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A Nonquiescent "Idling" Population State in Drug-Treated, BRAF-Mutated Melanoma.
Paudel BB, Harris LA, Hardeman KN, Abugable AA, Hayford CE, Tyson DR, Quaranta V
(2018) Biophys J 114: 1499-1511
MeSH Terms: Cell Line, Tumor, Drug Resistance, Neoplasm, Epigenesis, Genetic, Humans, Melanoma, Molecular Targeted Therapy, Mutation, Proto-Oncogene Proteins B-raf
Show Abstract · Added April 15, 2018
Targeted therapy is an effective standard of care in BRAF-mutated malignant melanoma. However, the duration of tumor remission varies unpredictably among patients, and relapse is almost inevitable. Here, we examine the responses of several BRAF-mutated melanoma cell lines (including isogenic subclones) to BRAF inhibitors. We observe complex response dynamics across cell lines, with short-term responses (<100 h) varying from cell line to cell line. In the long term, however, we observe equilibration of all drug-treated populations into a nonquiescent state characterized by a balanced rate of death and division, which we term the "idling" state, and to our knowledge, this state has not been previously reported. Using mathematical modeling, we propose that the observed population-level dynamics are the result of cells transitioning between basins of attraction within a drug-modified phenotypic landscape. Each basin is associated with a drug-induced proliferation rate, a recently introduced metric of an antiproliferative drug effect. The idling population state represents a new dynamic equilibrium in which cells are distributed across the landscape such that the population achieves zero net growth. By fitting our model to experimental drug-response data, we infer the phenotypic landscapes of all considered melanoma cell lines and provide a unifying view of how BRAF-mutated melanomas respond to BRAF inhibition. We hypothesize that the residual disease observed in patients after targeted therapy is composed of a significant number of idling cells. Thus, defining molecular determinants of the phenotypic landscape that idling populations occupy may lead to "targeted landscaping" therapies based on rational modification of the landscape to favor basins with greater drug susceptibility.
Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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8 MeSH Terms
lncRNA MIR100HG-derived miR-100 and miR-125b mediate cetuximab resistance via Wnt/β-catenin signaling.
Lu Y, Zhao X, Liu Q, Li C, Graves-Deal R, Cao Z, Singh B, Franklin JL, Wang J, Hu H, Wei T, Yang M, Yeatman TJ, Lee E, Saito-Diaz K, Hinger S, Patton JG, Chung CH, Emmrich S, Klusmann JH, Fan D, Coffey RJ
(2017) Nat Med 23: 1331-1341
MeSH Terms: Antineoplastic Agents, Immunological, Cell Line, Tumor, Cetuximab, Disease Progression, Drug Resistance, Neoplasm, Epigenesis, Genetic, GATA6 Transcription Factor, Humans, MicroRNAs, RNA, Long Noncoding, Signal Transduction, Wnt Proteins, beta Catenin
Show Abstract · Added April 3, 2018
De novo and acquired resistance, which are largely attributed to genetic alterations, are barriers to effective anti-epidermal-growth-factor-receptor (EGFR) therapy. To generate cetuximab-resistant cells, we exposed cetuximab-sensitive colorectal cancer cells to cetuximab in three-dimensional culture. Using whole-exome sequencing and transcriptional profiling, we found that the long non-coding RNA MIR100HG and two embedded microRNAs, miR-100 and miR-125b, were overexpressed in the absence of known genetic events linked to cetuximab resistance. MIR100HG, miR-100 and miR-125b overexpression was also observed in cetuximab-resistant colorectal cancer and head and neck squamous cell cancer cell lines and in tumors from colorectal cancer patients that progressed on cetuximab. miR-100 and miR-125b coordinately repressed five Wnt/β-catenin negative regulators, resulting in increased Wnt signaling, and Wnt inhibition in cetuximab-resistant cells restored cetuximab responsiveness. Our results describe a double-negative feedback loop between MIR100HG and the transcription factor GATA6, whereby GATA6 represses MIR100HG, but this repression is relieved by miR-125b targeting of GATA6. These findings identify a clinically actionable, epigenetic cause of cetuximab resistance.
