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Chung Y, Lee SH, Lee HK, Lim D, van der Werf J, Lee SH. THI Modulation of Genetic and Non-genetic Variance Components for Carcass Traits in Hanwoo Cattle. Front Genet 2021; 11:576377. [PMID: 33424920 PMCID: PMC7786192 DOI: 10.3389/fgene.2020.576377] [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: 06/26/2020] [Accepted: 11/25/2020] [Indexed: 11/15/2022] Open
Abstract
The phenotype of carcass traits in beef cattle are affected by random genetic and non-genetic effects, which both can be modulated by an environmental variable such as Temperature-Humidity Index (THI), a key environmental factor in cattle production. In this study, a multivariate reaction norm model (MRNM) was used to assess if the random genetic and non-genetic (i.e., residual) effects of carcass weight (CW), back fat thickness (BFT), eye muscle area (EMA), and marbling score (MS) were modulated by THI, using 9,318 Hanwoo steers (N = 8,964) and cows (N = 354) that were genotyped on the Illumina Bovine SNP50 BeadChip (50K). THI was measured based on the period of 15–45 days before slaughter. Both the correlation and the interaction between THI and random genetic and non-genetic effects were accounted for in the model. In the analyses, it was shown that the genetic effects of EMA and the non-genetic effects of CW and MS were significantly modulated by THI. No significant THI modulation of such effects was found for BFT. These results highlight the relevance of THI changes for the genetic and non-genetic variation of CW, EMA, and MS in Hanwoo beef cattle. Importantly, heritability estimates for CW, EMA, and MS from additive models without considering THI interactions were underestimated. Moreover, the significance of interaction can be biased if not properly accounting for the correlation between THI and genetic and non-genetic effects. Thus, we argue that the estimation of genetic parameters should be based on appropriate models to avoid any potential bias of estimates. Our finding should serve as a basis for future studies aiming at revealing genotype by environment interaction in estimation and genomic prediction of breeding values.
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Affiliation(s)
- Yoonji Chung
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Seung Hwan Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Hak-Kyo Lee
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, South Korea
| | - Dajeong Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju, South Korea
| | - Julius van der Werf
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - S Hong Lee
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, Australia.,UniSA Allied Health and Human Performance, University of South Australia, Adelaide, SA, Australia
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Zhang H, Guo L, Chen J. Rationale for Lung Adenocarcinoma Prevention and Drug Development Based on Molecular Biology During Carcinogenesis. Onco Targets Ther 2020; 13:3085-3091. [PMID: 32341654 PMCID: PMC7166063 DOI: 10.2147/ott.s248436] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/14/2020] [Indexed: 12/18/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common and aggressive subtype of lung cancer with the greatest heterogeneity and aggression. Inspite of recent years’ achievements in understanding the pathogenesis of this disease, as well as the development of new therapeutic approaches, our knowledge on crucial early molecular events during its development is still rudimentary. Recent classification and grading of LUAD has postulated that LUAD does not arise spontaneously, but through a stepwise process from lung adenomatous premalignancy atypical adenomatous hyperplasia to adenocarcinoma in situ, minimally invasive adenocarcinoma, and eventually frankly invasive predominant adenocarcinoma. In this review, we discuss the molecular processes that drive the evolutionary process that results in the formation of LUAD. We also describe how to handle lung premalignancy in clinical settings based on the most recent advances in genomic biology and our own understanding of lung cancer prevention.
