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Akuwudike P, López-Riego M, Ginter J, Cheng L, Wieczorek A, Życieńska K, Łysek-Gładysińska M, Wojcik A, Brzozowska B, Lundholm L. Mechanistic insights from high resolution DNA damage analysis to understand mixed radiation exposure. DNA Repair (Amst) 2023; 130:103554. [PMID: 37595330 DOI: 10.1016/j.dnarep.2023.103554] [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: 04/20/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 08/20/2023]
Abstract
Cells exposed to densely ionising high and scattered low linear energy transfer (LET) radiation (50 % dose of each) react more strongly than to the same dose of each separately. The relationship between DNA double strand break location inside the nucleus and chromatin structure was evaluated, using high-resolution transmission electron microscopy (TEM) in breast cancer MDA-MB-231 cells at 30 min post 5 Gy. Additionally, response to high and/or low LET radiation was assessed using single (1 ×1.5 Gy) versus fractionated dose delivery (5 ×0.3 Gy). By TEM analysis, the highest total number of γH2AX nanobeads were found in cells irradiated with alpha radiation just prior to gamma radiation (called mixed beam), followed by alpha, then gamma radiation. γH2AX foci induced by mixed beam radiation tended to be surrounded by open chromatin (lighter TEM regions), yet foci containing the highest number of beads, i.e. larger foci representing complex damage, remained in the heterochromatic areas. The γH2AX large focus area was also greater in mixed beam-treated cells when analysed by immunofluorescence. Fractionated mixed beams given daily induced the strongest reduction in cell viability and colony formation in MDA-MB-231 and osteosarcoma U2OS cells compared to the other radiation qualities, as well as versus acute exposure. This may partially be explained by recurring low LET oxidative DNA damage by every fraction together with a delay in recompaction of chromatin after high LET, demonstrated by low levels of heterochromatin marker H3K9me3 at 2 h after the last mixed beam fraction in MDA-MB-231. In conclusion, early differences in response to complex DNA damage may lead to a stronger cell kill induced by fractionated exposure, which suggest a therapeutic potential of combined high and low LET irradiation.
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Affiliation(s)
- Pamela Akuwudike
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Milagrosa López-Riego
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Józef Ginter
- Biomedical Physics Division, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Lei Cheng
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Anna Wieczorek
- Division of Medical Biology, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland
| | - Katarzyna Życieńska
- Biomedical Physics Division, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | | | - Andrzej Wojcik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Beata Brzozowska
- Biomedical Physics Division, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Lovisa Lundholm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden.
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Zhou F, Chen L, Lu P, Cao Y, Deng C, Liu G. An integrative bioinformatics investigation and experimental validation of chromobox family in diffuse large B-cell lymphoma. BMC Cancer 2023; 23:641. [PMID: 37430195 DOI: 10.1186/s12885-023-11108-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Diffuse large B-cell lymphoma (DLBCL) is one of the most aggressive malignant tumors. Chromobox (CBX) family plays the role of oncogenes in various malignancies. METHODS The transcriptional and protein levels of CBX family were confirmed by GEPIA, Oncomine, CCLE, and HPA database. Screening of co-expressed genes and gene function enrichment analysis were performed by GeneMANIA and DAVID 6.8. The prognostic value, immune cell infiltration and drug sensitivity analysis of CBX family in DLBCL were performed by Genomicscape, TIMER2.0, and GSCALite database. Confirmatory Tests of CBX family protein expression in DLBCL were performed by immunohistochemistry. RESULTS The mRNA and protein expressions of CBX1/2/3/5/6 were higher in DLBCL tissues than control groups. Enrichment analysis showed that the functions of CBX family were mainly related to chromatin remodeling, methylation-dependent protein binding, and VEGF signaling pathway. The high mRNA expressions of CBX2/3/5/6 were identified to be associated with short overall survival (OS) in DLBCL patients. Multivariate COX regression indicated that CBX3 was independent prognostic marker. Immune infiltration analysis revealed that the mRNA expressions of CBX family (especially CBX1, CBX5, and CBX6) in DLBCL were significantly correlated with the infiltration of most immune cells (including B cells, CD8 + T cells, CD4 + T cells, neutrophils, monocytes, macrophages, and Treg cells). Meanwhile, there was a strong correlation between the expression levels of CBX1/5/6 and surface markers of immune cells, such as the widely studied PVR-like protein receptor/ligand and PDL-1 immune checkpoint. Notably, our study found that DLBCL cells with CBX1 over-expression were resistant to the common anti-tumor drugs, but CBX2/5 had two polarities. Finally, we confirmed the higher expressions of CBX1/2/3/5/6 in DLBCL tissues compared with control groups by immunohistochemistry. CONCLUSION We provided a detailed analysis of the relationship between the CBX family and the prognosis of DLBCL. Distinguished from other studies, We found that high mRNA expressions of CBX2/3/5/6 were associated with poor prognosis in DLBCL patients, and Multivariate COX regression indicated that CBX3 was independent prognostic marker. Besides, our study also found an association between the CBX family and anti-tumour drug resistance, and provided a relationship between CBX family expression and immune cell infiltration.
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Affiliation(s)
- Fenling Zhou
- Institute of Hematology, Jinan University, HuangPu Da Dao Xi, Guangzhou, Guangdong, 510632, People's Republic of China
| | - Lu Chen
- Institute of Hematology, Jinan University, HuangPu Da Dao Xi, Guangzhou, Guangdong, 510632, People's Republic of China
| | - Peng Lu
- Departpent of Vascular Surgery, The Second Xiangya Hospital, Central South University, Hunan Province, No. 139, Renmin Road, Changsha, China
| | - Yuli Cao
- Institute of Hematology, Jinan University, HuangPu Da Dao Xi, Guangzhou, Guangdong, 510632, People's Republic of China
| | - Cuilan Deng
- Department of Hematology, First Affiliated Hospital, Jinan University, HuangPu Da Dao Xi, Guangzhou, Guangdong, 510632, People's Republic of China
| | - Gexiu Liu
- Institute of Hematology, Jinan University, HuangPu Da Dao Xi, Guangzhou, Guangdong, 510632, People's Republic of China.
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CBX5 loss drives EGFR inhibitor resistance and results in therapeutically actionable vulnerabilities in lung cancer. Proc Natl Acad Sci U S A 2023; 120:e2218118120. [PMID: 36652476 PMCID: PMC9942844 DOI: 10.1073/pnas.2218118120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Although epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (EGFRi) are approved for treating EGFR-mutant lung adenocarcinoma (LUAD), emergence of acquired resistance limits their clinical benefits. Several mechanisms for acquired resistance to EGFRi in LUAD have been identified; however, the molecular basis for this resistance remains unknown in ~30% of LUAD. Chromatin and DNA modifiers and their regulators play important roles in determining response to anticancer therapies. Therefore, to identify nongenetic mechanisms of EGFRi resistance in LUAD, we performed an epigenome-wide shRNA screen targeting 363 human epigenetic regulator genes. This screen identified loss of the transcriptional repressor chromobox homolog 5 (CBX5) as a driver of EGFRi resistance in EGFR-mutant LUAD. Loss of CBX5 confers resistance to multiple EGFRi in both cell culture and mice. We found that CBX5 loss in EGFR-mutant LUAD cells leads to increased expression of the transcription factor E2F1, which in turn stimulates expression of the antiapoptotic gene BIRC5 (survivin). This E2F1-mediated upregulation of BIRC5 in CBX5-knockdown LUAD cells attenuates apoptosis induction following EGFRi treatment. Consistent with these results, knockdown of E2F1 or BIRC5 partly rescues CBX5-knockdown-induced EGFRi resistance in cell culture and mice. EGFRi-resistant LUAD cell lines show reduced CBX5 expression compared to parental lines; however, bromo- and extra-terminal (BET)-domain inhibitors (BETi) restore CBX5 expression in these cells and sensitize them to EGFRi/BETi combination therapy. Similarly, treatment with a BIRC5 inhibitor suppresses growth of EGFRi-resistant LUAD cells. Collectively, these studies identify CBX5 loss as a driver of EGFRi resistance and reveal therapeutic opportunities for treating EGFRi-resistant LUAD.
