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Zafar S, Khan K, Badshah Y, Shahid K, Trembley JH, Hafeez A, Ashraf NM, Arslan H, Shabbir M, Afsar T, Almajwal A, Razak S. Exploring the prognostic significance of PKCε variants in cervical cancer. BMC Cancer 2023; 23:819. [PMID: 37667176 PMCID: PMC10476323 DOI: 10.1186/s12885-023-11236-z] [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: 06/07/2023] [Accepted: 07/29/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Protein Kinase C-epsilon (PKCε) is a member of the novel subfamily of PKCs (nPKCs) that plays a role in cancer development. Studies have revealed that its elevated expression levels are associated with cervical cancer. Previously, we identified pathogenic variations in its different domains through various bioinformatics tools and molecular dynamic simulation. In the present study, the aim was to find the association of its variants rs1553369874 and rs1345511001 with cervical cancer and to determine the influence of these variants on the protein-protein interactions of PKCε, which can lead towards cancer development and poor survival rates. METHODS The association of the variants with cervical cancer and its clinicopathological features was determined through genotyping analysis. Odds ratio and relative risk along with Fisher exact test were calculated to evaluate variants significance and disease risk. Protein-protein docking was performed and docked complexes were subjected to molecular dynamics simulation to gauge the variants impact on PKCε's molecular interactions. RESULTS This study revealed that genetic variants rs1553369874 and rs1345511001 were associated with cervical cancer. Smad3 interacts with PKCε and this interaction promotes cervical cancer angiogenesis; therefore, Smad3 was selected for protein-protein docking. The analysis revealed PKCε variants promoted aberrant interactions with Smad3 that might lead to the activation of oncogenic pathways. The data obtained from this study suggested the prognostic significance of PRKCE gene variants rs1553369874 and rs1345511001. CONCLUSION Through further in vitro and in vivo validation, these variants can be used at the clinical level as novel prognostic markers and therapeutic targets against cervical cancer.
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Affiliation(s)
- Sameen Zafar
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Khushbukhat Khan
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan.
| | - Kanza Shahid
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Janeen H Trembley
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Minneapolis VA Health Care System Research Service, Minneapolis, MN, USA
| | - Amna Hafeez
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Hamid Arslan
- University of Bonn, LIMES Institute (AG-Netea), Carl-Troll-Str. 31, 53115, Bonn, Germany
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
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2
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The association between single polymorphic positions and the risk of acute lymphoblastic leukemia. Meta Gene 2022. [DOI: 10.1016/j.mgene.2021.101006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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3
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Involvement of single nucleotide polymorphisms in acute lymphoblastic leukemia susceptibility. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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4
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Tan H, Kim P, Sun P, Zhou X. miRactDB characterizes miRNA-gene relation switch between normal and cancer tissues across pan-cancer. Brief Bioinform 2020; 22:5840023. [PMID: 32436932 DOI: 10.1093/bib/bbaa089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/05/2020] [Accepted: 04/26/2020] [Indexed: 12/26/2022] Open
Abstract
It has been increasingly accepted that microRNA (miRNA) can both activate and suppress gene expression, directly or indirectly, under particular circumstances. Yet, a systematic study on the switch in their interaction pattern between activation and suppression and between normal and cancer conditions based on multi-omics evidences is not available. We built miRactDB, a database for miRNA-gene interaction, at https://ccsm.uth.edu/miRactDB, to provide a versatile resource and platform for annotation and interpretation of miRNA-gene relations. We conducted a comprehensive investigation on miRNA-gene interactions and their biological implications across tissue types in both tumour and normal conditions, based on TCGA, CCLE and GTEx databases. We particularly explored the genetic and epigenetic mechanisms potentially contributing to the positive correlation, including identification of miRNA binding sites in the gene coding sequence (CDS) and promoter regions of partner genes. Integrative analysis based on this resource revealed that top-ranked genes derived from TCGA tumour and adjacent normal samples share an overwhelming part of biological processes, which are quite different than those from CCLE and GTEx. The most active miRNAs predicted to target CDS and promoter regions are largely overlapped. These findings corroborate that adjacent normal tissues might have undergone significant molecular transformations towards oncogenesis before phenotypic and histological change; and there probably exists a small yet critical set of miRNAs that profoundly influence various cancer hallmark processes. miRactDB provides a unique resource for the cancer and genomics communities to screen, prioritize and rationalize their candidates of miRNA-gene interactions, in both normal and cancer scenarios.
