1
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Reggiori F, Molinari M. ER-phagy: mechanisms, regulation and diseases connected to the lysosomal clearance of the endoplasmic reticulum. Physiol Rev 2022; 102:1393-1448. [PMID: 35188422 PMCID: PMC9126229 DOI: 10.1152/physrev.00038.2021] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
ER-phagy (reticulo-phagy) defines the degradation of portions of the endoplasmic reticulum (ER) within lysosomes or vacuoles. It is part of the self-digestion (i.e., auto-phagic) programs recycling cytoplasmic material and organelles, which rapidly mobilize metabolites in cells confronted with nutrient shortage. Moreover, selective clearance of ER subdomains participates to the control of ER size and activity during ER stress, the re-establishment of ER homeostasis after ER stress resolution and the removal of ER parts, in which aberrant and potentially cytotoxic material has been segregated. ER-phagy relies on the individual and/or concerted activation of the ER-phagy receptors, ER peripheral or integral membrane proteins that share the presence of LC3/Atg8-binding motifs in their cytosolic domains. ER-phagy involves the physical separation of portions of the ER from the bulk ER network, and their delivery to the endolysosomal/vacuolar catabolic district. This last step is accomplished by a variety of mechanisms including macro-ER-phagy (in which ER fragments are sequestered by double-membrane autophagosomes that eventually fuse with lysosomes/vacuoles), micro-ER-phagy (in which ER fragments are directly engulfed by endosomes/lysosomes/vacuoles), or direct fusion of ER-derived vesicles with lysosomes/vacuoles. ER-phagy is dysfunctional in specific human diseases and its regulators are subverted by pathogens, highlighting its crucial role for cell and organism life.
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Affiliation(s)
- Fulvio Reggiori
- Department of Biomedical Sciences of Cells & Systems, grid.4830.fUniversity of Groningen, Netherlands
| | - Maurizio Molinari
- Protein Folding and Quality Control, grid.7722.0Institute for Research in Biomedicine, Bellinzona, Switzerland
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2
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He L, Qian X, Cui Y. Advances in ER-Phagy and Its Diseases Relevance. Cells 2021; 10:cells10092328. [PMID: 34571977 PMCID: PMC8465915 DOI: 10.3390/cells10092328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/27/2021] [Accepted: 09/01/2021] [Indexed: 01/18/2023] Open
Abstract
As an important form of selective autophagy in cells, ER-phagy (endoplasmic reticulum-selective autophagy), the autophagic degradation of endoplasmic reticulum (ER), degrades ER membranes and proteins to maintain cellular homeostasis. The relationship between ER-phagy and human diseases, including neurodegenerative disorders, cancer, and other metabolic diseases has been unveiled by extensive research in recent years. Starting with the catabolic process of ER-phagy and key mediators in this pathway, this paper reviews the advances in the mechanism of ER-phagy and its diseases relevance. We hope to provide some enlightenment for further study on ER-phagy and the development of novel therapeutic strategies for related diseases.
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Affiliation(s)
- Lingang He
- Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan 430071, China; (L.H.); (X.Q.)
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan 430071, China
| | - Xuehong Qian
- Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan 430071, China; (L.H.); (X.Q.)
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan 430071, China
| | - Yixian Cui
- Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan 430071, China; (L.H.); (X.Q.)
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan 430071, China
- Correspondence: ; Tel.: +86-27-87267099
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3
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Zhao J, Chang L, Gu X, Liu J, Sun B, Wei X. Systematic profiling of alternative splicing signature reveals prognostic predictor for prostate cancer. Cancer Sci 2020; 111:3020-3031. [PMID: 32530556 PMCID: PMC7419053 DOI: 10.1111/cas.14525] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/21/2020] [Accepted: 06/02/2020] [Indexed: 01/14/2023] Open
Abstract
Alternative splicing (AS) provides the primary mechanism for producing protein diversity. There is growing evidence that AS is involved in the development and progression of cancers. The rapid accumulation of high‐throughput sequencing technologies and clinical data sets offers an opportunity to systematically profile the relationship between mRNA variants and clinical outcomes. However, there is a lack of systematic analysis of AS in prostate cancer: Download RNA‐seq data and clinical information from The Cancer Genome Atlas (TCGA) data portal. Evaluate RNA splicing patterns by SpliceSeq and calculate splicing percentage (PSI) values. Different expressions were identified as differently expressed AS events (DEAs) based on PSI values. Bioinformatics methods were used for further analysis of DEAs and their splicing networks. Kaplan‐Meier, Cox proportional regression, and unsupervised cluster analysis were used to assess the correlation between DEAs and clinical characteristics. In total, 43 834 AS events were identified, of which 1628 AS events were differentially expressed. The parental genes of these DEAs played a significant role in the regulation of prostate cancer‐related processes. In total, 226 DEAs events were found to be associated with disease‐free survival. Four clusters of molecules with different survival modes were revealed by unsupervised cluster analysis of DEAs. AS events may be important determinants of prognosis and bio‐modulation in prostate cancer. In this study, we established strong prognostic predictors, discovered a splicing network that may be a potential mechanism, and provided further validated therapeutic targets.