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Tian H, Zhao T, Li Y, Sun N, Ma D, Shi Q, Zhang G, Chen Q, Zhang K, Chen C, Zhang Y, Qi X. Chromobox Family Proteins as Putative Biomarkers for Breast Cancer Management: A Preliminary Study Based on Bioinformatics Analysis and qRT-PCR Validation. BREAST CANCER (DOVE MEDICAL PRESS) 2022; 14:515-535. [PMID: 36605919 PMCID: PMC9809168 DOI: 10.2147/bctt.s381856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022]
Abstract
Background Epigenetic modification of chromatin is an important step in the regulation of gene expression. The chromobox family proteins (CBXs), as epigenetic modifier, may play a vital role in tumorigenesis and cancer progression. Herein we explored the correlation between CBXs and breast cancer (BC) via the bioinformatics approach and qRT-PCR validation. Methods Several databases, including GEPIA, TCGA, GEO, K-M plotter, STRING, DAVID, cBioPortal, CIBERSORT, and HPA were employed to analyze the expression levels of CBXs and the correlations between CBXs and prognosis (overall and recurrence-free survival) in BC. We analyzed molecular functions, genetic variations, transcription factors of CBXs, and immune cell infiltration status. ROC curve analysis was performed to determine the predictive value of CBXs. RNA extracted from 11 human BC and paired adjacent normal tissues were subjected to qRT-PCR. Results The mRNA expression level of CBX1-5 was significantly upregulated, while that of CBX7 was significantly downregulated in BC; no expression disparities were observed in CBX6/8 expression. Further, high mRNA expression of CBX1/2/3/4/8 correlated with advanced BC, whereas high mRNA expression of CBX6/7 correlated with early BC. High mRNA expressions of CBX1/2/3/5 predict poor OS and RFS, while higher mRNA expressions of CBX6/7 predict better OS and RFS in patients with BC. ROC curve analysis revealed that CBX3 showed excellent discriminatory ability. Gene ontology enrichment analysis showed that CBXs primarily participated in SUMOylation and post-/transcriptional regulation. Moreover, they presented varying degrees of amplification in BC tissues and were related to the infiltration of various immune cells. Conclusion CBXs can serve as putative biomarkers for BC. Further studies are warranted to determine the exact molecular mechanisms underlying the action of CBXs in BC, particularly CBX1/2/3/5/7.
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Affiliation(s)
- Hao Tian
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China
| | - Tingting Zhao
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China
| | - Yanling Li
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China
| | - Na Sun
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China
| | - Dandan Ma
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China
| | - Qiyun Shi
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China
| | - Guozhi Zhang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China
| | - Qingqiu Chen
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China
| | - Kongyong Zhang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People’s Republic of China
| | - Yi Zhang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China
| | - Xiaowei Qi
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China,Correspondence: Xiaowei Qi; Yi Zhang, Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Gaotanyan Street 29, Chongqing, 400038, People’s Republic of China, Tel/Fax +86-23-68754160, Email ;
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CBX Family Members in Two Major Subtypes of Renal Cell Carcinoma: A Comparative Bioinformatic Analysis. Diagnostics (Basel) 2022; 12:diagnostics12102452. [PMID: 36292141 PMCID: PMC9600067 DOI: 10.3390/diagnostics12102452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/28/2022] [Accepted: 10/08/2022] [Indexed: 11/17/2022] Open
Abstract
The biological function and clinical values of Chromobox (CBX) family proteins in renal cell carcinoma (RCC) are still poorly investigated. This study aimed to compare the expression profiles and clinical relevance of CBXs between the two most frequent subtypes of RCC, clear cell renal cell carcinomas (ccRCC) and papillary renal cell carcinomas (pRCC), and to investigate whether CBXs would play a more or less similar role in the pathogenesis and progression of these RCC subtypes. Considering these two RCC populations in the TCGA database, we built a bioinformatics framework by integrating a computational pipeline with several online tools. CBXs showed a similar trend in ccRCC and pRCC tissues but with some features specific for each subtype. Specifically, the relative expressions of CBX3 and CBX2 were, respectively, the highest and lowest among all CBXs in both RCC subtypes. These data also found confirmation in cellular validation. Except for CBX4 and CBX8, all others were deregulated in the ccRCC subtype. CBX1, CBX6, and CBX7 were also significantly associated with the tumor stage. Further, low expression levels of CBX1, CBX5, CBX6, CBX7, and high expression of CBX8 were associated with poor prognosis. Otherwise, in the pRCC subtype, CBX2, CBX3, CBX7, and CBX8 were deregulated, and CBX2, CBX6, and CBX7 were associated with the tumor stage. In addition, in pRCC patients, low expression levels of CBX2, CBX4, and CBX7 were associated with an unfavorable prognosis. Similarly, CBX3, CBX6, and CBX7 presented the highest alteration rate in both subtypes and were found to be functionally related to histone binding, nuclear chromosomes, and heterochromatin. Furthermore, CBX gene expression levels correlated with immune cell infiltration, suggesting that CBXs might reflect the immune status of RCC subtypes. Our results highlight similarities and differences of CBXs within the two major RCC subtypes, providing new insights for future eligible biomarkers or possible molecular therapeutic targets for these diseases.
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Ye Y, Li L, Dai Q, Liu Y, Shen L. Comprehensive analysis of histone methylation modification regulators for predicting prognosis and drug sensitivity in lung adenocarcinoma. Front Cell Dev Biol 2022; 10:991980. [PMID: 36263018 PMCID: PMC9574078 DOI: 10.3389/fcell.2022.991980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/14/2022] [Indexed: 11/21/2022] Open
Abstract
Histone methylation is an epigenetic modification regulated by histone methyltransferases, histone demethylases, and histone methylation reader proteins that play important roles in the pathogenic mechanism of cancers. However, the prognostic value of histone methylation in lung adenocarcinoma (LUAD) remains unknown. Here, we found that LUAD cases could be divided into 2 subtypes by the 144 histone methylation modification regulators (HMMRs), with a significant difference in OS time. Ninety-five of the HMMRs were identified as differentially expressed genes (DEGs) between normal and tumor samples, and 13 of them were further discovered to be survival-related genes (SRGs). By applying the least absolute shrinkage and selector operator (LASSO) Cox regression, we constructed an 8-gene-based risk signature according to the TCGA (training) cohort, and the risk score calculated by the signature was proven to be an independent factor in both the training and validation cohorts. We then discovered that the immune functions were generally impaired in the high-risk groups defined by the HMMR signature (especially for the DCs and immune check-point pathway). Functional analyses showed that the DEGs between the low- and high-risk groups were related to the cell cycle. The drug sensitivity analysis indicated that our risk model could predict the sensitivity of commonly used drugs. Moreover, according to the DEGs between the low- and high-risk groups, we discovered several new compounds that showed potential therapeutic value for high-risk LUAD patients. In conclusion, our study demonstrated that HMMRs were promising predictors for the prognoses and drug therapeutic effects for LUAD patients.
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Affiliation(s)
- Ying Ye
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Li
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qinjin Dai
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yan Liu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lin Shen
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Lin Shen,
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Zheng ZQ, Yuan GQ, Kang NL, Nie QQ, Zhang GG, Wang Z. Chromobox 7/8 serve as independent indicators for glioblastoma via promoting proliferation and invasion of glioma cells. Front Neurol 2022; 13:912039. [PMID: 36034290 PMCID: PMC9403790 DOI: 10.3389/fneur.2022.912039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background The chromobox family, a critical component of epigenetic regulators, participates in the tumorigenesis and progression of many malignancies. However, the roles of the CBX family members (CBXs) in glioblastoma (GBM) remain unclear. Methods The mRNA expression of CBXs was analyzed in tissues and cell lines by Oncomine and Cancer Cell Line Encyclopedia (CCLE). The differential expression of CBXs at the mRNA level was explored in The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases with the “beeswarm” R package. The protein expression of CBXs in GBM was further examined on Human Protein Atlas (HPA). The correlations between CBXs and IDH mutation and between CBXs and GBM subtypes were investigated in the TCGA portal and CGGA database with the “survminer” R package. The alteration of CBXs and their prognostic value were further determined via the cBioPortal and CGGA database with the “survival” R package. The univariate and multivariate analyses were performed to screen out the independent prognostic roles of CBXs in the CGGA database. Cytoscape was used to visualize the functions and related pathways of CBXs in GBM. U251 and U87 glioma cells with gene intervention were used to validate the role of CBX7/8 in tumor proliferation and invasion. Proliferation/invasion-related markers were conducted by Western blot and immunostaining. Results CBXs presented significantly differential expressions in pan-cancers. CBX2/3/5/8 were upregulated, whereas CBX6/7 were downregulated at mRNA level in GBM of TCGA and CGGA databases. Similarly, high expression of CBX2/3/5 and low expression of CBX6/8 were further confirmed at the protein level in the HPA. CBX2/6/7 were positively correlated with IDH mutation and CBX1/2/4/5/8 were closely related to GBM subtypes. CBX7 and CBX8 presented the independent prognostic factors for GBM patient survival. GO and KEGG analyses indicated that CBXs were closely related to the histone H3-K36, PcG protein complex, ATPase, and Wnt pathway. The overexpression of CBX7 and underexpression of CBX8 significantly inhibited the proliferation and invasion of glioma cells in vivo and in vitro. Conclusion Our results suggested that CBX7 and CBX8 served as independent prognostic indicators that promoted the proliferation and invasion of glioma cells, providing a promising strategy for diagnosing and treating GBM.
