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Bai Z, Yan C, Nie Y, Zeng Q, Xu L, Wang S, Chang D. Glucose metabolism-based signature predicts prognosis and immunotherapy strategies for colon adenocarcinoma. J Gene Med 2024; 26:e3620. [PMID: 37973153 DOI: 10.1002/jgm.3620] [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: 08/30/2023] [Revised: 09/25/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The global prevalence and metastasis rates of colon adenocarcinoma (COAD) are high, and therapeutic success is limited. Although previous research has primarily explored changes in gene phenotypes, the incidence rate of COAD remains unchanged. Metabolic reprogramming is a crucial aspect of cancer research and therapy. The present study aims to develop cluster and polygenic risk prediction models for COAD based on glucose metabolism pathways to assess the survival status of patients and potentially identify novel immunotherapy strategies and related therapeutic targets. METHODS COAD-specific data (including clinicopathological information and gene expression profiles) were sourced from The Cancer Genome Atlas (TCGA) and two Gene Expression Omnibus (GEO) datasets (GSE33113 and GSE39582). Gene sets related to glucose metabolism were obtained from the MSigDB database. The Gene Set Variation Analysis (GSVA) method was utilized to calculate pathway scores for glucose metabolism. The hclust function in R, part of the Pheatmap package, was used to establish a clustering system. The mutation characteristics of identified clusters were assessed via MOVICS software, and differentially expressed genes (DEGs) were filtered using limma software. Signature analysis was performed using the least absolute shrinkage and selection operator (LASSO) method. Survival curves, survival receiver operating characteristic (ROC) curves and multivariate Cox regression were analyzed to assess the efficacy and accuracy of the signature for prognostic prediction. The pRRophetic program was employed to predict drug sensitivity, with data sourced from the Genomics of Drug Sensitivity in Cancer (GDSC) database. RESULTS Four COAD subgroups (i.e., C1, C2, C3 and C4) were identified based on glucose metabolism, with the C4 group having higher survival rates. These four clusters were bifurcated into a new Clust2 system (C1 + C2 + C3 and C4). In total, 2175 DEGs were obtained (C1 + C2 + C3 vs. C4), from which 139 prognosis-related genes were identified. ROC curves predicting 1-, 3- and 5-year survival based on a signature containing nine genes showed an area under the curve greater than 0.7. Meanwhile, the study also found this feature to be an important predictor of prognosis in COAD and accordingly assessed the risk score, with higher risk scores being associated with a worse prognosis. The high-risk and low-risk groups responded differently to immunotherapy and chemotherapeutic agents, and there were differences in functional enrichment pathways. CONCLUSIONS This unique signature based on glucose metabolism may potentially provide a basis for predicting patient prognosis, biological characteristics and more effective immunotherapy strategies for COAD.
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Affiliation(s)
- Zilong Bai
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Chunyu Yan
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Yuanhua Nie
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Qingnuo Zeng
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Longwen Xu
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Shilong Wang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Dongmin Chang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
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2
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Li K, Li Y, Nakamura F. Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin. Sci Rep 2023; 13:21723. [PMID: 38066085 PMCID: PMC10709462 DOI: 10.1038/s41598-023-49100-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
The contact inhibition of proliferation (CIP) denotes the cell density-dependent inhibition of growth, and the loss of CIP represents a hallmark of cancer. However, the mechanism by which CIP regulates gene expression remains poorly understood. Chromatin is a highly complex structure consisting of DNA, histones, and trans-acting factors (TAFs). The binding of TAF proteins to specific chromosomal loci regulates gene expression. Therefore, profiling chromatin is crucial for gaining insight into the gene expression mechanism of CIP. In this study, using modified proteomics of TAFs bound to DNA, we identified a protein that shuttles between the nucleus and cytosol in a cell density-dependent manner. We identified TIPARP, PTGES3, CBFB, and SMAD4 as cell density-dependent nucleocytoplasmic shuttling proteins. In low-density cells, these proteins predominantly reside in the nucleus; however, upon reaching high density, they relocate to the cytosol. Given their established roles in gene regulation, our findings propose their involvement as CIP-dependent TAFs. We also identified and characterized potential open chromatin regions sensitive to changes in cell density. These findings provide insights into the modulation of chromatin structure by CIP.
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Affiliation(s)
- Kangjing Li
- School of Pharmaceutical Science and Technology, Tianjin University, Nankai District, 92 Weijin Road, Tianjin, 300072, China
| | - Yaxin Li
- School of Pharmaceutical Science and Technology, Tianjin University, Nankai District, 92 Weijin Road, Tianjin, 300072, China
| | - Fumihiko Nakamura
- School of Pharmaceutical Science and Technology, Tianjin University, Nankai District, 92 Weijin Road, Tianjin, 300072, China.
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3
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Feng M, Wang J, Li K, Nakamura F. UBE2A/B is the trans-acting factor mediating mechanotransduction and contact inhibition. Biochem J 2023; 480:1659-1674. [PMID: 37818922 DOI: 10.1042/bcj20230208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023]
Abstract
Mechanotransduction and contact inhibition (CI) control gene expression to regulate proliferation, differentiation, and even tumorigenesis of cells. However, their downstream trans-acting factors (TAFs) are not well known due to a lack of a high-throughput method to quantitatively detect them. Here, we developed a method to identify TAFs on the cis-acting sequences that reside in open chromatin or DNaseI-hypersensitive sites (DHSs) and to detect nucleocytoplasmic shuttling TAFs using computational and experimental screening. The DHS-proteomics revealed over 1000 potential mechanosensing TAFs and UBE2A/B (Ubiquitin-conjugating enzyme E2 A) was experimentally identified as a force- and CI-dependent nucleocytoplasmic shuttling TAF. We found that translocation of YAP/TAZ and UBE2A/B are distinctively regulated by inhibition of myosin contraction, actin-polymerization, and CI depending on cell types. Next-generation sequence analysis revealed many downstream genes including YAP are transcriptionally regulated by ubiquitination of histone by UBE2A/B. Our results suggested a YAP-independent mechanotransduction and CI pathway mediated by UBE2A/B.
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Affiliation(s)
- Mingwei Feng
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jiale Wang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Kangjing Li
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Fumihiko Nakamura
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
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4
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Zhu P, Hou C, Liu M, Chen T, Li T, Wang L. Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediol. BMC Genomics 2023; 24:493. [PMID: 37641002 PMCID: PMC10464338 DOI: 10.1186/s12864-023-09600-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Chromatin-associated phase separation proteins establish various biomolecular condensates via liquid-liquid phase separation (LLPS), which regulates vital biological processes spatially and temporally. However, the widely used methods to characterize phase separation proteins are still based on low-throughput experiments, which consume time and could not be used to explore protein LLPS properties in bulk. RESULTS By combining gradient 1,6-hexanediol (1,6-HD) elution and quantitative proteomics, we developed chromatin enriching hexanediol separation coupled with liquid chromatography-mass spectrometry (CHS-MS) to explore the LLPS properties of different chromatin-associated proteins (CAPs). First, we found that CAPs were enriched more effectively in the 1,6-HD treatment group than in the isotonic solution treatment group. Further analysis showed that the 1,6-HD treatment group could effectively enrich CAPs prone to LLPS. Finally, we compared the representative proteins eluted by different gradients of 1,6-HD and found that the representative proteins of the 2% 1,6-HD treatment group had the highest percentage of IDRs and LCDs, whereas the 10% 1,6-HD treatment group had the opposite trend. CONCLUSION This study provides a convenient high-throughput experimental method called CHS-MS. This method can efficiently enrich proteins prone to LLPS and can be extended to explore LLPS properties of CAPs in different biological systems.
