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Ross C, Gong LY, Jenkins LM, Ha NH, Majocha M, Hunter KW. SMARCD1 is an essential expression-restricted metastasis modifier. Commun Biol 2024; 7:1299. [PMID: 39390150 PMCID: PMC11467182 DOI: 10.1038/s42003-024-07018-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 10/04/2024] [Indexed: 10/12/2024] Open
Abstract
Breast cancer is the most frequently diagnosed cancer worldwide, constituting 15% of cases in 2023. The predominant cause of breast cancer-related mortality is metastasis, and a lack of metastasis-targeted therapies perpetuates dismal outcomes for late-stage patients. By using meiotic genetics to study inherited transcriptional network regulation, we have identified, to the best of our knowledge, a new class of "essential expression-restricted" genes as potential candidates for metastasis-targeted therapeutics. Building upon previous work implicating the CCR4-NOT RNA deadenylase complex in metastasis, we demonstrate that RNA-binding proteins NANOS1, PUM2, and CPSF4 also regulate metastatic potential. Using various models and clinical data, we pinpoint Smarcd1 mRNA as a target of all three RNA-BPs. Strikingly, both high and low expression of Smarcd1 correlate with positive clinical outcomes, while intermediate expression significantly reduces the probability of survival. Applying the theory of "essential genes" from evolution, we identify 50 additional genes that require precise expression levels for metastasis to occur. Specifically, small perturbations in Smarcd1 expression significantly reduce metastasis in mouse models and alter splicing programs relevant to the ER+/HER2-enriched breast cancer. Identification subtype-specific essential expression-restricted metastasis modifiers introduces a novel class of genes that, when therapeutically "nudged" in either direction, may significantly improve late-stage breast cancer patients.
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Affiliation(s)
- Christina Ross
- Laboratory of Cancer Biology and Genetics, Metastasis Susceptibility Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Li-Yun Gong
- Laboratory of Cancer Biology and Genetics, Metastasis Susceptibility Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Guangdong Provincial Key Laboratory for Genome Stability and Disease Prevention, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Shenzhen University, 518060, Shenzhen, Guangdong, PR China
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Mass Spectrometry Resource, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Ngoc-Han Ha
- Laboratory of Cancer Biology and Genetics, Metastasis Susceptibility Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Megan Majocha
- Laboratory of Cancer Biology and Genetics, Metastasis Susceptibility Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Kent W Hunter
- Laboratory of Cancer Biology and Genetics, Metastasis Susceptibility Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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2
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Chen H, Pan Y, Lv C, He W, Wu D, Xuan Q. Telomere-related gene risk model for prognosis prediction in colorectal cancer. Transl Cancer Res 2024; 13:3495-3521. [PMID: 39145075 PMCID: PMC11319979 DOI: 10.21037/tcr-24-43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/02/2024] [Indexed: 08/16/2024]
Abstract
Background Colorectal cancer (CRC) is the third-most prevalent cancer globally. The biological significance of telomeres in CRC carcinogenesis and progression is underscored by accumulating data. Nevertheless, not much is known about how telomere-related genes (TRGs) affect CRC prognosis. Therefore, the aim of this study was to investigate the role of TRGs in CRC prognosis. Methods We retrospectively obtained the expression profiles and clinical data of CRC patients from public databases. Utilizing least absolute shrinkage and selection operator (LASSO) regression analysis, we created a telomere-related risk model to predict survival outcomes, identifying ten telomere-related differentially expressed genes (TRDEGs). Based on TRDEGs, we stratified patients from The Cancer Genome Atlas (TCGA) into low- and high-risk subsets. Subsequently, we conducted comprehensive analyses, including survival assessment, immune cell infiltration, drug sensitivity, and prediction of molecular interactions using Kaplan-Meier curves, ESTIMATE, CIBERSORT, OncoPredict, and other approaches. Results The model showed exceptional predictive accuracy for survival. Significant differences in survival were observed between the two groups of participants grouped according to the model (P<0.001), and this difference was further confirmed in the external validation set (GSE39582) (P=0.004). Additionally, compared to the low-risk group, the high-risk group exhibited significantly advanced tumor node metastasis (TNM) stages, lower proportions of activated CD4+ T cells, effector memory CD4+ T cells, and memory B cells, but increased ratios of M2 macrophages and regulatory T cells (Tregs), elevated tumor immune dysfunction and exclusion (TIDE) scores, and diminished sensitivity to dabrafenib, lapatinib, camptothecin, docetaxel, and telomerase inhibitor IX, reflecting the signature's capacity to distinguish clinical pathological characteristics, immune environment, and drug efficacy. Finally, we validated the expression of the ten TRDEGs (ACACB, TPX2, SRPX, PPARGC1A, CD36, MMP3, NAT2, MMP10, HIGD1A, and MMP1) through quantitative real-time polymerase chain reaction (qRT-PCR) and found that compared to normal cells, the expression levels of ACACB, HIGD1A, NAT2, PPARGC1A, and TPX2 in CRC cells were elevated, whereas those of CD36, SRPX, MMP1, MMP3, and MMP10 were reduced. Conclusions Overall, we constructed a telomere-related biomarker capable of predicting prognosis and treatment response in CRC individuals, offering potential guidance for drug therapy selection and prognosis prediction.
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Affiliation(s)
- Hao Chen
- Department of Medical Oncology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Yuhao Pan
- Department of Medical Oncology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Chenhui Lv
- Department of Medical Oncology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Wei He
- Department of Medical Oncology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Dingting Wu
- Department of Clinical Nutrition, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Qijia Xuan
- Department of Medical Oncology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
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Pena G, Rohrberg J, Goga A, Heald R. Changes in spindle morphology driven by TPX2 overexpression in MYC-driven breast cancer cells. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001182. [PMID: 38660563 PMCID: PMC11040394 DOI: 10.17912/micropub.biology.001182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/09/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
The MYC oncogene was previously shown to induce mitotic spindle defects, chromosome instability, and reliance on the microtubule-associated protein TPX2 to survive, but how TPX2 levels affect spindle morphology in cancer cells has not previously been examined in detail. We show that breast cancer cell lines expressing high levels of MYC and TPX2 possess shorter spindles with increased TPX2 localization at spindle poles. A similar effect was observed in non-transformed human RPE-1 cells compared to a tumor cell line (HeLa) that overexpresses MYC . These results demonstrate that TPX2 alters spindle length and morphology in cancer cells, which may contribute their ability to divide despite MYC-induced mitotic stress.
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Affiliation(s)
- Guadalupe Pena
- Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States
| | - Julia Rohrberg
- Medicine, University of California, San Francisco, San Francisco, California, United States
- Cell & Tissue Biology, University of California, San Francisco, San Francisco, California, United States
| | - Andrei Goga
- Medicine, University of California, San Francisco, San Francisco, California, United States
- Cell & Tissue Biology, University of California, San Francisco, San Francisco, California, United States
| | - Rebecca Heald
- Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States
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4
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Ross C, Gong LY, Jenkins LM, Ha NH, Majocha M, Hunter K. SMARCD1 is a "Goldilocks" metastasis modifier. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577061. [PMID: 38410477 PMCID: PMC10896335 DOI: 10.1101/2024.01.24.577061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Breast cancer is the most frequently diagnosed cancer worldwide, constituting around 15% of all diagnosed cancers in 2023. The predominant cause of breast cancer-related mortality is metastasis to distant essential organs, and a lack of metastasis-targeted therapies perpetuates dismal outcomes for late-stage patients. However, through our use of meiotic genetics to study inherited transcriptional network regulation, we have identified a new class of "Goldilocks" genes that are promising candidates for the development of metastasis-targeted therapeutics. Building upon previous work that implicated the CCR4-NOT RNA deadenylase complex in metastasis, we now demonstrate that the RNA-binding proteins (RNA-BPs) NANOS1, PUM2, and CPSF4 also regulate metastatic potential. Using cell lines, 3D culture, mouse models, and clinical data, we pinpoint Smarcd1 mRNA as a key target of all three RNA-BPs. Strikingly, both high and low expression of Smarcd1 is associated with positive clinical outcomes, while intermediate expression significantly reduces the probability of survival. Applying the theory of "essential genes" from evolution, we identify an additional 50 genes that span several cellular processes and must be maintained within a discrete window of expression for metastasis to occur. In the case of Smarcd1, small perturbations in its expression level significantly reduce metastasis in laboratory mouse models and alter splicing programs relevant to the ER+/HER2-enriched breast cancer subtype. The identification of subtype-specific "Goldilocks" metastasis modifier genes introduces a new class of genes and potential catalogue of novel targets that, when therapeutically "nudged" in either direction, may significantly improve late-stage patient outcomes.
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Affiliation(s)
- Christina Ross
- Laboratory of Cancer Biology and Genetics, Metastasis Susceptibility Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Li-Yun Gong
- Laboratory of Cancer Biology and Genetics, Metastasis Susceptibility Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
- Guangdong Provincial Key Laboratory for Genome Stability and Disease Prevention, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Shenzhen University, 518060, Shenzhen, Guangdong, P. R. China
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Mass Spectrometry Resource, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Ngoc-Han Ha
- Laboratory of Cancer Biology and Genetics, Metastasis Susceptibility Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Megan Majocha
- Laboratory of Cancer Biology and Genetics, Metastasis Susceptibility Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Kent Hunter
- Laboratory of Cancer Biology and Genetics, Metastasis Susceptibility Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
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5
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Zhu Q, Li M, Lu W, Wang Y, Li X, Cheng J. Transcriptomic Modulation Reveals the Specific Cellular Response in Chinese Sea Bass ( Lateolabrax maculatus) Gills under Salinity Change and Alkalinity Stress. Int J Mol Sci 2023; 24:ijms24065877. [PMID: 36982950 PMCID: PMC10056482 DOI: 10.3390/ijms24065877] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/27/2023] [Accepted: 03/12/2023] [Indexed: 03/30/2023] Open
Abstract
Salinity and alkalinity are among the important factors affecting the distribution, survival, growth and physiology of aquatic animals. Chinese sea bass (Lateolabrax maculatus) is an important aquaculture fish species in China that can widely adapt to diverse salinities from freshwater (FW) to seawater (SW) but moderately adapt to highly alkaline water (AW). In this study, juvenile L. maculatus were exposed to salinity change (SW to FW) and alkalinity stress (FW to AW). Coordinated transcriptomic responses in L. maculatus gills were investigated and based on the weighted gene co-expression network analysis (WGCNA), 8 and 11 stress-responsive modules (SRMs) were identified for salinity change and alkalinity stress, respectively, which revealed a cascade of cellular responses to oxidative and osmotic stress in L. maculatus gills. Specifically, four upregulated SRMs were enriched with induced differentially expressed genes (DEGs) for alkalinity stress, mainly corresponding to the functions of "extracellular matrix" and "anatomical structure", indicating a strong cellular response to alkaline water. Both "antioxidative activity" and "immune response" functions were enriched in the downregulated alkaline SRMs, which comprised inhibited alkaline specific DEGs, revealing the severely disrupted immune and antioxidative functions under alkalinity stress. These alkaline-specific responses were not revealed in the salinity change groups with only moderately inhibited osmoregulation and induced antioxidative response in L. maculatus gills. Therefore, the results revealed the diverse and correlated regulation of the cellular process and stress response in saline-alkaline water, which may have arisen through the functional divergence and adaptive recruitment of the co-expression genes and will provide vital insights for the development of L. maculatus cultivation in alkaline water.