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5
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Gray ID, Kross AR, Renfrew ME, Wood P. Precision Medicine in Lifestyle Medicine: The Way of the Future? Am J Lifestyle Med 2020; 14:169-186. [PMID: 32231483 PMCID: PMC7092395 DOI: 10.1177/1559827619834527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/21/2018] [Accepted: 02/08/2019] [Indexed: 02/06/2023] Open
Abstract
Precision medicine has captured the imagination of the medical community with visions of therapies precisely targeted to the specific individual's genetic, biological, social, and environmental profile. However, in practice it has become synonymous with genomic medicine. As such its successes have been limited, with poor predictive or clinical value for the majority of people. It adds little to lifestyle medicine, other than in establishing why a healthy lifestyle is effective in combatting chronic disease. The challenge of lifestyle medicine remains getting people to actually adopt, sustain, and naturalize a healthy lifestyle, and this will require an approach that treats the patient as a person with individual needs and providing them with suitable types of support. The future of lifestyle medicine is holistic and person-centered rather than technological.
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Affiliation(s)
- Ian D. Gray
- Avondale College of Higher Education, Cooranbong,
New South Wales, Australia
| | - Andrea R. Kross
- Avondale College of Higher Education, Cooranbong,
New South Wales, Australia
| | - Melanie E. Renfrew
- Avondale College of Higher Education, Cooranbong,
New South Wales, Australia
| | - Paul Wood
- Avondale College of Higher Education, Cooranbong,
New South Wales, Australia
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6
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Wang X, Zhong J, Chen F, Hu K, Sun S, Leng Y, Chen X, Gan F, Pan Y, Luo Q. Association between lncRNA H19 rs217727 polymorphism and the risk of cancer: an updated meta-analysis. BMC MEDICAL GENETICS 2019; 20:186. [PMID: 31752724 PMCID: PMC6873771 DOI: 10.1186/s12881-019-0904-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/02/2019] [Indexed: 12/11/2022]
Abstract
Background We have performed this study to evaluate the association between H19 rs217727 polymorphism and the risk of cancer. Methods An odds ratio (OR) with a 95% confidence interval (CI) was applied to determine a potential association. Results A total of 17 case–control publications were selected. This meta-analysis showed that H19 rs217727 has a significant increased association with cancer risk in allelic, homozygous, heterozygote, dominant and recessive models (T vs C: OR = 1.16, 95% CI = 1.06–1.27, I2 = 75.7; TT vs CC: OR = 1.29, 95% CI = 1.06–1.56, I2 = 71.6; CT vs CC: OR = 1.15, 95% CI = 1.01–1.31, I2 = 75.4; CT + TT vs CC: OR = 1.20, 95% CI = 1.05–1.36, I2 = 76.5; TT vs CT + CC: OR = 1.22, 95% CI = 1.02–1.45, I2 = 70.6;). In the subgroup analysis of smoking status, both smokers and nonsmokers showed an increase in cancer risk in allelic, homozygous, dominant and heterozygote models. Conclusion This meta-analysis revealed H19 rs217727 may influence cancer susceptibility.
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Affiliation(s)
- Xue Wang
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi, 563003, China.,The people's Hospital of Tongnan District, Chongqing, China
| | - Jialing Zhong
- Clinical Laboratory, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Fang Chen
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi, 563003, China
| | - Kang Hu
- Breast & Thyroid Disease Medical Center, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Suhong Sun
- Breast & Thyroid Disease Medical Center, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yuanxiu Leng
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi, 563003, China
| | - Xumei Chen
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi, 563003, China
| | - Fengjiao Gan
- Breast & Thyroid Disease Medical Center, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yana Pan
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi, 563003, China
| | - Qing Luo
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, No.149 Dalian Road, Zunyi, 563003, China.