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Affiliation(s)
- Peiyu Zhu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Chao Hou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Manlin Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Taoyu Chen
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, 100191, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, 100191, China.
| | - Likun Wang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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Pewklang T, Wet-osot S, Wangngae S, Ngivprom U, Chansaenpak K, Duangkamol C, Lai RY, Noisa P, Sukwattanasinitt M, Kamkaew A. Flavylium-Based Hypoxia-Responsive Probe for Cancer Cell Imaging. Molecules 2021; 26:4938. [PMID: 34443527 PMCID: PMC8400153 DOI: 10.3390/molecules26164938] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023] Open
Abstract
A hypoxia-responsive probe based on a flavylium dye containing an azo group (AZO-Flav) was synthesized to detect hypoxic conditions via a reductase-catalyzed reaction in cancer cells. In in vitro enzymatic investigation, the azo group of AZO-Flav was reduced by a reductase in the presence of reduced nicotinamide adenine dinucleotide phosphate (NADPH) followed by fragmentation to generate a fluorescent molecule, Flav-NH2. The response of AZO-Flav to the reductase was as fast as 2 min with a limit of detection (LOD) of 0.4 μM. Moreover, AZO-Flav displayed high enzyme specificity even in the presence of high concentrations of biological interferences, such as reducing agents and biothiols. Therefore, AZO-Flav was tested to detect hypoxic and normoxic environments in cancer cells (HepG2). Compared to the normal condition, the fluorescence intensity in hypoxic conditions increased about 10-fold after 15 min. Prolonged incubation showed a 26-fold higher fluorescent intensity after 60 min. In addition, the fluorescence signal under hypoxia can be suppressed by an electron transport process inhibitor, diphenyliodonium chloride (DPIC), suggesting that reductases take part in the azo group reduction of AZO-Flav in a hypoxic environment. Therefore, this probe showed great potential application toward in vivo hypoxia detection.
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Affiliation(s)
- Thitima Pewklang
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (T.P.); (S.W.-o.); (S.W.); (U.N.); (C.D.)
| | - Sirawit Wet-osot
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (T.P.); (S.W.-o.); (S.W.); (U.N.); (C.D.)
| | - Sirilak Wangngae
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (T.P.); (S.W.-o.); (S.W.); (U.N.); (C.D.)
| | - Utumporn Ngivprom
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (T.P.); (S.W.-o.); (S.W.); (U.N.); (C.D.)
| | - Kantapat Chansaenpak
- National Nanotechnology Center, National Science and Technology Development Agency, Thailand Science Park, Pathum Thani 12120, Thailand;
| | - Chuthamat Duangkamol
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (T.P.); (S.W.-o.); (S.W.); (U.N.); (C.D.)
| | - Rung-Yi Lai
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (T.P.); (S.W.-o.); (S.W.); (U.N.); (C.D.)
| | - Parinya Noisa
- Laboratory of Cell-Based Assays and Innovations, Institute of Agricultural Technology, School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
| | - Mongkol Sukwattanasinitt
- Thailand Nanotec-CU Center of Excellence on Food and Agriculture, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Anyanee Kamkaew
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (T.P.); (S.W.-o.); (S.W.); (U.N.); (C.D.)
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Alsagaby SA, Brewis IA, Vijayakumar R, Alhumaydhi FA, Alwashmi AS, Alharbi NK, Al Abdulmonem W, Premanathan M, Pratt G, Fegan C, Pepper C, Brennan P. Proteomics-based identification of cancer-associated proteins in chronic lymphocytic leukaemia. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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7
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Shang M, Weng L, Wu S, Liu B, Yin X, Wang Z, Mao A. HP1BP3 promotes tumor growth and metastasis by upregulating miR-23a to target TRAF5 in esophageal squamous cell carcinoma. Am J Cancer Res 2021; 11:2928-2943. [PMID: 34249436 PMCID: PMC8263663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 04/01/2021] [Indexed: 06/13/2023] Open
Abstract
HP1BP3, an ubiquitously expressed nuclear protein belonging to the H1 histone family of proteins, plays an important role in cell growth and viability. Recently, it was reported that HP1BP3 exclusively regulates miRNA biogenesis by enhancing transcriptional miRNA processing. Although HP1BP3 has previously been implicated in common cancer types, the mechanistic functions and effects of HP1BP3 and its role in the prognosis of esophageal squamous cell carcinoma (ESCC) remain unclear. Here, we report that ESCC tissues and cell lines show increased endogenous expression of HP1BP3. Knockdown of HP1BP3 in TE-1 cells significantly inhibited tumor growth and metastasis in vivo emphasizing its role in cell proliferation and invasion. In contrast, overexpression of HP1BP3 significantly enhanced tumor growth and metastasis in Eca-109 cells. Further, we found that HP1BP3 regulates these functions by upregulating miR-23a, which directly binds to the 3'UTR region of TRAF5 downstream to alter cell survival and proliferation. Our findings describe a role for HP1BP3 in promoting tumor growth and metastasis by upregulating miR-23a to target TRAF5 in esophageal cancer. This study provides novel insights into the potential of targeting miRNAs for therapy and as clinical markers for cancer progression.
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Affiliation(s)
- Mingyi Shang
- Department of Interventional Radiology, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
- Clinical Research Center, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Li Weng
- Department of Interventional Radiology, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
- Clinical Research Center, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Shaoqiu Wu
- Department of Interventional Radiology, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Bingyan Liu
- Department of Interventional Radiology, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Xiang Yin
- Department of Interventional Radiology, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Zhongmin Wang
- Clinical Research Center, Shanghai Jiao Tong University School of MedicineShanghai, China
- Department of Interventional Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Aiwu Mao
- Department of Interventional Radiology, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
- Clinical Research Center, Shanghai Jiao Tong University School of MedicineShanghai, China
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8
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Huang M, Lyu C, Li X, Qureshi AA, Han J, Li M. Identifying Susceptibility Loci for Cutaneous Squamous Cell Carcinoma Using a Fast Sequence Kernel Association Test. Front Genet 2021; 12:657499. [PMID: 34040636 PMCID: PMC8141858 DOI: 10.3389/fgene.2021.657499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/09/2021] [Indexed: 11/13/2022] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) accounts for about 20% of all skin cancers, the most common type of malignancy in the United States. Genome-wide association studies (GWAS) have successfully identified multiple genetic variants associated with the risk of cSCC. Most of these studies were single-locus-based, testing genetic variants one-at-a-time. In this article, we performed gene-based association tests to evaluate the joint effect of multiple variants, especially rare variants, on the risk of cSCC by using a fast sequence kernel association test (fastSKAT). The study included 1,710 cSCC cases and 24,304 cancer-free controls from the Nurses' Health Study, the Nurses' Health Study II and the Health Professionals Follow-up Study. We used UCSC Genome Browser to define gene units as candidate loci, and further evaluated the association between all variants within each gene unit and disease outcome. Four genes HP1BP3, DAG1, SEPT7P2, and SLFN12 were identified using Bonferroni adjusted significance level. Our study is complementary to the existing GWASs, and our findings may provide additional insights into the etiology of cSCC. Further studies are needed to validate these findings.
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Affiliation(s)
- Manyan Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University at Bloomington, Bloomington, IN, United States
| | - Chen Lyu
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University at Bloomington, Bloomington, IN, United States
| | - Xin Li
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University - Purdue University Indianapolis, Indianapolis, IN, United States.,Melvin and Bren Simon Cancer Center, Indianapolis, IN, United States
| | - Abrar A Qureshi
- Department of Dermatology, Alpert Medical School, Brown University, Providence, RI, United States
| | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University - Purdue University Indianapolis, Indianapolis, IN, United States.,Melvin and Bren Simon Cancer Center, Indianapolis, IN, United States
| | - Ming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University at Bloomington, Bloomington, IN, United States
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9
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Shen J, Varshney D, Simeone A, Zhang X, Adhikari S, Tannahill D, Balasubramanian S. Promoter G-quadruplex folding precedes transcription and is controlled by chromatin. Genome Biol 2021; 22:143. [PMID: 33962653 PMCID: PMC8103603 DOI: 10.1186/s13059-021-02346-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/09/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Four-stranded G-quadruplexes (G4s) are DNA secondary structures in the human genome that are primarily found in active promoters associated with elevated transcription. Here, we explore the relationship between the folding of promoter G4s, transcription and chromatin state. RESULTS Transcriptional inhibition by DRB or by triptolide reveals that promoter G4 formation, as assessed by G4 ChIP-seq, does not depend on transcriptional activity. We then show that chromatin compaction can lead to loss of promoter G4s and is accompanied by a corresponding loss of RNA polymerase II (Pol II), thus establishing a link between G4 formation and chromatin accessibility. Furthermore, pre-treatment of cells with a G4-stabilising ligand mitigates the loss of Pol II at promoters induced by chromatin compaction. CONCLUSIONS Overall, our findings show that G4 folding is coupled to the establishment of accessible chromatin and does not require active transcription.
