are needed to clarify the role of NEFL gene polymorphisms in neuroblastoma risk.
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Affiliation(s)
- Qiang Wu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Zhen-Jian Zhuo
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Jixiao Zeng
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Jiao Zhang
- Department of Pediatric Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Jinhong Zhu
- Molecular Epidemiology Laboratory and Department of Laboratory Medicine, Harbin Medical University Cancer Hospital, Harbin 150040, Heilongjiang, China
| | - Yan Zou
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Ruizhong Zhang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Tianyou Yang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Deli Zhu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
- ✉ Corresponding authors: Huimin Xia, Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou 510623, Guangdong, China, Tel.: (+86-020) 38076001, Fax: (+86-020) 38076020, ; or Jing He, Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou 510623, Guangdong, China, Tel./Fax: (+86-020) 38076560, or
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
- ✉ Corresponding authors: Huimin Xia, Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou 510623, Guangdong, China, Tel.: (+86-020) 38076001, Fax: (+86-020) 38076020, ; or Jing He, Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou 510623, Guangdong, China, Tel./Fax: (+86-020) 38076560, or
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He J, Zou Y, Wang T, Zhang R, Yang T, Zhu J, Wang F, Xia H. Genetic Variations of GWAS-Identified Genes and Neuroblastoma Susceptibility: a Replication Study in Southern Chinese Children. Transl Oncol 2017; 10:936-941. [PMID: 29024823 PMCID: PMC5704095 DOI: 10.1016/j.tranon.2017.09.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 09/17/2017] [Accepted: 09/18/2017] [Indexed: 02/07/2023] Open
Abstract
Neuroblastoma is one of the most commonly diagnosed solid cancers for children, and genetic factors may play a critical role in neuroblastoma development. Previous genome-wide association studies (GWASs) have identified nine genes associated with neuroblastoma susceptibility in Caucasians. To determine whether genetic variations in these genes are also associated with neuroblastoma susceptibility in Southern Chinese children, we genotyped 25 polymorphisms within these genes by the TaqMan method in 256 cases and 531 controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to evaluate the strength of the associations. We performed a meta-analysis to further evaluate the associations. Furthermore, we calculated the area under the receiver-operating characteristic curves (AUC) to assess which gene/genes may better predict neuroblastoma risk. We confirmed that CASC15 rs6939340 A>G, rs4712653 T>C, rs9295536 C>A, LIN28B rs221634 A>T, and LMO1 rs110419 A>G were associated with significantly altered neuroblastoma susceptibility. We also confirmed that rs6939340 A>G (G versus A: OR=1.30, 95% CI=1.13-1.50) and rs110419 G>A (A versus G: OR=1.37, 95% CI=1.19-1.58) were associated with increased neuroblastoma risk for all subjects. We also found that the combination of polymorphisms in CASC15, LIN28B, and LMO1 may be used to predict neuroblastoma risk (AUC=0.63, 95% CI=0.59-0.67). Overall, we verified five GWAS-identified polymorphisms that were associated with neuroblastoma susceptibility alteration for Southern Chinese population; however, these results need further validation in studies with larger sample sizes.
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Affiliation(s)
- Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China.
| | - Yan Zou
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Tongmin Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Ruizhong Zhang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Tianyou Yang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Jinhong Zhu
- Molecular Epidemiology Laboratory and Department of Laboratory Medicine, Harbin Medical University Cancer Hospital, Harbin 150040, Heilongjiang, China
| | - Fenghua Wang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China.
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