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Affiliation(s)
- Zong-Qing Zheng
- Department of Neurosurgery and Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Gui-Qiang Yuan
- Department of Neurosurgery and Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Neurosurgery, Changshu Second People's Hospital, Suzhou, China
| | - Na-Ling Kang
- Liver Center, The First Affiliated Hospital, Fujian Medical University, Fujian, China
| | - Qian-Qian Nie
- Department of Neurosurgery and Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Guo-Guo Zhang
- Department of Neurosurgery and Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhong Wang
- Department of Neurosurgery and Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Zhong Wang
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Atamaleki A, Yazdanbakhsh A, Gholizadeh A, Naimi N, Karimi P, Thai VN, Fakhri Y. Concentration of potentially harmful elements (PHEs) in eggplant vegetable ( Solanum melongena) irrigated with wastewater: a systematic review and meta-analysis and probabilistic health risk assessment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:1419-1431. [PMID: 33588645 DOI: 10.1080/09603123.2021.1887461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
The main objectives of this study were PHEs concentration meta-analysis (Fe, Zn, Cr, Ni, Cu, Pb, and Cd) in eggplant irrigated by wastewater and the following estimation of non-carcinogenic (n-CR) risk for the consumers based on countries. According to the results, the rank order of PHEs concentration in eggplant was Fe (88.3 mg/kg -dry weight) > Zn (10.1 mg/kg -dry weight) > Pb (3.0 mg/kg -dry weight) > Ni (2.7 mg/kg -dry weight) > Cu (1.1 mg/kg -dry weight) > Cd (0.9 mg/kg -dry weight) > Cr (0.05 mg/kg -dry weight). Moreover, n-CR risk showed that all investigated countries (China, India, Pakistan, Turkey, and Jordan) except for United Arab Emirates (UAE) had a considerable n-CR in both age groups (adults and children).
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Affiliation(s)
- Ali Atamaleki
- Student Research Committee, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ahmadreza Yazdanbakhsh
- Workplace Health Promotion Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abdolmajid Gholizadeh
- Department of Environmental Health Engineering, School of Public Health, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Nayera Naimi
- Department of Environmental Health Engineering, School of Public Health, North Khorasan University of Medical Sciences, Bojnurd, Iran
- PhD Student in Environmental Health Engineering, School Of Health, Student Research Committee, Mashhad University Of Medical Sciences, Mashhad, Iran
| | - Pouria Karimi
- Student Research Committee, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Workplace Health Promotion Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Van Nam Thai
- Ho Chi Minh City University of Technology (HUTECH) 475A, Ho Chi Minh City, Dien Bien Phu, Ward 25, Binh Thanh District, Vietnam
| | - Yadolah Fakhri
- Food Health Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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Sharma C, Hemler ME. Antioxidant and Anticancer Functions of Protein Acyltransferase DHHC3. Antioxidants (Basel) 2022; 11:antiox11050960. [PMID: 35624824 PMCID: PMC9137668 DOI: 10.3390/antiox11050960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/29/2022] [Accepted: 05/06/2022] [Indexed: 11/16/2022] Open
Abstract
Silencing of DHHC3, an acyltransferase enzyme in the DHHC family, extensively upregulates oxidative stress (OS). Substrates for DHHC3-mediated palmitoylation include several antioxidant proteins and many other redox regulatory proteins. This helps to explain why DHHC3 ablation upregulates OS. DHHC3 also plays a key role in cancer. DHHC3 ablation leads to diminished xenograft growth of multiple cancer cell types, along with diminished metastasis. Furthermore, DHHC3 protein is upregulated on malignant/metastatic cancer samples, and upregulated gene expression correlates with diminished patient survival in several human cancers. Decreased primary tumor growth due to DHHC3 ablation may be partly explained by an elevated OS → senescence → innate immune cell recruitment mechanism. Elevated OS due to DHHC3 ablation may also contribute to adaptive anticancer immunity and impair tumor metastasis. In addition, DHHC3 ablation disrupts antioxidant protection mechanisms, thus enhancing the efficacy of OS-inducing anticancer drugs. A major focus has thus far been on OS regulation by DHHC3. However, remaining to be studied are multiple DHHC3 substrates that may affect tumor behavior independent of OS. Nonetheless, the currently established properties of DHHC3 make it an attractive candidate for therapeutic targeting in situations in which antioxidant protections need to be downmodulated, and also in cancer.
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Li J, Xu Z, Zhou L, Hu K. Expression profile and prognostic values of Chromobox family members in human glioblastoma. Aging (Albany NY) 2022; 14:1910-1931. [PMID: 35210369 PMCID: PMC8908931 DOI: 10.18632/aging.203912] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/28/2022] [Indexed: 02/05/2023]
Abstract
Glioblastoma (GBM) is the most common and deadly malignant primary brain tumor. Chromobox (CBX) family proteins are essential components of the epigenetic regulatory complex and are involved in the occurrence and development of various cancers. However, the roles of CBX members in GBM is little known. In this analysis, we synthesized several mainstream bioinformatics databases to comprehensively explore the expression profiles, prognostic implications, genetic alterations, immune infiltration, and potential biological functions of the CBXs in GBM, and cell experiments were also conducted to investigate the role of CBX8 in GBM. We found that the elevated mRNA expression of CBX2/3/5/8 and reduced mRNA expression of CBX6/7 were found in GBM. The protein levels of CBX2/3/5/8 were elevated in GBM tissues, whereas the protein levels of CBX6/7 showed no significant difference. The upregulated expression of CBX2/3/8 was found to be both correlated with the tumor grade and recurrent status. The overexpression of CBX3/8 and underexpression of CBX6 mRNA were associated with the poor prognosis. These findings suggested that CBX3 and CBX8 might be useful diagnostic and prognostic biomarkers in GBM. Further cell experiment results supported that CBX8 promoted the proliferation of glioma cells. Moreover, a high genetic alteration rate of CBXs (37%) was found in GBM and to varying degrees. The expression of CBXs was significantly related to the immune cells infiltration. CBX7 methylation level was significantly increased in GBM tissues. Our results may provide novel ideas to find potential prognostic markers and new therapeutic targets among CBX family members in glioblastoma.
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Affiliation(s)
- Juanni Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Lei Zhou
- Department of Anesthesiology, Third Xiangya Hospital of Central South University, Changsha 410008, Hunan, China
| | - Kuan Hu
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
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Kean KM, Baril SA, Lamb KN, Dishman SN, Treacy JW, Houk KN, Brustad EM, James LI, Waters ML. Systematic Variation of Both the Aromatic Cage and Dialkyllysine via GCE-SAR Reveal Mechanistic Insights in CBX5 Reader Protein Binding. J Med Chem 2022; 65:2646-2655. [PMID: 35014255 PMCID: PMC9048841 DOI: 10.1021/acs.jmedchem.1c02049] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Development of inhibitors for histone methyllysine reader proteins is an active area of research due to the importance of reader protein-methyllysine interactions in transcriptional regulation and disease. Optimized peptide-based chemical probes targeting methyllysine readers favor larger alkyllysine residues in place of methyllysine. However, the mechanism by which these larger substituents drive tighter binding is not well understood. This study describes the development of a two-pronged approach combining genetic code expansion (GCE) and structure-activity relationships (SAR) through systematic variation of both the aromatic binding pocket in the protein and the alkyllysine residues in the peptide to probe inhibitor recognition in the CBX5 chromodomain. We demonstrate a novel change in driving force for larger alkyllysines, which weaken cation-π interactions but increases dispersion forces, resulting in tighter binding. This GCE-SAR approach establishes discrete energetic contributions to binding from both ligand and protein, providing a powerful tool to gain mechanistic understanding of SAR trends.