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Affiliation(s)
- Jiazhen Shen
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Dhaval Varshney
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Angela Simeone
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Xiaoyun Zhang
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Santosh Adhikari
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - David Tannahill
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Shankar Balasubramanian
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK.
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10
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Cabrera-Licona A, Pérez-Añorve IX, Flores-Fortis M, Moral-Hernández OD, González-de la Rosa CH, Suárez-Sánchez R, Chávez-Saldaña M, Aréchaga-Ocampo E. Deciphering the epigenetic network in cancer radioresistance. Radiother Oncol 2021; 159:48-59. [PMID: 33741468 DOI: 10.1016/j.radonc.2021.03.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 02/15/2021] [Accepted: 03/09/2021] [Indexed: 12/16/2022]
Abstract
Radiotherapy, in addition to surgery and systemic chemotherapy, remains the core of the current clinical management of cancer. Radioresistance is one of the major causes of disease progression and mortality in cancer; therefore, it is a significant challenge in the treatment of locally advanced, recurrent and metastatic cancer. Epigenetic mechanisms that control hallmarks of cancer have a key role in the development of radiation resistance of cancer cells. Recent advances in DNA methylation, histone modification, chromatin remodeling and non-coding RNAs identified in the control of signal transduction pathways in cancer and cancer stem cells have provided even greater promise in the improvement of understanding cancer radioresistance. Many epigenetic drugs that target epigenetic enzymes revert the radioresistant phenotypes decreasing the possibility that resistant cancer cells will develop refractory tumors to radiotherapy. Epigenetic profiles identified as regulators of DNA damage repair, hypoxia, cell survival, apoptosis and invasion are determinants in the development of tumor radioresistance; hence, they also are promising in personalized medicine to develop novel targeted therapies or biomarkers to follow-up the effectiveness of radiotherapy. Now, it is clear that radiotherapy can influence a complex epigenetic network for transcriptional reprogramming, enabling the cells to adapt and avoid the effect of radiotherapy. This review aims to highlight the epigenetic modifications identified in cancer radioresistance and to discuss approaches to disable epigenetic networks to increase the sensitivity and specificity of radiotherapy.
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Affiliation(s)
- Ariana Cabrera-Licona
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autonoma Metropolitana, Ciudad de Mexico, Mexico; Posgrado en Ciencias Naturales e Ingenieria, Unidad Cuajimalpa, Universidad Autonoma Metropolitana, Ciudad de Mexico, Mexico
| | - Isidro X Pérez-Añorve
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autonoma Metropolitana, Ciudad de Mexico, Mexico
| | - Mauricio Flores-Fortis
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autonoma Metropolitana, Ciudad de Mexico, Mexico; Posgrado en Ciencias Naturales e Ingenieria, Unidad Cuajimalpa, Universidad Autonoma Metropolitana, Ciudad de Mexico, Mexico
| | - Oscar Del Moral-Hernández
- Laboratorio de Virologia y Epigenetica del Cancer, Facultad de Ciencias Quimico Biologicas, Universidad Autonoma de Guerrero, Chilpancingo, Mexico
| | | | - Rocio Suárez-Sánchez
- Laboratorio de Medicina Genomica, Departamento de Genetica, Instituto Nacional de Rehabilitacion LGII, Ciudad de Mexico, Mexico
| | - Margarita Chávez-Saldaña
- Laboratorio de Biologia de la Reproduccion, Instituto Nacional de Pediatria, Ciudad de Mexico, Mexico
| | - Elena Aréchaga-Ocampo
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autonoma Metropolitana, Ciudad de Mexico, Mexico.
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11
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Federation AJ, Nandakumar V, Searle BC, Stergachis A, Wang H, Pino LK, Merrihew G, Ting YS, Howard N, Kutyavin T, MacCoss MJ, Stamatoyannopoulos JA. Highly Parallel Quantification and Compartment Localization of Transcription Factors and Nuclear Proteins. Cell Rep 2021; 30:2463-2471.e5. [PMID: 32101728 DOI: 10.1016/j.celrep.2020.01.096] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/15/2019] [Accepted: 01/28/2020] [Indexed: 01/12/2023] Open
Abstract
Transcription factors and other chromatin-associated proteins are difficult to quantify comprehensively. Here, we combine facile nuclear sub-fractionation with data-independent acquisition mass spectrometry to achieve rapid, sensitive, and highly parallel quantification of the nuclear proteome in human cells. We apply this approach to quantify the response to acute degradation of BET bromodomains, revealing unexpected chromatin regulatory dynamics. The method is simple and enables system-level study of previously inaccessible chromatin and genome regulators.
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Affiliation(s)
| | - Vivek Nandakumar
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Brian C Searle
- University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA
| | - Andrew Stergachis
- University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA
| | - Hao Wang
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Lindsay K Pino
- University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA
| | - Gennifer Merrihew
- University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA
| | - Ying S Ting
- University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA
| | - Nicholas Howard
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Tanya Kutyavin
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Michael J MacCoss
- University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA.
| | - John A Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA; University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA.
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12
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Vinaiphat A, Low JK, Yeoh KW, Chng WJ, Sze SK. Application of Advanced Mass Spectrometry-Based Proteomics to Study Hypoxia Driven Cancer Progression. Front Oncol 2021; 11:559822. [PMID: 33708620 PMCID: PMC7940826 DOI: 10.3389/fonc.2021.559822] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/07/2021] [Indexed: 12/24/2022] Open
Abstract
Cancer is one of the largest contributors to the burden of chronic disease in the world and is the second leading cause of death globally. It is associated with episodes of low-oxygen stress (hypoxia or ischemia/reperfusion) that promotes cancer progression and therapeutic resistance. Efforts have been made in the past using traditional proteomic approaches to decipher oxygen deprivation stress-related mechanisms of the disease initiation and progression and to identify key proteins as a therapeutic target for the treatment and prevention. Despite the potential benefits of proteomic in translational research for the discovery of new drugs, the therapeutic outcome with this approach has not met expectations in clinical trials. This is mainly due to the disease complexity which possess a multifaceted molecular pathology. Therefore, novel strategies to identify and characterize clinically important sets of modulators and molecular events for multi-target drug discovery are needed. Here, we review important past and current studies on proteomics in cancer with an emphasis on recent pioneered labeling approaches in mass spectrometry (MS)-based systematic quantitative analysis to improve clinical success. We also discuss the results of the selected innovative publications that integrate advanced proteomic technologies (e.g. MALDI-MSI, pSILAC/SILAC/iTRAQ/TMT-LC-MS/MS, MRM-MS) for comprehensive analysis of proteome dynamics in different biosystems, including cell type, cell species, and subcellular proteome (i.e. secretome and chromatome). Finally, we discuss the future direction and challenges in the application of these technological advancements in mass spectrometry within the context of cancer and hypoxia.