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Affiliation(s)
- Qing Zhu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China
| | - Moli Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China
| | - Wei Lu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China
| | - Yapeng Wang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China
| | - Xujian Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China
| | - Jie Cheng
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Qingdao 266237, China
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Mosler T, Baymaz HI, Gräf JF, Mikicic I, Blattner G, Bartlett E, Ostermaier M, Piccinno R, Yang J, Voigt A, Gatti M, Pellegrino S, Altmeyer M, Luck K, Ahel I, Roukos V, Beli P. PARP1 proximity proteomics reveals interaction partners at stressed replication forks. Nucleic Acids Res 2022; 50:11600-11618. [PMID: 36350633 PMCID: PMC9723622 DOI: 10.1093/nar/gkac948] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022] Open
Abstract
PARP1 mediates poly-ADP-ribosylation of proteins on chromatin in response to different types of DNA lesions. PARP inhibitors are used for the treatment of BRCA1/2-deficient breast, ovarian, and prostate cancer. Loss of DNA replication fork protection is proposed as one mechanism that contributes to the vulnerability of BRCA1/2-deficient cells to PARP inhibitors. However, the mechanisms that regulate PARP1 activity at stressed replication forks remain poorly understood. Here, we performed proximity proteomics of PARP1 and isolation of proteins on stressed replication forks to map putative PARP1 regulators. We identified TPX2 as a direct PARP1-binding protein that regulates the auto-ADP-ribosylation activity of PARP1. TPX2 interacts with DNA damage response proteins and promotes homology-directed repair of DNA double-strand breaks. Moreover, TPX2 mRNA levels are increased in BRCA1/2-mutated breast and prostate cancers, and high TPX2 expression levels correlate with the sensitivity of cancer cells to PARP-trapping inhibitors. We propose that TPX2 confers a mitosis-independent function in the cellular response to replication stress by interacting with PARP1.
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Affiliation(s)
| | - H Irem Baymaz
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Justus F Gräf
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Ivan Mikicic
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | | | - Edward Bartlett
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | | | | | - Jiwen Yang
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Marco Gatti
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich CH-8057, Switzerland
| | - Stefania Pellegrino
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich CH-8057, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich CH-8057, Switzerland
| | - Katja Luck
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | | | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
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7
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Zhou S, Han Y, Yang R, Pi X, Li J. TIMM13 as a prognostic biomarker and associated with immune infiltration in skin cutaneous melanoma (SKCM). Front Surg 2022; 9:990749. [PMID: 36061054 PMCID: PMC9428353 DOI: 10.3389/fsurg.2022.990749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/01/2022] [Indexed: 11/21/2022] Open
Abstract
Objective Providing protection against aggregation and guiding hydrophobic precursors through the mitochondria’s intermembrane space, this protein functions as a chaperone-like protein. SLC25A12 is imported by TIMM8 as a result of its interaction with TIMM13. In spite of this, it is still unknown how TIMM13 interacts with skin cutaneous melanoma (SKCM) and tumor-infiltrating lymphocytes (TILs). Methods Aberrant expression of TIMM13 in SKCM and its clinical outcome was evaluated with the help of multiple databases, including the Xiantao tool (https://www.xiantao.love/), HPA, and UALCAN. TISIDB and Tumor Immune Estimation Resources (TIMER) databases were applied to explore the association between TIMM13 and tumor infiltration immune cells. OS nomogram was constructed, and model performance was examined. Finally, TIMM13 protein expression was validated by immunohistochemistry (IHC). Results TIMM13 expression was higher in SKCM samples than in peritumor samples. TIMM13 was strongly associated with sample type, subgroup, cancer stage, lymph node stage, and worse survival. Further, upregulation of TIMM13 was significantly associated with immunoregulators, and chemokines, as well as T cells, B cells, monocytes, neutrophils, macrophages, and T-cell regulators. An analysis of bioinformatic data uncovered that TIMM13 expression was strongly associated with PD1 (T-cell exhaustion marker). The nomogram showed good predictive performance based on calibration plot. TIMM13 was highly expressed in melanoma tissue samples than in normal samples. Conclusion In brief, TIMM13 may be a prognostic biomarker for SKCM. It might modulate the tumor immune microenvironment and lead to a poorer prognosis. In addition, it is necessary to study the targeted therapy of TIMM13.
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Affiliation(s)
- Sitong Zhou
- Department of Dermatology, The First People’s Hospital of Foshan, Foshan, China
| | - Yuanyuan Han
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China
| | - Ronghua Yang
- Department of Burn and Plastic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
- Correspondence: Jiehua Li Xiaobing Pi Ronghua Yang
| | - Xiaobing Pi
- Department of Dermatology, The First People’s Hospital of Foshan, Foshan, China
- Correspondence: Jiehua Li Xiaobing Pi Ronghua Yang
| | - Jiehua Li
- Department of Dermatology, The First People’s Hospital of Foshan, Foshan, China
- Correspondence: Jiehua Li Xiaobing Pi Ronghua Yang
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8
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Ding FP, Tian JY, Wu J, Han DF, Zhao D. Identification of key genes as predictive biomarkers for osteosarcoma metastasis using translational bioinformatics. Cancer Cell Int 2021; 21:640. [PMID: 34856991 PMCID: PMC8638136 DOI: 10.1186/s12935-021-02308-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/31/2021] [Indexed: 11/30/2022] Open
Abstract
Background Osteosarcoma (OS) metastasis is the most common cause of cancer-related mortality, however, no sufficient clinical biomarkers have been identified. In this study, we identified five genes to help predict metastasis at diagnosis. Methods We performed weighted gene co-expression network analysis (WGCNA) to identify the most relevant gene modules associated with OS metastasis. An important machine learning algorithm, the support vector machine (SVM), was employed to predict key genes for classifying the OS metastasis phenotype. Finally, we investigated the clinical significance of key genes and their enriched pathways. Results Eighteen modules were identified in WGCNA, among which the pink, red, brown, blue, and turquoise modules demonstrated good preservation. In the five modules, the brown and red modules were highly correlated with OS metastasis. Genes in the two modules closely interacted in protein–protein interaction networks and were therefore chosen for further analysis. Genes in the two modules were primarily enriched in the biological processes associated with tumorigenesis and development. Furthermore, 65 differentially expressed genes were identified as common hub genes in both WGCNA and protein–protein interaction networks. SVM classifiers with the maximum area under the curve were based on 30 and 15 genes in the brown and red modules, respectively. The clinical significance of the 45 hub genes was analyzed. Of the 45 genes, 17 were found to be significantly correlated with survival time. Finally, 5/17 genes, including ADAP2 (P = 0.0094), LCP2 (P = 0.013), ARHGAP25 (P = 0.0049), CD53 (P = 0.016), and TLR7 (P = 0.04) were significantly correlated with the metastatic phenotype. In vitro verification, western blotting, wound healing analyses, transwell invasion assays, proliferation assays, and colony formation assays indicated that ARHGAP25 promoted OS cell migration, invasion, proliferation, and epithelial–mesenchymal transition. Conclusion We identified five genes, namely ADAP2, LCP2, ARHGAP25, CD53, and TLR7, as candidate biomarkers for the prediction of OS metastasis; ARHGAP25 inhibits MG63 OS cell growth, migration, and invasion in vitro, indicating that ARHGAP25 can serve as a promising specific and prognostic biomarker for OS metastasis. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02308-w.
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Affiliation(s)
- Fu-Peng Ding
- Department of Orthopedics Surgery, The First Hospital of Jilin University, Changchun, 130021, China
| | - Jia-Yi Tian
- Department of Reproductive Medicine and Center for Prenatal Diagnosis, The First Hospital of Jilin University, Changchun, 130000, China
| | - Jing Wu
- Department of General Practice, The First Hospital of Jilin University, Changchun, 130000, China
| | - Dong-Feng Han
- Department of Emergency Medicine, The First Hospital of Jilin University, Changchun, 130021, China.
| | - Ding Zhao
- Department of Orthopedics Surgery, The First Hospital of Jilin University, Changchun, 130021, China.
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9
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Malvezzi F, Stubbs CJ, Jowitt TA, Dale IL, Guo X, DeGnore JP, Degliesposti G, Skehel JM, Bannister AJ, McAlister MS. Phosphorylation-dependent BRD4 dimerization and implications for therapeutic inhibition of BET family proteins. Commun Biol 2021; 4:1273. [PMID: 34754068 PMCID: PMC8578508 DOI: 10.1038/s42003-021-02750-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/27/2021] [Indexed: 01/12/2023] Open
Abstract
Bromodomain-containing protein 4 (BRD4) is an epigenetic reader and oncology drug target that regulates gene transcription through binding to acetylated chromatin via bromodomains. Phosphorylation by casein kinase II (CK2) regulates BRD4 function, is necessary for active transcription and is involved in resistance to BRD4 drug inhibition in triple-negative breast cancer. Here, we provide the first biophysical analysis of BRD4 phospho-regulation. Using integrative structural biology, we show that phosphorylation by CK2 modulates the dimerization of human BRD4. We identify two conserved regions, a coiled-coil motif and the Basic-residue enriched Interaction Domain (BID), essential for the BRD4 structural rearrangement, which we term the phosphorylation-dependent dimerization domain (PDD). Finally, we demonstrate that bivalent inhibitors induce a conformational change within BRD4 dimers in vitro and in cancer cells. Our results enable the proposal of a model for BRD4 activation critical for the characterization of its protein-protein interaction network and for the development of more specific therapeutics.