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7
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Zhuo Z, Fu W, Liu J, Cheng J, Zhou H, Zhang J, Zhu J, Xia H, Liu G, He J. LIN28A gene polymorphisms confer Wilms tumour susceptibility: A four-centre case-control study. J Cell Mol Med 2019; 23:7105-7110. [PMID: 31338973 PMCID: PMC6787499 DOI: 10.1111/jcmm.14561] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 06/10/2019] [Accepted: 07/07/2019] [Indexed: 02/06/2023] Open
Abstract
Wilms tumour is a renal malignancy that commonly occurs in children. LIN28A gene overexpression has been reported to be involved in various human malignancies, while its roles in Wilms tumour risk are still under investigation. Here, we genotyped four LIN28A polymorphisms in 355 Wilms tumour patients and 1070 healthy controls from four hospitals in China. The genotyped single nucleotide polymorphisms (SNPs) include the following: rs3811464 G>A, rs3811463 T>C, rs34787247 G>A and rs11247957 G>A. Overall, we found that rs3811463 T>C and rs34787247 G>A were associated with increased risk of Wilms tumour. Combination analysis of risk genotypes showed that, compared to non-carriers, subjects with 1 risk genotype and 1-3 risk genotypes were more likely to develop Wilms tumour, with an adjusted odds ratio (OR) of 1.58 and 1.56, respectively. Stratified analysis further demonstrated that the risk effect remained prominent in some subgroups. We also found that presence of 1-3 risk genotypes was associated with Wilms tumour risk in subgroups > 18 months of age, females, males and those with clinical stage I + II diseases. Furthermore, expression quantitative trait locus (eQTL) analysis indicated that rs3811463 C allele was significantly associated with increased transcripts of LIN28A gene. These findings suggest that LIN28A gene polymorphisms may be associated with increased predisposition to Wilms tumour.
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Affiliation(s)
- Zhenjian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
- School of Chinese Medicine, Faculty of MedicineThe Chinese University of Hong KongHong KongChina
| | - Wen Fu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
| | - Jiabin Liu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
| | - Jiwen Cheng
- Department of Pediatric SurgeryThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Haixia Zhou
- Department of HematologyThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Jiao Zhang
- Department of Pediatric SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Jin‐Hong Zhu
- Department of Clinical LaboratoryMolecular Epidemiology LaboratoryHarbin Medical University Cancer HospitalHarbinChina
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
| | - Guochang Liu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
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Wang J, Wu P. Correlation analysis of mRNA expression and prognosis of hOGG1 gene polymorphism in patients with non-small cell lung cancer. Oncol Lett 2019; 18:2310-2315. [PMID: 31402936 PMCID: PMC6676738 DOI: 10.3892/ol.2019.10586] [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: 09/18/2018] [Accepted: 05/22/2019] [Indexed: 11/14/2022] Open
Abstract
Level of mRNA expression and gene polymorphism of human 8-hydroxyguanine glycosidase 1 (hOGG1) in patients with non-small cell lung cancer (NSCLC) were investigated. A polymorphism analysis of hOGG1 gene rs1052133 locus in 182 NSCLC patients (NSCLC group) surgically treated in Xiang Yang No. 1 People's Hospital, Hubei University of Medicine from January 2008 to January 2012 and 200 healthy individuals (control group) was performed. The expression level of hOGG1 was compared between cancer tissues and adjacent tissues of NSCLC patients, and the survival rate was analyzed. The expression level of hOGG1 was significantly higher in cancer tissues than that in adjacent tissues (P<0.001). Taqman probe method was used to detect the genotypes of hOGG1 polymorphism locus rs1052133, with the genotype distribution frequencies of NSCLC group (P=0.411) and control group (P=0.354) consistent with the Hardy-Weinberg equilibrium. The proportion of C/C gene was significantly higher in NSCLC group than that in control group (P=0.008, OR=2.2, 95%, CI=1.27–4.52). The median value of the hOGG1 expression level in detection results as the boundary, NSCLC patients were divided into hOGG1 high expression group (≥3.61) with 91 cases and hOGG1 low expression group (<3.61) with 91 cases. The 1-, 2- and 3-year survival rates of patients in hOGG1 low expression group were significantly higher than those in hOGG1 high expression group (P=0.007). The 3-year survival rate in hOGG1 low expression group is significantly higher than that in hOGG1 high expression group (P=0.007). The sensitivity, specificity and AUC of hOGG1 to patient survival prediction were 83.33%, 64.29%, and 0.816, respectively. In conclusion, hOGG1 is highly expressed in NSCLC tissues. Compared to S/S and S/C genotypes, the C/C gene was found to be more common in NSCLC group than in control group. Thus, hOGG1 has a high predictive value for patient survival.
