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Nemsick S, Hansen AS. Molecular models of bidirectional promoter regulation. Curr Opin Struct Biol 2024; 87:102865. [PMID: 38905929 DOI: 10.1016/j.sbi.2024.102865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/30/2024] [Accepted: 05/27/2024] [Indexed: 06/23/2024]
Abstract
Approximately 11% of human genes are transcribed by a bidirectional promoter (BDP), defined as two genes with <1 kb between their transcription start sites. Despite their evolutionary conservation and enrichment for housekeeping genes and oncogenes, the regulatory role of BDPs remains unclear. BDPs have been suggested to facilitate gene coregulation and/or decrease expression noise. This review discusses these potential regulatory functions through the context of six prospective underlying mechanistic models: a single nucleosome free region, shared transcription factor/regulator binding, cooperative negative supercoiling, bimodal histone marks, joint activation by enhancer(s), and RNA-mediated recruitment of regulators. These molecular mechanisms may act independently and/or cooperatively to facilitate the coregulation and/or decreased expression noise predicted of BDPs.
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Affiliation(s)
- Sarah Nemsick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA.
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Wang T, Li Z, Yan L, Yan F, Shen H, Tian X. Long Non-Coding RNA Neighbor of BRCA1 Gene 2: A Crucial Regulator in Cancer Biology. Front Oncol 2021; 11:783526. [PMID: 34926299 PMCID: PMC8674783 DOI: 10.3389/fonc.2021.783526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in fundamental biochemical and cellular processes. The neighbor of BRCA1 gene 2 (NBR2) is a long intergenic non-coding RNA (lincRNA) whose gene locus is adjacent to the tumor suppressor gene breast cancer susceptibility gene 1 (BRCA1). In human cancers, NBR2 expression is dysregulated and correlates with clinical outcomes. Moreover, NBR2 is crucial for glucose metabolism and affects the proliferation, survival, metastasis, and therapeutic resistance in different types of cancer. Here, we review the precise molecular mechanisms underlying NBR2-induced changes in cancer. In addition, the potential application of NBR2 in the diagnosis and treatment of cancer is also discussed, as well as the challenges of exploiting NBR2 for cancer intervention.
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Affiliation(s)
- Ting Wang
- Department of Laboratory Medicine, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Zhaosheng Li
- Department of Laboratory Medicine, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Liujia Yan
- Department of Laboratory Medicine, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Yan
- Department of Laboratory Medicine, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Xinyu Tian
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
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Yu H, Xie Y, Zhou Z, Wu Z, Dai X, Xu B. Curcumin Regulates the Progression of Colorectal Cancer via LncRNA NBR2/AMPK Pathway. Technol Cancer Res Treat 2020; 18:1533033819870781. [PMID: 31888414 PMCID: PMC6732852 DOI: 10.1177/1533033819870781] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Objective: To identify the effect of curcumin on tumor suppression and the possible molecular
pathways involved. Methods: The expression of long noncoding RNA neighbor of BRCA1 lncRNA 2 (NBR2) was quantified
using reverse transcription-polymerase chain reaction on cultured colorectal cancer
cells. Next, we used Western blot to measure the activation of adenosine
monophosphate-activated protein kinase and mechanistic target of rapamycin kinase (mTOR)
signaling molecules. Both cell proliferation and viability were measured via MTT assay,
and the cell ratio and S phase were detected by BrdU assay. Colorectal cancer cells were
pretreated with curcumin or transfected with shNBR2 or adenosine monophosphate-activated
protein kinase inhibitor Compound C to examine the molecular pathway involved. Results: Current data showed that glucose deficiency increased the expression of NBR2 in
colorectal cancer cells, and NBR2 knockdown affected the progression of colorectal
cancer cells under glucose starvation conditions. When NBR2 was silenced in the treated
colorectal cancer cells, the proliferation, the clone formation, and the percentage of
S-phase cells suppressed by glucose deprivation were compromised. Furthermore, NBR2
knockdown could suppress glucose deprivation-induced adenosine monophosphate-activated
protein kinase activation plus mTOR inactivation. Similarly, when colorectal cancer
cells were treated with curcumin, the expression of NBR2 was significantly increased.