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MeSH Terms
Loss of claudin-3 expression induces IL6/gp130/Stat3 signaling to promote colon cancer malignancy by hyperactivating Wnt/β-catenin signaling.
Ahmad R, Kumar B, Chen Z, Chen X, Müller D, Lele SM, Washington MK, Batra SK, Dhawan P, Singh AB
(2017) Oncogene 36: 6592-6604
MeSH Terms: Adenocarcinoma, Animals, Carcinogenesis, Cell Transformation, Neoplastic, Claudin-3, Colon, Colonic Neoplasms, Colorectal Neoplasms, Cytokine Receptor gp130, Epigenesis, Genetic, Epithelial-Mesenchymal Transition, Gene Expression Regulation, Neoplastic, Humans, Intestinal Mucosa, Mice, Mice, Knockout, Permeability, STAT3 Transcription Factor, Up-Regulation, Wnt Signaling Pathway, beta Catenin
Show Abstract · Added March 14, 2018
The hyperactivated Wnt/β-catenin signaling acts as a switch to induce epithelial to mesenchymal transition and promote colorectal cancer. However, due to its essential role in gut homeostasis, therapeutic targeting of this pathway has proven challenging. Additionally, IL-6/Stat-3 signaling, activated by microbial translocation through the dysregulated mucosal barrier in colon adenomas, facilitates the adenoma to adenocarcinomas transition. However, inter-dependence between these signaling pathways and key mucosal barrier components in regulating colon tumorigenesis and cancer progression remains unclear. In current study, we have discovered, using a comprehensive investigative regimen, a novel and tissue-specific role of claudin-3, a tight junction integral protein, in inhibiting colon cancer progression by serving as the common rheostat of Stat-3 and Wnt-signaling activation. Loss of claudin-3 also predicted poor patient survival. These findings however contrasted an upregulated claudin-3 expression in other cancer types and implicated role of the epigenetic regulation. Claudin-3-/- mice revealed dedifferentiated and leaky colonic epithelium, and developed invasive adenocarcinoma when subjected to colon cancer. Wnt-signaling hyperactivation, albeit in GSK-3β independent manner, differentiated colon cancer in claudin-3-/- mice versus WT-mice. Claudin-3 loss also upregulated the gp130/IL6/Stat3 signaling in colonic epithelium potentially assisted by infiltrating immune components. Genetic and pharmacological studies confirmed that claudin-3 loss induces Wnt/β-catenin activation, which is further exacerbated by Stat-3-activation and help promote colon cancer. Overall, these novel findings identify claudin-3 as a therapeutic target for inhibiting overactivation of Wnt-signaling to prevent CRC malignancy.
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21 MeSH Terms
Mathematical models of cell phenotype regulation and reprogramming: Make cancer cells sensitive again!
Wooten DJ, Quaranta V
(2017) Biochim Biophys Acta Rev Cancer 1867: 167-175
MeSH Terms: Adaptation, Physiological, Animals, Antineoplastic Agents, Biomarkers, Tumor, Cell Transformation, Neoplastic, Cellular Reprogramming, Drug Resistance, Neoplasm, Epigenesis, Genetic, Evolution, Molecular, Gene Expression Regulation, Neoplastic, Genetic Fitness, Genetic Predisposition to Disease, Heredity, Humans, Models, Genetic, Mutation, Neoplasms, Pedigree, Phenotype, Signal Transduction, Time Factors
Show Abstract · Added May 5, 2017
A cell's phenotype is the observable actualization of complex interactions between its genome, epigenome, and local environment. While traditional views in cancer have held that cellular and tumor phenotypes are largely functions of genomic instability, increasing attention has recently been given to epigenetic and microenvironmental influences. Such non-genetic factors allow cancer cells to experience intrinsic diversity and plasticity, and at the tumor level can result in phenotypic heterogeneity and treatment evasion. In 2006, Takahashi and Yamanaka exploited the epigenome's plasticity by "reprogramming" differentiated cells into a pluripotent state by inducing expression of a cocktail of four transcription factors. Recent advances in cancer biology have shown not only that cellular reprogramming is possible for malignant cells, but it may provide a foundation for future therapies. Nevertheless, cell reprogramming experiments are frequently plagued by low efficiency, activation of aberrant transcriptional programs, instability, and often rely on expertise gathered from systems which may not translate directly to cancer. Here, we review a theoretical framework tracing back to Waddington's epigenetic landscape which may be used to derive quantitative and qualitative understanding of cellular reprogramming. Implications for tumor heterogeneity, evolution and adaptation are discussed in the context of designing new treatments to re-sensitize recalcitrant tumors. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby.