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Affiliation(s)
- Kelsey M. Kean
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Stefanie A. Baril
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Kelsey N. Lamb
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Sarah N. Dishman
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Joseph W. Treacy
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, CA 90095 USA
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, CA 90095 USA
| | - Eric M. Brustad
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Marcey L. Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA,Corresponding Author: Marcey L. Waters – Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States;
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12
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Jeon YH, Kim GW, Kim SY, Yi SA, Yoo J, Kim JY, Lee SW, Kwon SH. Heterochromatin Protein 1: A Multiplayer in Cancer Progression. Cancers (Basel) 2022; 14:cancers14030763. [PMID: 35159030 PMCID: PMC8833910 DOI: 10.3390/cancers14030763] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 11/16/2022] Open
Abstract
Dysregulation of epigenetic mechanisms as well as genomic mutations contribute to the initiation and progression of cancer. In addition to histone code writers, including histone lysine methyltransferase (KMT), and histone code erasers, including histone lysine demethylase (KDM), histone code reader proteins such as HP1 are associated with abnormal chromatin regulation in human diseases. Heterochromatin protein 1 (HP1) recognizes histone H3 lysine 9 methylation and broadly affects chromatin biology, such as heterochromatin formation and maintenance, transcriptional regulation, DNA repair, chromatin remodeling, and chromosomal segregation. Molecular functions of HP1 proteins have been extensively studied, although their exact roles in diseases require further study. Here, we comprehensively review the studies that have revealed the altered expression of HP1 and its functions in tumorigenesis. In particular, the distinctive effects of each HP1 subtype, namely HP1α, HP1β, and HP1γ, have been thoroughly explored in various cancer types. We also highlight how HP1 can serve as a potential biomarker for cancer prognosis and therapeutic target for cancer patients.
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Affiliation(s)
- Yu Hyun Jeon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - So Yeon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - Sang Ah Yi
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea;
| | - Jung Yoo
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - Ji Yoon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - Sang Wu Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
- Correspondence: ; Tel.: +82-32-749-4513
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13
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Hu CY, Li X, Zeng T, Ye DM, Li YK, Yan HX. Significance of chromobox protein (CBX) expression in diffuse LBCL. Gene 2021; 813:146092. [PMID: 34896523 DOI: 10.1016/j.gene.2021.146092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/24/2021] [Accepted: 11/23/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND Diffuse large B-cell lymphoma (DLBCL) is the main pathological type of non-Hodgkin lymphoma (NHL). Chromobox (CBX) family proteins are classical components of polycomb group (PcG) complexes in many cancer types, resulting in accelerated carcinogenesis. Nevertheless, the prognostic, functional and expression significance of these CBX family members in DLBCL remain unclear and elusive. METHODS CBX transcriptional levels were confirmed using Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA) and Cancer Cell Line Encyclopedia (CCLE) databases. The protein levels of CBX family members were analysed using The Human Protein Atlas (HPA) database. Information on the PPI network, functional enrichment, drug sensitivity, prognostic value, miRNA network, protein structure, genetic alteration and immune cell infiltration were generated using the GeneMANIA, Metascape, GSCALite, GEPIA, PDB, cBioPortal, and TIMER databases, and the correlation of these factors with CBX expression levels in DLBCL was assessed. RESULTS CBX1/2/3/5/6/8 mRNA levels were significantly enhanced in DLBCL tissues compared to corresponding normal tissues. CBX1/3/4/5/8 protein expression levels were obviously increased, whereas CBX7 was obviously decreased. This difference might be attributed to miRNA regulation based on the miRNA network. Overall survival (OS) analysis showed that CBX levels were not correlated with prognosis in DLBCL patients, indicating that CBXs are not good biomarkers for DLBCL patients. Furthermore, functional enrichment analyses indicated that CBXs were closely related to DNA duplex unwinding, covalent chromatin modification, and histone lysine methylation. The levels of CBXs were also significantly associated with diverse immune cell infiltration in DLBCL. CONCLUSIONS This study reveals that dysregulated CBXs are involved in DLBCL development and might represent potential therapeutic targets for DLBCL.
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Affiliation(s)
- Chun-Yan Hu
- Department of Pediatrics, The Second Affiliated Hospital of University of South China, Hengyang, Hunan 421001, PR China
| | - Xuan Li
- Department of Embryo Laboratory, Changsha Reproductive Medical Hospital, Changsha, Hunan 410000, PR China
| | - Tian Zeng
- Hengyang Medical College & Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study & Department of Pharmacy and Pharmacology, University of South China, Hengyang 421001, PR China
| | - Dong-Mei Ye
- Department of Pathology, The First Hospital of Nanchang City, Nanchang, Jiangxi 330008, PR China
| | - Yu-Kun Li
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of University of South China, Hengyang, Hunan 421001, PR China
| | - Hong-Xia Yan
- Department of Pediatrics, The Second Affiliated Hospital of University of South China, Hengyang, Hunan 421001, PR China.
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14
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Zhu Y, Pu Z, Li Z, Lin Y, Li N, Peng F. Comprehensive Analysis of the Expression and Prognosis Value of Chromobox Family Members in Clear Cell Renal Cell Carcinoma. Front Oncol 2021; 11:700528. [PMID: 34395271 PMCID: PMC8357267 DOI: 10.3389/fonc.2021.700528] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) accounts for 80% of all renal cancers and has a poor prognosis. Chromobox (CBX) family protein expression has been reported in a variety of human malignancies, but the roles of CBXs in ccRCC remain unclear. In this study, by using ONCOMINE, UALCAN, GEPIA, Kaplan-Meier Plotter, cBioPortal, and TIMER, we found the transcriptional levels of CBX3 and CBX4 in ccRCC tissues were significantly higher than those in normal kidney tissues, whereas the transcriptional levels of CBX1, CBX5, CBX6, and CBX7 were significantly reduced in ccRCC tissues. The promoters of CBX2, CBX3, CBX4, CBX5, CBX6, CBX7, and CBX8 were hypermethylated, whereas the CBX1 promoter was hypomethylated in ccRCC. The expression of CBX1, CBX3, CBX4, CBX5, CBX6, and CBX7 was significantly associated with clinicopathological parameters in ccRCC patients. ccRCC patients with high expression levels of CBX3, CBX4, and CBX8 and low expression levels of CBX1, CBX5, CBX6, and CBX7 showed a strong association with poor overall survival. Genetic alterations in CBXs were correlated with poor overall survival and disease-free survival in patients with ccRCC. Moreover, we found significant associations between the expression of CBXs and infiltration of immune cells (B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells). Our results provide novel insights into the development of CBX-based biomarkers and therapeutic targets for ccRCC.