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Affiliation(s)
- Jiyu Zhao
- Department of Urology, ChuiYangLiu Hospital affiliated to Tsinghua University, Beijing, China
| | - Luchen Chang
- Department of Diagnostic and Therapeutic Ultrasonography, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Xianen Gu
- Department of Urology, ChuiYangLiu Hospital affiliated to Tsinghua University, Beijing, China
| | - Jia Liu
- Department of Urology, ChuiYangLiu Hospital affiliated to Tsinghua University, Beijing, China
| | - Bei Sun
- Department of Outpatient Office, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Xi Wei
- Department of Diagnostic and Therapeutic Ultrasonography, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
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4
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Stefely JA, Zhang Y, Freiberger EC, Kwiecien NW, Thomas HE, Davis AM, Lowry ND, Vincent CE, Shishkova E, Clark NA, Medvedovic M, Coon JJ, Pagliarini DJ, Mercer CA. Mass spectrometry proteomics reveals a function for mammalian CALCOCO1 in MTOR-regulated selective autophagy. Autophagy 2020; 16:2219-2237. [PMID: 31971854 DOI: 10.1080/15548627.2020.1719746] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Macroautophagy/autophagy is suppressed by MTOR (mechanistic target of rapamycin kinase) and is an anticancer target under active investigation. Yet, MTOR-regulated autophagy remains incompletely mapped. We used proteomic profiling to identify proteins in the MTOR-autophagy axis. Wild-type (WT) mouse cell lines and cell lines lacking individual autophagy genes (Atg5 or Ulk1/Ulk2) were treated with an MTOR inhibitor to induce autophagy and cultured in media with either glucose or galactose. Mass spectrometry proteome profiling revealed an elevation of known autophagy proteins and candidates for new autophagy components, including CALCOCO1 (calcium binding and coiled-coil domain protein 1). We show that CALCOCO1 physically interacts with MAP1LC3C, a key protein in the machinery of autophagy. Genetic deletion of CALCOCO1 disrupted autophagy of the endoplasmic reticulum (reticulophagy). Together, these results reveal a role for CALCOCO1 in MTOR-regulated selective autophagy. More generally, the resource generated by this work provides a foundation for establishing links between the MTOR-autophagy axis and proteins not previously linked to this pathway. Abbreviations: ATG: autophagy-related; CALCOCO1: calcium binding and coiled-coil domain protein 1; CALCOCO2/NDP52: calcium binding and coiled-coil domain protein 2; CLIR: MAP1LC3C-interacting region; CQ: chloroquine; KO: knockout; LIR: MAP1LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; MLN: MLN0128 ATP-competitive MTOR kinase inhibitor; MTOR: mechanistic target of rapamycin kinase; reticulophagy: selective autophagy of the endoplasmic reticulum; TAX1BP1/CALCOCO3: TAX1 binding protein 1; ULK: unc 51-like autophagy activating kinase; WT: wild-type.
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Affiliation(s)
- Jonathan A Stefely
- Morgridge Institute for Research , Madison, WI, USA.,Medical Scientist Training Program, School of Medicine and Public Health, University of Wisconsin-Madison , Madison, WI, USA.,Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Yu Zhang
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Elyse C Freiberger
- Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Nicholas W Kwiecien
- Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Hala Elnakat Thomas
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Alexander M Davis
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Nathaniel D Lowry
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Catherine E Vincent
- Genome Center of Wisconsin , Madison, WI, USA.,Department of Chemistry, Hartwick College , Oneonta, NY, USA
| | | | - Nicholas A Clark
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati , Cincinnati, OH, USA
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati , Cincinnati, OH, USA
| | - Joshua J Coon
- Morgridge Institute for Research , Madison, WI, USA.,Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA
| | - David J Pagliarini
- Morgridge Institute for Research , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Carol A Mercer
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
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5
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Zavala VA, Serrano-Gomez SJ, Dutil J, Fejerman L. Genetic Epidemiology of Breast Cancer in Latin America. Genes (Basel) 2019; 10:E153. [PMID: 30781715 PMCID: PMC6410045 DOI: 10.3390/genes10020153] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 12/20/2022] Open
Abstract
The last 10 years witnessed an acceleration of our understanding of what genetic factors underpin the risk of breast cancer. Rare high- and moderate-penetrance variants such as those in the BRCA genes account for a small proportion of the familial risk of breast cancer. Low-penetrance alleles are expected to underlie the remaining heritability. By now, there are about 180 genetic polymorphisms that are associated with risk, most of them of modest effect. In combination, they can be used to identify women at the lowest or highest ends of the risk spectrum, which might lead to more efficient cancer prevention strategies. Most of these variants were discovered in populations of European descent. As a result, we might be failing to discover additional polymorphisms that could explain risk in other groups. This review highlights breast cancer genetic epidemiology studies conducted in Latin America, and summarizes the information that they provide, with special attention to similarities and differences with studies in other populations. It includes studies of common variants, as well as moderate- and high-penetrance variants. In addition, it addresses the gaps that need to be bridged in order to better understand breast cancer genetic risk in Latin America.
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Affiliation(s)
- Valentina A Zavala
- Department of Medicine, Division of General Internal Medicine, University of California San Francisco, San Francisco, CA 94143-1793, USA.
| | - Silvia J Serrano-Gomez
- Grupo de investigación en biología del cáncer, Instituto Nacional de Cancerología, Bogotá 11001000, Colombia.
| | - Julie Dutil
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, PR 00732, USA.
| | - Laura Fejerman
- Department of Medicine, Division of General Internal Medicine, University of California San Francisco, San Francisco, CA 94143-1793, USA.