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Affiliation(s)
- Francesca Malvezzi
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Molecular Partners AG, Schlieren, Switzerland
| | - Christopher J Stubbs
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Thomas A Jowitt
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - Ian L Dale
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Xieyang Guo
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jon P DeGnore
- Mechanistic Biology & Profiling, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Boston, USA
| | - Gianluca Degliesposti
- Biological Mass Spectrometry and Proteomics, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - J Mark Skehel
- Biological Mass Spectrometry and Proteomics, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Andrew J Bannister
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - Mark S McAlister
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
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10
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El-Masry OS, Goja A, Rateb M, Owaidah AY, Alsamman K. RNA sequencing identified novel target genes for Adansonia digitata in breast and colon cancer cells. Sci Prog 2021; 104:368504211032084. [PMID: 34251294 PMCID: PMC10450698 DOI: 10.1177/00368504211032084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Adansonia digitata exhibits numerous beneficial effects. In the current study, we investigated the anti-cancer effects of four different extracts of A. digitata (polar and non-polar extracts of fruit powder and fibers) on the proliferation of human colon cancer (HCT116), human breast cancer (MCF-7), and human ovarian cancer (OVCAR-3 and OVCAR-4) cell lines. RNA sequencing revealed the influence of the effective A. digitata fraction on the gene expression profiles of responsive cells. The results indicated that only the polar extract of the A. digitata fibers exhibited anti-proliferative activities against HCT116 and MCF-7 cells, but not ovarian cancer cells. Moreover, the polar extract of the fibers resulted in the modulation of the expression of multiple genes in HCT116 and MCF-7 cells. We propose that casein kinase 2 alpha 3 (CSNK2A3) is a novel casein kinase 2 (CSNK2) isoform in HCT116 cells and report, for the first time, the potential involvement of FYVE, RhoGEF, and PH domain-containing 3 (FGD3) in colon cancer. Together, these findings provide evidence supporting the anti-cancer potential of the polar extract of A. digitata fibers in this experimental model of breast and colon cancers.
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Affiliation(s)
- Omar S. El-Masry
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Arafat Goja
- Department of Clinical Nutrition, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mostafa Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley, UK
- Marine Biodiscovery Centre, School of Natural & Computing Sciences, University of Aberdeen, Aberdeen, UK
| | - Amani Y Owaidah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Khaldoon Alsamman
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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11
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Deciphering the nexus between the tumor immune microenvironment and DNA methylation in subgrouping estrogen receptor-positive breast cancer. Breast Cancer 2021; 28:1252-1260. [PMID: 33966175 DOI: 10.1007/s12282-021-01262-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/06/2021] [Indexed: 01/15/2023]
Abstract
BACKGROUND Based on variable DNA methylation (DNAm), estrogen receptor (ER)-positive breast cancer (BRCA) is composed of two major subtypes, with the hypomethylated subgroup displaying good survival. Evidence indicates that the tumor microenvironment (TME) plays an important role in tumor progression and metastasis; however, its role and biological characteristics in DNAm-based subtypes of ER-positive BRCA remain largely unknown. METHODS Transcriptome data and matched clinical information of BRCA were downloaded from the Cancer Genome Atlas. Immune (ISs) and stromal scores (SSs) of BRCA patients were calculated using the ESTIMATE algorithm. Inferred fractions of 22 types of infiltrating immune cells of BRCA were collected from the Cancer Immunome Atlas. RESULTS The hypomethylated ER-positive BRCA subtype displayed high ISs, echoing the finding that higher ISs are associated with good BRCA survival. In addition, we analyzed the differentially expressed genes between the hypo-high-IS and hyper-low-IS BRCA subtypes in ER-positive patients and identified a co-expressed gene module (i.e., red module) enriched in immune-related biological processes (e.g., leukocyte activation involved in immune response). Moreover, four hub genes (i.e., PLEK, CD53, EVI2B, and CD4) in this module showed significant association between their expression and ER-positive BRCA survival. CONCLUSIONS We found differences in the tumor immune microenvironment (TIME) between DNAm-based BRCA subgroups in ER-positive patients and identified a specific module and hub genes involved to these differences. These findings elucidate the immunological basis for ER-positive BRCA progression and classification and provide potential gene biomarkers and targets for ER-positive BRCA diagnosis and treatment.
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12
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Marchetti P, Antonov A, Anemona L, Vangapandou C, Montanaro M, Botticelli A, Mauriello A, Melino G, Catani MV. New immunological potential markers for triple negative breast cancer: IL18R1, CD53, TRIM, Jaw1, LTB, PTPRCAP. Discov Oncol 2021; 12:6. [PMID: 35201443 PMCID: PMC8777524 DOI: 10.1007/s12672-021-00401-0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/22/2021] [Indexed: 12/31/2022] Open
Abstract
Breast cancer (BC) is the second leading cause of cancer death in women worldwide, and settings of specific prognostic factors and efficacious therapies are made difficult by phenotypic heterogeneity of BC subtypes. Therefore, there is a current urgent need to define novel predictive genetic predictors that may be useful for stratifying patients with distinct prognostic outcomes. Here, we looked for novel molecular signatures for triple negative breast cancers (TNBCs). By a bioinformatic approach, we identified a panel of genes, whose expression was positively correlated with disease-free survival in TNBC patients, namely IL18R1, CD53, TRIM, Jaw1, LTB, and PTPRCAP, showing specific immune expression profiles linked to survival prediction; most of these genes are indeed expressed in immune cells and are required for productive lymphocyte activation. According to our hypothesis, these genes were not, or poorly, expressed in different TNBC cell lines, derived from either primary breast tumours or metastatic pleural effusions. This conclusion was further supported in vivo, as immuno-histochemical analysis on biopsies of TNBC invasive ductal carcinomas highlighted differential expression of these six genes in cancer cells, as well as in intra- and peri-tumoral infiltrating lymphocytes. Our data open to the possibility that inter-tumour heterogeneity of immune markers might have predictive value; further investigations are recommended in order to establish the real power of cancer-related immune profiles as prognostic factors.
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Affiliation(s)
- Paolo Marchetti
- Oncology Unit, Department of Clinical and Molecular Medicine, University of Rome La Sapienza, 00185 Rome, Italy
| | - Alexey Antonov
- MRC Toxicology Unit, University of Cambridge, Cambridge, CB2 1QR UK
| | - Lucia Anemona
- Department of Experimental Medicine, Torvergata Oncoscience Research (TOR), University of Rome Tor Vergata, via Montpellier 1, 00133 Rome, Italy
| | - Chaitania Vangapandou
- Department of Experimental Medicine, Torvergata Oncoscience Research (TOR), University of Rome Tor Vergata, via Montpellier 1, 00133 Rome, Italy
| | - Manuela Montanaro
- Department of Experimental Medicine, Torvergata Oncoscience Research (TOR), University of Rome Tor Vergata, via Montpellier 1, 00133 Rome, Italy
| | - Andrea Botticelli
- Oncology Unit, Department of Clinical and Molecular Medicine, University of Rome La Sapienza, 00185 Rome, Italy
| | - Alessandro Mauriello
- Department of Experimental Medicine, Torvergata Oncoscience Research (TOR), University of Rome Tor Vergata, via Montpellier 1, 00133 Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, Torvergata Oncoscience Research (TOR), University of Rome Tor Vergata, via Montpellier 1, 00133 Rome, Italy
| | - M. Valeria Catani
- Department of Experimental Medicine, Torvergata Oncoscience Research (TOR), University of Rome Tor Vergata, via Montpellier 1, 00133 Rome, Italy
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13
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Matson DR, Denu RA, Zasadil LM, Burkard ME, Weaver BA, Flynn C, Stukenberg PT. High nuclear TPX2 expression correlates with TP53 mutation and poor clinical behavior in a large breast cancer cohort, but is not an independent predictor of chromosomal instability. BMC Cancer 2021; 21:186. [PMID: 33622270 PMCID: PMC7901195 DOI: 10.1186/s12885-021-07893-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/08/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Targeting Protein for Xenopus Kinesin Like Protein 2 (TPX2) is a microtubule associated protein that functions in mitotic spindle assembly. TPX2 also localizes to the nucleus where it functions in DNA damage repair during S-phase. We and others have previously shown that TPX2 RNA levels are strongly associated with chromosomal instability (CIN) in breast and other cancers, and TPX2 RNA levels have been demonstrated to correlate with aggressive behavior and poor clinical outcome across a range of solid malignancies, including breast cancer. METHODS We perform TPX2 IHC on a cohort of 253 primary breast cancers and adopt a clinically amenable scoring system to separate tumors into low, intermediate, or high TPX2 expression. We then correlate TPX2 expression against diverse pathologic parameters and important measures of clinical outcome, including disease-specific and overall survival. We link TPX2 expression to TP53 mutation and evaluate whether TPX2 is an independent predictor of chromosomal instability (CIN). RESULTS We find that TPX2 nuclear expression strongly correlates with high grade morphology, elevated clinical stage, negative ER and PR status, and both disease-specific and overall survival. We also show that increased TPX2 nuclear expression correlates with elevated ploidy, supernumerary centrosomes, and TP53 mutation. TPX2 nuclear expression correlates with CIN via univariate analyses but is not independently predictive when compared to ploidy, Ki67, TP53 mutational status, centrosome number, and patient age. CONCLUSIONS Our findings demonstrate a strong correlation between TPX2 nuclear expression and aggressive tumor behavior, and show that TPX2 overexpression frequently occurs in the setting of TP53 mutation and elevated ploidy. However, TPX2 expression is not an independent predictor of CIN where it fails to outperform existing clinical and pathologic metrics.
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Affiliation(s)
- Daniel R Matson
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792, USA.
| | - Ryan A Denu
- Department of Medicine, University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Lauren M Zasadil
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark E Burkard
- Department of Medicine, University of Wisconsin Hospitals and Clinics, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Beth A Weaver
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Christopher Flynn
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792, USA
| | - P Todd Stukenberg
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
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14
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Liu F, Dong H, Mei Z, Huang T. Investigation of miRNA and mRNA Co-expression Network in Ependymoma. Front Bioeng Biotechnol 2020; 8:177. [PMID: 32266223 PMCID: PMC7096354 DOI: 10.3389/fbioe.2020.00177] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/20/2020] [Indexed: 12/18/2022] Open
Abstract
Ependymoma (EPN) is a rare primary tumor of the central nervous system (CNS) that affects both children and adults. Despite the definition and classification of distinct molecular subgroups, there remains a group of EPNs with a balanced genome, which makes it difficult to predict a prognosis of patients with EPN. The role of miRNA-mRNA network on EPN is still poorly understood. We assessed the involvement of miRNA-mRNA pairs in EPN by applying a weighted co-expression network analysis (WGCNA) approach. Using whole genome expression profile analysis followed by functional enrichment, we detected hub genes involved in active proliferation and DNA replication of nerve cells. Key genes including CYP11B1, KRT33B, RUNX1T1, SIK1, MAP3K4, MLANA, and SFRP5 identified in co-expression networks were regulated by miR-15a and miR-24-1. These seven miRNA-mRNA pairs were considered to influence not only pathways in cancer and tumor suppression process, but also MAPK, NF-kappaB, and WNT signaling pathways which were associated with tumorigenesis and development. This study provides a novel insight into potential diagnostic biomarkers of EPN and may have value in choosing therapeutic targets with clinical utility.