Copyright © 2017. Published by Elsevier B.V.
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21 MeSH Terms
Integrated molecular analysis reveals complex interactions between genomic and epigenomic alterations in esophageal adenocarcinomas.
Peng D, Guo Y, Chen H, Zhao S, Washington K, Hu T, Shyr Y, El-Rifai W
(2017) Sci Rep 7: 40729
MeSH Terms: Adenocarcinoma, Cell Line, Tumor, Comparative Genomic Hybridization, Computational Biology, DNA Copy Number Variations, DNA Methylation, Epigenesis, Genetic, Epigenomics, Esophageal Neoplasms, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Gene Ontology, Gene Regulatory Networks, Genomics, Humans
Show Abstract · Added April 18, 2017
The incidence of esophageal adenocarcinoma (EAC) is rapidly rising in the United States and Western countries. In this study, we carried out an integrative molecular analysis to identify interactions between genomic and epigenomic alterations in regulating gene expression networks in EAC. We detected significant alterations in DNA copy numbers (CN), gene expression levels, and DNA methylation profiles. The integrative analysis demonstrated that altered expression of 1,755 genes was associated with changes in CN or methylation. We found that expression alterations in 84 genes were associated with changes in both CN and methylation. These data suggest a strong interaction between genetic and epigenetic events to modulate gene expression in EAC. Of note, bioinformatics analysis detected a prominent K-RAS signature and predicted activation of several important transcription factor networks, including β-catenin, MYB, TWIST1, SOX7, GATA3 and GATA6. Notably, we detected hypomethylation and overexpression of several pro-inflammatory genes such as COX2, IL8 and IL23R, suggesting an important role of epigenetic regulation of these genes in the inflammatory cascade associated with EAC. In summary, this integrative analysis demonstrates a complex interaction between genetic and epigenetic mechanisms providing several novel insights for our understanding of molecular events in EAC.
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15 MeSH Terms
Epigenomic reprogramming during pancreatic cancer progression links anabolic glucose metabolism to distant metastasis.
McDonald OG, Li X, Saunders T, Tryggvadottir R, Mentch SJ, Warmoes MO, Word AE, Carrer A, Salz TH, Natsume S, Stauffer KM, Makohon-Moore A, Zhong Y, Wu H, Wellen KE, Locasale JW, Iacobuzio-Donahue CA, Feinberg AP
(2017) Nat Genet 49: 367-376
MeSH Terms: Carcinogenesis, Carcinoma, Pancreatic Ductal, Chromatin, Epigenesis, Genetic, Epigenomics, Gene Expression, Glucose, Heterochromatin, Histones, Humans, Neoplasm Metastasis, Pancreatic Neoplasms
Show Abstract · Added July 20, 2018
During the progression of pancreatic ductal adenocarcinoma (PDAC), heterogeneous subclonal populations emerge that drive primary tumor growth, regional spread, distant metastasis, and patient death. However, the genetics of metastases largely reflects that of the primary tumor in untreated patients, and PDAC driver mutations are shared by all subclones. This raises the possibility that an epigenetic process might operate during metastasis. Here we report large-scale reprogramming of chromatin modifications during the natural evolution of distant metastasis. Changes were targeted to thousands of large chromatin domains across the genome that collectively specified malignant traits, including euchromatin and large organized chromatin histone H3 lysine 9 (H3K9)-modified (LOCK) heterochromatin. Remarkably, distant metastases co-evolved a dependence on the oxidative branch of the pentose phosphate pathway (oxPPP), and oxPPP inhibition selectively reversed reprogrammed chromatin, malignant gene expression programs, and tumorigenesis. These findings suggest a model whereby linked metabolic-epigenetic programs are selected for enhanced tumorigenic fitness during the evolution of distant metastasis.