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6
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McNamara KM, Kannai A, Sasano H. Possible roles for glucocorticoid signalling in breast cancer. Mol Cell Endocrinol 2018; 466:38-50. [PMID: 28687451 DOI: 10.1016/j.mce.2017.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 07/03/2017] [Accepted: 07/03/2017] [Indexed: 12/15/2022]
Abstract
Our understanding of breast cancer biology, and our ability to manipulate breast cancers have grown exponentially in the last 20 years. Much of that expansion has focused on the roles of steroids in driving these neoplasms. Initially this research focused on estrogens and progesterone receptors, and more recently on androgen actions in breast cancers. This review aims to make the case for glucocorticoids as the next essential steroid subclass that contributes significantly to our understanding of steroidogenic regulation of these neoplasms. Glucocorticoids have the potential to play multiple roles in the regulation of breast cancers including their control of cellular differentiation, apoptosis and proliferation. Beyond this they also act as a master integrator of organ homeostats in relation to such as circadian rhythms and stress responses. Therefore a better understanding of glucocorticoids and breast cancer could help to explain some of the epidemiological links between circadian disruption and/or stress and breast cancer development. Finally glucocorticoids are currently used during chemotherapeutic treatment in breast cancer therapy and yet results of various studies suggest that this may have an adverse impact on treatment success. This review aims to summarise the current evidence for glucocorticoids as actors in breast cancer and then suggest future essential approaches in order to determine the roles of glucocorticoids in this disease.
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Affiliation(s)
- Keely M McNamara
- Department of Anatomical Pathology, School of Graduate Medicine, Tohoku University, Sendai, Japan.
| | - Ayako Kannai
- Department of Anatomical Pathology, School of Graduate Medicine, Tohoku University, Sendai, Japan
| | - Hironobu Sasano
- Department of Anatomical Pathology, School of Graduate Medicine, Tohoku University, Sendai, Japan
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7
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Shi X, Jin H, Peng M, Li B, She M, Zhu T, Wen S, Qin D. Association between NME1 polymorphisms and cancer susceptibility: A meta-analysis based on 1644 cases and 2038 controls. Pathol Res Pract 2018. [PMID: 29525404 DOI: 10.1016/j.prp.2018.02.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The association between polymorphisms in the nucleoside diphosphate kinase 1 (NME1) gene and overall risk of cancer remains to be elucidated. Here, we performed a meta-analysis of the association between rs16949649, rs2302254, and rs34214448 polymorphisms in the NME1 gene and cancer risk. PubMed, Web of Science, and CNKI databases (as of June 6, 2017) were searched. Eight studies, encompassing 1644 cases and 2038 controls, were selected. The results revealed no significant relationship between NME1 polymorphisms and overall cancer susceptibility. Interestingly, the rs16949649 polymorphism was associated with increased susceptibility to gynecological cancer (heterozygous model: odds ratio [OR] = 1.74, 95% confidence interval [CI] = 1.06-2.86, P = 0.029). The rs2302254 polymorphism was linked to decreased susceptibility to gastric cancer in the other groups (recessive model: OR = 0.53, 95% CI = 0.28-0.98, P = 0.045). The rs34214448 polymorphism correlated significantly with increased susceptibility to non-small cell lung cancer according to all genetic models (P < 0.05) and was linked to decreased risk in cervical cancer (recessive model: OR = 0.51, 95% CI = 0.27-0.94, P = 0.031). Thus, our meta-analysis found rs16949649 associated with increased susceptibility to gynecological cancer and rs2302254 was linked to reduced gastric cancer risk; additional, larger studies are required to confirm these findings.
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Affiliation(s)
- Xiaoqing Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, Henan, China
| | - Huifang Jin
- Department of Blood Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mengle Peng
- Department of Clinical Laboratory, The Third People's Hospital of Henan Province, Zhengzhou, China
| | - Bingjie Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, Henan, China
| | - Mingcong She
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Tao Zhu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, Henan, China
| | - Shuang Wen
- Reproductive Medical Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dongchun Qin
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, Henan, China.
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8
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Lynce F, Graves KD, Jandorf L, Ricker C, Castro E, Moreno L, Augusto B, Fejerman L, Vadaparampil ST. Genomic Disparities in Breast Cancer Among Latinas. Cancer Control 2017; 23:359-372. [PMID: 27842325 DOI: 10.1177/107327481602300407] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Breast cancer is the most common cancer diagnosed among Latinas in the United States and the leading cause of cancer-related death among this population. Latinas tend to be diagnosed at a later stage and have worse prognostic features than their non-Hispanic white counterparts. Genetic and genomic factors may contribute to observed breast cancer health disparities in Latinas. METHODS We provide a landscape of our current understanding and the existing gaps that need to be filled across the cancer prevention and control continuum. RESULTS We summarize available data on mutations in high and moderate penetrance genes for inherited risk of breast cancer and the associated literature on disparities in awareness of and uptake of genetic counseling and testing in Latina populations. We also discuss common genetic polymorphisms and risk of breast cancer in Latinas. In the treatment setting, we examine tumor genomics and pharmacogenomics in Latina patients with breast cancer. CONCLUSIONS As the US population continues to diversify, extending genetic and genomic research into this underserved and understudied population is critical. By understanding the risk of breast cancer among ethnically diverse populations, we will be better positioned to make treatment advancements for earlier stages of cancer, identify more effective and ideally less toxic treatment regimens, and increase rates of survival.