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Affiliation(s)
- Feili Liu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Hang Dong
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zi Mei
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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15
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Rohrberg J, Van de Mark D, Amouzgar M, Lee JV, Taileb M, Corella A, Kilinc S, Williams J, Jokisch ML, Camarda R, Balakrishnan S, Shankar R, Zhou A, Chang AN, Chen B, Rugo HS, Dumont S, Goga A. MYC Dysregulates Mitosis, Revealing Cancer Vulnerabilities. Cell Rep 2020; 30:3368-3382.e7. [PMID: 32160543 PMCID: PMC7085414 DOI: 10.1016/j.celrep.2020.02.041] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 11/18/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022] Open
Abstract
Tumors that overexpress the MYC oncogene are frequently aneuploid, a state associated with highly aggressive cancers and tumor evolution. However, how MYC causes aneuploidy is not well understood. Here, we show that MYC overexpression induces mitotic spindle assembly defects and chromosomal instability (CIN) through effects on microtubule nucleation and organization. Attenuating MYC expression reverses mitotic defects, even in established tumor cell lines, indicating an ongoing role for MYC in CIN. MYC reprograms mitotic gene expression, and we identify TPX2 to be permissive for spindle assembly in MYC-high cells. TPX2 depletion blocks mitotic progression, induces cell death, and prevents tumor growth. Further elevating TPX2 expression reduces mitotic defects in MYC-high cells. MYC and TPX2 expression may be useful biomarkers to stratify patients for anti-mitotic therapies. Our studies implicate MYC as a regulator of mitosis and suggest that blocking MYC activity can attenuate the emergence of CIN and tumor evolution.
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Affiliation(s)
- Julia Rohrberg
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, CA, USA.
| | - Daniel Van de Mark
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Meelad Amouzgar
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Joyce V Lee
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Moufida Taileb
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Alexandra Corella
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Seda Kilinc
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Jeremy Williams
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Marie-Lena Jokisch
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Roman Camarda
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Sanjeev Balakrishnan
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Rama Shankar
- Department of Pediatrics and Human Development and Department of Pharmacology and Toxicology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Alicia Zhou
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Bin Chen
- Department of Pediatrics and Human Development and Department of Pharmacology and Toxicology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Hope S Rugo
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sophie Dumont
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Andrei Goga
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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16
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Pang L, Hu J, Li F, Yuan H, Yan M, Liao G, Xu L, Pang B, Ping Y, Xiao Y, Li X. Discovering Rare Genes Contributing to Cancer Stemness and Invasive Potential by GBM Single-Cell Transcriptional Analysis. Cancers (Basel) 2019; 11:E2025. [PMID: 31888172 PMCID: PMC6966673 DOI: 10.3390/cancers11122025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 12/12/2022] Open
Abstract
Single-cell RNA sequencing presents the sophisticated delineation of cell transcriptomes in many cancer types and highlights the tumor heterogeneity at higher resolution, which provides a new chance to explore the molecular mechanism in a minority of cells. In this study, we utilized publicly available single-cell RNA-seq data to discover and comprehensively dissect rare genes existing in few glioblastoma (GBM) cells. Moreover, we designed a framework to systematically identify 51 rare protein-coding genes (PCGs) and 47 rare long non-coding RNAs (lncRNAs) in GBM. Patients with high expression levels of rare genes like CYB5R2 and TPPP3 had worse overall survival and disease-free survival, implying their potential implication in GBM progression and prognosis. We found that these rare genes tended to be specifically expressed in GBM cancer stem cells, which emphasized their ability to characterize stem-like cancer cells and implied their contribution to GBM growth. Furthermore, rare genes were enriched in a 17-cell subset, which was located in an individual branch of the pseudotime trajectory of cancer progression and exhibited high cell cycle activity and invasive potential. Our study captures the rare genes highly expressed in few cells, deepens our understanding of special states during GBM tumorigenesis and progression such as cancer stemness and invasion, and proposes potential targets for cancer therapy.
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Affiliation(s)
- Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (L.P.); (J.H.); (F.L.); (H.Y.); (M.Y.); (G.L.); (L.X.); (B.P.); (Y.P.)
| | - Jing Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (L.P.); (J.H.); (F.L.); (H.Y.); (M.Y.); (G.L.); (L.X.); (B.P.); (Y.P.)
| | - Feng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (L.P.); (J.H.); (F.L.); (H.Y.); (M.Y.); (G.L.); (L.X.); (B.P.); (Y.P.)
| | - Huating Yuan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (L.P.); (J.H.); (F.L.); (H.Y.); (M.Y.); (G.L.); (L.X.); (B.P.); (Y.P.)
| | - Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (L.P.); (J.H.); (F.L.); (H.Y.); (M.Y.); (G.L.); (L.X.); (B.P.); (Y.P.)
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (L.P.); (J.H.); (F.L.); (H.Y.); (M.Y.); (G.L.); (L.X.); (B.P.); (Y.P.)
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (L.P.); (J.H.); (F.L.); (H.Y.); (M.Y.); (G.L.); (L.X.); (B.P.); (Y.P.)
| | - Bo Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (L.P.); (J.H.); (F.L.); (H.Y.); (M.Y.); (G.L.); (L.X.); (B.P.); (Y.P.)
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (L.P.); (J.H.); (F.L.); (H.Y.); (M.Y.); (G.L.); (L.X.); (B.P.); (Y.P.)
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (L.P.); (J.H.); (F.L.); (H.Y.); (M.Y.); (G.L.); (L.X.); (B.P.); (Y.P.)
- Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin 150086, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (L.P.); (J.H.); (F.L.); (H.Y.); (M.Y.); (G.L.); (L.X.); (B.P.); (Y.P.)
- Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin 150086, China
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18
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Jia Y, Xiao Z, Gongsun X, Xin Z, Shang B, Chen G, Wang Z, Jiang W. CEP55 promotes the proliferation, migration and invasion of esophageal squamous cell carcinoma via the PI3K/Akt pathway. Onco Targets Ther 2018; 11:4221-4232. [PMID: 30050313 PMCID: PMC6055835 DOI: 10.2147/ott.s168861] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background Centrosomal protein 55 (CEP55) is an important prognostic biomarker that plays an essential role in the proliferation, migration and invasion of multiple tumors. We aimed to investigate the prognostic value of CEP55 in pN0 esophageal squamous cell carcinoma (ESCC) and explore its biological function in ESCC cells. Methods We used immunohistochemistry and Western blot analysis to detect the expression of CEP55 in ESCC. Furthermore, both in vitro and in vivo assays were used to determine the effect of CEP55 on malignant behavior in ESCC cells. Results As expected, we found that CEP55 was overexpressed in ESCC. Univariate and multivariate analyses demonstrated that patients with CEP55 overexpression had a poor prognosis. Additionally, the abilities of proliferation, migration and invasion of cells, as well as the epithelial–mesenchymal transition markers, were all altered with the changed CEP55 expression levels in ESCC cells. Further study elucidated that CEP55 facilitated ESCC via the PI3K/Akt pathway. Blockade of this pathway markedly attenuated CEP55-mediated proliferation, migration, invasion and epithelial–mesenchymal transition of ESCC cells. Conclusion Oncogenic CEP55 correlates with a poor prognosis by regulating tumor cell proliferation, migration and invasion via the PI3K/Akt pathway. It can serve as a promising prognostic biomarker and therapeutic target of pN0 ESCC after Ivor-Lewis esophagectomy.
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Affiliation(s)
- Yang Jia
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China,
| | - Zhaohua Xiao
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China,
| | - Xin Gongsun
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China,
| | - Zhongwei Xin
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China,
| | - Bin Shang
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China,
| | - Gang Chen
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China,
| | - Zhou Wang
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China,
| | - Wenpeng Jiang
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China,
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19
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Zhao J, Cheng F, Jia P, Cox N, Denny JC, Zhao Z. An integrative functional genomics framework for effective identification of novel regulatory variants in genome-phenome studies. Genome Med 2018; 10:7. [PMID: 29378629 PMCID: PMC5789733 DOI: 10.1186/s13073-018-0513-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 01/04/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Genome-phenome studies have identified thousands of variants that are statistically associated with disease or traits; however, their functional roles are largely unclear. A comprehensive investigation of regulatory mechanisms and the gene regulatory networks between phenome-wide association study (PheWAS) and genome-wide association study (GWAS) is needed to identify novel regulatory variants contributing to risk for human diseases. METHODS In this study, we developed an integrative functional genomics framework that maps 215,107 significant single nucleotide polymorphism (SNP) traits generated from the PheWAS Catalog and 28,870 genome-wide significant SNP traits collected from the GWAS Catalog into a global human genome regulatory map via incorporating various functional annotation data, including transcription factor (TF)-based motifs, promoters, enhancers, and expression quantitative trait loci (eQTLs) generated from four major functional genomics databases: FANTOM5, ENCODE, NIH Roadmap, and Genotype-Tissue Expression (GTEx). In addition, we performed a tissue-specific regulatory circuit analysis through the integration of the identified regulatory variants and tissue-specific gene expression profiles in 7051 samples across 32 tissues from GTEx. RESULTS We found that the disease-associated loci in both the PheWAS and GWAS Catalogs were significantly enriched with functional SNPs. The integration of functional annotations significantly improved the power of detecting novel associations in PheWAS, through which we found a number of functional associations with strong regulatory evidence in the PheWAS Catalog. Finally, we constructed tissue-specific regulatory circuits for several complex traits: mental diseases, autoimmune diseases, and cancer, via exploring tissue-specific TF-promoter/enhancer-target gene interaction networks. We uncovered several promising tissue-specific regulatory TFs or genes for Alzheimer's disease (e.g. ZIC1 and STX1B) and asthma (e.g. CSF3 and IL1RL1). CONCLUSIONS This study offers powerful tools for exploring the functional consequences of variants generated from genome-phenome association studies in terms of their mechanisms on affecting multiple complex diseases and traits.
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Affiliation(s)
- Junfei Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Feixiong Cheng
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Center for Complex Networks Research, Northeastern University, Boston, MA, 02215, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Nancy Cox
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Joshua C Denny
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA.