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Affiliation(s)
- Jing Wang
- Department of Oncology, Xiang Yang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei 441000, P.R. China
| | - Puzhao Wu
- Department of Interventional Oncology, Xiang Yang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei 441000, P.R. China
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Canadas A, Santos M, Medeiros R, Dias-Pereira P. Influence of E-cadherin genetic variation in canine mammary tumour risk, clinicopathological features and prognosis. Vet Comp Oncol 2019; 17:489-496. [PMID: 31100200 DOI: 10.1111/vco.12510] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 12/14/2022]
Abstract
E-cadherin is a cell adhesion molecule that participates in several cellular processes that guarantee the maintenance of structural and functional integrity of epithelial tissues. E-cadherin plays an important role in mammary carcinogenesis, and various studies have demonstrated the effect of CDH1 genetic variation in risk, progression and biological behaviour of human breast cancer. Although there are some recognized genetic variations in canine CDH1 gene, their influence in canine mammary tumour development and progression has not been previously evaluated. In this study, we aim to assess the influence of CDH1 SNPs rs850805755, rs852280880 and rs852639930 in the risk, clinicopathological features and clinical outcome of canine mammary tumours. A case-control study was conducted involving 206 bitches with mammary tumours and 161 bitches free of mammary neoplasia. CDH1 SNPs rs850805755 and rs852280880 were associated with a decreased risk and a later onset of mammary tumour development. Furthermore, these SNPs were related to the development of small size carcinomas, of low histological grade and low nuclear pleomorphism. SNP rs852639930 was associated with the development of small size tumours with a non-infiltrative, non-invasive growth pattern. Data from the present investigation demonstrate that these CDH1 genetic variants could have a protective role in canine mammary tumours, by being associated with low risk of tumour development, delayed onset of the disease and less aggressive clinicopathological features.
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Affiliation(s)
- Ana Canadas
- Department of Pathology and Molecular Immunology, Instituto Ciências Biomédicas Abel Salazar, ICBAS - UPorto, University of Porto, Porto, Portugal
| | - Marta Santos
- Department of Microscopy, Instituto Ciências Biomédicas Abel Salazar, ICBAS - UPorto, University of Porto, Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, IPO-Porto Research Centre, Portuguese Institute of Oncology of Porto, (IPO-Porto), Porto, Portugal.,CEBIMED, Biomedical Research Centre, Faculty of Health Sciences of Fernando Pessoa University, Porto, Portugal.,FMUP, Faculty of Medicine of Porto, University of Porto, Porto, Portugal.,LPCC, Research Department-Portuguese League Against Cancer (LPCC-NRNorte), Porto, Portugal
| | - Patrícia Dias-Pereira
- Department of Pathology and Molecular Immunology, Instituto Ciências Biomédicas Abel Salazar, ICBAS - UPorto, University of Porto, Porto, Portugal
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Tan H, Huang S, Zhang Z, Qian X, Sun P, Zhou X. Pan-cancer analysis on microRNA-associated gene activation. EBioMedicine 2019; 43:82-97. [PMID: 30956173 PMCID: PMC6557760 DOI: 10.1016/j.ebiom.2019.03.082] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/21/2019] [Accepted: 03/27/2019] [Indexed: 12/26/2022] Open
Abstract
Background While microRNAs (miRNAs) were widely considered to repress target genes at mRNA and/or protein levels, emerging evidence from in vitro experiments has shown that miRNAs can also activate gene expression in particular contexts. However, this counterintuitive observation has rarely been reported or interpreted in in vivo conditions. Methods We systematically explored the positive correlation between miRNA and gene expressions and its potential implications in tumorigenesis, based on 8375 patient samples across 31 major human cancers from The Cancer Genome Atlas (TCGA). Findings We found that positive miRNA-gene correlations are surprisingly prevalent and consistent across cancer types, and show distinct patterns than negative correlations. The top-ranked positive correlations are significantly involved in the immune cell differentiation and cell membrane signaling related processes, and display strong power in stratifying patients in terms of survival rate. Although intragenic miRNAs generally tend to co-express with their host genes, a substantial portion of miRNAs shows no obvious correlation with their host gene plausibly due to non-conservation. A miRNA can upregulate a gene by inhibiting its upstream suppressor, or shares transcription factors with that gene, both leading to positive correlation. The miRNA/gene sites associated with the top-ranked positive correlations are more likely to form super-enhancers compared to randomly chosen pairs. Wet-lab experiments revealed that positive correlations partially remain in in vitro condition. Interpretation Our study brings new insights into the critical role of miRNA in gene regulation and the complex mechanisms underlying miRNA functions, and reveals both biological and clinical significance of miRNA-associated gene activation.