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Affiliation(s)
- Yuanyuan Zhu
- Department of Blood Transfusion, Xiangya Hospital, Central South University, Changsha, China.,National Health Commission (NHC) Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhangya Pu
- Department of Infectious Diseases and Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenfen Li
- National Health Commission (NHC) Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, China
| | - Ying Lin
- Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Ning Li
- Department of Blood Transfusion, Xiangya Hospital, Central South University, Changsha, China
| | - Fang Peng
- Department of Blood Transfusion, Xiangya Hospital, Central South University, Changsha, China.,National Health Commission (NHC) Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, China
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15
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Sun Y, Wang X, Bu X. LINC02381 contributes to cell proliferation and hinders cell apoptosis in glioma by transcriptionally enhancing CBX5. Brain Res Bull 2021; 176:121-129. [PMID: 34274429 DOI: 10.1016/j.brainresbull.2021.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/25/2021] [Accepted: 07/12/2021] [Indexed: 01/11/2023]
Abstract
Glioma, featured with high incidence and low survival rate, is the most common type of primary brain tumor, severely affecting human life worldwide. LINC02381 is an interesting lncRNA functioning as oncogenic lncRNA in some cancers but as tumor-suppressor in others, but no report demonstrates its association with and function in glioma. Intriguingly, we found in a bioinformatics website LncRNADisease that LINC02381 was closely related to malignant glioma, so this study aimed to figure out the expression and function of LINC02381 in glioma. By RT-qPCR, we confirmed LINC02381 upregulation in glioma cells. Functional experiments demonstrated that LINC02381 knockdown repressed glioma cell proliferation and induced apoptosis. Boinformatics tools and RT-qPCR revealed the positive correlation between LINC02381 and CBX5 in glioma cells. More importantly, we confirmed that LINC02381 could interact and work synergistically with CEBPβ to bind to CBX5 promoter and activate CBX5 transcriptionally. Additionally, rescue experiments indicated that CBX5 up-regulation reversed the decline in cell proliferation and the augment in cell apoptosis caused by LINC02381 knockdown. To conclude, LINC02381 could facilitate CBX5 transcription via interaction with CEBPβ, thus exerting its oncogenic role in glioma cells, which could contribute to better understanding of glioma.
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Affiliation(s)
- Yong Sun
- Department of Neurosurgery, Henan Provincial People's Hospital, No.7 Weiwu Road, Jinshui District, Zhengzhou, 450003, Henan, China
| | - Xinjun Wang
- Department of Neurosurgery, Fifth Affiliated Hospital of Zhengzhou University, No.3 Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450052, China
| | - Xingyao Bu
- Department of Neurosurgery, Henan Provincial People's Hospital, No.7 Weiwu Road, Jinshui District, Zhengzhou, 450003, Henan, China.
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16
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He M, Yue L, Wang H, Yu F, Yu M, Ni P, Zhang K, Chen S, Duan G, Zhang R. Evaluation of the prognostic value of CBXs in gastric cancer patients. Sci Rep 2021; 11:12375. [PMID: 34117289 PMCID: PMC8196000 DOI: 10.1038/s41598-021-91649-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 04/26/2021] [Indexed: 12/23/2022] Open
Abstract
Chromobox (CBX) proteins were suggested to exert epigenetic regulatory and transcriptionally repressing effects on target genes and might play key roles in the carcinogenesis of a variety of carcinomas. Nevertheless, the functions and prognostic significance of CBXs in gastric cancer (GC) remain unclear. The current study investigated the roles of CBXs in the prognosis of GC using the Oncomine, The Gene Expression Profiling Interactive Analysis (GEPIA), UALCAN, The Cancer Genome Atlas (TCGA), and cBioPortal databases. CBX1/2/3/4/5 were significantly upregulated in GC tissues compared with normal tissues, and CBX7 was downregulated. Multivariate analysis showed that high mRNA expression levels of CBX3/8 were independent prognostic factors for prolonged OS in GC patients. In addition, the genetic mutation rate of CBXs was 37% in GC patients, and genetic alterations in CBXs showed no association with OS or disease-free survival (DFS) in GC patients. These results indicated that CBX3/8 can be prognostic biomarkers for the survival of GC patients.
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Affiliation(s)
- Mengya He
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China
| | - Limin Yue
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China.
| | - Haiyan Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China
| | - Feiyan Yu
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China
| | - Mingyang Yu
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China
| | - Peng Ni
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China
| | - Ke Zhang
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China.
| | - Rongguang Zhang
- Department of Epidemiology, College of Public Health, Hainan Medical University, Longhua District, No.3 Xueyuan Road, Haikou, 570216, China. .,Department of Experimentation Center, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China.
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17
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Comertpay B, Gulfidan G, Arga KY, Gov E. Cancer Stem Cell Transcriptome Profiling Reveals Seed Genes of Tumorigenesis: New Avenues for Cancer Precision Medicine. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:372-388. [PMID: 34037481 DOI: 10.1089/omi.2021.0021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer stem-like cells (CSCs) possess the ability to self-renew and differentiate, and they are among the major factors driving tumorigenesis, metastasis, and resistance to chemotherapy. Therefore, it is critical to understand the molecular substrates of CSC biology so as to discover novel molecular biosignatures that distinguish CSCs and tumor cells. Here, we report new findings and insights by employing four transcriptome datasets associated with CSCs, with CSC and tumor samples from breast, lung, oral, and ovarian tissues. The CSC samples were analyzed to identify differentially expressed genes between CSC and tumor phenotypes. Through comparative profiling of expression levels in different cancer types, we identified 17 "seed genes" that showed a mutual differential expression pattern. We showed that these seed genes were strongly associated with cancer-associated signaling pathways and biological processes, the immune system, and the key cancer hallmarks. Further, the seed genes presented significant changes in their expression profiles in different cancer types and diverse mutation rates, and they also demonstrated high potential as diagnostic and prognostic biomarkers in various cancers. We report a number of seed genes that represent significant potential as "systems biomarkers" for understanding the pathobiology of tumorigenesis. Seed genes offer a new innovation avenue for potential applications toward cancer precision medicine in a broad range of cancers in oncology in the future.
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Affiliation(s)
- Betul Comertpay
- Department of Bioengineering, Faculty of Engineering, Adana Alparslan Türkeş Science and Technology University, Adana, Turkey
| | - Gizem Gulfidan
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | | | - Esra Gov
- Department of Bioengineering, Faculty of Engineering, Adana Alparslan Türkeş Science and Technology University, Adana, Turkey
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18
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Zhao N, Ruan M, Koestler DC, Lu J, Marsit CJ, Kelsey KT, Platz EA, Michaud DS. Epigenome-wide scan identifies differentially methylated regions for lung cancer using pre-diagnostic peripheral blood. Epigenetics 2021; 17:460-472. [PMID: 34008478 DOI: 10.1080/15592294.2021.1923615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
BACKGROUND DNA methylation markers have been associated with lung cancer risk and may identify aetiologically relevant genomic regions, or alternatively, be markers of disease risk factors or biological processes associated with disease development. METHODS In a nested case-control study, we measured blood leukocyte DNA methylation levels in pre-diagnostic samples collected from 430 participants (208 cases; 222 controls) in the 1989 CLUE II cohort. We compared DNA methylation levels with case/control status to identify novel genomic regions, both single CpG sites and differentially methylated regions (DMRs), while controlling for known DNA methylation changes associated with smoking using a previously described pack-years-based smoking methylation score. Stratification analyses were conducted over time from blood draw to diagnosis, histology, and smoking status. RESULTS We identified 16 single CpG sites and 40 DMRs significantly associated with lung cancer risk (q < 0.05). The identified genomic regions were associated with genes including H19, HOXA3/HOXA4, RUNX3, BRICD5, PLXNB2, and RP13. For the single CpG sites, the strongest association was noted for cg09736286 in the DIABLO gene (OR [for 1 SD] = 2.99, 95% CI: 1.95-4.59, P-value = 4.81 × 10-7). We found that CpG sites in the HOXA3/HOXA4 region were hypermethylated in cases compared to controls. CONCLUSION The single CpG sites and DMRs that we identified represented significant measurable differences in lung cancer risk, providing potential biomarkers for lung cancer risk stratification. Future studies will need to examine whether these regions are causally related to lung cancer.