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Affiliation(s)
- Arada Vinaiphat
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jee Keem Low
- Department of Surgery, Tan Tock Seng Hospital, Singapore, Singapore
| | - Kheng Wei Yeoh
- Department of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Wee Joo Chng
- Department of Hematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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13
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Gene transcription and chromatin regulation in hypoxia. Biochem Soc Trans 2021; 48:1121-1128. [PMID: 32369557 PMCID: PMC7329336 DOI: 10.1042/bst20191106] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/02/2020] [Accepted: 04/06/2020] [Indexed: 12/30/2022]
Abstract
Oxygen sensing is an essential feature of metazoan biology and reductions in oxygen availability (hypoxia) have both physiological and pathophysiological implications. Co-ordinated mechanisms have evolved for sensing and responding to hypoxia, which involve diverse biological outputs, with the main aim of restoring oxygen homeostasis. This includes a dynamic gene transcriptional response, the central drivers of which are the hypoxia-inducible factor (HIF) family of transcription factors. HIFs are regulated in an oxygen-dependent manner and while their role in hypoxia is well established, it is apparent that other key players are required for gene expression control in hypoxia. In this review, we highlight the current understanding of the known and potential molecular mechanisms underpinning gene transcriptional responses to hypoxia in mammals, with a focus on oxygen-dependent effects on chromatin structure.
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14
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Belrose JL, Prasad A, Sammons MA, Gibbs KM, Szaro BG. Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons. BMC Genomics 2020; 21:540. [PMID: 32758133 PMCID: PMC7430912 DOI: 10.1186/s12864-020-06954-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The South African claw-toed frog, Xenopus laevis, is uniquely suited for studying differences between regenerative and non-regenerative responses to CNS injury within the same organism, because some CNS neurons (e.g., retinal ganglion cells after optic nerve crush (ONC)) regenerate axons throughout life, whereas others (e.g., hindbrain neurons after spinal cord injury (SCI)) lose this capacity as tadpoles metamorphose into frogs. Tissues from these CNS regions (frog ONC eye, tadpole SCI hindbrain, frog SCI hindbrain) were used in a three-way RNA-seq study of axotomized CNS axons to identify potential core gene expression programs for successful CNS axon regeneration. RESULTS Despite tissue-specific changes in expression dominating the injury responses of each tissue, injury-induced changes in gene expression were nonetheless shared between the two axon-regenerative CNS regions that were not shared with the non-regenerative region. These included similar temporal patterns of gene expression and over 300 injury-responsive genes. Many of these genes and their associated cellular functions had previously been associated with injury responses of multiple tissues, both neural and non-neural, from different species, thereby demonstrating deep phylogenetically conserved commonalities between successful CNS axon regeneration and tissue regeneration in general. Further analyses implicated the KEGG adipocytokine signaling pathway, which links leptin with metabolic and gene regulatory pathways, and a novel gene regulatory network with genes regulating chromatin accessibility at its core, as important hubs in the larger network of injury response genes involved in successful CNS axon regeneration. CONCLUSIONS This study identifies deep, phylogenetically conserved commonalities between CNS axon regeneration and other examples of successful tissue regeneration and provides new targets for studying the molecular underpinnings of successful CNS axon regeneration, as well as a guide for distinguishing pro-regenerative injury-induced changes in gene expression from detrimental ones in mammals.
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Affiliation(s)
- Jamie L Belrose
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Aparna Prasad
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Morgan A Sammons
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Kurt M Gibbs
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, 40351, USA
| | - Ben G Szaro
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.
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15
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Luo A, Gong Y, Kim H, Chen Y. Proteome dynamics analysis identifies functional roles of SDE2 and hypoxia in DNA damage response in prostate cancer cells. NAR Cancer 2020; 2:zcaa010. [PMID: 32743553 PMCID: PMC7380487 DOI: 10.1093/narcan/zcaa010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/19/2020] [Accepted: 06/08/2020] [Indexed: 12/20/2022] Open
Abstract
Mechanistic understanding of hypoxia-responsive signaling pathways provides important insights into oxygen- and metabolism-dependent cellular phenotypes in diseases. Using SILAC-based quantitative proteomics, we provided a quantitative map identifying over 6300 protein groups in response to hypoxia in prostate cancer cells and identified both canonical and novel cellular networks dynamically regulated under hypoxia. Particularly, we identified SDE2, a DNA stress response modulator, that was significantly downregulated by hypoxia, independent of HIF (hypoxia-inducible factor) transcriptional activity. Mechanistically, hypoxia treatment promoted SDE2 polyubiquitination and degradation. Such regulation is independent of previously identified Arg/N-end rule proteolysis or the ubiquitin E3 ligase, CDT2. Depletion of SDE2 increased cellular sensitivity to DNA damage and inhibited cell proliferation. Interestingly, either SDE2 depletion or hypoxia treatment potentiated DNA damage-induced PCNA (proliferating cell nuclear antigen) monoubiquitination, a key step for translesion DNA synthesis. Furthermore, knockdown of SDE2 desensitized, while overexpression of SDE2 protected the hypoxia-mediated regulation of PCNA monoubiquitination upon DNA damage. Taken together, our quantitative proteomics and biochemical study revealed diverse hypoxia-responsive pathways that strongly associated with prostate cancer tumorigenesis and identified the functional roles of SDE2 and hypoxia in regulating DNA damage-induced PCNA monoubiquitination, suggesting a possible link between hypoxic microenvironment and the activation of error-prone DNA repair pathway in tumor cells.
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Affiliation(s)
- Ang Luo
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Yao Gong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
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16
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Zhang Y, Kang Z, Lv D, Zhang X, Liao Y, Li Y, Liu R, Li P, Tong M, Tian J, Shao Y, Huang C, Ge D, Zhang J, Bai W, Wang Y, Liu Q, Li Z, Yan J. Longitudinal whole-genome sequencing reveals the evolution of MPAL. Cancer Genet 2020; 240:59-65. [DOI: 10.1016/j.cancergen.2019.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/21/2019] [Accepted: 11/21/2019] [Indexed: 12/30/2022]
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17
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Gupta N, Park JE, Tse W, Low JK, Kon OL, McCarthy N, Sze SK. ERO1α promotes hypoxic tumor progression and is associated with poor prognosis in pancreatic cancer. Oncotarget 2019; 10:5970-5982. [PMID: 31666928 PMCID: PMC6800261 DOI: 10.18632/oncotarget.27235] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/24/2019] [Indexed: 01/04/2023] Open
Abstract
Pancreatic cancer is a leading cause of mortality worldwide due to the difficulty of detecting early-stage disease and our poor understanding of the mediators that drive progression of hypoxic solid tumors. We therefore used a heavy isotope 'pulse/trace' proteomic approach to determine how hypoxia (Hx) alters pancreatic tumor expression of proteins that confer treatment resistance, promote metastasis, and suppress host immunity. Using this method, we identified that hypoxia stress stimulates pancreatic cancer cells to rapidly translate proteins that enhance metastasis (NOTCH2, NCS1, CD151, NUSAP1), treatment resistance (ABCB6), immune suppression (NFIL3, WDR4), angiogenesis (ANGPT4, ERO1α, FOS), alter cell metabolic activity (HK2, ENO2), and mediate growth-promoting cytokine responses (CLK3, ANGPTL4). Database mining confirmed that elevated gene expression of these hypoxia-induced mediators is significantly associated with poor patient survival in various stages of pancreatic cancer. Among these proteins, the oxidoreductase enzyme ERO1α was highly sensitive to induction by hypoxia stress across a range of different pancreatic cancer cell lines and was associated with particularly poor prognosis in human patients. Consistent with these data, genetic deletion of ERO1α substantially reduced growth rates and colony formation by pancreatic cancer cells when assessed in a series of functional assays in vitro. Accordingly, when transferred into a mouse xenograft model, ERO1α-deficient tumor cells exhibited severe growth restriction and negligible disease progression in vivo. Together, these data indicate that ERO1α is potential prognostic biomarker and novel drug target for pancreatic cancer therapy.