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Affiliation(s)
- Hua Tan
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Shan Huang
- Department of Cancer Biology, Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Zhigang Zhang
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaohua Qian
- Institute for Medical Imaging Technology, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Peiqing Sun
- Department of Cancer Biology, Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
| | - Xiaobo Zhou
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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Abstract
PURPOSE OF REVIEW Over the last decade over 40 loci have been associated with risk of Alzheimer's disease (AD). However, most studies have either focused on identifying risk loci or performing unbiased screens without a focus on protective variation in AD. Here, we provide a review of known protective variants in AD and their putative mechanisms of action. Additionally, we recommend strategies for finding new protective variants. RECENT FINDINGS Recent Genome-Wide Association Studies have identified both common and rare protective variants associated with AD. These include variants in or near APP, APOE, PLCG2, MS4A, MAPT-KANSL1, RAB10, ABCA1, CCL11, SORL1, NOCT, SCL24A4-RIN3, CASS4, EPHA1, SPPL2A, and NFIC. SUMMARY There are very few protective variants with functional evidence and a derived allele with a frequency below 20%. Additional fine mapping and multi-omic studies are needed to further validate and characterize known variants as well as specialized genome-wide scans to identify novel variants.
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Affiliation(s)
- Shea J Andrews
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Equal first author
| | - Brian Fulton-Howard
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Equal first author
| | - Alison Goate
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Downs B, Sherman S, Cui J, Kim YC, Snyder C, Christensen M, Luo J, Lynch H, Wang SM. Common genetic variants contribute to incomplete penetrance: evidence from cancer-free BRCA1 mutation carriers. Eur J Cancer 2018; 107:68-78. [PMID: 30551077 DOI: 10.1016/j.ejca.2018.10.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 10/27/2022]
Abstract
PURPOSE The presence of pathogenic germline mutation in BRCA1 gene is considered as the most penetrant genetic predisposition for breast cancer. However, a portion of BRCA1 mutation carriers never develops breast cancer throughout their lifetime. This phenomenon is called incomplete penetrance. Genetic factor is proposed to contribute to this phenomenon, but the details regarding the genetic factor remain elusive. BRCA1 mutations were inherited from the ancestors of the mutation carrier families during human evolution, and their presence is a consistent threat to the survival of the mutation carrier population. In the present study, we hypothesize that evolution could positively select genetic components in the mutation carrier population to suppress the oncogenesis imposed by the predisposition. EXPERIMENTAL DESIGN To test our hypothesis, we used whole exome sequencing to compare germline variation of all genes in pairs of breast cancer-unaffected and breast cancer-affected BRCA1 mutation carriers, each pair was from the same family carrying the same BRCA1 mutation. RESULTS We identified a group of 'beneficial' variants enriched in the breast cancer-unaffected carrier group. These were the common variants in human population distributed in multiple genes involved in multiple functionally important pathways. We found a single-nucleotide polymorphism, rs3735400 located in ANLN gene, which plays an essential role in controlling cytokinesis and is often found to be overexpressed in cancer. The carriers of this variant had lower cumulative risk of developing breast cancer; overexpression of the variant-containing ANLN decreased ANLN nuclear localization suppressed expression of the variant-containing ANLN, and decreased the cellular proliferation respectively. CONCLUSION Our findings support our hypothesis that common genetic variants can be evolutionarily selected in BRCA1 mutation carrier population to counterpart the oncogenic effects imposed by mutation predisposition in BRCA1, contributing to the incomplete penetrance.
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Affiliation(s)
- Bradley Downs
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, USA
| | - Simon Sherman
- Eppley Institute for Research in Cancer and Allied Diseases, USA
| | - Jian Cui
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, USA
| | - Yeong C Kim
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, USA
| | - Carrie Snyder
- Hereditary Cancer Center, Department of Preventive Medicine, Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Maria Christensen
- Hereditary Cancer Center, Department of Preventive Medicine, Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Jiangtao Luo
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Henry Lynch
- Hereditary Cancer Center, Department of Preventive Medicine, Creighton University School of Medicine, Omaha, NE 68178, USA.
| | - San Ming Wang
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, USA; Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau, SAR, China.
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