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Affiliation(s)
- Naisi Zhao
- Department of Public Health & Community Medicine, Tufts University School of Medicine, Tufts University, Boston, MA, USA
| | - Mengyuan Ruan
- Department of Public Health & Community Medicine, Tufts University School of Medicine, Tufts University, Boston, MA, USA
| | - Devin C Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA.,University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jiayun Lu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Carmen J Marsit
- Department of Environmental Health and Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI, USA.,Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Dominique S Michaud
- Department of Public Health & Community Medicine, Tufts University School of Medicine, Tufts University, Boston, MA, USA.,Department of Epidemiology, Brown University, Providence, RI, USA
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19
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CloneSeq: A highly sensitive analysis platform for the characterization of 3D-cultured single-cell-derived clones. Dev Cell 2021; 56:1804-1817.e7. [PMID: 34010629 DOI: 10.1016/j.devcel.2021.04.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 03/07/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022]
Abstract
Single-cell assays have revealed the importance of heterogeneity in many biological systems. However, limited sensitivity is a major hurdle for uncovering cellular variation. To overcome it, we developed CloneSeq, combining clonal expansion inside 3D hydrogel spheres and droplet-based RNA sequencing (RNA-seq). We show that clonal cells maintain similar transcriptional profiles and cell states. CloneSeq of lung cancer cells revealed cancer-specific subpopulations, including cancer stem-like cells, that were not revealed by scRNA-seq. Clonal expansion within 3D soft microenvironments supported cellular stemness of embryonic stem cells (ESCs) even without pluripotent media, and it improved epigenetic reprogramming efficiency of mouse embryonic fibroblasts. CloneSeq of ESCs revealed that the differentiation decision is made early during Oct4 downregulation and is maintained during early clonal expansion. Together, we show CloneSeq can be adapted to different biological systems to discover rare subpopulations by leveraging the enhanced sensitivity within clones.
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20
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Zhou J, Chen Z, Zou M, Wan R, Wu T, Luo Y, Wu G, Wang W, Liu T. Prognosis and Immune Infiltration of Chromobox Family Genes in Sarcoma. Front Oncol 2021; 11:657595. [PMID: 34046352 PMCID: PMC8147558 DOI: 10.3389/fonc.2021.657595] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/13/2021] [Indexed: 12/16/2022] Open
Abstract
Background Chromobox family genes (CBXs) are known to play roles in numerous modifications of the chromatin in order to inhibit the transcription of target genes. CBXs have been shown to be expressed at high levels in many types of cancer and can also serve as a target gene for therapeutic purposes. However, little is known about the expression and prognostic value of CBXs in human sarcomas. Methods The transcription level of CBXs was analyzed using the Oncomine dataset, and the differential expression of CBXs in sarcoma was reported by the Gene Expression Profiling Interactive Analysis (GEPIA) dataset. We also used the CCLE dataset to evaluate the expression of CBXs in a sarcoma cell line. The prognostic value of CBXs was analyzed using GEPIA and Kaplan–Meier analysis. In addition, the corrections between CBXs and their co-expressed genes were reported using Oncomine and GEPIA datasets. DAVID was used to perform GO function enrichment analysis for the CBXs and their co-expression genes. Finally, TIMER was used to analyze the immune cell infiltration of CBXs in patients with sarcoma. Results HP1-α/β/γ (CBX1/3/5) and CBX4/6/8 were found to be overexpressed in human sarcoma, and CBXs were upregulated in almost all the sarcoma cell line. The expression levels of HP1-α/β/γ (CBX1/3/5) and CBX7 were associated with overall survival (OS) in patients with sarcoma, while high expression levels of CBX7 were related to disease-free survival (DFS). In addition, the expression levels of CBX2/6/7 were related to recurrence-free survival (RFS). We also found that the CBX family was positively correlated with the infiltration of immune cells, including CD8+ T cells, CD4+ T cells, B cells, macrophages, neutrophils, and dendritic cells, in sarcoma. Conclusions The results from the present study indicated that CBXs were significantly associated with prognosis and immunological status in sarcoma. These data suggest that CBXs could serve as potential biomarkers for prognosis and immune infiltration in human sarcoma.
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Affiliation(s)
- Jian Zhou
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ziyuan Chen
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ming Zou
- Department of Orthopedics, Brain Hospital of Hunan Province (The Second People's Hospital of Hunan Province), Changsha, China
| | - Rongjun Wan
- Department of Respiratory and Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Tong Wu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yingquan Luo
- Department of General Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Gen Wu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Clinical Medicine Eight-Year Program, Central South University, Changsha, China
| | - Wanchun Wang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
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Merino GA, Raad J, Bugnon LA, Yones C, Kamenetzky L, Claus J, Ariel F, Milone DH, Stegmayer G. Novel SARS-CoV-2 encoded small RNAs in the passage to humans. Bioinformatics 2021; 36:5571-5581. [PMID: 33244583 PMCID: PMC7717134 DOI: 10.1093/bioinformatics/btaa1002] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/15/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
Motivation The Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has recently emerged as the responsible for the pandemic outbreak of the coronavirus disease (COVID-19). This virus is closely related to coronaviruses infecting bats and Malayan pangolins, species suspected to be an intermediate host in the passage to humans. Several genomic mutations affecting viral proteins have been identified, contributing to the understanding of the recent animal-to-human transmission. However, the capacity of SARS-CoV-2 to encode functional putative microRNAs (miRNAs) remains largely unexplored. Results We have used deep learning to discover 12 candidate stem-loop structures hidden in the viral protein-coding genome. Among the precursors, the expression of eight mature miRNAs-like sequences was confirmed in small RNA-seq data from SARS-CoV-2 infected human cells. Predicted miRNAs are likely to target a subset of human genes of which 109 are transcriptionally deregulated upon infection. Remarkably, 28 of those genes potentially targeted by SARS-CoV-2 miRNAs are down-regulated in infected human cells. Interestingly, most of them have been related to respiratory diseases and viral infection, including several afflictions previously associated with SARS-CoV-1 and SARS-CoV-2. The comparison of SARS-CoV-2 pre-miRNA sequences with those from bat and pangolin coronaviruses suggests that single nucleotide mutations could have helped its progenitors jumping inter-species boundaries, allowing the gain of novel mature miRNAs targeting human mRNAs. Our results suggest that the recent acquisition of novel miRNAs-like sequences in the SARS-CoV-2 genome may have contributed to modulate the transcriptional reprogramming of the new host upon infection.
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Affiliation(s)
- Gabriela A Merino
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina.,Bioengineering and Bioinformatics Research and Development Institute (IBB), FI-UNER, CONICET, Entre Ríos 3100, Argentina.,European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridgeshire CB101SD, UK
| | - Jonathan Raad
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Leandro A Bugnon
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Cristian Yones
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, UBA-CONICET, Ciudad Autónoma de Buenos Aires 1121, Argentina.,Laboratorio de Genómica y Bioinformática de Patógenos, iB3, Instituto de Biociencias, Biotecnología y Biología traslacional, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1121, Argentina
| | - Juan Claus
- Laboratorio de Virología, FBCB, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral (IAL), CONICET, FBCB, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Diego H Milone
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Georgina Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
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22
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Li H, Wu N, Liu ZY, Chen YC, Cheng Q, Wang J. Development of a novel transcription factors-related prognostic signature for serous ovarian cancer. Sci Rep 2021; 11:7207. [PMID: 33785763 PMCID: PMC8010122 DOI: 10.1038/s41598-021-86294-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/12/2021] [Indexed: 12/20/2022] Open
Abstract
Growing evidence suggest that transcription factors (TFs) play vital roles in serous ovarian cancer (SOC). In the present study, TFs mRNA expression profiles of 564 SOC subjects in the TCGA database, and 70 SOC subjects in the GEO database were screened. A 17-TFs related prognostic signature was constructed using lasso cox regression and validated in the TCGA and GEO cohorts. Consensus clustering analysis was applied to establish a cluster model. The 17-TFs related prognostic signature, risk score and cluster models were effective at accurately distinguishing the overall survival of SOC. Analysis of genomic alterations were used to elaborate on the association between the 17-TFs related prognostic signature and genomic aberrations. The GSEA assay results suggested that there was a significant difference in the inflammatory and immune response pathways between the high-risk and low-risk score groups. The potential immune infiltration, immunotherapy, and chemotherapy responses were analyzed due to the significant difference in the regulation of lymphocyte migration and T cell-mediated cytotoxicity between the two groups. The results indicated that patients with low-risk score were more likely to respond anti-PD-1, etoposide, paclitaxel, and veliparib but not to gemcitabine, doxorubicin, docetaxel, and cisplatin. Also, the prognostic nomogram model revealed that the risk score was a good prognostic indicator for SOC patients. In conclusion, we explored the prognostic values of TFs in SOC and developed a 17-TFs related prognostic signature to predict the survival of SOC patients.
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Affiliation(s)
- He Li
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China
| | - Nayiyuan Wu
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China
| | - Zhao-Yi Liu
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China
| | - Yong-Chang Chen
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
| | - Jing Wang
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China.