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
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20
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Brinker AE, Vivian CJ, Koestler DC, Tsue TT, Jensen RA, Welch DR. Mitochondrial Haplotype Alters Mammary Cancer Tumorigenicity and Metastasis in an Oncogenic Driver-Dependent Manner. Cancer Res 2017; 77:6941-6949. [PMID: 29070615 DOI: 10.1158/0008-5472.can-17-2194] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/20/2017] [Accepted: 10/19/2017] [Indexed: 12/13/2022]
Abstract
Using a novel mouse model, a mitochondrial-nuclear exchange model termed MNX, we tested the hypothesis that inherited mitochondrial haplotypes alter primary tumor latency and metastatic efficiency. Male FVB/N-Tg(MMTVneu)202Mul/J (Her2) transgenic mice were bred to female MNX mice having FVB/NJ nuclear DNA with either FVB/NJ, C57BL/6J, or BALB/cJ mtDNA. Pups receiving the C57BL/6J or BALB/cJ mitochondrial genome (i.e., females crossed with Her2 males) showed significantly (P < 0.001) longer tumor latency (262 vs. 293 vs. 225 days), fewer pulmonary metastases (5 vs. 7 vs. 15), and differences in size of lung metastases (1.2 vs. 1.4 vs. 1.0 mm diameter) compared with FVB/NJ mtDNA. Although polyoma virus middle T-driven tumors showed altered primary and metastatic profiles in previous studies, depending upon nuclear and mtDNA haplotype, the magnitude and direction of changes were not the same in the HER2-driven mammary carcinomas. Collectively, these results establish mitochondrial polymorphisms as quantitative trait loci in mammary carcinogenesis, and they implicate distinct interactions between tumor drivers and mitochondria as critical modifiers of tumorigenicity and metastasis. Cancer Res; 77(24); 6941-9. ©2017 AACR.
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Affiliation(s)
- Amanda E Brinker
- Department of Cancer Biology, The University of Kansas Medical Center, Kansas City, Kansas.,Department of Molecular and Integrative Physiology, The University of Kansas Medical Center, Kansas City, Kansas.,Heartland Center for Mitochondrial Medicine, The University of Kansas Medical Center, Kansas City, Kansas
| | - Carolyn J Vivian
- Department of Cancer Biology, The University of Kansas Medical Center, Kansas City, Kansas.,Heartland Center for Mitochondrial Medicine, The University of Kansas Medical Center, Kansas City, Kansas
| | - Devin C Koestler
- Department of Biostatistics, The University of Kansas Medical Center, Kansas City, Kansas.,The University Kansas Cancer Center, The University of Kansas Medical Center, Kansas City, Kansas
| | - Trevor T Tsue
- Department of Cancer Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Roy A Jensen
- The University Kansas Cancer Center, The University of Kansas Medical Center, Kansas City, Kansas.,Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, Kansas
| | - Danny R Welch
- Department of Cancer Biology, The University of Kansas Medical Center, Kansas City, Kansas. .,Department of Molecular and Integrative Physiology, The University of Kansas Medical Center, Kansas City, Kansas.,Heartland Center for Mitochondrial Medicine, The University of Kansas Medical Center, Kansas City, Kansas.,The University Kansas Cancer Center, The University of Kansas Medical Center, Kansas City, Kansas
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21
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Conrad RJ, Fozouni P, Thomas S, Sy H, Zhang Q, Zhou MM, Ott M. The Short Isoform of BRD4 Promotes HIV-1 Latency by Engaging Repressive SWI/SNF Chromatin-Remodeling Complexes. Mol Cell 2017; 67:1001-1012.e6. [PMID: 28844864 DOI: 10.1016/j.molcel.2017.07.025] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 05/24/2017] [Accepted: 07/25/2017] [Indexed: 11/18/2022]
Abstract
BET proteins commonly activate cellular gene expression, yet inhibiting their recruitment paradoxically reactivates latent HIV-1 transcription. Here we identify the short isoform of BET family member BRD4 (BRD4S) as a corepressor of HIV-1 transcription. We found that BRD4S was enriched in chromatin fractions of latently infected T cells, and it was more rapidly displaced from chromatin upon BET inhibition than the long isoform. BET inhibition induced marked nucleosome remodeling at the latent HIV-1 promoter, which was dependent on the activity of BRG1-associated factors (BAF), an SWI/SNF chromatin-remodeling complex with known repressive functions in HIV-1 transcription. BRD4S directly bound BRG1, a catalytic subunit of BAF, via its bromodomain and extraterminal (ET) domain, and this isoform was necessary for BRG1 recruitment to latent HIV-1 chromatin. Using chromatin immunoprecipitation sequencing (ChIP-seq) combined with assay for transposase-accessible chromatin coupled to high-throughput sequencing (ATAC-seq) data, we found that the latent HIV-1 promoter phenotypically resembles endogenous long terminal repeat (LTR) sequences, pointing to a select role of BRD4S-BRG1 complexes in genomic silencing of invasive retroelements.
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Affiliation(s)
- Ryan J Conrad
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158, USA; Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Parinaz Fozouni
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sean Thomas
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hendrik Sy
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Qiang Zhang
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Melanie Ott
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158, USA; Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA.
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22
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Espinal-Enríquez J, Fresno C, Anda-Jáuregui G, Hernández-Lemus E. RNA-Seq based genome-wide analysis reveals loss of inter-chromosomal regulation in breast cancer. Sci Rep 2017; 7:1760. [PMID: 28496157 PMCID: PMC5431987 DOI: 10.1038/s41598-017-01314-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 03/27/2017] [Indexed: 12/21/2022] Open
Abstract
Breast cancer is a complex heterogeneous disease. Common hallmark features of cancer can be found. Their origin may be traced back to their intricate relationships governing regulatory programs during the development of this disease. To unveil distinctive features of the transcriptional regulation program in breast cancer, a pipeline for RNA-seq analysis in 780 breast cancer and 101 healthy breast samples, at gene expression and network level, was implemented. Inter-chromosomal relationships between genes resulted strikingly scarce in a cancer network, in comparison to its healthy counterpart. We suggest that inter-chromosomal regulation loss may be a novel feature in breast cancer. Additional evidence was obtained by independent validation in microarray and Hi-C data as well as supplementary computational analyses. Functional analysis showed upregulation in processes related to cell cycle and division; while migration, adhesion and cell-to-cell communication, were downregulated. Both the BRCA1 DNA repairing signalling and the Estrogen-mediated G1/S phase entry pathways were found upregulated. In addition, a synergistic underexpression of the γ-protocadherin complex, located at Chr5q31 is also shown. This region has previously been reported to be hypermethylated in breast cancer. These findings altogether provide further evidence for the central role of transcriptional regulatory programs in shaping malignant phenotypes.
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Affiliation(s)
- Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine (INMEGEN), 14610, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México (UNAM), 04510, Mexico City, Mexico
| | - Cristóbal Fresno
- Computational Genomics Division, National Institute of Genomic Medicine (INMEGEN), 14610, Mexico City, Mexico
- UA AREA CS. AGR. ING. BIO Y S, CONICET - Universidad Católica de Córdoba, Córdoba, Argentina
| | - Guillermo Anda-Jáuregui
- Computational Genomics Division, National Institute of Genomic Medicine (INMEGEN), 14610, Mexico City, Mexico
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Rd Stop 9061, Grand Forks, ND, 58203, USA
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine (INMEGEN), 14610, Mexico City, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México (UNAM), 04510, Mexico City, Mexico.
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23
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Buckberry S, Bianco-Miotto T, Bent SJ, Clifton V, Shoubridge C, Shankar K, Roberts CT. Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation. BMC Genomics 2017; 18:10. [PMID: 28049421 PMCID: PMC5209944 DOI: 10.1186/s12864-016-3384-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 12/07/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Mammalian development in utero is absolutely dependent on proper placental development, which is ultimately regulated by the placental genome. The regulation of the placental genome can be directly studied by exploring the underlying organisation of the placental transcriptome through a systematic analysis of gene-wise co-expression relationships. RESULTS In this study, we performed a comprehensive analysis of human placental co-expression using RNA sequencing and intergrated multiple transcriptome datasets spanning human gestation. We identified modules of co-expressed genes that are preserved across human gestation, and also identifed modules conserved in the mouse indicating conserved molecular networks involved in placental development and gene expression patterns more specific to late gestation. Analysis of co-expressed gene flanking sequences indicated that conserved co-expression modules in the placenta are regulated by a core set of transcription factors, including ZNF423 and EBF1. Additionally, we identified a gene co-expression module enriched for genes implicated in the pregnancy pathology preeclampsia. By using an independnet transcriptome dataset, we show that these co-expressed genes are differentially expressed in preeclampsia. CONCLUSIONS This study represents a comprehensive characterisation of placental co-expression and provides insight into potential transcriptional regulators that govern conserved molecular programs fundamental to placental development.
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Affiliation(s)
- Sam Buckberry
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.,University of Western Australia, Harry Perkins Institute of Medical Research, Perth, 6009, Australia.,University of Western Australia, Australian Research Council Centre of Excellence in Plant Energy Biology, Perth, 6009, Australia
| | - Tina Bianco-Miotto
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.,The University of Adelaide, School of agriculture, food and wine, Adelaide, 5005, Australia
| | - Stephen J Bent
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia
| | - Vicki Clifton
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia
| | - Cheryl Shoubridge
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia
| | - Kartik Shankar
- University of Arkansas for Medical Sciences, The Department of Pediatrics, Little Rock, 72202, USA
| | - Claire T Roberts
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.
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24
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Abstract
A key characteristic of systems genetics is its reliance on populations that vary to a greater or lesser degree in genetic complexity-from highly admixed populations such as the Collaborative Cross and Diversity Outcross to relatively simple crosses such as sets of consomic strains and reduced complexity crosses. This protocol is intended to help investigators make more informed decisions about choices of resources given different types of questions. We consider factors such as costs, availability, and ease of breeding for common scenarios. In general, we recommend using complementary resources and minimizing depth of resampling of any given genome or strain.
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Affiliation(s)
- Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, 77 S. Manassas Street, Memphis, TN, 38163, USA.
| | - Evan G Williams
- Department of Biology, Institute for Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
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25
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Gao C, McDowell IC, Zhao S, Brown CD, Engelhardt BE. Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering. PLoS Comput Biol 2016; 12:e1004791. [PMID: 27467526 PMCID: PMC4965098 DOI: 10.1371/journal.pcbi.1004791] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 02/03/2016] [Indexed: 01/15/2023] Open
Abstract
Identifying latent structure in high-dimensional genomic data is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes that are co-regulated by shared biological mechanisms. To do this, we develop a Bayesian statistical model for biclustering to infer subsets of co-regulated genes that covary in all of the samples or in only a subset of the samples. Our biclustering method, BicMix, allows overcomplete representations of the data, computational tractability, and joint modeling of unknown confounders and biological signals. Compared with related biclustering methods, BicMix recovers latent structure with higher precision across diverse simulation scenarios as compared to state-of-the-art biclustering methods. Further, we develop a principled method to recover context specific gene co-expression networks from the estimated sparse biclustering matrices. We apply BicMix to breast cancer gene expression data and to gene expression data from a cardiovascular study cohort, and we recover gene co-expression networks that are differential across ER+ and ER- samples and across male and female samples. We apply BicMix to the Genotype-Tissue Expression (GTEx) pilot data, and we find tissue specific gene networks. We validate these findings by using our tissue specific networks to identify trans-eQTLs specific to one of four primary tissues.