NBR2 knockdown reversed curcumin-suppressed proliferation, clone formation, and the
percentage of S-phase colorectal cancer cells. Furthermore, NBR2 knockdown abolished
curcumin-induced activation of adenosine monophosphate-activated protein kinase and
inactivation of the mTOR signaling pathway. Conclusion: This study revealed a novel mechanism by which long noncoding RNA NBR2 mediates
curcumin suppression of colorectal cancer proliferation by activating adenosine
monophosphate-activated protein kinase and inactivating the mTOR signaling pathway.
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Affiliation(s)
- Hua Yu
- Department of Nutrition, The Second Hospital of Ningbo, Ningbo, People's Republic of China
| | - Yangyang Xie
- Department of Anorectal Surgery, The Second Hospital of Ningbo, Ningbo, People's Republic of China
| | - Zhendong Zhou
- Department of Anorectal Surgery, The Second Hospital of Ningbo, Ningbo, People's Republic of China
| | - Zhou Wu
- Department of Anorectal Surgery, The Second Hospital of Ningbo, Ningbo, People's Republic of China
| | - Xiaoyu Dai
- Department of Anorectal Surgery, The Second Hospital of Ningbo, Ningbo, People's Republic of China
| | - Binbin Xu
- Department of Nutrition, The Second Hospital of Ningbo, Ningbo, People's Republic of China
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Non-Coding Variants in BRCA1 and BRCA2 Genes: Potential Impact on Breast and Ovarian Cancer Predisposition. Cancers (Basel) 2018; 10:cancers10110453. [PMID: 30453575 PMCID: PMC6266896 DOI: 10.3390/cancers10110453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/04/2018] [Accepted: 11/12/2018] [Indexed: 12/21/2022] Open
Abstract
BRCA1 and BRCA2 are major breast cancer susceptibility genes whose pathogenic variants are associated with a significant increase in the risk of breast and ovarian cancers. Current genetic screening is generally limited to BRCA1/2 exons and intron/exon boundaries. Most identified pathogenic variants cause the partial or complete loss of function of the protein. However, it is becoming increasingly clear that variants in these regions only account for a small proportion of cancer risk. The role of variants in non-coding regions beyond splice donor and acceptor sites, including those that have no qualitative effect on the protein, has not been thoroughly investigated. The key transcriptional regulatory elements of BRCA1 and BRCA2 are housed in gene promoters, untranslated regions, introns, and long-range elements. Within these sequences, germline and somatic variants have been described, but the clinical significance of the majority is currently unknown and it remains a significant clinical challenge. This review summarizes the available data on the impact of variants on non-coding regions of BRCA1/2 genes and their role on breast and ovarian cancer predisposition.
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Wiedmeier JE, Ohlrich A, Chu A, Rountree MR, Turker MS. Induction of the long noncoding RNA NBR2 from the bidirectional BRCA1 promoter under hypoxic conditions. Mutat Res 2017; 796:13-19. [PMID: 28249151 DOI: 10.1016/j.mrfmmm.2017.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 01/27/2017] [Accepted: 02/09/2017] [Indexed: 06/06/2023]
Abstract
BRCA1 plays an important role in preventing breast cancer and is often silenced or repressed in sporadic cancer. The BRCA1 promoter is bidirectional: it drives transcription of the long non-coding (lnc) NBR2 transcript in the opposite orientation relative to the BRCA1 transcript. Hypoxic conditions repress BRCA1 transcription, but their effect on expression of the NBR2 transcript has not been reported. We used quantitative RT-PCR to measure BRCA1 and NBR2 transcript levels in 0% and 1% oxygen in MCF-7 breast cancer cells and found that NBR2 transcript levels increased as a function of time under hypoxic conditions, whereas BRCA1 mRNA levels were repressed. Hypoxic conditions were ineffective in reducing BRCA1 mRNA in the UACC-3199 breast cancer cell line, which is reported to have an epigenetically silenced BRCA1 promoter, even though appreciable levels of BRCA1 and NBR2 mRNA were detected. Significant recovery back to baseline RNA levels occurred within 48h after the MCF-7 cells were restored to normoxic conditions. We used a construct with the 218bp minimal BRCA1 promoter linked to marker genes to show that this minimal promoter repressed expression bidirectionally under hypoxic conditions, which suggests that the elements necessary for induction of NBR2 are located elsewhere.
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Affiliation(s)
- J Erin Wiedmeier
- University of Utah School of Medicine, Salt Lake City, UT 84132, United States
| | - Anna Ohlrich
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97239, United States
| | - Adrian Chu
- University of Utah School of Medicine, Salt Lake City, UT 84132, United States
| | | | - Mitchell S Turker
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, United States.