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23
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Lin K, Zhu J, Hu C, Bu F, Luo C, Zhu X, Zhu Z. Comprehensive analysis of the prognosis for chromobox family in gastric cancer. J Gastrointest Oncol 2020; 11:932-951. [PMID: 33209489 DOI: 10.21037/jgo-20-208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Chromobox (CBX) family proteins are a class of transcriptional repressors involved in epigenetic regulation and developmental processes of various tumors, including gastric cancer. However, the function and prognosis of different CBXs in gastric cancer remain unknown. Methods This study addresses this issue by synthesizing several mainstream databases (Oncomine, GEPIA2, cBioportal, and Kaplan-Meier plotter, among others) that currently contain many tumor samples and provide very reliable analysis results, investigating the role of CBXs in the prognosis of gastric cancer. Results The mRNA of CBX1/2/3/4/5/8 was highly expressed in gastric cancer, the mRNA of CBX7 was lowly expressed in gastric cancer, and the mRNA expression of CBX6 was not significantly different in CRC. Besides, high and low CBXs mRNA expression correlated with cancer stage, node metastasis status, H. pylori infection status, and tumor grade in CRC patients. We found that high mRNA expression of CBX4/5/6/7/8 was significantly associated with worse overall survival (OS), progression-free survival (FP), and post-progression survival (PPS) in a large number of CRC patients. High mRNA expression of CBX3 was significantly associated with better OS and FP. We also found that none of the eight CBXs family genes had a mutation rate of less than 5% in gastric cancer, and the highest mutation rate was in CBX3 (14%). Conclusions These results suggest that CBX3/4/5/6/7/8 could be a prognostic biomarker in gastric cancer patients.
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Affiliation(s)
- Kang Lin
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jinfeng Zhu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Cegui Hu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Fanqin Bu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chen Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaojian Zhu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhengming Zhu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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24
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Ma T, Ma N, Chen JL, Tang FX, Zong Z, Yu ZM, Chen S, Zhou TC. Expression and prognostic value of Chromobox family members in gastric cancer. J Gastrointest Oncol 2020; 11:983-998. [PMID: 33209492 DOI: 10.21037/jgo-20-223] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background The Chromobox (CBX) protein family, which is a crucial part of the epigenetic regulatory complex, plays an important role in the occurrence and development of cancer; however, the function and prognostic value of CBX family members in gastric cancer is not clear. Methods we investigated the relationship between CBX members and gastric cancer using a range of tools and databases: Oncomine, Kaplan-Meier plotter, cBioPortal, ULCAN, Metascape, and GEPIA. Results The results showed that, relative to normal gastric tissue, mRNA expression levels of CBX1-6 were significantly higher in gastric cancer tissue, whereas the level of CBX7 was significantly lower. Furthermore, overexpression of CBX3-6 and underexpression of CBX7 mRNAs was significantly related to the poor prognosis and survival of gastric cancer patients, making these CBX family members useful biomarkers. Finally, overexpression of CBX1 mRNA was significantly related to the poor prognosis of gastric cancer patients treated with adjuvant 5-fluorouracil-based chemotherapy. Conclusions The members of the CBX family can be used as prognosis and survival biomarkers for gastric cancer and CBX1 may be a biomarker for choosing the chemotherapy regimen of gastric cancer patients.
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Affiliation(s)
- Tao Ma
- Department of Gastrointestinal Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, China
| | - Ning Ma
- Department of Gastrointestinal Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, China
| | - Jia-Lin Chen
- Department of Gastrointestinal Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, China
| | - Fu-Xin Tang
- Department of Gastrointestinal Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, China
| | - Zhen Zong
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhuo-Min Yu
- Department of Gastrointestinal Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, China
| | - Shuang Chen
- Department of Gastrointestinal Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, China
| | - Tai-Cheng Zhou
- Department of Gastrointestinal Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, China
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25
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Xie X, Ning Y, Long J, Wang H, Chen X. Diverse CBX family members as potential prognostic biomarkers in non-small-cell lung cancer. FEBS Open Bio 2020; 10:2206-2215. [PMID: 32894652 PMCID: PMC7530393 DOI: 10.1002/2211-5463.12971] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/19/2020] [Accepted: 09/01/2020] [Indexed: 12/11/2022] Open
Abstract
Chromobox (CBX) family members are vital epigenetic regulators that repress the transcription of target genes through chromatin modification. Several studies have investigated the role of CBX family members in cancer. However, the function and prognostic value of diverse CBX family members in non‐small‐cell lung cancer remain largely unknown. In this study, we reveal that CBX family members are overexpressed in non‐small‐cell lung cancer tissue compared with normal lung tissue, with the exception of CBX6. Kaplan–Meier analysis demonstrated that high expressions of CBX1 and CBX3 are correlated with overall survival, disease‐specific survival, disease‐free interval, and progression‐free interval for patients with lung adenocarcinoma (LUAD). Furthermore, regression model analysis suggests that CBX3 may be suitable as an independent prediction factor for overall survival and progression‐free interval in patients with LUAD. In addition, CBX3 mRNA expression was found to be associated with tumor diameter and lymph node metastasis. Gene enrichment analysis suggests that CBX3 is involved in the cell cycle and P53 signaling pathways. Aberrant expression of CBX3 in LUAD is correlated with DNA copy number alteration. In summary, our data imply that CBX3 plays an important role in the promotion of LUAD and may thus have potential as a prognostic biomarker and molecular therapeutic target for the disease.
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Affiliation(s)
- Xiaobin Xie
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Yue Ning
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jie Long
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Hongyan Wang
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xiaowei Chen
- Department of Hematology, Guangzhou First People's Hospital, South China University of Technology School of Medicine, Guangzhou, China
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26
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Li Q, Pan Y, Cao Z, Zhao S. Comprehensive Analysis of Prognostic Value and Immune Infiltration of Chromobox Family Members in Colorectal Cancer. Front Oncol 2020; 10:582667. [PMID: 33014884 PMCID: PMC7498700 DOI: 10.3389/fonc.2020.582667] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022] Open
Abstract
Objective: Colorectal cancer (CRC) is one of the common malignant tumors worldwide. Chromobox (CBX) family proteins are important components of epigenetic regulation complexes and are implicated in the development of multiple cancers by blocking differentiation and promoting proliferation. However, little is known about the function of distinct CBX proteins in colorectal cancer. Methods: Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), Kaplan-Meier plotter, cBioPortal, GeneMANIA, and TIMER were utilized to analyze differential expression, prognostic value, genetic alteration and immune cell infiltration of CBXs in colorectal cancer patients. Results: The expression levels of CBX1/2/3/4/5 and CBX8 were significantly elevated in CRC tissues, whereas the expression levels of CBX6/7 were reduced. CBX3 was significantly associated with the clinical cancer stage and short disease-free survival (DFS) in CRC patients. High mRNA expression of CBX5/6 was associated with short overall survival (OS) in rectal cancer patients. CBX3/5/6 could be potential prognostic biomarkers for the survival of CRC patients. Moreover, the functions of the differentially expressed CBXs were primarily related to the SUMOylation of DNA methylation proteins and chromatin organization and may regulate the pluripotency of stem cells. The expression of CBXs were significantly correlated with the infiltration of diverse immune cells, including six types of CD4+ T cells, macrophages, neutrophils, B cells, CD8+ T cells, and dendritic cells in colon cancers and rectal cancers. Conclusions: Our study may provide novel insights for the selection of prognostic biomarkers of CBX family in colorectal cancer.