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Affiliation(s)
- Hongming Zhang
- Department of Respiratory Medicine, Yancheng Third People's Hospital, Affiliated Yancheng Hospital of Southeast University Medical College, Yancheng, Jiangsu Province, People's Republic of China
| | - Liting Guo
- Department of Oncology, Ruijin Hospital,affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Jibei Chen
- Department of Respiratory Medicine, Yancheng Third People's Hospital, Affiliated Yancheng Hospital of Southeast University Medical College, Yancheng, Jiangsu Province, People's Republic of China
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Moghaddar N, van der Werf JHJ. Genomic estimation of additive and dominance effects and impact of accounting for dominance on accuracy of genomic evaluation in sheep populations. J Anim Breed Genet 2017; 134:453-462. [DOI: 10.1111/jbg.12287] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 07/19/2017] [Indexed: 11/28/2022]
Affiliation(s)
- N. Moghaddar
- School of Environmental and Rural Science; University of New England; Armidale NSW Australia
- Cooperative Research Centre for Sheep Industry Innovation; Armidale NSW Australia
| | - J. H. J. van der Werf
- School of Environmental and Rural Science; University of New England; Armidale NSW Australia
- Cooperative Research Centre for Sheep Industry Innovation; Armidale NSW Australia
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Baykara O, Dalay N, Bakir B, Bulut P, Kaynak K, Buyru N. The EMSY Gene Collaborates with CCND1 in Non-Small Cell Lung Carcinogenesis. Int J Med Sci 2017; 14:675-679. [PMID: 28824300 PMCID: PMC5562119 DOI: 10.7150/ijms.19355] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/23/2017] [Indexed: 12/13/2022] Open
Abstract
Background: Lung cancer is the leading cause of cancer deaths. The main risk factor is smoking but the risk is also associated with various genetic and epigenetic components in addition to environmental factors. Increases in the gene copy numbers due to chromosomal amplifications constitute a common mechanism for oncogene activation. A gene-dense region on chromosome 11q13 which harbors four core regions that are frequently amplified, has been associated with various types of cancer. The important cell cycle regulatory protein cyclin D1 (CCND1) is an essential driver of the first core region of the Chr11q13 amplicon. Deregulation of CCND1 has been associated with different kinds of human malignancies including lung cancer. The EMSY (c11orf30) gene has been proposed as the possible driver of the fourth core of the 11q13 amplicon and its amplification has been associated with breast and ovarian cancers. There is no report in the literature investigating the EMSY gene in lung cancer. Methods: In this study, expression levels of the EMSY and CCND1 genes were investigated in 85 patients with non small cell lung cancer by Real Time PCR. Results: Expression of the EMSY and CCND1 genes were increased in 56 (65.8%) and 50 (58.8%) of the patients, respectively. Both genes showed a higher expression in the tumors when compared to normal tissues. A strong correlation was present between the expression rates of both genes (p<0.001). Patients with adenocarcinoma had higher expression levels of both genes (p=0.02). Conclusion: We conclude that EMSY and CCND1 work in collaboration and contribute to the pathogenesis of lung cancer.
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Affiliation(s)
- Onur Baykara
- Istanbul University, Department of Medical Biology, Cerrahpasa Medical Faculty, Istanbul 34303, Turkey
| | - Nejat Dalay
- Istanbul University, Department of Medical Biology, Cerrahpasa Medical Faculty, Istanbul 34303, Turkey
| | - Burak Bakir
- Istanbul University, Department of Medical Biology, Cerrahpasa Medical Faculty, Istanbul 34303, Turkey
| | - Pelin Bulut
- Istanbul University, Department of Medical Biology, Cerrahpasa Medical Faculty, Istanbul 34303, Turkey
| | - Kamil Kaynak
- Istanbul University, Department of Chest Surgery, Cerrahpasa Medical Faculty, Istanbul 34303, Turkey
| | - Nur Buyru
- Istanbul University, Department of Medical Biology, Cerrahpasa Medical Faculty, Istanbul 34303, Turkey
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Lee SH, Goddard ME, Visscher PM, van der Werf JHJ. Using the realized relationship matrix to disentangle confounding factors for the estimation of genetic variance components of complex traits. Genet Sel Evol 2010; 42:22. [PMID: 20546624 PMCID: PMC2903499 DOI: 10.1186/1297-9686-42-22] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 06/15/2010] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND In the analysis of complex traits, genetic effects can be confounded with non-genetic effects, especially when using full-sib families. Dominance and epistatic effects are typically confounded with additive genetic and non-genetic effects. This confounding may cause the estimated genetic variance components to be inaccurate and biased. METHODS In this study, we constructed genetic covariance structures from whole-genome marker data, and thus used realized relationship matrices to estimate variance components in a heterogenous population of approximately 2200 mice for which four complex traits were investigated. These mice were genotyped for more than 10,000 single nucleotide polymorphisms (SNP) and the variances due to family, cage and genetic effects were estimated by models based on pedigree information only, aggregate SNP information, and model selection for specific SNP effects. RESULTS AND CONCLUSIONS We show that the use of genome-wide SNP information can disentangle confounding factors to estimate genetic variances by separating genetic and non-genetic effects. The estimated variance components using realized relationship were more accurate and less biased, compared to those based on pedigree information only. Models that allow the selection of individual SNP in addition to fitting a relationship matrix are more efficient for traits with a significant dominance variance.