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Affiliation(s)
- Filipa Lynce
- Health Outcomes and Behavior Program, Moffitt Cancer Center, Tampa, FL, USA.
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9
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Chen L, Zhang YH, Huang T, Cai YD. Gene expression profiling gut microbiota in different races of humans. Sci Rep 2016; 6:23075. [PMID: 26975620 PMCID: PMC4791684 DOI: 10.1038/srep23075] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/22/2016] [Indexed: 12/14/2022] Open
Abstract
The gut microbiome is shaped and modified by the polymorphisms of microorganisms in the intestinal tract. Its composition shows strong individual specificity and may play a crucial role in the human digestive system and metabolism. Several factors can affect the composition of the gut microbiome, such as eating habits, living environment, and antibiotic usage. Thus, various races are characterized by different gut microbiome characteristics. In this present study, we studied the gut microbiomes of three different races, including individuals of Asian, European and American races. The gut microbiome and the expression levels of gut microbiome genes were analyzed in these individuals. Advanced feature selection methods (minimum redundancy maximum relevance and incremental feature selection) and four machine-learning algorithms (random forest, nearest neighbor algorithm, sequential minimal optimization, Dagging) were employed to capture key differentially expressed genes. As a result, sequential minimal optimization was found to yield the best performance using the 454 genes, which could effectively distinguish the gut microbiomes of different races. Our analyses of extracted genes support the widely accepted hypotheses that eating habits, living environments and metabolic levels in different races can influence the characteristics of the gut microbiome.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China.,College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People's Republic of China
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China
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10
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Abstract
Nuclear receptors (NR) act as an integrated conduit for environmental and hormonal signals to govern genomic responses, which relate to cell fate decisions. We review how their integrated actions with each other, shared co-factors and other transcription factors are disrupted in cancer. Steroid hormone nuclear receptors are oncogenic drivers in breast and prostate cancer and blockade of signaling is a major therapeutic goal. By contrast to blockade of receptors, in other cancers enhanced receptor function is attractive, as illustrated initially with targeting of retinoic acid receptors in leukemia. In the post-genomic era large consortia, such as The Cancer Genome Atlas, have developed a remarkable volume of genomic data with which to examine multiple aspects of nuclear receptor status in a pan-cancer manner. Therefore to extend the review of NR function we have also undertaken bioinformatics analyses of NR expression in over 3000 tumors, spread across six different tumor types (bladder, breast, colon, head and neck, liver and prostate). Specifically, to ask how the NR expression was distorted (altered expression, mutation and CNV) we have applied bootstrapping approaches to simulate data for comparison, and also compared these NR findings to 12 other transcription factor families. Nuclear receptors were uniquely and uniformly downregulated across all six tumor types, more than predicted by chance. These approaches also revealed that each tumor type had a specific NR expression profile but these were most similar between breast and prostate cancer. Some NRs were down-regulated in at least five tumor types (e.g. NR3C2/MR and NR5A2/LRH-1)) whereas others were uniquely down-regulated in one tumor (e.g. NR1B3/RARG). The downregulation was not driven by copy number variation or mutation and epigenetic mechanisms maybe responsible for the altered nuclear receptor expression.
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Affiliation(s)
- Mark D Long
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
| | - Moray J Campbell
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
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11
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Long MD, van den Berg PR, Russell JL, Singh PK, Battaglia S, Campbell MJ. Integrative genomic analysis in K562 chronic myelogenous leukemia cells reveals that proximal NCOR1 binding positively regulates genes that govern erythroid differentiation and Imatinib sensitivity. Nucleic Acids Res 2015; 43:7330-48. [PMID: 26117541 PMCID: PMC4551916 DOI: 10.1093/nar/gkv642] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/10/2015] [Indexed: 01/05/2023] Open
Abstract
To define the functions of NCOR1 we developed an integrative analysis that combined ENCODE and NCI-60 data, followed by in vitro validation. NCOR1 and H3K9me3 ChIP-Seq, FAIRE-seq and DNA CpG methylation interactions were related to gene expression using bootstrapping approaches. Most NCOR1 combinations (24/44) were associated with significantly elevated level expression of protein coding genes and only very few combinations related to gene repression. DAVID's biological process annotation revealed that elevated gene expression was uniquely associated with acetylation and ETS binding. A matrix of gene and drug interactions built on NCI-60 data identified that Imatinib significantly targeted the NCOR1 governed transcriptome. Stable knockdown of NCOR1 in K562 cells slowed growth and significantly repressed genes associated with NCOR1 cistrome, again, with the GO terms acetylation and ETS binding, and significantly dampened sensitivity to Imatinib-induced erythroid differentiation. Mining public microarray data revealed that NCOR1-targeted genes were significantly enriched in Imatinib response gene signatures in cell lines and chronic myelogenous leukemia (CML) patients. These approaches integrated cistrome, transcriptome and drug sensitivity relationships to reveal that NCOR1 function is surprisingly most associated with elevated gene expression, and that these targets, both in CML cell lines and patients, associate with sensitivity to Imatinib.