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Affiliation(s)
- Nikhil Gupta
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jung Eun Park
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Wilford Tse
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jee Keem Low
- Department of Surgery, Tan Tock Seng Hospital, Singapore
| | - Oi Lian Kon
- National Cancer Centre Singapore, Division of Medical Sciences, Singapore
| | - Neil McCarthy
- Centre for Immunobiology, The Blizard Institute, Bart’s and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore
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18
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van Mierlo G, Wester RA, Marks H. A Mass Spectrometry Survey of Chromatin-Associated Proteins in Pluripotency and Early Lineage Commitment. Proteomics 2019; 19:e1900047. [PMID: 31219242 DOI: 10.1002/pmic.201900047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/07/2019] [Indexed: 12/12/2022]
Abstract
Pluripotency can be captured in vitro in the form of Embryonic Stem Cells (ESCs). These ESCs can be either maintained in the unrestricted "naïve" state of pluripotency, adapted to developmentally more constrained "primed" pluripotency or differentiated towards each of the three germ layers. Epigenetic protein complexes and transcription factors have been shown to specify and instruct transitions from ESCs to distinct cell states. In this study, proteomic profiling of the chromatin landscape by chromatin enrichment for proteomics (ChEP) is used in mouse naive pluripotent ESCs, primed pluripotent Epiblast stem cells (EpiSCs), and cells in early stages of differentiation. A comprehensive overview of epigenetic protein complexes associated with the chromatin is provided and proteins associated with the maintenance and loss of pluripotency are identified. The data reveal major compositional alterations of epigenetic complexes during priming and differentiation of naïve pluripotent ESCs. These results contribute to the understanding of ESC differentiation and provide a framework for future studies of lineage commitment of ESCs.
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Affiliation(s)
- Guido van Mierlo
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands.,Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Roelof Alexander Wester
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands
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19
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Irmak D, Fatima A, Gutiérrez-Garcia R, Rinschen MM, Wagle P, Altmüller J, Arrigoni L, Hummel B, Klein C, Frese CK, Sawarkar R, Rada-Iglesias A, Vilchez D. Mechanism suppressing H3K9 trimethylation in pluripotent stem cells and its demise by polyQ-expanded huntingtin mutations. Hum Mol Genet 2019; 27:4117-4134. [PMID: 30452683 DOI: 10.1093/hmg/ddy304] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/10/2018] [Indexed: 02/06/2023] Open
Abstract
Pluripotent stem cells are invaluable resources to study development and disease, holding a great promise for regenerative medicine. Here we use human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) from patients with Huntington's disease (HD-iPSCs) to shed light into the normal function of huntingtin (HTT) and its demise in disease. We find that HTT binds ATF7IP, a regulator of the histone H3 methyltransferase SETDB1. HTT inhibits the interaction of the ATF7IP-SETDB1 complex with other heterochromatin regulators and transcriptional repressors, maintaining low levels of H3K9 trimethylation (H3K9me3) in hESCs. Loss of HTT promotes global increased H3K9me3 levels and enrichment of H3K9me3 marks at distinct genes, including transcriptional regulators of neuronal differentiation. Although these genes are normally expressed at low amounts in hESCs, HTT knockdown (KD) reduces their induction during neural differentiation. Notably, mutant expanded polyglutamine repeats in HTT diminish its interaction with ATF7IP-SETDB1 complex and trigger H3K9me3 in HD-iPSCs. Conversely, KD of ATF7IP in HD-iPSCs reduces H3K9me3 alterations and ameliorates gene expression changes in their neural counterparts. Taken together, our results indicate ATF7IP as a potential target to correct aberrant H3K9me3 levels induced by mutant HTT.
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Affiliation(s)
- Dilber Irmak
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| | - Azra Fatima
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| | - Ricardo Gutiérrez-Garcia
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| | - Markus M Rinschen
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| | - Prerana Wagle
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| | - Janine Altmüller
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Strasse 21, Cologne, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Barbara Hummel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Corinna Klein
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| | - Christian K Frese
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| | - Ritwick Sawarkar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Alvaro Rada-Iglesias
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Strasse 21, Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
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20
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Park JE, Tse SW, Xue G, Assisi C, Maqueda AS, Ramon GPX, Low JK, Kon OL, Tay CY, Tam JP, Sze SK. Pulsed SILAC-based proteomic analysis unveils hypoxia- and serum starvation-induced de novo protein synthesis with PHD finger protein 14 (PHF14) as a hypoxia sensitive epigenetic regulator in cell cycle progression. Oncotarget 2019; 10:2136-2150. [PMID: 31040906 PMCID: PMC6481330 DOI: 10.18632/oncotarget.26669] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 12/27/2018] [Indexed: 12/27/2022] Open
Abstract
Hypoxia is an environmental cue that is associated with multiple tumorigenic processes such as immunosuppression, angiogenesis, cancer invasion, metastasis, drug resistance, and poor clinical outcomes. When facing hypoxic stress, cells initiate several adaptive responses such as cell cycle arrest to reduce excessive oxygen consumption and co-activation of oncogenic factors. In order to identify the critical novel proteins for hypoxia responses, we used pulsed-SILAC method to trace the active cellular translation events in A431 cells. Proteomic discovery data and biochemical assays showed that cancer cells selectively activate key glycolytic enzymes and novel ER-stress markers, while protein synthesis is severely suppressed. Interestingly, deprivation of oxygen affected the expression of various epigenetic regulators such as histone demethylases and NuRD (nucleosome remodeling and deacetylase) complex in A431 cells. In addition, we identified PHF14 (the plant homeodomain finger-14) as a novel hypoxia-sensitive epigenetic regulator that plays a key role in cell cycle progress and protein synthesis. Hypoxia-mediated inhibition of PHF14 was associated with increase of key cell cycle inhibitors, p14ARF, p15INK4b, and p16INK4a, which are responsible for G1-S phase transition and decrease of AKT-mTOR-4E-BP1/pS6K signaling pathway, a master regulator of protein synthesis, in response to environmental cues. Analysis of TCGA colon cancer (n=461) and skin cancer (n=470) datasets revealed a positive correlation between PHF14 expression and protein translation initiation factors, eIF4E, eIF4B, and RPS6. Significance of PHF14 gene was further demonstrated by in vivo mouse xenograft model using PHF14 KD cell lines.
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Affiliation(s)
- Jung Eun Park
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Shun Wilford Tse
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Guo Xue
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Christina Assisi
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Aida Serra Maqueda
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Gallart Palau Xavier Ramon
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Jee Keem Low
- Department of Oncology, Tan Tock Seng Hospital, Singapore 308433
| | - Oi Lian Kon
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore 169610
| | - Chor Yong Tay
- Division of Materials Technology School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798
| | - James P Tam
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Siu Kwan Sze
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
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21
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22
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Dutta B, Park JE, Qing ITY, Kon OL, Sze SK. Soy-Derived Phytochemical Genistein Modifies Chromatome Topology to Restrict Cancer Cell Proliferation. Proteomics 2018; 18:e1700474. [PMID: 29963755 DOI: 10.1002/pmic.201700474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/22/2018] [Indexed: 12/18/2022]
Abstract
Epidemiological data indicate that human cancer risk is significantly reduced by the consumption of soy-based foods containing the "phytoestrogen" genistein, which can signal via host cell estrogen receptors. While additional chemoprotective effects of genistein induced by epigenetic factors have also been reported, the key molecules and mechanisms involved are poorly defined. We therefore investigated genistein effects on chromatin-bound proteins in the estrogen receptor-deficient cell line MDA-MB-231 which is insensitive to phytoestrogen signaling. After exposure to low-dose genistein for >1 month, MDA-MB-231 cells exhibited stable epigenetic alterations that are analyzed via partial MNase digestion and TMT-based quantitative proteomics. 3177 chromatin-bound proteins are identified with high confidence, including 882 molecules that displayed altered binding topology after cell conditioning with genistein. Prolonged phytochemical exposure conferred heritable changes in the binding topology of key epigenetic regulators including ATRX, SUV39H1/H2, and HP1BP3 that are preserved in untreated progeny, resulting in sustained downregulation of proliferation genes and reduced cell growth. These data indicate that soy derivative genistein exerts complex estrogen receptor-independent effects on the epigenome likely to influence tumorigenesis by restricting cell growth.