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Affiliation(s)
- Chuan Gao
- Department of Statistical Science, Duke University, Durham, North Carolina, United States of America
| | - Ian C. McDowell
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | - Shiwen Zhao
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | - Christopher D. Brown
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Barbara E. Engelhardt
- Department of Computer Science, Center for Statistics and Machine Learning, Princeton University, Princeton, New Jersey, United States of America
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26
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Bai L, Yang HH, Hu Y, Shukla A, Ha NH, Doran A, Faraji F, Goldberger N, Lee MP, Keane T, Hunter KW. An Integrated Genome-Wide Systems Genetics Screen for Breast Cancer Metastasis Susceptibility Genes. PLoS Genet 2016; 12:e1005989. [PMID: 27074153 PMCID: PMC4830524 DOI: 10.1371/journal.pgen.1005989] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/24/2016] [Indexed: 12/31/2022] Open
Abstract
Metastasis remains the primary cause of patient morbidity and mortality in solid tumors and is due to the action of a large number of tumor-autonomous and non-autonomous factors. Here we report the results of a genome-wide integrated strategy to identify novel metastasis susceptibility candidate genes and molecular pathways in breast cancer metastasis. This analysis implicates a number of transcriptional regulators and suggests cell-mediated immunity is an important determinant. Moreover, the analysis identified novel or FDA-approved drugs as potentially useful for anti-metastatic therapy. Further explorations implementing this strategy may therefore provide a variety of information for clinical applications in the control and treatment of advanced neoplastic disease. Metastasis, the spread and growth of tumor cells from the original tumor to secondary sites throughout the body, is the primary cause of cancer-related death for most solid tumor types. The process of metastasis is very complex, requiring multiple individual steps and the cooperation of different cell types during the dissemination and proliferation steps. Many genes are involved in this process, but at present few have been identified and characterized. In this study, we have integrated multiple genome-wide analysis methods to try to identify large numbers of candidate metastasis-associated genes and pathways based on a highly metastatic mouse model. Using this strategy, we have identified a number of genes that predict outcome of human breast cancer. These genes implicate specific molecular and cellular pathways in the metastatic process that might be used to intervene in the process. Furthermore, this integrated analysis implicates pre-existing drugs that might be re-purposed to help prevent or reduce metastatic burden in patients. The combined results obtained from this analytical strategy therefore provide an important platform for further genome-wide analysis into the etiology of metastatic disease.
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Affiliation(s)
- Ling Bai
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Howard H. Yang
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ying Hu
- Center for Bioinformatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Anjali Shukla
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ngoc-Han Ha
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Anthony Doran
- Computational Genomics Program, Welcome Trust Sanger Centre, Hinxton, Cambridge, United Kingdom
| | - Farhoud Faraji
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Natalie Goldberger
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maxwell P. Lee
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Thomas Keane
- Computational Genomics Program, Welcome Trust Sanger Centre, Hinxton, Cambridge, United Kingdom
| | - Kent W. Hunter
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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27
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Abstract
Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing, diagnosing, or curing disease. In this chapter we discuss how bioinformatics critically contributes to systems medicine. First, we explain the role of bioinformatics in the management and analysis of data. In particular we show the importance of publicly available biological and clinical repositories to support systems medicine studies. Second, we discuss how the integration and analysis of multiple types of omics data through integrative bioinformatics may facilitate the determination of more predictive and robust disease signatures, lead to a better understanding of (patho)physiological molecular mechanisms, and facilitate personalized medicine. Third, we focus on network analysis and discuss how gene networks can be constructed from omics data and how these networks can be decomposed into smaller modules. We discuss how the resulting modules can be used to generate experimentally testable hypotheses, provide insight into disease mechanisms, and lead to predictive models. Throughout, we provide several examples demonstrating how bioinformatics contributes to systems medicine and discuss future challenges in bioinformatics that need to be addressed to enable the advancement of systems medicine.
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Affiliation(s)
- Ulf Schmitz
- Dept of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany
| | - Olaf Wolkenhauer
- Dept of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany
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28
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Khirade MF, Lal G, Bapat SA. Derivation of a fifteen gene prognostic panel for six cancers. Sci Rep 2015; 5:13248. [PMID: 26272668 PMCID: PMC4536526 DOI: 10.1038/srep13248] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/22/2015] [Indexed: 12/21/2022] Open
Abstract
The hallmarks of cancer deem biological pathways and molecules to be conserved. This approach may be useful for deriving a prognostic gene signature. Weighted Gene Co-expression Network Analysis of gene expression datasets in eleven cancer types identified modules of highly correlated genes and interactive networks conserved across glioblastoma, breast, ovary, colon, rectal and lung cancers, from which a universal classifier for tumor stratification was extracted. Specific conserved gene modules were validated across different microarray platforms and datasets. Strikingly, preserved genes within these modules defined regulatory networks associated with immune regulation, cell differentiation, metastases, cell migration, metastases, oncogenic transformation, and resistance to apoptosis and senescence, with AIF1 and PRRX1 being suggested to be master regulators governing these biological processes. A universal classifier from these conserved networks enabled execution of common set of principles across different cancers that revealed distinct, differential correlation of biological functions with patient survival in a cancer-specific manner. Correlation analysis further identified a panel of 15 risk genes with potential prognostic value, termed as the GBOCRL-IIPr panel [(GBM-Breast-Ovary-Colon-Rectal-Lung)–Immune–Invasion–Prognosis], that surprisingly, were not amongst the master regulators or important network hubs. This panel may now be integrated in predicting patient outcomes in the six cancers.
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Affiliation(s)
- Mamata F Khirade
- National Centre for Cell Science, NCCS Complex, Pune 411007, India
| | - Girdhari Lal
- National Centre for Cell Science, NCCS Complex, Pune 411007, India
| | - Sharmila A Bapat
- National Centre for Cell Science, NCCS Complex, Pune 411007, India
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29
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Jeffery J, Sinha D, Srihari S, Kalimutho M, Khanna KK. Beyond cytokinesis: the emerging roles of CEP55 in tumorigenesis. Oncogene 2015; 35:683-90. [PMID: 25915844 DOI: 10.1038/onc.2015.128] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 03/16/2015] [Accepted: 03/16/2015] [Indexed: 01/10/2023]
Abstract
CEP55 was initially identified as a pivotal component of abscission, the final stage of cytokinesis, serving to regulate the physical separation of two daughter cells. Over the past 10 years, several studies have illuminated additional roles for CEP55 including regulating the PI3K/AKT pathway and midbody fate. Concurrently, CEP55 has been studied in the context of cancers including those of the breast, lung, colon and liver. CEP55 overexpression has been found to significantly correlate with tumor stage, aggressiveness, metastasis and poor prognosis across multiple tumor types and therefore has been included as part of several prognostic 'gene signatures' for cancer. Here by discussing in depth the functions of CEP55 across different effector pathways, and also its roles as a biomarker and driver of tumorigenesis, we assemble an exhaustive review, thus commemorating a decade of research on CEP55.
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Affiliation(s)
- J Jeffery
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - D Sinha
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,School of Natural Sciences, Griffith University, Brisbane, Queensland, Australia
| | - S Srihari
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - M Kalimutho
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - K K Khanna
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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30
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Geiger TR, Ha NH, Faraji F, Michael HT, Rodriguez L, Walker RC, Green JE, Simpson RM, Hunter KW. Functional analysis of prognostic gene expression network genes in metastatic breast cancer models. PLoS One 2014; 9:e111813. [PMID: 25368990 PMCID: PMC4219783 DOI: 10.1371/journal.pone.0111813] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 10/06/2014] [Indexed: 12/17/2022] Open
Abstract
Identification of conserved co-expression networks is a useful tool for clustering groups of genes enriched for common molecular or cellular functions [1]. The relative importance of genes within networks can frequently be inferred by the degree of connectivity, with those displaying high connectivity being significantly more likely to be associated with specific molecular functions [2]. Previously we utilized cross-species network analysis to identify two network modules that were significantly associated with distant metastasis free survival in breast cancer. Here, we validate one of the highly connected genes as a metastasis associated gene. Tpx2, the most highly connected gene within a proliferation network specifically prognostic for estrogen receptor positive (ER+) breast cancers, enhances metastatic disease, but in a tumor autonomous, proliferation-independent manner. Histologic analysis suggests instead that variation of TPX2 levels within disseminated tumor cells may influence the transition between dormant to actively proliferating cells in the secondary site. These results support the co-expression network approach for identification of new metastasis-associated genes to provide new information regarding the etiology of breast cancer progression and metastatic disease.
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Affiliation(s)
- Thomas R. Geiger
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ngoc-Han Ha
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Farhoud Faraji
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Helen T. Michael
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Loren Rodriguez
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Renard C. Walker
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeffery E. Green
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - R. Mark Simpson
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kent W. Hunter
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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31
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Neumayer G, Belzil C, Gruss OJ, Nguyen MD. TPX2: of spindle assembly, DNA damage response, and cancer. Cell Mol Life Sci 2014; 71:3027-47. [PMID: 24556998 PMCID: PMC11114040 DOI: 10.1007/s00018-014-1582-7] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/28/2014] [Accepted: 01/30/2014] [Indexed: 10/25/2022]
Abstract
For more than 15 years, TPX2 has been studied as a factor critical for mitosis and spindle assembly. These functions of TPX2 are attributed to its Ran-regulated microtubule-associated protein properties and to its control of the Aurora A kinase. Overexpressed in cancers, TPX2 is being established as marker for the diagnosis and prognosis of malignancies. During interphase, TPX2 resides preferentially in the nucleus where its function had remained elusive until recently. The latest finding that TPX2 plays a role in amplification of the DNA damage response, combined with the characterization of TPX2 knockout mice, open new perspectives to understand the biology of this protein. This review provides an historic overview of the discovery of TPX2 and summarizes its cytoskeletal and signaling roles with relevance to cancer therapies. Finally, the review aims to reconcile discrepancies between the experimental and pathological effects of TPX2 overexpression and advances new roles for compartmentalized TPX2.
