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Thomsen H, Chattopadhyay S, Weinhold N, Vodicka P, Vodickova L, Hoffmann P, Nöthen MM, Jöckel KH, Schmidt B, Hajek R, Hallmans G, Pettersson-Kymmer U, Späth F, Goldschmidt H, Hemminki K, Försti A. Haplotype analysis identifies functional elements in monoclonal gammopathy of unknown significance. Blood Cancer J 2024; 14:140. [PMID: 39164264 PMCID: PMC11335940 DOI: 10.1038/s41408-024-01121-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 08/22/2024] Open
Abstract
Genome-wide association studies (GWASs) based on common single nucleotide polymorphisms (SNPs) have identified several loci associated with the risk of monoclonal gammopathy of unknown significance (MGUS), a precursor condition for multiple myeloma (MM). We hypothesized that analyzing haplotypes might be more useful than analyzing individual SNPs, as it could identify functional chromosomal units that collectively contribute to MGUS risk. To test this hypothesis, we used data from our previous GWAS on 992 MGUS cases and 2910 controls from three European populations. We identified 23 haplotypes that were associated with the risk of MGUS at the genome-wide significance level (p < 5 × 10-8) and showed consistent results among all three populations. In 10 genomic regions, strong promoter, enhancer and regulatory element-related histone marks and their connections to target genes as well as genome segmentation data supported the importance of these regions in MGUS susceptibility. Several associated haplotypes affected pathways important for MM cell survival such as ubiquitin-proteasome system (RNF186, OTUD3), PI3K/AKT/mTOR (HINT3), innate immunity (SEC14L1, ZBP1), cell death regulation (BID) and NOTCH signaling (RBPJ). These pathways are important current therapeutic targets for MM, which may highlight the advantage of the haplotype approach homing to functional units.
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Affiliation(s)
- Hauke Thomsen
- MSB Medical School Berlin, Hochschule für Gesundheit und Medizin, Berlin, Germany
| | - Subhayan Chattopadhyay
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Niels Weinhold
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Pavel Vodicka
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Börge Schmidt
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Roman Hajek
- Department of Hematooncology, University Hospital Ostrava and Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Umea University, Umea, Sweden
| | - Ulrika Pettersson-Kymmer
- Clinical Pharmacology, Department of Pharmacology and Clinical Neuroscience, Umea University, Umea, Sweden
| | - Florentin Späth
- Department of Diagnostics and Intervention, Cancer Center, Hematology, Umeå University, Umeå, Sweden
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- National Centre of Tumor Diseases, Heidelberg, Germany
| | - Kari Hemminki
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Pilsen, Czech Republic
- Department of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Asta Försti
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.
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The relationship between RAGE gene four common polymorphisms and breast cancer risk in northeastern Han Chinese. Sci Rep 2014; 4:4355. [PMID: 24619131 PMCID: PMC5394748 DOI: 10.1038/srep04355] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 02/24/2014] [Indexed: 12/03/2022] Open
Abstract
We aimed to evaluate the association of four common polymorphisms (rs1800625, rs1800624, rs2070600, and rs184003) in receptor for advanced glycation end products (RAGE) gene to evaluate their epistatic influence on breast cancer risk in northeastern Han Chinese. This is a hospital-based case-control study involving 509 histologically-proven breast cancer patients and 504 cancer-free controls. The genotype and allele distributions of rs184003 differed significantly between patients and controls, even after the Bonferroni correction. Individuals carrying the rs184003 T allele exhibited 1.62-fold increased risk of breast cancer (odds ratio (OR) = 1.62; 95% confidence interval (95% CI): 1.26–2.08; P < 0.001) after adjusting for confounders. The frequency of haplotype T-T-G-T (alleles in order of rs1800625, rs1800624, rs2070600, and rs184003) was remarkably higher in patients than in controls (Simulated P = 0.001), and this haplotype was significantly associated with a 1.43-fold (95% CI: 1.01–2.01; P = 0.041) increase in adjusted risk of breast cancer. Further analysis indicated that there was synergistic interaction between rs184003 and rs2070600, whereas their joint information gain value was relatively small (0.27%). Taken together, although there was no suggestive evidence for the presence of epistasis in RAGE gene, our findings clearly demonstrate that rs184003 might play a predominant role in the development of breast cancer.