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Affiliation(s)
- Bamaprasad Dutta
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jung Eun Park
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Ivan Toh Yi Qing
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Oi Lian Kon
- Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, 169610, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
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23
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Batie M, Del Peso L, Rocha S. Hypoxia and Chromatin: A Focus on Transcriptional Repression Mechanisms. Biomedicines 2018; 6:biomedicines6020047. [PMID: 29690561 PMCID: PMC6027312 DOI: 10.3390/biomedicines6020047] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/26/2018] [Accepted: 04/19/2018] [Indexed: 12/20/2022] Open
Abstract
Hypoxia or reduced oxygen availability has been studied extensively for its ability to activate specific genes. Hypoxia-induced gene expression is mediated by the HIF transcription factors, but not exclusively so. Despite the extensive knowledge about how hypoxia activates genes, much less is known about how hypoxia promotes gene repression. In this review, we discuss the potential mechanisms underlying hypoxia-induced transcriptional repression responses. We highlight HIF-dependent and independent mechanisms as well as the potential roles of dioxygenases with functions at the nucleosome and DNA level. Lastly, we discuss recent evidence regarding the involvement of transcriptional repressor complexes in hypoxia.
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Affiliation(s)
- Michael Batie
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L697ZB, UK.
| | - Luis Del Peso
- Department of Biochemistry, Institute of Biomedical Research, Autonomous Madrid University, Arturo Duperier, 4. 28029 Madrid, Spain.
| | - Sonia Rocha
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L697ZB, UK.
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24
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Hao D, Li J, Jia S, Meng Y, Zhang C, Wang L, Di LJ. Integrated Analysis Reveals Tubal- and Ovarian-Originated Serous Ovarian Cancer and Predicts Differential Therapeutic Responses. Clin Cancer Res 2017; 23:7400-7411. [PMID: 28939742 DOI: 10.1158/1078-0432.ccr-17-0638] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 07/12/2017] [Accepted: 09/19/2017] [Indexed: 11/16/2022]
Abstract
Purpose: The relative importance of fallopian tube (FT) compared with ovarian surface epithelium (OSE) in the genesis of serous type of ovarian cancer (SOC) is still unsettled. Here, we followed an integrated approach to study the tissue origin of SOC, as well as its association with clinical outcome and response to therapeutic drugs.Experimental Design: A collection of transcriptome data of 80 FTs, 89 OSEs, and 2,668 SOCs was systematically analyzed to determine the characteristic of FT-like and OSE-like tumors. A molecular signature was developed for identifying tissue origin of SOC and then was used to reevaluate the prognostic genes and therapeutic biomarkers of SOC of different tissue origins. IHC staining of tissue array and functional experiments on a panel of ovarian cancer cell lines were used to further validate the key findings.Results: The expression patterns of tissue-specific genes, prognostic genes, and molecular markers all support a dualistic tissue origin of SOC, from either FT or OSE. A molecular signature was established to identify the tissue identity of SOCs. Surprisingly, the signature showed a strong association with overall survival (OSE-like vs. FT-like, HR = 4.16; 95% CI, 2.67-6.48; P < 10-9). The pharmacogenomic approach revealed AXL to be a therapeutic target of the aggressive OSE-derived SOC.Conclusions: SOC has two subtypes originated from either FT or OSE, which show different clinical and pathologic features. Clin Cancer Res; 23(23); 7400-11. ©2017 AACR.
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Affiliation(s)
- Dapeng Hao
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China
| | - Jingjing Li
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China
| | - Shanshan Jia
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China
| | - Yuan Meng
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China
| | - Chao Zhang
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China
| | - Li Wang
- Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, China
| | - Li-Jun Di
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China.
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Gao Z, Luo G, Ni B. Progress in mass spectrometry-based proteomic research of tumor hypoxia (Review). Oncol Rep 2017; 38:676-684. [PMID: 28656308 DOI: 10.3892/or.2017.5748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 05/31/2017] [Indexed: 11/06/2022] Open
Abstract
A hypoxic microenvironment effects various signaling pathways in the human body, including those that are critical for normal physiology and those that support tumorigenesis or cancer progression. A hypoxic tumor microenvironment, in particular, modulates cell migration, invasion and resistance to radiotherapy and chemotherapy. Development of the mass spectrometry (MS) technique has allowed for expansion of proteomic study to a wide variety of fields, with the study of tumor hypoxia being among the latest to enjoy its benefits. In such studies, changes in the proteome of tumor tissue or cells induced by the hypoxic conditions are analyzed. A multitude of hypoxic regulatory proteins have already been identified, increasing our understanding of the mechanisms underlying tumor occurrence and development and representing candidate reference markers for tumor diagnosis and therapy. The present review provides the first summary of the collective studies on tumor microenvironment hypoxia that have been completed using MS-based proteomic techniques, providing a systematic discussion of the benefits and current challenges of the various applications.
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Affiliation(s)
- Zhiqi Gao
- Department of Pathophysiology and High Altitude Pathology/Key Laboratory of High Altitude Environment Medicine (Third Military Medical University), Ministry of Education/Key Laboratory of High Altitude Medicine, College of High Altitude Military Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Gang Luo
- Department of Pathophysiology and High Altitude Pathology/Key Laboratory of High Altitude Environment Medicine (Third Military Medical University), Ministry of Education/Key Laboratory of High Altitude Medicine, College of High Altitude Military Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Bing Ni
- Department of Pathophysiology and High Altitude Pathology/Key Laboratory of High Altitude Environment Medicine (Third Military Medical University), Ministry of Education/Key Laboratory of High Altitude Medicine, College of High Altitude Military Medicine, Third Military Medical University, Chongqing 400038, P.R. China
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26
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Dick JM. Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. PeerJ 2017; 5:e3421. [PMID: 28603672 PMCID: PMC5463988 DOI: 10.7717/peerj.3421] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/16/2017] [Indexed: 12/19/2022] Open
Abstract
The changes of protein expression that are monitored in proteomic experiments are a type of biological transformation that also involves changes in chemical composition. Accompanying the myriad molecular-level interactions that underlie any proteomic transformation, there is an overall thermodynamic potential that is sensitive to microenvironmental conditions, including local oxidation and hydration potential. Here, up- and down-expressed proteins identified in 71 comparative proteomics studies were analyzed using the average oxidation state of carbon (ZC) and water demand per residue (\documentclass[12pt]{minimal}
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}{}${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$\end{document}n¯H2O), calculated using elemental abundances and stoichiometric reactions to form proteins from basis species. Experimental lowering of oxygen availability (hypoxia) or water activity (hyperosmotic stress) generally results in decreased ZC or \documentclass[12pt]{minimal}
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}{}${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$\end{document}n¯H2O of up-expressed compared to down-expressed proteins. This correspondence of chemical composition with experimental conditions provides evidence for attraction of the proteomes to a low-energy state. An opposite compositional change, toward higher average oxidation or hydration state, is found for proteomic transformations in colorectal and pancreatic cancer, and in two experiments for adipose-derived stem cells. Calculations of chemical affinity were used to estimate the thermodynamic potentials for proteomic transformations as a function of fugacity of O2 and activity of H2O, which serve as scales of oxidation and hydration potential. Diagrams summarizing the relative potential for formation of up- and down-expressed proteins have predicted equipotential lines that cluster around particular values of oxygen fugacity and water activity for similar datasets. The changes in chemical composition of proteomes are likely linked with reactions among other cellular molecules. A redox balance calculation indicates that an increase in the lipid to protein ratio in cancer cells by 20% over hypoxic cells would generate a large enough electron sink for oxidation of the cancer proteomes. The datasets and computer code used here are made available in a new R package, canprot.