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Gazy I, Zeevi DA, Renbaum P, Zeligson S, Eini L, Bashari D, Smith Y, Lahad A, Goldberg M, Ginsberg D, Levy-Lahad E. TODRA, a lncRNA at the RAD51 Locus, Is Oppositely Regulated to RAD51, and Enhances RAD51-Dependent DSB (Double Strand Break) Repair. PLoS One 2015; 10:e0134120. [PMID: 26230935 PMCID: PMC4521930 DOI: 10.1371/journal.pone.0134120] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 07/06/2015] [Indexed: 12/18/2022] Open
Abstract
Expression of RAD51, a crucial player in homologous recombination (HR) and DNA double-strand break (DSB) repair, is dysregulated in human tumors, and can contribute to genomic instability and tumor progression. To further understand RAD51 regulation we functionally characterized a long non-coding (lnc) RNA, dubbed TODRA (Transcribed in the Opposite Direction of RAD51), transcribed 69bp upstream to RAD51, in the opposite direction. We demonstrate that TODRA is an expressed transcript and that the RAD51 promoter region is bidirectional, supporting TODRA expression (7-fold higher than RAD51 in this assay, p = 0.003). TODRA overexpression in HeLa cells induced expression of TPIP, a member of the TPTE family which includes PTEN. Similar to PTEN, we found that TPIP co-activates E2F1 induction of RAD51. Analysis of E2F1's effect on the bidirectional promoter showed that E2F1 binding to the same site that promotes RAD51 expression, results in downregulation of TODRA. Moreover, TODRA overexpression induces HR in a RAD51-dependent DSB repair assay, and increases formation of DNA damage-induced RAD51-positive foci. Importantly, gene expression in breast tumors supports our finding that E2F1 oppositely regulates RAD51 and TODRA: increased RAD51 expression, which is associated with an aggressive tumor phenotype (e.g. negative correlation with positive ER (r = -0.22, p = 0.02) and positive PR status (r = -0.27, p<0.001); positive correlation with ki67 status (r = 0.36, p = 0.005) and HER2 amplification (r = 0.41, p = 0.001)), correlates as expected with lower TODRA and higher E2F1 expression. However, although E2F1 induction resulted in TPIP downregulation in cell lines, we find that TPIP expression in tumors is not reduced despite higher E2F1 expression, perhaps contributing to increased RAD51 expression. Our results identify TPIP as a novel E2F1 co-activator, suggest a similar role for other TPTEs, and indicate that the TODRA lncRNA affects RAD51 dysregulation and RAD51-dependent DSB repair in malignancy. Importantly, gene expression in breast tumors supports our finding that E2F1 oppositely regulates RAD51 and TODRA: increased RAD51 expression, which is associated with an aggressive tumor phenotype (e.g. negative correlation with positive ER (r = -0.22, p = 0.02) and positive PR status (r = -0.27, p<0.001); positive correlation with ki67 status (r = 0.36, p = 0.005) and HER2 amplification (r = 0.41, p = 0.001)), correlates as expected with lower TODRA and higher E2F1 expression. However, although E2F1 induction resulted in TPIP downregulation in cell lines, we find that TPIP expression in tumors is not reduced despite higher E2F1 expression, perhaps contributing to increased RAD51 expression. Our results identify TPIP as a novel E2F1 co-activator, suggest a similar role for other TPTEs, and indicate that the TODRA lncRNA affects RAD51 dysregulation and RAD51-dependent DSB repair in malignancy.