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Affiliation(s)
- Mark D Long
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
| | - Patrick R van den Berg
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
| | - James L Russell
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
| | - Prashant K Singh
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
| | - Sebastiano Battaglia
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
| | - Moray J Campbell
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
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12
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Genetic association between cyclin D1 polymorphism and breast cancer susceptibility. Tumour Biol 2014; 35:11959-65. [PMID: 25399071 DOI: 10.1007/s13277-014-2489-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 08/12/2014] [Indexed: 01/15/2023] Open
Abstract
Cyclin D1 polymorphism has been reported to be associated with risk of breast cancer, but the published studies have yielded controversial results. This study was undertaken to derive a precise risk estimate for the cyclin D1 polymorphism associated with breast cancer risk. We performed a search of EMBASE, PubMed, and Web of Science. In total, data from 18 publications were pooled and the association was assessed by odds ratios (ORs) with 95 % confidence intervals (CIs). This analysis showed that there was no obvious association between the cyclin D1 polymorphism and breast cancer risk in any of the analyzed genetic model. We found the same negative association in stratified analyses by ethnicity, source of controls, and sample size. Our meta-analysis provides an estimate that the presence of cyclin D1 polymorphism may not confer susceptibility to breast cancer.
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13
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Blackmore JK, Karmakar S, Gu G, Chaubal V, Wang L, Li W, Smith CL. The SMRT coregulator enhances growth of estrogen receptor-α-positive breast cancer cells by promotion of cell cycle progression and inhibition of apoptosis. Endocrinology 2014; 155:3251-61. [PMID: 24971610 PMCID: PMC4138560 DOI: 10.1210/en.2014-1002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The SMRT coregulator functions as a dual coactivator and corepressor for estrogen receptor-α (ERα) in a gene-specific manner, and in several studies its elevated expression correlates with poor outcome for breast cancer patients. A specific role of SMRT in breast cancer progression has not been elucidated, but SMRT knock-down limits estradiol-dependent growth of MCF-7 breast cancer cells. In this study, small-interfering RNA (siRNA) and short-hairpin RNA (shRNA) approaches were used to determine the effects of SMRT depletion on growth of ERα-positive MCF-7 and ZR-75-1 breast cancer cells, as well as the ERα-negative MDA-MB-231 breast cancer line. Depletion of SMRT inhibited growth of ERα-positive cells grown in monolayer but had no effect on growth of the ERα-negative cells. Reduced SMRT levels also negatively impacted the anchorage-independent growth of MCF-7 cells as assessed by soft agar colony formation assays. The observed growth inhibitions were due to a loss of estradiol-induced progression through the G1/S transition of the cell cycle and increased apoptosis in SMRT-depleted compared with control cells. Gene expression analyses indicated that SMRT inhibits apoptosis by a coordinated regulation of genes involved in apoptosis. Functioning as a dual coactivator for anti-apoptotic genes and corepressor for pro-apoptotic genes, SMRT can limit apoptosis. Together these data indicate that SMRT promotes breast cancer progression through multiple pathways leading to increased proliferation and decreased apoptosis.
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Affiliation(s)
- Julia K Blackmore
- Molecular and Cellular Biology (J.K.B., S.K., V.C., C.L.S.), Lester and Sue Smith Breast Center (G.G.), and Dan L Duncan Cancer Center (L.W., W.L.), Baylor College of Medicine, Houston, Texas 77030
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14
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Amankwah EK, Thompson RC, Nabors LB, Olson JJ, Browning JE, Madden MH, Egan KM. SWI/SNF gene variants and glioma risk and outcome. Cancer Epidemiol 2012; 37:162-5. [PMID: 23276717 DOI: 10.1016/j.canep.2012.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/27/2012] [Accepted: 12/01/2012] [Indexed: 12/31/2022]
Abstract
BACKGROUND The human SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays essential roles in a variety of cellular processes and has been implicated in human cancer. However, the role of germline genetic variants in this complex in relation to cancer risk is not well studied. METHODS We assessed the association of 16 variants in the catalytic subunits (SMARCA2 and SMARCA4) of the SWI/SNF complex with the risk of glioma subtypes (lower grade astrocytoma, oligodendroglioma and glioblastoma [GBM]) and with mortality from high-grade tumors (GBM) in a multicenter US case-control study that included 561 cases and 574 controls. Associations were estimated with odds ratios (OR, for risk) or hazards ratios (HR, for mortality) with 95% confidence intervals (CI). False discovery rate (FDR-q) was used to control for multiple testing in risk associations. RESULTS None of the investigated SNPs was associated with overall glioma risk. However, analyses according to histological subtypes revealed a statistically significant increased risk of oligodendroglioma in association with SMARCA2 rs2296212 (OR = 4.05, 95% CI = 1.11-14.80, P = 0.030, q = 0.08) and rs4741651 (OR = 4.68, 95% CI = 1.43-15.30, P = 0.011, q = 0.08) and SMARCA4 rs11672232 (OR = 1.90, 95% CI = 1.01-3.58, P = 0.048, q = 0.08) and rs12232780 (OR = 2.14, 95% CI = 1.06-4.33, P = 0.035, q = 0.08). No significant risk associations were observed for GBM or lower grade astrocytoma. Suggestive associations with GBM mortality were not validated in the Cancer Genome Atlas. CONCLUSION Our findings suggest that genetic variants in SMARCA2 and SMARCA4 influence the risk of oligodendroglioma. Further research is warranted on the SWI/SNF complex genes and epigenetic mechanisms more generally in the development of glioma in adults.
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Affiliation(s)
- Ernest K Amankwah
- Department of Cancer Epidemiology & Genetics, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA.