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Xu D, Yang Q, Cui M, Zhang Q. The novel transcriptional factor HP1BP3 negatively regulates Hsp70 transcription in Crassostrea hongkongensis. Sci Rep 2017; 7:1401. [PMID: 28469151 PMCID: PMC5431216 DOI: 10.1038/s41598-017-01573-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/29/2017] [Indexed: 11/29/2022] Open
Abstract
ChHP1BP3, a chromatin complex-related protein known with dynamic features, was identified as a ChHsp70 promoter-associated factor in Crassostrea hongkongensis by DNA-affinity purification and mass spectrometry analysis. Direct interaction between purified ChHP1BP3 and the ChHsp70 promoter region was demonstrated using EMSA. ChHp1bp3 depletion led to clear enhancements in ChHsp70 mRNA expression in C. hongkongensis hemocytes. However, ChHp1bp3 overexpression in heterologous HEK293T cells correlated with fluctuations in ChHsp70 transcription. Quantitative RT-PCR analysis showed that both ChHsp70 and ChHp1bp3 transcription were responsive to external physical/chemical stresses by heat, CdCl2 and NP. This indicated a plausible correlation between ChHsp70 and ChHp1bp3 in the stress-induced genetic regulatory pathway. While, the distinctive ChHp1bp3 expression patterns upon physical and chemical stresses suggest that the mechanisms that mediate ChHp1bp3 induction might be stress-specific. This study discovered a novel role for HP1BP3 as a negative regulator in controlling Hsp70 transcription in C. hongkongensis, and contributed to better understanding the complex regulatory mechanisms governing Hsp70 transcription.
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Affiliation(s)
- Delin Xu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China
| | - Qin Yang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China
| | - Miao Cui
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China.
| | - Qizhong Zhang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China.
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Hollerer I, Curk T, Haase B, Benes V, Hauer C, Neu-Yilik G, Bhuvanagiri M, Hentze MW, Kulozik AE. The differential expression of alternatively polyadenylated transcripts is a common stress-induced response mechanism that modulates mammalian mRNA expression in a quantitative and qualitative fashion. RNA (NEW YORK, N.Y.) 2016; 22:1441-1453. [PMID: 27407180 PMCID: PMC4986898 DOI: 10.1261/rna.055657.115] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
Stress adaptation plays a pivotal role in biological processes and requires tight regulation of gene expression. In this study, we explored the effect of cellular stress on mRNA polyadenylation and investigated the implications of regulated polyadenylation site usage on mammalian gene expression. High-confidence polyadenylation site mapping combined with global pre-mRNA and mRNA expression profiling revealed that stress induces an accumulation of genes with differentially expressed polyadenylated mRNA isoforms in human cells. Specifically, stress provokes a global trend in polyadenylation site usage toward decreased utilization of promoter-proximal poly(A) sites in introns or ORFs and increased utilization of promoter-distal polyadenylation sites in intergenic regions. This extensively affects gene expression beyond regulating mRNA abundance by changing mRNA length and by altering the configuration of open reading frames. Our study highlights the impact of post-transcriptional mechanisms on stress-dependent gene regulation and reveals the differential expression of alternatively polyadenylated transcripts as a common stress-induced mechanism in mammalian cells.
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Affiliation(s)
- Ina Hollerer
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
| | - Tomaz Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana 1001, Slovenia
| | - Bettina Haase
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Vladimir Benes
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Christian Hauer
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
| | - Gabriele Neu-Yilik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
| | - Madhuri Bhuvanagiri
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
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Admoni-Elisha L, Nakdimon I, Shteinfer A, Prezma T, Arif T, Arbel N, Melkov A, Zelichov O, Levi I, Shoshan-Barmatz V. Novel Biomarker Proteins in Chronic Lymphocytic Leukemia: Impact on Diagnosis, Prognosis and Treatment. PLoS One 2016; 11:e0148500. [PMID: 27078856 PMCID: PMC4831809 DOI: 10.1371/journal.pone.0148500] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 01/19/2016] [Indexed: 12/31/2022] Open
Abstract
In many cancers, cells undergo re-programming of metabolism, cell survival and anti-apoptotic defense strategies, with the proteins mediating this reprogramming representing potential biomarkers. Here, we searched for novel biomarker proteins in chronic lymphocytic leukemia (CLL) that can impact diagnosis, treatment and prognosis by comparing the protein expression profiles of peripheral blood mononuclear cells from CLL patients and healthy donors using specific antibodies, mass spectrometry and binary logistic regression analyses and other bioinformatics tools. Mass spectrometry (LC-HR-MS/MS) analysis identified 1,360 proteins whose expression levels were modified in CLL-derived lymphocytes. Some of these proteins were previously connected to different cancer types, including CLL, while four other highly expressed proteins were not previously reported to be associated with cancer, and here, for the first time, DDX46 and AK3 are linked to CLL. Down-regulation expression of two of these proteins resulted in cell growth inhibition. High DDX46 expression levels were associated with shorter survival of CLL patients and thus can serve as a prognosis marker. The proteins with modified expression include proteins involved in RNA splicing and translation and particularly mitochondrial proteins involved in apoptosis and metabolism. Thus, we focused on several metabolism- and apoptosis-modulating proteins, particularly on the voltage-dependent anion channel 1 (VDAC1), regulating both metabolism and apoptosis. Expression levels of Bcl-2, VDAC1, MAVS, AIF and SMAC/Diablo were markedly increased in CLL-derived lymphocytes. VDAC1 levels were highly correlated with the amount of CLL-cancerous CD19+/CD5+ cells and with the levels of all other apoptosis-modulating proteins tested. Binary logistic regression analysis demonstrated the ability to predict probability of disease with over 90% accuracy. Finally, based on the changes in the levels of several proteins in CLL patients, as revealed from LC-HR-MS/MS, we could distinguish between patients in a stable disease state and those who would be later transferred to anti-cancer treatments. The over-expressed proteins can thus serve as potential biomarkers for early diagnosis, prognosis, new targets for CLL therapy, and treatment guidance of CLL, forming the basis for personalized therapy.
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MESH Headings
- Aged
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Blotting, Western
- Chromatography, Liquid
- Female
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/blood
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukocytes, Mononuclear/metabolism
- Male
- Prognosis
- Proteome/analysis
- RNA, Messenger/genetics
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Tandem Mass Spectrometry/methods
- Tumor Cells, Cultured
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Affiliation(s)
- Lee Admoni-Elisha
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Itay Nakdimon
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Anna Shteinfer
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Tal Prezma
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Tasleem Arif
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Nir Arbel
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Anna Melkov
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ori Zelichov
- Department of Hematology, Soroka University Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Itai Levi
- Department of Hematology, Soroka University Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Varda Shoshan-Barmatz
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
- * E-mail:
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30
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Maekawa R, Lee L, Okada M, Asada H, Shinagawa M, Tamura I, Sato S, Tamura H, Sugino N. Changes in gene expression of histone modification enzymes in rat granulosa cells undergoing luteinization during ovulation. J Ovarian Res 2016; 9:15. [PMID: 26979106 PMCID: PMC4793631 DOI: 10.1186/s13048-016-0225-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/09/2016] [Indexed: 12/20/2022] Open
Abstract
Background The ovulatory LH surge rapidly alters the expression of steroidogenesis-related genes such as steroidogenic acute regulatory protein (StAR) in granulosa cells (GCs) undergoing luteinization. We recently reported that histone modifications contribute to these changes. Histone modifications are regulated by a variety of histone modification enzymes. This study investigated the changes in gene expression of histone modification enzymes in rat GCs undergoing luteinization after the induction of ovulation. The extracellular regulated kinase (ERK)-1/2 is a mediator in the intracellular signaling pathway stimulated by the ovulatory LH surge and regulates the expression of a number of genes in GCs. We further investigated whether ERK-1/2 is involved in the regulation of the histone modification at the StAR promoter region in GCs undergoing luteinization. Results GCs were obtained from rats treated with equine chorionic gonadotropin (CG) before (0 h) and after human (h) CG injection. The expressions of 84 genes regulating histone modifications or DNA methylation were measured using a PCR array. Five genes (HDAC4, HDAC10, EZH2, SETDB2, and CIITA) were identified as histone acetylation- or histone methylation-related genes, and were significantly altered after hCG injection. None of the genes were related to DNA methylation. mRNA levels of EZH2, SETDB2, HDAC4, and HDAC10 decreased and CIITA mRNA levels increased 4 or 12 h after hCG injection. GCs isolated after eCG injection were incubated with hCG for 4 h to induce luteinization. StAR mRNA levels were significantly increased by hCG accompanied by the increase in H3K4me3 of the StAR promoter region. StAR mRNA expression was inhibited by the ERK inhibitor with the significant decrease of H3K4me3. These results suggest that hCG increases StAR gene expression through the ERK-1/2-mediated signaling which is also associated with histone modification of the promoter region. Conclusions Gene expressions of histone modification enzymes change in GCs undergoing luteinization after ovulation induction. This change may play important roles in regulating the expression of various genes during the early stage of luteinization, which may be critical for the subsequent corpus luteum formation.