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Affiliation(s)
- Inbal Gazy
- Human Genetics, Hebrew University Medical School, Jerusalem, Israel
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - David A. Zeevi
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Paul Renbaum
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Sharon Zeligson
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Lital Eini
- Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dana Bashari
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, Israel
| | - Yoav Smith
- Genomic Data Analysis Unit, Hebrew University Medical School, Jerusalem, Israel
| | - Amnon Lahad
- Department of Family Medicine, Hebrew University Medical School, Jerusalem, Israel
- Clalit Health Services, Jerusalem, Israel
| | - Michal Goldberg
- Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Doron Ginsberg
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, Israel
| | - Ephrat Levy-Lahad
- Human Genetics, Hebrew University Medical School, Jerusalem, Israel
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
- * E-mail:
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Wang Y, Zhang Y, Zhang C, Weng H, Li Y, Cai W, Xie M, Long Y, Ai Q, Liu Z, Du G, Wang S, Niu Y, Song F, Ozaki T, Bu Y. The gene pair PRR11 and SKA2 shares a NF-Y-regulated bidirectional promoter and contributes to lung cancer development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1133-44. [PMID: 26162986 DOI: 10.1016/j.bbagrm.2015.07.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/03/2015] [Accepted: 07/06/2015] [Indexed: 12/21/2022]
Abstract
Head-to-head gene pairs represent a unique feature of gene organization in eukaryotes, accounting for >10% of genes in the human genome. Identification and functional analysis of such gene pairs is only in its infancy. Recently, we identified PRR11 as a novel cancer-related gene that is implicated in cell cycle and lung cancer. Here we demonstrate that PRR11 is oriented in a head-to-head configuration with its neighboring gene, SKA2. 5'-RACE assay revealed that the intergenic spacer region between the two genes is <500 bp. Serial luciferase reporter assays demonstrated that a minimal 80-bp intergenic region functions as a core bidirectional promoter to drive basal transcription in both the PRR11 and SKA2 orientations. EMSA and ChIP assays demonstrated that NF-Y binds to and directly transactivates the PRR11-SKA2 bidirectional promoter. SiRNA-mediated NF-Y depletion significantly downregulated PRR11 and SKA2 expression. Expression of both PRR11 and SKA2 was significantly upregulated in lung cancer. Expression of the two genes was highly correlated with each other and with NF-Y expression. Remarkably, high expression of both PRR11 and SKA2 was associated with poorer prognosis in lung cancer patients compared with high expression of one gene or low expression of both genes. Knockdown of PRR11 and/or SKA2 remarkably reduced cell proliferation, migration, and invasion in lung cancer cells. Thus, the PRR11-SKA2 bidirectional transcription unit, which is a novel direct target of NF-Y, is essential for the accelerated proliferation and motility of lung cancer cells and may represent a potential target in the diagnosis and/or treatment of human lung cancer.
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Affiliation(s)
- Yitao Wang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Chundong Zhang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Huali Weng
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yi Li
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Wei Cai
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Mengyu Xie
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yinjiang Long
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Qing Ai
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Zhu Liu
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Gang Du
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Sen Wang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yulong Niu
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Fangzhou Song
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Toshinori Ozaki
- Laboratory of DNA Damage Signaling, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuohku, Chiba 260-8717, Japan
| | - Youquan Bu
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China.
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Abstract
Background We develop a new concept that reflects how genes are connected based on microarray data using the coefficient of determination (the squared Pearson correlation coefficient). Our gene rank combines a priori knowledge about gene connectivity, say, from the Gene Ontology (GO) database, and the microarray expression data at hand, called the microarray enriched gene rank, or simply gene rank (GR). GR, similarly to Google PageRank, is defined in a recursive fashion and is computed as the left maximum eigenvector of a stochastic matrix derived from microarray expression data. An efficient algorithm is devised that allows computation of GR for 50 thousand genes with 500 samples within minutes on a personal computer using the public domain statistical package R. Results Computation of GR is illustrated with several microarray data sets. In particular, we apply GR (1) to answer whether bad genes are more connected than good genes in relation with cancer patient survival, (2) to associate gene connectivity with cluster/subtypes in ovarian cancer tumors, and to determine whether gene connectivity changes (3) from organ to organ within the same organism and (4) between organisms. Conclusions We have shown by examples that findings based on GR confirm biological expectations. GR may be used for hypothesis generation on gene pathways. It may be used for a homogeneous sample or for comparison of gene connectivity among cases and controls, or in longitudinal setting.
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Affiliation(s)
- Eugene Demidenko
- Department of Biomedical Data Science, Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, 03755 NH USA
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Zhou L, Graves M, MacDonald G, Cipollone J, Mueller CR, Roskelley CD. Microenvironmental regulation of BRCA1 gene expression by c-Jun and Fra2 in premalignant human ovarian surface epithelial cells. Mol Cancer Res 2013; 11:272-81. [PMID: 23339184 DOI: 10.1158/1541-7786.mcr-12-0395] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Reduced BRCA1 gene expression is common in the sporadic form of ovarian carcinoma. The spread of this highly lethal cancer often begins when tumor cell clusters are shed into the fluid of the abdominopelvic cavity such that they can float freely before seeding distant sites on the peritoneal walls and organs. Thus, the microenvironment that tumor cells find themselves in changes dramatically during these early shedding and floating stages of transperitoneal metastasis. To mimic this microenvironmental change in vitro, we released premalignant human ovarian surface epithelial cells from the substratum and forced them to cluster in suspension. Under these conditions, steady state levels of BRCA1 mRNA and protein fell significantly and the transcriptional activation state of the BRCA1 promoter was suppressed. Analysis of the promoter indicated that the previously identified "CRE" element located within the "positive regulatory region" (PRR) contributed to this suppression. More specifically, we show that the suppression was mediated, at least in part, by a suspension culture-driven decrease in the levels of two members of the AP1 transcription factor complex, c-Jun and Fra2, that bind to the CRE element. Therefore, a microenvironmental change that is manifested during the initial stages of ovarian carcinoma dissemination may, potentially, help suppress BRCA1 expression in sporadic tumors and thus promote their progression.