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Histone Adduction and Its Functional Impact on Epigenetics.
Galligan JJ, Marnett LJ
(2017) Chem Res Toxicol 30: 376-387
MeSH Terms: Animals, DNA, Epigenesis, Genetic, Gene Expression, Histones, Humans, Protein Binding, Protein Processing, Post-Translational
Show Abstract · Added April 22, 2018
Bioactive electrophiles generated from the oxidation of endogenous and exogenous compounds are a contributing factor in numerous disease states. Their toxicity is largely attributed to the covalent modification of cellular nucleophiles, including protein and DNA. With regard to protein modification, the side-chains of Cys, His, Lys, and Arg residues are critical targets. This results in the generation of undesired protein post-translational modifications (PTMs) that can trigger dire cellular consequences. Notably, histones are Lys- and Arg-rich proteins, providing a fertile source for adduction by both exogenous and endogenous electrophiles. The regulation of histone PTMs plays a critical role in the regulation of chromatin structure and thus gene expression. This perspective focuses on the role of electrophilic protein adduction within the context of chromatin and its potential consequences on cellular law and order.
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Reprogramming cell fate with a genome-scale library of artificial transcription factors.
Eguchi A, Wleklinski MJ, Spurgat MC, Heiderscheit EA, Kropornicka AS, Vu CK, Bhimsaria D, Swanson SA, Stewart R, Ramanathan P, Kamp TJ, Slukvin I, Thomson JA, Dutton JR, Ansari AZ
(2016) Proc Natl Acad Sci U S A 113: E8257-E8266
MeSH Terms: Animals, Binding Sites, Cell Lineage, Cellular Reprogramming, Chaperonin Containing TCP-1, Epigenesis, Genetic, Fibroblasts, Gene Expression Regulation, Neoplastic, Gene Regulatory Networks, Genomic Library, HEK293 Cells, Humans, Mice, Protein Domains, Protein Engineering, Sequence Analysis, RNA, Transcription Factors, Transcription, Genetic, Zinc Fingers
Show Abstract · Added September 5, 2017
Artificial transcription factors (ATFs) are precision-tailored molecules designed to bind DNA and regulate transcription in a preprogrammed manner. Libraries of ATFs enable the high-throughput screening of gene networks that trigger cell fate decisions or phenotypic changes. We developed a genome-scale library of ATFs that display an engineered interaction domain (ID) to enable cooperative assembly and synergistic gene expression at targeted sites. We used this ATF library to screen for key regulators of the pluripotency network and discovered three combinations of ATFs capable of inducing pluripotency without exogenous expression of Oct4 (POU domain, class 5, TF 1). Cognate site identification, global transcriptional profiling, and identification of ATF binding sites reveal that the ATFs do not directly target Oct4; instead, they target distinct nodes that converge to stimulate the endogenous pluripotency network. This forward genetic approach enables cell type conversions without a priori knowledge of potential key regulators and reveals unanticipated gene network dynamics that drive cell fate choices.
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19 MeSH Terms
Imbalance between HDAC and HAT activities drives aberrant STAT1/MyD88 expression in macrophages from type 1 diabetic mice.
Filgueiras LR, Brandt SL, Ramalho TR, Jancar S, Serezani CH
(2017) J Diabetes Complications 31: 334-339
MeSH Terms: Acetylation, Animals, Bone Marrow Cells, Cells, Cultured, Diabetes Mellitus, Type 1, Enzyme Inhibitors, Epigenesis, Genetic, Gene Expression Regulation, Glucose, Histone Acetyltransferases, Histone Deacetylases, Histones, Macrophages, Macrophages, Peritoneal, Male, Mice, Inbred C57BL, Myeloid Differentiation Factor 88, Osmolar Concentration, Promoter Regions, Genetic, Protein Processing, Post-Translational, STAT1 Transcription Factor, Streptozocin
Show Abstract · Added May 4, 2017
AIMS - To investigate the hypothesis that alteration in histone acetylation/deacetylation triggers aberrant STAT1/MyD88 expression in macrophages from diabetics. Increased STAT1/MyD88 expression is correlated with sterile inflammation in type 1 diabetic (T1D) mice.