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15
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Wallace SS, Murphy DL, Sweasy JB. Base excision repair and cancer. Cancer Lett 2012; 327:73-89. [PMID: 22252118 DOI: 10.1016/j.canlet.2011.12.038] [Citation(s) in RCA: 224] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/20/2011] [Accepted: 12/24/2011] [Indexed: 01/13/2023]
Abstract
Base excision repair is the system used from bacteria to man to remove the tens of thousands of endogenous DNA damages produced daily in each human cell. Base excision repair is required for normal mammalian development and defects have been associated with neurological disorders and cancer. In this paper we provide an overview of short patch base excision repair in humans and summarize current knowledge of defects in base excision repair in mouse models and functional studies on short patch base excision repair germ line polymorphisms and their relationship to cancer. The biallelic germ line mutations that result in MUTYH-associated colon cancer are also discussed.
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Affiliation(s)
- Susan S Wallace
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, 05405-0068, United States.
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16
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Cai Q, Long J, Lu W, Qu S, Wen W, Kang D, Lee JY, Chen K, Shen H, Shen CY, Sung H, Matsuo K, Haiman CA, Khoo US, Ren Z, Iwasaki M, Gu K, Xiang YB, Choi JY, Park SK, Zhang L, Hu Z, Wu PE, Noh DY, Tajima K, Henderson BE, Chan KYK, Su F, Kasuga Y, Wang W, Cheng JR, Yoo KY, Lee JY, Zheng H, Liu Y, Shieh YL, Kim SW, Lee JW, Iwata H, Le Marchand L, Chan SY, Xie X, Tsugane S, Lee MH, Wang S, Li G, Levy S, Huang B, Shi J, Delahanty R, Zheng Y, Li C, Gao YT, Shu XO, Zheng W. Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium. Hum Mol Genet 2011; 20:4991-9. [PMID: 21908515 DOI: 10.1093/hmg/ddr405] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Although approximately 20 common genetic susceptibility loci have been identified for breast cancer risk through genome-wide association studies (GWASs), genetic risk variants reported to date explain only a small fraction of heritability for this common cancer. We conducted a four-stage GWAS including 17 153 cases and 16 943 controls among East-Asian women to search for new genetic risk factors for breast cancer. After analyzing 684 457 SNPs in 2062 cases and 2066 controls (Stage I), we selected for replication among 5969 Chinese women (4146 cases and 1823 controls) the top 49 SNPs that had neither been reported previously nor were in strong linkage disequilibrium with reported SNPs (Stage II). Three SNPs were further evaluated in up to 13 152 Chinese and Japanese women (6436 cases and 6716 controls) (Stage III). Finally, two SNPs were evaluated in 10 847 Korean women (4509 cases and 6338 controls) (Stage IV). SNP rs10822013 on chromosome 10q21.2, located in the zinc finger protein 365 (ZNF365) gene, showed a consistent association with breast cancer risk in all four stages with a combined per-risk allele odds ratio of 1.10 (95% CI: 1.07-1.14) (P-value for trend = 5.87 × 10(-9)). In vitro electrophoretic mobility shift assays demonstrated the potential functional significance of rs10822013. Our results strongly implicate rs10822013 at 10q21.2 as a genetic risk variant for breast cancer among East-Asian women.
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Affiliation(s)
- Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN 37203-1738, USA
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17
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Sharma S, Murphy A, Howrylak J, Himes B, Cho MH, Chu JH, Hunninghake GM, Fuhlbrigge A, Klanderman B, Ziniti J, Senter-Sylvia J, Liu A, Szefler SJ, Strunk R, Castro M, Hansel NN, Diette GB, Vonakis BM, Adkinson NF, Carey VJ, Raby BA. The impact of self-identified race on epidemiologic studies of gene expression. Genet Epidemiol 2011; 35:93-101. [PMID: 21254216 DOI: 10.1002/gepi.20560] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Although population differences in gene expression have been established, the impact on differential gene expression studies in large populations is not well understood. We describe the effect of self-reported race on a gene expression study of lung function in asthma. We generated gene expression profiles for 254 young adults (205 non-Hispanic whites and 49 African Americans) with asthma on whom concurrent total RNA derived from peripheral blood CD4(+) lymphocytes and lung function measurements were obtained. We identified four principal components that explained 62% of the variance in gene expression. The dominant principal component, which explained 29% of the total variance in gene expression, was strongly associated with self-identified race (P<10(-16)). The impact of these racial differences was observed when we performed differential gene expression analysis of lung function. Using multivariate linear models, we tested whether gene expression was associated with a quantitative measure of lung function: pre-bronchodilator forced expiratory volume in one second (FEV(1)). Though unadjusted linear models of FEV(1) identified several genes strongly correlated with lung function, these correlations were due to racial differences in the distribution of both FEV(1) and gene expression, and were no longer statistically significant following adjustment for self-identified race. These results suggest that self-identified race is a critical confounding covariate in epidemiologic studies of gene expression and that, similar to genetic studies, careful consideration of self-identified race in gene expression profiling studies is needed to avoid spurious association.