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Affiliation(s)
- Lixin Zhou
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
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10
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MacDonald G, Stramwasser M, Mueller CR. Characterization of a negative transcriptional element in the BRCA1 promoter. Breast Cancer Res 2008; 9:R49. [PMID: 17663789 PMCID: PMC2206725 DOI: 10.1186/bcr1753] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Revised: 06/22/2007] [Accepted: 07/30/2007] [Indexed: 01/18/2023] Open
Abstract
Introduction Decreased transcription of the BRCA1 gene has previously been observed to occur in sporadic breast tumours, making elucidation of the mechanisms regulating the expression of this gene important for our understanding of the etiology of the disease. Methods Transcriptional elements involved in the regulation of the BRCA1 promoter were analysed by co-transfection experiments into the human MCF-7 and T-47D breast cancer cell lines. Results We have identified a repressor element, referred to as the UP site, within the proximal BRCA1 promoter whose inactivation results in increased promoter activity. An E2F recognition element, previously suggested to mediate repression via E2F-6, is adjacent to the UP site and its inactivation also leads to increased BRCA1 expression. These two elements appear to form a composite repressor element whose combined effect is additive. The UP element is composed of two sequences, one of which binds the ubiquitously expressed ets family transcription factor GABP alpha/beta. This site is distinct from a previously identified GABP alpha/beta site, the RIBS element, though the RIBS site appears to be necessary for derepression of the promoter via mutations in the UP site. Knockdown of GABP alpha using an shRNA vector confirms that this protein is important for the function of both the RIBS and UP sites. Conclusion The identification of a repressor element in the BRCA1 promoter brings a new level of complexity to the regulation of BRCA1 expression. The elements characterized here may play a normal role in the integration of a variety of signals, including two different growth related pathways, and it is possible that loss of the ability to derepress the BRCA1 promoter during critical periods may contribute to breast transformation.
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Affiliation(s)
- Gwen MacDonald
- Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada, K7L 3N6
- Department of Biochemistry, Queen's University, Kingston, Ontario, Canada, K7L 3N6
| | - Melissa Stramwasser
- Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada, K7L 3N6
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada, K7L 3N6
| | - Christopher R Mueller
- Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada, K7L 3N6
- Department of Biochemistry, Queen's University, Kingston, Ontario, Canada, K7L 3N6
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada, K7L 3N6
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Han K, Lee J, Meyer TJ, Wang J, Sen SK, Srikanta D, Liang P, Batzer MA. Alu recombination-mediated structural deletions in the chimpanzee genome. PLoS Genet 2007; 3:1939-49. [PMID: 17953488 PMCID: PMC2041999 DOI: 10.1371/journal.pgen.0030184] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Accepted: 09/07/2007] [Indexed: 12/02/2022] Open
Abstract
With more than 1.2 million copies, Alu elements are one of the most important sources of structural variation in primate genomes. Here, we compare the chimpanzee and human genomes to determine the extent of Alu recombination-mediated deletion (ARMD) in the chimpanzee genome since the divergence of the chimpanzee and human lineages (∼6 million y ago). Combining computational data analysis and experimental verification, we have identified 663 chimpanzee lineage-specific deletions (involving a total of ∼771 kb of genomic sequence) attributable to this process. The ARMD events essentially counteract the genomic expansion caused by chimpanzee-specific Alu inserts. The RefSeq databases indicate that 13 exons in six genes, annotated as either demonstrably or putatively functional in the human genome, and 299 intronic regions have been deleted through ARMDs in the chimpanzee lineage. Therefore, our data suggest that this process may contribute to the genomic and phenotypic diversity between chimpanzees and humans. In addition, we found four independent ARMD events at orthologous loci in the gorilla or orangutan genomes. This suggests that human orthologs of loci at which ARMD events have already occurred in other nonhuman primate genomes may be “at-risk” motifs for future deletions, which may subsequently contribute to human lineage-specific genetic rearrangements and disorders. The recent sequencing of a number of primate genomes shows that small segments of DNA known as Alu elements are found repeatedly along all chromosomes, and indeed comprise ∼10% of the human genome. Although older Alu elements that have been in the genome for a long time accumulate some random mutations, overall these elements retain high levels of sequence identity among themselves. The presence of many near-identical Alu elements located close to each other makes primate genomes prone to DNA recombination events that generate genomic deletions of varying sizes. Here, by scanning the chimpanzee genome for such deletions, we determined the role of the Alu recombination-mediated deletion process in creating structural differences between the chimpanzee and human genomes. Using a combination of computational and experimental techniques, we identified 663 deletions, involving the removal of ∼771 kb of genomic sequence. Interestingly, about half of these deletions were located within known or predicted genes, and in several cases, the deletions removed coding exons from chimpanzee genes as compared to their human counterparts. Alu recombination-mediated deletion shows signs of being a major sculptor of primate genomes and may be responsible for generating some of the genetic differences between humans and chimpanzees.