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Affiliation(s)
- Gernot Neumayer
- Department of Clinical Neurosciences, Department of Cell Biology and Anatomy, Department of Biochemistry and Molecular Biology, Hotchkiss Brain Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, T2N 4N1, Canada,
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32
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Hollern DP, Andrechek ER. A genomic analysis of mouse models of breast cancer reveals molecular features of mouse models and relationships to human breast cancer. Breast Cancer Res 2014; 16:R59. [PMID: 25069779 PMCID: PMC4078930 DOI: 10.1186/bcr3672] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/04/2013] [Indexed: 02/11/2023] Open
Abstract
INTRODUCTION Genomic variability limits the efficacy of breast cancer therapy. To simplify the study of the molecular complexity of breast cancer, researchers have used mouse mammary tumor models. However, the degree to which mouse models model human breast cancer and are reflective of the human heterogeneity has yet to be demonstrated with gene expression studies on a large scale. METHODS To this end, we have built a database consisting of 1,172 mouse mammary tumor samples from 26 different major oncogenic mouse mammary tumor models. RESULTS In this dataset we identified heterogeneity within mouse models and noted a surprising amount of interrelatedness between models, despite differences in the tumor initiating oncogene. Making comparisons between models, we identified differentially expressed genes with alteration correlating with initiating events in each model. Using annotation tools, we identified transcription factors with a high likelihood of activity within these models. Gene signatures predicted activation of major cell signaling pathways in each model, predictions that correlated with previous genetic studies. Finally, we noted relationships between mouse models and human breast cancer at both the level of gene expression and predicted signal pathway activity. Importantly, we identified individual mouse models that recapitulate human breast cancer heterogeneity at the level of gene expression. CONCLUSIONS This work underscores the importance of fully characterizing mouse tumor biology at molecular, histological and genomic levels before a valid comparison to human breast cancer may be drawn and provides an important bioinformatic resource.
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33
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Liu W, Li L, Li W. Gene co-expression analysis identifies common modules related to prognosis and drug resistance in cancer cell lines. Int J Cancer 2014; 135:2795-803. [PMID: 24771271 DOI: 10.1002/ijc.28935] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/12/2014] [Accepted: 04/16/2014] [Indexed: 11/08/2022]
Abstract
To discover a common gene co-expression network in cancer cell, we applied weighted gene co-expression network analysis to transcriptional profiles of 917 cancer cell lines. Fourteen biologically meaningful modules were identified, including cytoskeleton, cell cycle, RNA splicing, signaling pathway, transcription, translation and others. These modules were robust in an independent human cancer microarray dataset. Furthermore, we collected 11 independent cancer microarray datasets, and correlated these modules with clinical outcome. Most of these modules could predict patient survival in one or more cancer types. Some modules were predictive of relapse, metastasis and drug resistance. Novel regulatory mechanisms were also implicated. In summary, our findings, for the first time, provide a modular map for cancer cell lines, new targets for therapy and modules for regulatory mechanism of cancer development and drug resistance.
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Affiliation(s)
- Wei Liu
- Department of Pathology, Human Centrifuge Medical Training Center, Institute of Aviation Medicine of Chinese PLA Air Force, Beijing, China
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34
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Song L, Craney A, Rape M. Microtubule-dependent regulation of mitotic protein degradation. Mol Cell 2014; 53:179-92. [PMID: 24462202 DOI: 10.1016/j.molcel.2013.12.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 10/18/2013] [Accepted: 12/20/2013] [Indexed: 01/10/2023]
Abstract
Accurate cell division depends on tightly regulated ubiquitylation events catalyzed by the anaphase-promoting complex (APC/C). Among its many substrates, the APC/C triggers the degradation of proteins that stabilize the mitotic spindle, and loss or accumulation of such spindle assembly factors can result in aneuploidy and cancer. Although critical for cell division, it has remained poorly understood how the timing of spindle assembly factor degradation is established during mitosis. Here, we report that active spindle assembly factors are protected from APC/C-dependent degradation by microtubules. In contrast, those molecules that are not bound to microtubules are highly susceptible to proteolysis and turned over immediately after APC/C activation. The correct timing of spindle assembly factor degradation, as achieved by this regulatory circuit, is required for accurate spindle structure and function. We propose that the localized stabilization of APC/C substrates provides a mechanism for the selective disposal of cell-cycle regulators that have fulfilled their mitotic roles.
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Affiliation(s)
- Ling Song
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Allison Craney
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael Rape
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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35
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Wang P, Wang Y, Yan H, Xie Q, Zhao L, Xu S, Zhao Q. Genetic variation in the major mitotic checkpoint genes and risk of breast cancer: a multigenic study on cancer susceptibility. Tumour Biol 2014; 35:6701-5. [PMID: 24711138 DOI: 10.1007/s13277-014-1906-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/28/2014] [Indexed: 11/28/2022] Open
Abstract
The mitotic checkpoint system is a mechanism essential for maintaining genomic stability and defects which have been linked to cancer development. We conducted this hospital-based case-control study to investigate whether genetic variants in three major spindle checkpoint genes (BUB3, MAD2L1, and BUB1) had any bearing on an individual risk of breast cancer (BC). A total of 462 incident BC patients and 529 cancer-free controls were enrolled in this study. Results showed that neither variants in BUB3 nor variants in MAD2L1 caused any significant effect on the risk of BC. However, the variant rs12623473 in BUB1 was significantly associated with increased BC risk with the odds ratio (OR) of 1.30 (95 % confidence interval (CI) 1.03-1.64) under the allelic model. The estimated population attributable risk of one copy of the risk allele for developing BC was 10.3 %. The bioinformatics analysis suggested that this variant may regulate the transcriptional ability of BUB1.
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Affiliation(s)
- Ping Wang
- Department of Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, 310009, Hangzhou, China
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36
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Wang X, Cui L, Liu W. Network-based analysis reveals the difference between inflammatory and fibrogenic livers of children with biliary atresia. J Pediatr Surg 2014; 49:500. [PMID: 24650486 DOI: 10.1016/j.jpedsurg.2013.11.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 10/25/2022]
Affiliation(s)
- Xiaohui Wang
- Department of Gastroenterology, Navy General Hospital, Beijing 100048, China
| | - Lihong Cui
- Department of Gastroenterology, Navy General Hospital, Beijing 100048, China
| | - Wei Liu
- Department of pathology, Human centrifuge Medical Training Center, Institute of Aviation Medicine of Chinese PLA Air Force, Beijing 100089, China.
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37
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Schramm HM. Should EMT of Cancer Cells Be Understood as Epithelial-Myeloid Transition? J Cancer 2014; 5:125-32. [PMID: 24494030 PMCID: PMC3909767 DOI: 10.7150/jca.8242] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/02/2014] [Indexed: 12/11/2022] Open
Abstract
Cancer cells express epithelial markers, and when progressing in malignancy they may express markers of the mesenchymal cell type. Therefore an epithelial-mesenchymal transition of the cancer cells is assumed. However the mesenchymal markers can equally well be interpreted as myeloid markers since they are common in both types of cell lineages. Moreover, cancer cells express multiple specific markers of the myeloid lineages thus giving rise to the hypothesis that the transition of cancer cells may be from epithelial to myeloid cells and not to mesenchymal cells. This interpretation would better explain why cancer cells, often already in their primary cancer site, frequently show properties common to those of macrophages, platelets and pre-/osteoclasts.
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Affiliation(s)
- Henning M. Schramm
- Institute Hiscia, Society for Cancer Research, CH-4144 Arlesheim/Switzerland
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38
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Faraji F, Hu Y, Wu G, Goldberger NE, Walker RC, Zhang J, Hunter KW. An integrated systems genetics screen reveals the transcriptional structure of inherited predisposition to metastatic disease. Genome Res 2013; 24:227-40. [PMID: 24322557 PMCID: PMC3912413 DOI: 10.1101/gr.166223.113] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Metastasis is the result of stochastic genomic and epigenetic events leading to gene expression profiles that drive tumor dissemination. Here we exploit the principle that metastatic propensity is modified by the genetic background to generate prognostic gene expression signatures that illuminate regulators of metastasis. We also identify multiple microRNAs whose germline variation is causally linked to tumor progression and metastasis. We employ network analysis of global gene expression profiles in tumors derived from a panel of recombinant inbred mice to identify a network of co-expressed genes centered on Cnot2 that predicts metastasis-free survival. Modulating Cnot2 expression changes tumor cell metastatic potential in vivo, supporting a functional role for Cnot2 in metastasis. Small RNA sequencing of the same tumor set revealed a negative correlation between expression of the Mir216/217 cluster and tumor progression. Expression quantitative trait locus analysis (eQTL) identified cis-eQTLs at the Mir216/217 locus, indicating that differences in expression may be inherited. Ectopic expression of Mir216/217 in tumor cells suppressed metastasis in vivo. Finally, small RNA sequencing and mRNA expression profiling data were integrated to reveal that miR-3470a/b target a high proportion of network transcripts. In vivo analysis of Mir3470a/b demonstrated that both promote metastasis. Moreover, Mir3470b is a likely regulator of the Cnot2 network as its overexpression down-regulated expression of network hub genes and enhanced metastasis in vivo, phenocopying Cnot2 knockdown. The resulting data from this strategy identify Cnot2 as a novel regulator of metastasis and demonstrate the power of our systems-level approach in identifying modifiers of metastasis.
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Affiliation(s)
- Farhoud Faraji
- Metastasis Susceptibility Section, Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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39
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Chen X, Stewart E, Shelat AA, Qu C, Bahrami A, Hatley M, Wu G, Bradley C, McEvoy J, Pappo A, Spunt S, Valentine MB, Valentine V, Krafcik F, Lang WH, Wierdl M, Tsurkan L, Tolleman V, Federico SM, Morton C, Lu C, Ding L, Easton J, Rusch M, Nagahawatte P, Wang J, Parker M, Wei L, Hedlund E, Finkelstein D, Edmonson M, Shurtleff S, Boggs K, Mulder H, Yergeau D, Skapek S, Hawkins DS, Ramirez N, Potter PM, Sandoval JA, Davidoff AM, Mardis ER, Wilson RK, Zhang J, Downing JR, Dyer MA. Targeting oxidative stress in embryonal rhabdomyosarcoma. Cancer Cell 2013; 24:710-24. [PMID: 24332040 PMCID: PMC3904731 DOI: 10.1016/j.ccr.2013.11.002] [Citation(s) in RCA: 223] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 08/28/2013] [Accepted: 11/06/2013] [Indexed: 10/25/2022]
Abstract
Rhabdomyosarcoma is a soft-tissue sarcoma with molecular and cellular features of developing skeletal muscle. Rhabdomyosarcoma has two major histologic subtypes, embryonal and alveolar, each with distinct clinical, molecular, and genetic features. Genomic analysis shows that embryonal tumors have more structural and copy number variations than alveolar tumors. Mutations in the RAS/NF1 pathway are significantly associated with intermediate- and high-risk embryonal rhabdomyosarcomas (ERMS). In contrast, alveolar rhabdomyosarcomas (ARMS) have fewer genetic lesions overall and no known recurrently mutated cancer consensus genes. To identify therapeutics for ERMS, we developed and characterized orthotopic xenografts of tumors that were sequenced in our study. High-throughput screening of primary cultures derived from those xenografts identified oxidative stress as a pathway of therapeutic relevance for ERMS.