METHODS - To induce diabetes, we injected low-doses of streptozotocin in C57BL/6 mice. Peritoneal or bone marrow-differentiated macrophages were cultured in 5mM (low) or 25mM (high glucose). ChIP analysis of macrophages from nondiabetic or diabetic mice was performed to determine acetylation of lysine 9 in histone H3 in MyD88 and STAT1 promoter regions. Macrophages from diabetic mice were treated with the histone acetyltransferase inhibitor anacardic acid (AA), followed by determination of mRNA expression by qPCR.
RESULTS - Increased STAT1 and MyD88 expression in macrophages from diabetic but not naive mice cultured in low glucose persisted for up to 6days. Macrophages from diabetic mice exhibited increased activity of histone acetyltransferases (HAT) and decreased histone deacetylases (HDAC) activity. We detected increased H3K9Ac binding to Stat1/Myd88 promoters in macrophages from T1D mice and AA in vitro treatment reduced STAT1 and MyD88 mRNA expression.
CONCLUSIONS/INTERPRETATION - These results indicate that histone acetylation drives elevated Stat1/Myd88 expression in macrophages from diabetic mice, and this mechanism may be involved in sterile inflammation and diabetes comorbidities.
Copyright © 2016 Elsevier Inc. All rights reserved.
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22 MeSH Terms
Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus.
Zeng C, Guo X, Long J, Kuchenbaecker KB, Droit A, Michailidou K, Ghoussaini M, Kar S, Freeman A, Hopper JL, Milne RL, Bolla MK, Wang Q, Dennis J, Agata S, Ahmed S, Aittomäki K, Andrulis IL, Anton-Culver H, Antonenkova NN, Arason A, Arndt V, Arun BK, Arver B, Bacot F, Barrowdale D, Baynes C, Beeghly-Fadiel A, Benitez J, Bermisheva M, Blomqvist C, Blot WJ, Bogdanova NV, Bojesen SE, Bonanni B, Borresen-Dale AL, Brand JS, Brauch H, Brennan P, Brenner H, Broeks A, Brüning T, Burwinkel B, Buys SS, Cai Q, Caldes T, Campbell I, Carpenter J, Chang-Claude J, Choi JY, Claes KB, Clarke C, Cox A, Cross SS, Czene K, Daly MB, de la Hoya M, De Leeneer K, Devilee P, Diez O, Domchek SM, Doody M, Dorfling CM, Dörk T, Dos-Santos-Silva I, Dumont M, Dwek M, Dworniczak B, Egan K, Eilber U, Einbeigi Z, Ejlertsen B, Ellis S, Frost D, Lalloo F, EMBRACE, Fasching PA, Figueroa J, Flyger H, Friedlander M, Friedman E, Gambino G, Gao YT, Garber J, García-Closas M, Gehrig A, Damiola F, Lesueur F, Mazoyer S, Stoppa-Lyonnet D, behalf of GEMO Study Collaborators, Giles GG, Godwin AK, Goldgar DE, González-Neira A, Greene MH, Guénel P, Haeberle L, Haiman CA, Hallberg E, Hamann U, Hansen TV, Hart S, Hartikainen JM, Hartman M, Hassan N, Healey S, Hogervorst FB, Verhoef S, HEBON, Hendricks CB, Hillemanns P, Hollestelle A, Hulick PJ, Hunter DJ, Imyanitov EN, Isaacs C, Ito H, Jakubowska A, Janavicius R, Jaworska-Bieniek K, Jensen UB, John EM, Joly Beauparlant C, Jones M, Kabisch M, Kang D, Karlan BY, Kauppila S, Kerin MJ, Khan S, Khusnutdinova E, Knight JA, Konstantopoulou I, Kraft P, Kwong A, Laitman Y, Lambrechts D, Lazaro C, Le Marchand L, Lee CN, Lee MH, Lester J, Li J, Liljegren A, Lindblom A, Lophatananon A, Lubinski J, Mai PL, Mannermaa A, Manoukian S, Margolin S, Marme F, Matsuo K, McGuffog L, Meindl A, Menegaux F, Montagna M, Muir K, Mulligan AM, Nathanson KL, Neuhausen SL, Nevanlinna H, Newcomb PA, Nord S, Nussbaum RL, Offit K, Olah E, Olopade OI, Olswold C, Osorio A, Papi L, Park-Simon TW, Paulsson-Karlsson Y, Peeters S, Peissel B, Peterlongo P, Peto J, Pfeiler G, Phelan CM, Presneau N, Radice P, Rahman N, Ramus SJ, Rashid MU, Rennert