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Affiliation(s)
- Kyudong Han
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jungnam Lee
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Thomas J Meyer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jianxin Wang
- Department of Cancer Genetics, Roswell Park Cancer Institute, New York, United States of America
| | - Shurjo K Sen
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Deepa Srikanta
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Ping Liang
- Department of Cancer Genetics, Roswell Park Cancer Institute, New York, United States of America
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * To whom correspondence should be addressed. E-mail:
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Graves ML, Zhou L, MacDonald G, Mueller CR, Roskelley CD. Regulation of the BRCA1 promoter in ovarian surface epithelial cells and ovarian carcinoma cells. FEBS Lett 2007; 581:1825-33. [PMID: 17434164 DOI: 10.1016/j.febslet.2007.03.072] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Revised: 03/20/2007] [Accepted: 03/27/2007] [Indexed: 11/18/2022]
Abstract
As BRCA1 expression is often suppressed in sporadic ovarian carcinoma we characterized the regulation of the 231nt proximal 'L6' fragment of the BRCA1 promoter in two human ovarian surface epithelial cell and two sporadic ovarian carcinoma cell lines. Two individual regulatory elements within L6, the 'RIBS' element and the potential 'CRE' element were each necessary, but alone not sufficient for L6 activation in all four cell lines. The latter element showed some affinity for the CREB transcription factor, but cAMP pathway stimulation failed to promote its activation. This element did, however, interact with, and was activated by, c-Jun and Fra2 which suggests that it can interact with AP1-like transcription factors and that it may act co-operatively with RIBS-binding factors to regulate BRCA1 transcription in ovarian cells.
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Affiliation(s)
- Marcia L Graves
- Life Sciences Institute, Department of Cellular and Physiological Sciences, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3
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Scholzová E, Malík R, Sevcík J, Kleibl Z. RNA regulation and cancer development. Cancer Lett 2006; 246:12-23. [PMID: 16675105 DOI: 10.1016/j.canlet.2006.03.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Revised: 03/20/2006] [Accepted: 03/24/2006] [Indexed: 12/23/2022]
Abstract
Cancer is viewed as a genetic disease. According to the currently accepted model of carcinogenesis, several consequential mutations in oncogenes or tumor suppressor genes are necessary for cancer development. In this model, mutated DNA sequence is transcribed to mRNA that is finally translated into functionally aberrant protein. mRNA is viewed solely as an intermediate between DNA (with 'coding' potential) and protein (with 'executive' function). However, recent findings suggest that (m)RNA is actively regulated by a variety of processes including nonsense-mediated decay, alternative splicing, RNA editing or RNA interference. Moreover, RNA molecules can regulate a variety of cellular functions through interactions with RNA, DNA as well as protein molecules. Although, the precise contribution of RNA molecules by themselves and RNA-regulated processes on cancer development is currently unknown, recent data suggest their important role in carcinogenesis. Here, we summarize recent knowledge on RNA-related processes and discuss their potential role in cancer development.
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Affiliation(s)
- Eva Scholzová
- First Medical Faculty, Institute of Biochemistry and Experimental Oncology, Charles University, U Nemocnice 5, 128 53 Prague 2, Czech Republic.
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