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Affiliation(s)
- Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elizabeth Stewart
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chunxu Qu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Armita Bahrami
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mark Hatley
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cori Bradley
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Justina McEvoy
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Alberto Pappo
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sheri Spunt
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Marcus B Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Virginia Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Fred Krafcik
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Walter H Lang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Monika Wierdl
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lyudmila Tsurkan
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Viktor Tolleman
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sara M Federico
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chris Morton
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles Lu
- The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Li Ding
- The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Panduka Nagahawatte
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jianmin Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Matthew Parker
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lei Wei
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Erin Hedlund
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michael Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sheila Shurtleff
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kristy Boggs
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Heather Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Donald Yergeau
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Steve Skapek
- Division of Pediatric Hematology-Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Douglas S Hawkins
- Division of Hematology-Oncology, Seattle Children's Hospital, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98105, USA
| | - Nilsa Ramirez
- Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Philip M Potter
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - John A Sandoval
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elaine R Mardis
- The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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40
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Hu Y, Bai L, Geiger T, Goldberger N, Walker RC, Green JE, Wakefield LM, Hunter KW. Genetic background may contribute to PAM50 gene expression breast cancer subtype assignments. PLoS One 2013; 8:e72287. [PMID: 24015230 PMCID: PMC3756056 DOI: 10.1371/journal.pone.0072287] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/12/2013] [Indexed: 01/02/2023] Open
Abstract
Recent advances in genome wide transcriptional analysis have provided greater insights into the etiology and heterogeneity of breast cancer. Molecular signatures have been developed that stratify the conventional estrogen receptor positive or negative categories into subtypes that are associated with differing clinical outcomes. It is thought that the expression patterns of the molecular subtypes primarily reflect cell-of-origin or tumor driver mutations. In this study however, using a genetically engineered mouse mammary tumor model we demonstrate that the PAM50 subtype signature of tumors driven by a common oncogenic event can be significantly influenced by the genetic background on which the tumor arises. These results have important implications for interpretation of "snapshot" expression profiles, as well as suggesting that incorporation of genetic background effects may allow investigation into phenotypes not initially anticipated in individual mouse models of cancer.
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Affiliation(s)
- Ying Hu
- Center for Biomedical Informatics and Information Technology, Bethesda, Maryland, United States of America
| | - Ling Bai
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, Maryland, United States of America
| | - Thomas Geiger
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, Maryland, United States of America
| | - Natalie Goldberger
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, Maryland, United States of America
| | - Renard C. Walker
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, Maryland, United States of America
| | - Jeffery E. Green
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, Maryland, United States of America
| | - Lalage M. Wakefield
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, Maryland, United States of America
| | - Kent W. Hunter
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, Maryland, United States of America
- * E-mail:
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41
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Ha NH, Hunter KW. Using a systems biology approach to understand and study the mechanisms of metastasis. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 6:107-14. [PMID: 23873855 DOI: 10.1002/wsbm.1237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/11/2013] [Accepted: 06/21/2013] [Indexed: 11/07/2022]
Abstract
Metastasis remains the main cause for cancer-related deaths due to the lack of effective therapy. The clonal selection model has long been thought to be the primary mechanism of metastatic progression but many different mechanisms have been hypothesized for the progression from tumorigenesis to the successful dissemination and expansion of tumor cells at the secondary site. MicroRNAs, germline polymorphisms in combination with the tumor microenvironment are few of the different pathways to explain the metastatic cascade. Technological advances for high-throughput screening of cells such as expression profiling, next generation sequencing, as well as global network analyses have advanced the studies of these mechanisms. Combined with new insights into the various mechanisms of metastasis a systems biology approach has also been shown to be useful in identifying metastasis-specific gene signatures as well as predicting disease outcome. Furthermore, the results of these studies have been relevant for identifying biomarkers for metastatic disease.
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Affiliation(s)
- Ngoc-Han Ha
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, USA
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42
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Pérez de Castro I, Malumbres M. Mitotic Stress and Chromosomal Instability in Cancer: The Case for TPX2. Genes Cancer 2013; 3:721-30. [PMID: 23634259 DOI: 10.1177/1947601912473306] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cell cycle deregulation is a common motif in human cancer, and multiple therapeutic strategies are aimed to prevent tumor cell proliferation. Whereas most current therapies are designed to arrest cell cycle progression either in G1/S or in mitosis, new proposals include targeting the intrinsic chromosomal instability (CIN, an increased rate of gain or losses of chromosomes during cell division) or aneuploidy (a genomic composition that differs from diploid) that many tumor cells display. Why tumors cells are chromosomally unstable or aneuploid and what are the consequences of these alterations are not completely clear at present. Several mitotic regulators are overexpressed as a consequence of oncogenic alterations, and they are likely to alter the proper regulation of chromosome segregation in cancer cells. In this review, we propose the relevance of TPX2, a mitotic regulator involved in the formation of the mitotic spindle, in oncogene-induced mitotic stress. This protein, as well as its partner Aurora-A, is frequently overexpressed in human cancer, and its deregulation may participate not only in chromosome numeric aberrations but also in other forms of genomic instability in cancer cells.
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Affiliation(s)
- Ignacio Pérez de Castro
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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43
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Gusev Y, Riggins RB, Bhuvaneshwar K, Gauba R, Sheahan L, Clarke R, Madhavan S. In silico discovery of mitosis regulation networks associated with early distant metastases in estrogen receptor positive breast cancers. Cancer Inform 2013; 12:31-51. [PMID: 23470717 PMCID: PMC3579429 DOI: 10.4137/cin.s10329] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The aim of this study was to perform comparative analysis of multiple public datasets of gene expression in order to identify common genes as potential prognostic biomarkers. Additionally, the study sought to identify biological processes and pathways that are most significantly associated with early distant metastases (<5 years) in women with estrogen receptor-positive (ER+) breast tumors. Datasets from three published studies were selected for in silico analysis of gene expression profiles of ER+ breast cancer, using time to distant metastasis as the clinical endpoint. A subset of 44 differently expressed genes (DEGs) was found common to all three studies and characterized by mitotic checkpoint genes and pathways that regulate mitotic spindle and chromosome dynamics. DEG promoter regions were enriched with NFY binding sites. Analysis of miRNA target sites identified significant enrichment of miR-192, miR-193B, and miR-16-1 targets. Aberrant mitotic regulation could drive increased genomic instability leading to a progression towards an early onset metastatic phenotype. The relative importance of mitotic instability may reflect the clinical utility of mitotic poisons in metastatic breast cancer, including poisons such as the taxanes, epothilones, and vinca alkaloids.
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Affiliation(s)
- Yuriy Gusev
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - Rebecca B. Riggins
- Breast Cancer Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Krithika Bhuvaneshwar
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - Robinder Gauba
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | | | - Robert Clarke
- Breast Cancer Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
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44
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Hasegawa K, Ryu SJ, Kaláb P. Chromosomal gain promotes formation of a steep RanGTP gradient that drives mitosis in aneuploid cells. ACTA ACUST UNITED AC 2013; 200:151-61. [PMID: 23319601 PMCID: PMC3549973 DOI: 10.1083/jcb.201206142] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The chromosome-centered RanGTP gradient, which is strongly reduced in slow-growing normal cells, is amplified by chromosomal gain and is required for mitosis in rapidly growing aneuploid cells. Many mitotic factors were shown to be activated by Ran guanosine triphosphatase. Previous studies in Xenopus laevis egg extracts and in highly proliferative cells showed that mitotic chromosomes were surrounded by steep Ran guanosine triphosphate (GTP) concentration gradients, indicating that RanGTP-activated factors promote spindle assembly around chromosomes. However, the mitotic role of Ran in normal differentiated cells is not known. In this paper, we show that although the steep mitotic RanGTP gradients were present in rapidly growing cell lines and were required for chromosome congression in mitotic HeLa cells, the gradients were strongly reduced in slow-growing primary cells, such as HFF-1 fibroblasts. The overexpression of RCC1, the guanine nucleotide exchange factor for Ran, induced steeper mitotic RanGTP gradients in HFF-1 cells, showing the critical role of RCC1 levels in the regulation of mitosis by Ran. Remarkably, in vitro fusion of HFF-1 cells produced cells with steep mitotic RanGTP gradients comparable to HeLa cells, indicating that chromosomal gain can promote mitosis in aneuploid cancer cells via Ran.
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Affiliation(s)
- Keisuke Hasegawa
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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45
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Winter SF, Lukes L, Walker RC, Welch DR, Hunter KW. Allelic variation and differential expression of the mSIN3A histone deacetylase complex gene Arid4b promote mammary tumor growth and metastasis. PLoS Genet 2012; 8:e1002735. [PMID: 22693453 PMCID: PMC3364935 DOI: 10.1371/journal.pgen.1002735] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/12/2012] [Indexed: 12/26/2022] Open
Abstract
Accumulating evidence suggests that breast cancer metastatic progression is modified by germline polymorphism, although specific modifier genes have remained largely undefined. In the current study, we employ the MMTV-PyMT transgenic mouse model and the AKXD panel of recombinant inbred mice to identify AT-rich interactive domain 4B (Arid4b; NM_194262) as a breast cancer progression modifier gene. Ectopic expression of Arid4b promoted primary tumor growth in vivo as well as increased migration and invasion in vitro, and the phenotype was associated with polymorphisms identified between the AKR/J and DBA/2J alleles as predicted by our genetic analyses. Stable shRNA-mediated knockdown of Arid4b caused a significant reduction in pulmonary metastases, validating a role for Arid4b as a metastasis modifier gene. ARID4B physically interacts with the breast cancer metastasis suppressor BRMS1, and we detected differential binding of the Arid4b alleles to histone deacetylase complex members mSIN3A and mSDS3, suggesting that the mechanism of Arid4b action likely involves interactions with chromatin modifying complexes. Downregulation of the conserved Tpx2 gene network, which is comprised of many factors regulating cell cycle and mitotic spindle biology, was observed concomitant with loss of metastatic efficiency in Arid4b knockdown cells. Consistent with our genetic analysis and in vivo experiments in our mouse model system, ARID4B expression was also an independent predictor of distant metastasis-free survival in breast cancer patients with ER+ tumors. These studies support a causative role of ARID4B in metastatic progression of breast cancer.
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Affiliation(s)
- Scott F Winter
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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