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Affiliation(s)
- Sang Hong Lee
- Queensland Statistical Genetics, Queensland Institute of Medical Research, Brisbane, Australia
| | - Michael E Goddard
- Biosciences Research Division, Department of Primary Industries, Victoria, Australia
- Department of Agriculture and Food Systems, University of Melbourne, Melbourne, Australia
| | - Peter M Visscher
- Queensland Statistical Genetics, Queensland Institute of Medical Research, Brisbane, Australia
| | - Julius HJ van der Werf
- School of Environmental and Rural Science, University of New England, Armidale, Australia
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Yang P, Li Y, Jiang R, Cunningham JM, Li Y, Zhang F, de Andrade M. A rigorous and comprehensive validation: common genetic variations and lung cancer. Cancer Epidemiol Biomarkers Prev 2010; 19:240-4. [PMID: 20056643 DOI: 10.1158/1055-9965.epi-09-0710] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Multiple recent genome-wide studies of single nucleotide polymorphisms (SNP) reported associations between candidate chromosome loci and lung cancer susceptibility. We evaluated five of the top candidate SNPs (rs402710, rs2736100, rs4324798, rs16969968, and rs8034191) for their effects on lung cancer risk and overall survival. METHODS Over 1,700 cases and 2,200 controls were included in this study. Seven independent, complementary case-control data sets were tested for risk assessment encompassing cigarette smokers and never smokers, using unrelated controls and unaffected full-sibling controls. Five patient groups were tested for survival prediction stratified by smoking status, histology subtype, and treatment. RESULTS After considering a history of chronic obstructive pulmonary disease as a risk factor altering lung cancer risk and comparing to sibling controls, none of the five SNPs remained significant. However, the variant rs4324798 was significant in predicting overall survival (hazard ratio, 0.46; 95% confidence interval, 0.30-0.73; P = 0.001) in small cell lung cancer. CONCLUSIONS None of the five candidate SNPs in lung cancer risk can be confirmed in our study. The previously reported association could be explained by disparity in tobacco smoke exposure and chronic obstructive pulmonary disease history between cases and controls. Instead, we found rs4324798 to be an independent predictor in small cell lung cancer survival, warranting further elucidation of the underlying mechanisms.
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Affiliation(s)
- Ping Yang
- Department of 1Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA.
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Hemminki K, Li X. FAMILIAL RISK FOR LUNG CANCER BY HISTOLOGY AND AGE OF ONSET: EVIDENCE FOR RECESSIVE INHERITANCE. Exp Lung Res 2009; 31:205-15. [PMID: 15824021 DOI: 10.1080/01902140490495606] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The authors used the Swedish Family-Cancer Database to search for evidence for a genetic predisposition in lung cancer. Familial risks in offspring were increased for all lung cancer to 1.77 when a parent was affected with any lung cancers; the comparable risk among siblings was 2.15. At young age, risks between siblings were higher than those between offspring and parents for all histological types of lung cancer. The present data suggest that 1.7% of lung cancers up to age 68 years are heritable and probably due to a high-penetrant recessive gene or genes that predispose to tobacco carcinogens.
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Affiliation(s)
- Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany.