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Scoccianti C, Lauby-Secretan B, Bello PY, Chajes V, Romieu I. Female breast cancer and alcohol consumption: a review of the literature. Am J Prev Med 2014; 46:S16-25. [PMID: 24512927 DOI: 10.1016/j.amepre.2013.10.031] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 10/29/2013] [Accepted: 10/29/2013] [Indexed: 10/25/2022]
Abstract
CONTEXT Consumption of alcoholic beverages is one of the single most important known and modifiable risk factor for human cancer. Among women, breast cancer is the most common cancer worldwide and the leading cause of cancer-related mortality. Consumption of alcoholic beverages is causally associated with female breast cancer and the association shows a linear dose-response relationship. The role of heavy drinking has been long recognized and even a moderate intake is associated with an increased risk for breast cancer. The present review is an update of the current evidence on the association between alcohol consumption and breast cancer risk. The aim is to gain further insight into this association and to improve our current understanding of the effects of the major modifying factors. EVIDENCE ACQUISITION Epidemiologic and experimental studies published since the most recent International Agency for Research on Cancer (IARC) Monograph on alcoholic beverages were identified in PubMed using a combination of keywords such as alcohol, breast cancer, polymorphisms, menopausal status. EVIDENCE SYNTHESIS Cumulative lifetime consumption, drinking frequency, drinking patterns and timing of exposure each modulate the association between alcohol consumption and breast cancer. Hormonal status, genetic polymorphisms, and nutritional factors may interact with ethanol metabolism and further influence breast cancer risk. CONCLUSIONS Better standardization among experimental and epidemiologic designs in assessing alcohol intake and timing of exposure may improve our understanding of the heterogeneity observed across studies, possibly allowing the quantification of the effects of occasional heavy drinking and the identification of a window of higher susceptibility to breast cancer development.
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Affiliation(s)
- Chiara Scoccianti
- Nutritional Epidemiology Group, International Agency for Research on Cancer, Lyon
| | | | | | - Véronique Chajes
- Nutritional Epidemiology Group, International Agency for Research on Cancer, Lyon
| | - Isabelle Romieu
- Nutritional Epidemiology Group, International Agency for Research on Cancer, Lyon.
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Batra J, Lose F, Chambers S, Gardiner RA, Aitken J, Yaxley J, Clements JA, Spurdle AB. A replication study examining novel common single nucleotide polymorphisms identified through a prostate cancer genome-wide association study in a Japanese population. Am J Epidemiol 2011; 174:1391-5. [PMID: 22085625 DOI: 10.1093/aje/kwr271] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Five novel prostate cancer risk loci were identified in a recent genome-wide association study (GWAS) of Japanese persons (Takata et al., Nat Genet. 2010;42(9):751-754). Those authors proposed that apart from population-specific linkage disequilibrium patterns, limitations of GWAS single nucleotide polymorphism (SNP) prioritization and/or study design could explain the lack of identification of these loci in GWAS previously conducted among Caucasians. Thus, the authors undertook a replication study in 1,357 prostate cancer patients and 1,403 healthy Australian males of European descent (2004-2008). The rs12653946 SNP at 5p15 was found to be significantly associated with prostate cancer risk (odds ratio = 1.20, 95% confidence interval: 1.07, 1.34; P = 0.002). On the basis of linkage disequilibrium calculations, the rs12653946 SNP represents an independent locus, distinct from the previously identified TERT-CLPTM1L cancer nexus region. Further, analysis from AceView (Thierry-Mieg and Thierry-Mieg, Genome Biol. 2006;7(suppl 1):S12) indicated that rs12653946 falls within the intron of a testis-expressed gene strongly predicted to translate a conceptual 8.1-kilodalton protein named tojy.aApr07. The authors' findings suggest that follow-up of apparently ethnicity-specific risk associations are warranted in order to highlight risk-associated loci for experimental studies and for incorporation into future risk prediction models for prostate cancer.
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Affiliation(s)
- Jyotsna Batra
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Brisbane, Queensland 4059, Australia.