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Affiliation(s)
- Sunita Sharma
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
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18
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Cai Q, Wen W, Qu S, Li G, Egan KM, Chen K, Deming SL, Shen H, Shen CY, Gammon MD, Blot WJ, Matsuo K, Haiman CA, Khoo US, Iwasaki M, Santella RM, Zhang L, Fair AM, Hu Z, Wu PE, Signorello LB, Titus-Ernstoff L, Tajima K, Henderson BE, Chan KYK, Kasuga Y, Newcomb PA, Zheng H, Cui Y, Wang F, Shieh YL, Iwata H, Le Marchand L, Chan SY, Shrubsole MJ, Trentham-Dietz A, Tsugane S, Garcia-Closas M, Long J, Li C, Shi J, Huang B, Xiang YB, Gao YT, Lu W, Shu XO, Zheng W. Replication and functional genomic analyses of the breast cancer susceptibility locus at 6q25.1 generalize its importance in women of chinese, Japanese, and European ancestry. Cancer Res 2011; 71:1344-55. [PMID: 21303983 DOI: 10.1158/0008-5472.can-10-2733] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We evaluated the generalizability of a single nucleotide polymorphism (SNP), rs2046210 (A/G allele), associated with breast cancer risk that was initially identified at 6q25.1 in a genome-wide association study conducted among Chinese women. In a pooled analysis of more than 31,000 women of East-Asian, European, and African ancestry, we found a positive association for rs2046210 and breast cancer risk in Chinese women [ORs (95% CI) = 1.30 (1.22-1.38) and 1.64 (1.50-1.80) for the AG and AA genotypes, respectively, P for trend = 1.54 × 10⁻³⁰], Japanese women [ORs (95% CI) = 1.31 (1.13-1.52) and 1.37 (1.06-1.76), P for trend = 2.51 × 10⁻⁴], and European-ancestry American women [ORs (95% CI) = 1.07 (0.99-1.16) and 1.18 (1.04-1.34), P for trend = 0.0069]. No association with this SNP, however, was observed in African American women [ORs (95% CI) = 0.81 (0.63-1.06) and 0.85 (0.65-1.11) for the AG and AA genotypes, respectively, P for trend = 0.4027]. In vitro functional genomic studies identified a putative functional variant, rs6913578. This SNP is 1,440 bp downstream of rs2046210 and is in high linkage disequilibrium with rs2046210 in Chinese (r(2) = 0.91) and European-ancestry (r² = 0.83) populations, but not in Africans (r² = 0.57). SNP rs6913578 was found to be associated with breast cancer risk in Chinese and European-ancestry American women. After adjusting for rs2046210, the association of rs6913578 with breast cancer risk in African Americans approached borderline significance. Results from this large consortium study confirmed the association of rs2046210 with breast cancer risk among women of Chinese, Japanese, and European ancestry. This association may be explained in part by a putatively functional variant (rs6913578) identified in the region.
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Affiliation(s)
- Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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19
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Li Y, Li Y, Wedrén S, Li G, Charn TH, Desai KV, Bonnard C, Czene K, Humphreys K, Darabi H, Einarsdóttir K, Heikkinen T, Aittomäki K, Blomqvist C, Chia KS, Nevanlinna H, Hall P, Liu ET, Liu J. Genetic variation of ESR1 and its co-activator PPARGC1B is synergistic in augmenting the risk of estrogen receptor-positive breast cancer. Breast Cancer Res 2011; 13:R10. [PMID: 21269472 PMCID: PMC3109578 DOI: 10.1186/bcr2817] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 12/03/2010] [Accepted: 01/26/2011] [Indexed: 12/27/2022] Open
Abstract
Introduction Given the role of estrogen in breast carcinogenesis and the modification of estrogen receptor (ER) activity by its biochemical cofactors, we hypothesize that genetic variation within ER cofactor genes alters cellular response to estrogen exposure and consequently modifies the risk for ER-positive breast cancer. Methods We genotyped 790 tagging SNPs within 60 ER cofactor genes in 1,257 cases and 1,464 controls from Sweden and in 2,215 cases and 1,265 controls from Finland, and tested their associations with either ER-positive or ER-negative breast cancer. Results Seven SNPs showed consistent association with ER-positive breast cancer in the two independent samples, and six of them were located within PPARGC1B, encoding an ER co-activator, with the strongest association at rs741581 (odds ratio = 1.41, P = 4.84 × 10-5) that survived Bonferroni correction for multiple testing in the combined ER-positive breast cancer sample (Pcorrected = 0.03). Moreover, we also observed significant synergistic interaction (Pinteraction = 0.008) between the genetic polymorphisms within PPARGC1B and ESR1 in ER-positive breast cancer. By contrast, no consistent association was observed in ER-negative breast cancer. Furthermore, we found that administration of estrogen in the MCF-7 cell line induced PPARGC1B expression and enhanced occupancies of ER and RNA polymerase II within the region of SNP association, suggesting the upregulation of PPARGC1B expression by ESR1 activation. Conclusions Our study revealed that DNA polymorphisms of PPARGC1B, coding a bona fide ER co-activator, are associated with ER-positive breast cancer risk. The feed-forward transcriptional regulatory loop between PPARGC1B and ESR1 further augments their protein interaction, which provides a plausible mechanistic explanation for the synergistic genetic interaction between PPARGC1B and ESR1 in ER-positive breast cancer. Our study also highlights that biochemically and genomically informed candidate gene studies can enhance the discovery of interactive disease susceptibility genes.