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Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 2008; 455:1069-75. [PMID: 18948947 PMCID: PMC2694412 DOI: 10.1038/nature07423] [Citation(s) in RCA: 2035] [Impact Index Per Article: 127.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Accepted: 09/10/2008] [Indexed: 02/08/2023]
Abstract
Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers--including NF1, APC, RB1 and ATM--and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment.
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Affiliation(s)
- Li Ding
- The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
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Li X, Hemminki K. Familial multiple primary lung cancers: a population-based analysis from Sweden. Lung Cancer 2005; 47:301-7. [PMID: 15713513 DOI: 10.1016/j.lungcan.2004.07.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2004] [Revised: 07/01/2004] [Accepted: 07/14/2004] [Indexed: 10/26/2022]
Abstract
Multiple primary cancers arise because of inherited or acquired deficiencies, and their causes may depend on the first primary cancer, or they may be entirely independent. We used a nation-wide family dataset to search for evidence for a genetic predisposition to lung cancer. The Swedish Family-Cancer Database includes all Swedes born in 1932 and later with their parents, totalling over 10.2 million individuals. Cancer cases were retrieved from the Swedish Cancer Registry up to year 2000. Standardized incidence ratios (SIR) and 95% confidence limits (CI) were calculated for first and second primary lung cancers by a family history. The incidence of second primary lung cancer was nine times higher among cases with familial lung cancer compare to that of first primary lung cancer. The proportion of multiple primary lung cancer patients with family history for lung cancer was 4.7% (9/190) for men and 6.5% (5/77) for women. Lung cancer patients with a family history of lung cancer were at a significantly increased risk for subsequent primary lung cancer among both men (SIR=9.89, 95%CI 4.48-18.66) and women (SIR=17.86, 95%CI 5.63-42.00). The corresponding SIRs in patients without a family history were 2.04 (95%CI 1.75-2.36) and 5.10 (95%CI 3.99-6.43) for men and women, respectively. The present study suggests that the development from the first primary lung cancer to the second primary lung cancer may be more strongly affected by genetic factor than the first primary lung cancer.
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Affiliation(s)
- Xinjun Li
- Department of Biosciences at Novum, Karolinska Institute, Huddinge 14157, Sweden
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Li X, Hemminki K. Inherited predisposition to early onset lung cancer according to histological type. Int J Cancer 2004; 112:451-7. [PMID: 15382071 DOI: 10.1002/ijc.20436] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The role of hereditary factors in lung cancer is less well understood than in many other human neoplastic diseases. We used a nation-wide family dataset to search for evidence for a genetic predisposition in lung cancer. The Swedish Family-Cancer Database includes all Swedes born in 1932 and later (0- to 68-year-old offspring) with their parents, totaling over 10.2 million individuals. Cancer cases were retrieved from the Swedish Cancer Registry up to year 2000. Standardized incidence ratios (SIR) and 95% confidence limits (CI) were calculated for age-specific familial risks in offspring by parental or sibling proband, separately. A Kappa test was used to examine the association between familial risk and histology. Compared to the rate of lung cancers among persons without family history, a high risk by parental family history in adenocarcinoma (2.03) and large cell carcinoma (2.14) was found, and only a slightly lower risk was found among patients with squamous cell carcinoma (1.63) and small cell carcinoma (1.55). Among siblings, an increased risk was shown for concordant adenocarcinoma and small cell carcinoma at all ages and for all histological types when cancer was diagnosed before age 50. At young age, risks between siblings were higher than those between offspring and parents. The present data suggest that a large proportion of lung cancers before age 50 years appears to be heritable and probably due to a high-penetrant recessive gene or genes that predispose to tobacco carcinogens; however, this hypothesis needs to be tested in segregation analysis with a large number of pedigrees.
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Affiliation(s)
- Xinjun Li
- Department of Biosciences at Novum, Karolinska Institute, Huddinge, Sweden
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Cheng LSC, Wang TN, Ko YC. Reply to correspondence from Axenovich and Borodin--"Some pitfalls of segregation analysis of complex traits". Am J Med Genet A 2003; 117A:101-2. [PMID: 12548752 DOI: 10.1002/ajmg.a.10531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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