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Affiliation(s)
- Ryo Maekawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Lifa Lee
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Maki Okada
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Hiromi Asada
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Masahiro Shinagawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Isao Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Shun Sato
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Hiroshi Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Norihiro Sugino
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan.
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Hadac JN, Miller DD, Grimes IC, Clipson L, Newton MA, Schelman WR, Halberg RB. Heterochromatin Protein 1 Binding Protein 3 Expression as a Candidate Marker of Intrinsic 5-Fluorouracil Resistance. Anticancer Res 2016; 36:845-852. [PMID: 26976970 PMCID: PMC4876978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
BACKGROUND Despite receiving post-operative 5-fluorouracil (5-FU)-based chemotherapy, approximately 50% of patients with stage IIIC colon cancer experience recurrence. Currently, no molecular signature can predict response to 5-FU. MATERIALS AND METHODS Mouse models of colon cancer have been developed and characterized. Individual tumors in these mice can be longitudinally monitored and assessed to identify differences between those that are responsive and those that are resistant to therapy. Gene expression was analyzed in serial biopsies that were collected before and after treatment with 5-FU. Colon tumors had heterogeneous responses to treatment with 5-FU. Microarray analysis of pre-treatment biopsies revealed that Hp1bp3, a gene encoding heterochromatin protein 1 binding protein 3, was differentially expressed between sensitive and resistant tumors. CONCLUSION Using mouse models of human colorectal cancer, Hp1bp3 was identified as a candidate marker of intrinsic 5-FU resistance and may represent a potential biomarker for patient stratification or a target of clinical importance.
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Affiliation(s)
- Jamie N Hadac
- Department of Oncology, K4/532 Clinical Science Center, Madison, WI, U.S.A
| | - Devon D Miller
- Department of Medicine, Division of Gastroenterology and Hepatology, K4/532 Clinical Science Center, Madison, WI, U.S.A
| | - Ian C Grimes
- Department of Medicine, Division of Gastroenterology and Hepatology, K4/532 Clinical Science Center, Madison, WI, U.S.A
| | - Linda Clipson
- Department of Oncology, K4/532 Clinical Science Center, Madison, WI, U.S.A
| | - Michael A Newton
- Departments of Statistics and of Biostatistics and Medical Informatics, 1245a, K6/434 Medical Sciences Center, Madison, WI, U.S.A
| | - William R Schelman
- Department of Medicine, Division of Hematology and Oncology, K4/532 Clinical Science Center, Madison, WI, U.S.A
| | - Richard B Halberg
- Department of Medicine, Division of Gastroenterology and Hepatology, K4/532 Clinical Science Center, Madison, WI, U.S.A. Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, U.S.A.
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Zhang Q, Gou W, Wang X, Zhang Y, Ma J, Zhang H, Zhang Y, Zhang H. Genome Resequencing Identifies Unique Adaptations of Tibetan Chickens to Hypoxia and High-Dose Ultraviolet Radiation in High-Altitude Environments. Genome Biol Evol 2016; 8:765-76. [PMID: 26907498 PMCID: PMC4824011 DOI: 10.1093/gbe/evw032] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Tibetan chicken, unlike their lowland counterparts, exhibit specific adaptations to high-altitude conditions. The genetic mechanisms of such adaptations in highland chickens were determined by resequencing the genomes of four highland (Tibetan and Lhasa White) and four lowland (White Leghorn, Lindian, and Chahua) chicken populations. Our results showed an evident genetic admixture in Tibetan chickens, suggesting a history of introgression from lowland gene pools. Genes showing positive selection in highland populations were related to cardiovascular and respiratory system development, DNA repair, response to radiation, inflammation, and immune responses, indicating a strong adaptation to oxygen scarcity and high-intensity solar radiation. The distribution of allele frequencies of nonsynonymous single nucleotide polymorphisms between highland and lowland populations was analyzed using chi-square test, which showed that several differentially distributed genes with missense mutations were enriched in several functional categories, especially in blood vessel development and adaptations to hypoxia and intense radiation. RNA sequencing revealed that several differentially expressed genes were enriched in gene ontology terms related to blood vessel and respiratory system development. Several candidate genes involved in the development of cardiorespiratory system (FGFR1, CTGF, ADAM9, JPH2, SATB1, BMP4, LOX, LPR, ANGPTL4, and HYAL1), inflammation and immune responses (AIRE, MYO1F, ZAP70, DDX60, CCL19, CD47, JSC, and FAS), DNA repair, and responses to radiation (VCP, ASH2L, and FANCG) were identified to play key roles in the adaptation to high-altitude conditions. Our data provide new insights into the unique adaptations of highland animals to extreme environments.
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Affiliation(s)
- Qian Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Wenyu Gou
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, China
| | - Yawen Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Jun Ma
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Hongliang Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Ying Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
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Scanlon SE, Glazer PM. Multifaceted control of DNA repair pathways by the hypoxic tumor microenvironment. DNA Repair (Amst) 2015; 32:180-189. [PMID: 25956861 DOI: 10.1016/j.dnarep.2015.04.030] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hypoxia, as a pervasive feature in the microenvironment of solid tumors, plays a significant role in cancer progression, metastasis, and ultimately clinical outcome. One key cellular consequence of hypoxic stress is the regulation of DNA repair pathways, which contributes to the genomic instability and mutator phenotype observed in human cancers. Tumor hypoxia can vary in severity and duration, ranging from acute fluctuating hypoxia arising from temporary blockages in the immature microvasculature, to chronic moderate hypoxia due to sparse vasculature, to complete anoxia at distances more than 150 μM from the nearest blood vessel. Paralleling the intra-tumor heterogeneity of hypoxia, the effects of hypoxia on DNA repair occur through diverse mechanisms. Acutely, hypoxia activates DNA damage signaling pathways, primarily via post-translational modifications. On a longer timescale, hypoxia leads to transcriptional and/or translational downregulation of most DNA repair pathways including DNA double-strand break repair, mismatch repair, and nucleotide excision repair. Furthermore, extended hypoxia can lead to long-term persistent silencing of certain DNA repair genes, including BRCA1 and MLH1, revealing a mechanism by which tumor suppressor genes can be inactivated. The discoveries of the hypoxic modulation of DNA repair pathways have highlighted many potential ways to target susceptibilities of hypoxic cancer cells. In this review, we will discuss the multifaceted hypoxic control of DNA repair at the transcriptional, post-transcriptional, and epigenetic levels, and we will offer perspective on the future of its clinical implications.
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Affiliation(s)
- Susan E Scanlon
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA; Department of Experimental Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
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34
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Uncovering Neurodegenerative Protein Modifications via Proteomic Profiling. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2015; 121:87-116. [DOI: 10.1016/bs.irn.2015.06.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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