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Affiliation(s)
- Yuqing Li
- Human Genetics, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
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Sergentanis TN, Economopoulos KP. Cyclin D1 G870A polymorphism and breast cancer risk: a meta-analysis comprising 9,911 cases and 11,171 controls. Mol Biol Rep 2010; 38:4955-63. [PMID: 21161398 DOI: 10.1007/s11033-010-0639-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 12/03/2010] [Indexed: 12/12/2022]
Abstract
Cyclin D1 represents a key molecule in the regulation of cell cycle. CCND1 G870A (rs603965) polymorphism has drawn considerable attention as the A allele may generate a variant splice product with possible oncogenic actions. A meta-analysis examining the association between CCND1 G870A polymorphism and breast cancer risk was performed. Separate analyses on Caucasian and Chinese populations were also implemented. Eligible articles were identified for the period up to July 2010. Pooled odds ratios (OR) were appropriately derived from fixed-effects or random-effects models. Sensitivity analysis excluding studies whose genotype frequencies in controls significantly deviated from Hardy-Weinberg Equilibrium (HWE) was performed. Nine case-control studies on Caucasians (7,304 cases and 8,149 controls) and four case-control studies on Chinese (2,607 cases and 3,022 controls) were eligible. At the overall analysis the A allele seemed to be associated with elevated breast cancer risk; the effect seemed to be confined to homozygous carriers (pooled OR = 1.091, 95% CI: 1.008-1.179, P = 0.030, fixed effects) as heterozygous carriers did not exhibit significantly elevated breast cancer risk. No statistically significant associations were demonstrated in Caucasians. On the other hand, Chinese AA carriers exhibited marginally elevated breast cancer risk (pooled OR = 1.144, 95% CI: 0.984-1.329, P = 0.080, fixed effects). Nevertheless, the controls in two out of the four Chinese studies deviated from HWE. In conclusion, this meta-analysis suggests that the A allele of the CCND1 G870A polymorphism may confer additional breast cancer risk when it comes to homozygosity and Chinese populations. The need for additional, methodologically sound studies on Chinese populations seems warranted.
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Hartmaier RJ, Tchatchou S, Richter AS, Wang J, McGuire SE, Skaar TC, Rae JM, Hemminki K, Sutter C, Ditsch N, Bugert P, Weber BHF, Niederacher D, Arnold N, Varon-Mateeva R, Wappenschmidt B, Schmutzler RK, Meindl A, Bartram CR, Burwinkel B, Oesterreich S. Nuclear receptor coregulator SNP discovery and impact on breast cancer risk. BMC Cancer 2009; 9:438. [PMID: 20003447 PMCID: PMC2804710 DOI: 10.1186/1471-2407-9-438] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 12/14/2009] [Indexed: 11/10/2022] Open
Abstract
Background Coregulator proteins are "master regulators", directing transcriptional and posttranscriptional regulation of many target genes, and are critical in many normal physiological processes, but also in hormone driven diseases, such as breast cancer. Little is known on how genetic changes in these genes impact disease development and progression. Thus, we set out to identify novel single nucleotide polymorphisms (SNPs) within SRC-1 (NCoA1), SRC-3 (NCoA3, AIB1), NCoR (NCoR1), and SMRT (NCoR2), and test the most promising SNPs for associations with breast cancer risk. Methods The identification of novel SNPs was accomplished by sequencing the coding regions of these genes in 96 apparently normal individuals (48 Caucasian Americans, 48 African Americans). To assess their association with breast cancer risk, five SNPs were genotyped in 1218 familial BRCA1/2-mutation negative breast cancer cases and 1509 controls (rs1804645, rs6094752, rs2230782, rs2076546, rs2229840). Results Through our resequencing effort, we identified 74 novel SNPs (30 in NCoR, 32 in SMRT, 10 in SRC-3, and 2 in SRC-1). Of these, 8 were found with minor allele frequency (MAF) >5% illustrating the large amount of genetic diversity yet to be discovered. The previously shown protective effect of rs2230782 in SRC-3 was strengthened (OR = 0.45 [0.21-0.98], p = 0.04). No significant associations were found with the other SNPs genotyped. Conclusions This data illustrates the importance of coregulators, especially SRC-3, in breast cancer development and suggests that more focused studies, including functional analyses, should be conducted.
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Affiliation(s)
- Ryan J Hartmaier
- Program in Translational Biology & Molecular Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
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Hsia EYC, Zou JX, Chen HW. The roles and action mechanisms of p160/SRC coactivators and the ANCCA coregulator in cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 87:261-98. [PMID: 20374707 DOI: 10.1016/s1877-1173(09)87008-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chromosomal aberrations involving genes encoding members of the p160/SRC transcriptional coactivator family such as AIB1/ACTR and TIF2 implicated the coactivators in malignancy of human cells. Significant progress has been made in the last decade toward uncovering their roles in the development and progression of solid tissue tumors as well as leukemia and understanding of the underlying molecular mechanisms. Here, we review their genetic aberrations and dysregulation in expression in breast cancer, prostate cancer, and other nonhormone-responsive cancers. The experimental evidence gathered from studies using cell culture and animal models strongly supports a critical and, in some circumstances, their oncogenic function. We summarize results that the SRCs may contribute to tumorigenesis and disease progression through transcription factors such as E2F, PEA3, and AP-1 and through an intimate control of signaling pathways of growth factors-Akt and the receptor tyrosine kinases. The finding that a recently identified nuclear receptor coregulator ANCCA, like the SRCs, is frequently overexpressed in many types of cancers again underscores their broader roles in cancer.
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Affiliation(s)
- Elaine Y C Hsia
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Sacramento, California 95817, USA
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