G, Rhiem K, Rudolph A, Salani R, Sangrajrang S, Sawyer EJ, Schmidt MK, Schmutzler RK, Schoemaker MJ, Schürmann P, Seynaeve C, Shen CY, Shrubsole MJ, Shu XO, Sigurdson A, Singer CF, Slager S, Soucy P, Southey M, Steinemann D, Swerdlow A, Szabo CI, Tchatchou S, Teixeira MR, Teo SH, Terry MB, Tessier DC, Teulé A, Thomassen M, Tihomirova L, Tischkowitz M, Toland AE, Tung N, Turnbull C, van den Ouweland AM, van Rensburg EJ, Ven den Berg D, Vijai J, Wang-Gohrke S, Weitzel JN, Whittemore AS, Winqvist R, Wong TY, Wu AH, Yannoukakos D, Yu JC, Pharoah PD, Hall P, Chenevix-Trench G, KConFab, AOCS Investigators, Dunning AM, Simard J, Couch FJ, Antoniou AC, Easton DF, Zheng W
(2016) Breast Cancer Res 18: 64
MeSH Terms: Alleles, BRCA1 Protein, Breast Neoplasms, Case-Control Studies, Chromosome Mapping, Chromosomes, Human, Pair 12, Computational Biology, Databases, Genetic, Enhancer Elements, Genetic, Epigenesis, Genetic, European Continental Ancestry Group, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Haplotypes, Heterozygote, Humans, Mutation, Odds Ratio, Polymorphism, Single Nucleotide, Population Surveillance, Promoter Regions, Genetic, Quantitative Trait Loci, Risk
Show Abstract · Added April 18, 2017
BACKGROUND - Multiple recent genome-wide association studies (GWAS) have identified a single nucleotide polymorphism (SNP), rs10771399, at 12p11 that is associated with breast cancer risk.
METHOD - We performed a fine-scale mapping study of a 700 kb region including 441 genotyped and more than 1300 imputed genetic variants in 48,155 cases and 43,612 controls of European descent, 6269 cases and 6624 controls of East Asian descent and 1116 cases and 932 controls of African descent in the Breast Cancer Association Consortium (BCAC; http://bcac.ccge.medschl.cam.ac.uk/ ), and in 15,252 BRCA1 mutation carriers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Stepwise regression analyses were performed to identify independent association signals. Data from the Encyclopedia of DNA Elements project (ENCODE) and the Cancer Genome Atlas (TCGA) were used for functional annotation.
RESULTS - Analysis of data from European descendants found evidence for four independent association signals at 12p11, represented by rs7297051 (odds ratio (OR) = 1.09, 95 % confidence interval (CI) = 1.06-1.12; P = 3 × 10(-9)), rs805510 (OR = 1.08, 95 % CI = 1.04-1.12, P = 2 × 10(-5)), and rs1871152 (OR = 1.04, 95 % CI = 1.02-1.06; P = 2 × 10(-4)) identified in the general populations, and rs113824616 (P = 7 × 10(-5)) identified in the meta-analysis of BCAC ER-negative cases and BRCA1 mutation carriers. SNPs rs7297051, rs805510 and rs113824616 were also associated with breast cancer risk at P < 0.05 in East Asians, but none of the associations were statistically significant in African descendants. Multiple candidate functional variants are located in putative enhancer sequences. Chromatin interaction data suggested that PTHLH was the likely target gene of these enhancers. Of the six variants with the strongest evidence of potential functionality, rs11049453 was statistically significantly associated with the expression of PTHLH and its nearby gene CCDC91 at P < 0.05.
CONCLUSION - This study identified four independent association signals at 12p11 and revealed potentially functional variants, providing additional insights into the underlying biological mechanism(s) for the association observed between variants at 12p11 and breast cancer risk.
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25 MeSH Terms