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Pelletier C, Speed WC, Paranjape T, Keane K, Blitzblau R, Hollestelle A, Safavi K, van den Ouweland A, Zelterman D, Slack FJ, Kidd KK, Weidhaas JB. Rare BRCA1 haplotypes including 3'UTR SNPs associated with breast cancer risk. Cell Cycle 2011; 10:90-9. [PMID: 21191178 DOI: 10.4161/cc.10.1.14359] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Genetic markers identifying women at an increased risk of developing breast cancer exist, yet the majority of inherited risk remains elusive. While numerous BRCA1 coding sequence mutations are associated with breast cancer risk, BRCA1 mutations account for less then 5% of breast cancer risk. Since 3' untranslated region (3'UTR) polymorphisms disrupting microRNA (miRNA) binding can be functional and can act as genetic markers of cancer risk, we tested the hypothesis that such polymorphisms in the 3'UTR of BRCA1 and haplotypes containing these functional polymorphisms may be associated with breast cancer risk. We sequenced the BRCA1 3'UTR from breast cancer patients to identify miRNA disrupting polymorphisms. We further evaluated haplotypes of this region including the identified 3'UTR variants in a large population of controls and breast cancer patients (n = 221) with known breast cancer subtypes and ethnicities. We identified three 3'UTR variants in BRCA1 that are polymorphic in breast cancer populations, and haplotype analysis including these variants revealed that breast cancer patients harbor five rare haplotypes not generally found among controls (9.50% for breast cancer chromosomes, 0.11% for control chromosomes, p = 0.0001). Three of these rare haplotypes contain the rs8176318 BRCA1 3'UTR functional variant. These haplotypes are not biomarkers for BRCA1 coding mutations, as they are found rarely in BRCA1 mutant breast cancer patients (1/129 patients = 0.78%). These rare BRCA1 haplotypes and 3'UTR SNPs may represent new genetic markers of breast cancer risk.
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Affiliation(s)
- Cory Pelletier
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
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Mizuno H, Atwal G, Wang H, Levine AJ, Vazquez A. Fine-scale detection of population-specific linkage disequilibrium using haplotype entropy in the human genome. BMC Genet 2010; 11:27. [PMID: 20416085 PMCID: PMC2873552 DOI: 10.1186/1471-2156-11-27] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Accepted: 04/23/2010] [Indexed: 01/14/2023] Open
Abstract
Background The creation of a coherent genomic map of recent selection is one of the greatest challenges towards a better understanding of human evolution and the identification of functional genetic variants. Several methods have been proposed to detect linkage disequilibrium (LD), which is indicative of natural selection, from genome-wide profiles of common genetic variations but are designed for large regions. Results To find population-specific LD within small regions, we have devised an entropy-based method that utilizes differences in haplotype frequency between populations. The method has the advantages of incorporating multilocus association, conciliation with low allele frequencies, and independence from allele polarity, which are ideal for short haplotype analysis. The comparison of HapMap SNPs data from African and Caucasian populations with a median resolution size of ~23 kb gave us novel candidates as well as known selection targets. Enrichment analysis for the yielded genes showed associations with diverse diseases such as cardiovascular, immunological, neurological, and skeletal and muscular diseases. A possible scenario for a selective force is discussed. In addition, we have developed a web interface (ENIGMA, available at http://gibk21.bse.kyutech.ac.jp/ENIGMA/index.html), which allows researchers to query their regions of interest for population-specific LD. Conclusion The haplotype entropy method is powerful for detecting population-specific LD embedded in short regions and should contribute to further studies aiming to decipher the evolutionary histories of modern humans.
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Affiliation(s)
- Hideaki Mizuno
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, USA.
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GARRE P, DE LA HOYA M, INIESTA P, ROMERA A, LLOVET P, GONZALEZ S, PEREZ-SEGURA P, CAPELLA G, DIAZ-RUBIO E, CALDES T. APC Yin-Yang haplotype associated with colorectal cancer risk. Exp Ther Med 2010; 1:879-883. [DOI: 10.3892/etm.2010.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 07/15/2010] [Indexed: 11/06/2022] Open
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