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Affiliation(s)
- Qingshang Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, School of Medicine, Shanghai Institute of Digestive Disease, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Pan
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, School of Medicine, Shanghai Institute of Digestive Disease, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhijun Cao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, School of Medicine, Shanghai Institute of Digestive Disease, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Shuliang Zhao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, School of Medicine, Shanghai Institute of Digestive Disease, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
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27
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Alpha Radiation as a Way to Target Heterochromatic and Gamma Radiation-Exposed Breast Cancer Cells. Cells 2020; 9:cells9051165. [PMID: 32397212 PMCID: PMC7291130 DOI: 10.3390/cells9051165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/19/2020] [Accepted: 05/06/2020] [Indexed: 12/21/2022] Open
Abstract
Compact chromatin is linked to a poor tumour prognosis and resistance to radiotherapy from photons. We investigated DNA damage induction and repair in the context of chromatin structure for densely ionising alpha radiation as well as its therapeutic potential. Chromatin opening by histone deacetylase inhibitor trichostatin A (TSA) pretreatment reduced clonogenic survival and increased γH2AX foci in MDA-MB-231 cells, indicative of increased damage induction by free radicals using gamma radiation. In contrast, TSA pretreatment tended to improve survival after alpha radiation while γH2AX foci were similar or lower; therefore, an increased DNA repair is suggested due to increased access of repair proteins. MDA-MB-231 cells exposed to fractionated gamma radiation (2 Gy × 6) expressed high levels of stem cell markers, elevated heterochromatin H3K9me3 marker, and a trend towards reduced clonogenic survival in response to alpha radiation. There was a higher level of H3K9me3 at baseline, and the ratio of DNA damage induced by alpha vs. gamma radiation was higher in the aggressive MDA-MB-231 cells compared to hormone receptor-positive MCF7 cells. We demonstrate that heterochromatin structure and stemness properties are induced by fractionated radiation exposure. Gamma radiation-exposed cells may be targeted using alpha radiation, and we provide a mechanistic basis for the involvement of chromatin in these effects.
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Transcriptional expressions of Chromobox 1/2/3/6/8 as independent indicators for survivals in hepatocellular carcinoma patients. Aging (Albany NY) 2019; 10:3450-3473. [PMID: 30481161 PMCID: PMC6286817 DOI: 10.18632/aging.101658] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 11/15/2018] [Indexed: 12/27/2022]
Abstract
Chromobox (CBX) proteins are important components of epigenetic regulation complexes known to play key roles in hepatocellular carcinoma (HCC). Little is known about the function of distinct CBXs in HCC. To address this issue, the study investigated the roles of CBXs in the prognosis of HCC using ONCOMINE, UALCAN, Human Protein Atlas, Kaplan-Meier Plotter, c-BioPortal databases. Over expressions of 8 CBXs members were found to be significantly associated with clinical cancer stages and pathological tumor grades in HCC patients. Besides, higher mRNA expressions of CBX1/2/3/6/8 were found to be significantly associated with shorter overall survival (OS) in HCC patients, while higher mRNA expression of CBX7 was associated with favorable OS. Multivariate analysis also showed that high mRNA expressions of CBX1/2/3/6/8 were independent prognostic factors for shorter OS of HCC patients. Moreover, high mutation rate of CBXs (51%) was also observed in HCC patients, and genetic alteration in CBXs was associated with shorter OS and disease-free survival (DFS) in HCC patients. Taken together, these results indicated that CBX1/2/3/6/8 could be prognostic biomarkers for survivals of HCC patients.
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29
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Yu YH, Wilk K, Waldon PL, Intini G. In vivo identification of Bmp2-correlation networks during fracture healing by means of a limb-specific conditional inactivation of Bmp2. Bone 2018; 116:103-110. [PMID: 30048819 PMCID: PMC6613210 DOI: 10.1016/j.bone.2018.07.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 05/09/2018] [Accepted: 07/21/2018] [Indexed: 12/31/2022]
Abstract
Bmp2 is known to play an essential role in the initiation of fracture healing via periosteal activation. Specifically, activation and subsequent differentiation of periosteal progenitor cells requires Bmp2 signaling for activation of the osteo-chondrogenic pathway. Here, we explored the interactive transcriptional gene-gene interplays between Bmp2 and 150 known candidate genes during fracture repair. We constructed the interactive Bmp2 signaling pathways in vivo, by comparing gene expression levels prior and 24 h post femur fracture, in presence (wild type) and in absence of Bmp2 (Bmp2c/c;Prx1::cre limb-specific conditional knockout). Twenty-six differentially expressed genes (pre- vs. post-fracture), which demonstrated high correlations within each experimental condition, were used to construct the co-expression networks. Topological dynamic shifts across different co-expression networks characterized the 26 differentially expressed genes as non-redundant focal linking hubs, redundant connecting hubs, periphery genes, or non-existent. Top-ranked up- or down-regulated genes were identified and discussed. Protein-protein interactions in public databases support our findings. Thus, the co-expression networks from this study can be used for future experimental hypotheses.
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Affiliation(s)
- Yau-Hua Yu
- Dept. of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA; Dept. of Periodontology, Tufts University School of Dental Medicine, Boston MA, USA.
| | - Katarzyna Wilk
- Dept. of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - PhiAnh L Waldon
- Dept. of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Giuseppe Intini
- Dept. of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USAa.
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Yang Y, Meng Q, Wang C, Li X, Lu Y, Xin X, Zheng Q, Lu D. MicroRNA 675 cooperates PKM2 to aggravate progression of human liver cancer stem cells induced from embryonic stem cells. J Mol Med (Berl) 2018; 96:1119-1130. [PMID: 30140938 DOI: 10.1007/s00109-018-1687-9] [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: 01/22/2018] [Revised: 08/08/2018] [Accepted: 08/13/2018] [Indexed: 01/17/2023]
Abstract
Both miR675 and pyruvate kinase M2 (PKM2) contribute to malignant progression of tumor, but its functions in liver cancer stem cells remain unclear. Herein, our findings indicate that miR675 plus PKM2 strongly promotes the growth of liver cancer stem cells. Mechanistically, miR675 plus PKM2 enhances the transcriptional activity of SUV39h2. On the other hand, the excessive SUV39h2 binds to more substrate histone H3, triggering an increase of tri-methylation of histone H3 on the ninth lysine. Furthermore, the tri-methylation of histone 3 on the ninth lysine (H3K9me3)-heterochromatin protein 1 alpha (HP1α) complex is increased when the complex occupancy ability on the C-myc promoter region is raised, recruiting CREB, P300, and RNApolII to the special position that results in C-myc high abundance. Therefore, miR675 plus PKM2 triggered the upregulation of C-myc by increasing the interaction between H3K9me3 and HP1α. Understanding the signaling pathways that miR675 plus PKM2 epigenetically possesses during the malignant transformation of liver cancer stem cells will contribute to more effective liver cancer therapies.
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Affiliation(s)
- Yuxin Yang
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Qiuyu Meng
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Chen Wang
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Xiaonan Li
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Yanan Lu
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Xiaoru Xin
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Qidi Zheng
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Dongdong Lu
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China.
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Lai X, Deng Z, Guo H, Zhu X, Tu W. HP1α is highly expressed in glioma cells and facilitates cell proliferation and survival. Cancer Biomark 2018; 20:453-460. [DOI: 10.3233/cbm-170249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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32
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Ci X, Hao J, Dong X, Choi SY, Xue H, Wu R, Qu S, Gout PW, Zhang F, Haegert AM, Fazli L, Crea F, Ong CJ, Zoubeidi A, He HH, Gleave ME, Collins CC, Lin D, Wang Y. Heterochromatin Protein 1α Mediates Development and Aggressiveness of Neuroendocrine Prostate Cancer. Cancer Res 2018; 78:2691-2704. [PMID: 29487201 DOI: 10.1158/0008-5472.can-17-3677] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/19/2018] [Accepted: 02/23/2018] [Indexed: 11/16/2022]
Abstract
Neuroendocrine prostate cancer (NEPC) is a lethal subtype of prostate cancer arising mostly from adenocarcinoma via neuroendocrine transdifferentiation following androgen deprivation therapy. Mechanisms contributing to both NEPC development and its aggressiveness remain elusive. In light of the fact that hyperchromatic nuclei are a distinguishing histopathologic feature of NEPC, we utilized transcriptomic analyses of our patient-derived xenograft (PDX) models, multiple clinical cohorts, and genetically engineered mouse models to identify 36 heterochromatin-related genes that are significantly enriched in NEPC. Longitudinal analysis using our unique, first-in-field PDX model of adenocarcinoma-to-NEPC transdifferentiation revealed that, among those 36 heterochromatin-related genes, heterochromatin protein 1α (HP1α) expression increased early and steadily during NEPC development and remained elevated in the developed NEPC tumor. Its elevated expression was further confirmed in multiple PDX and clinical NEPC samples. HP1α knockdown in the NCI-H660 NEPC cell line inhibited proliferation, ablated colony formation, and induced apoptotic cell death, ultimately leading to tumor growth arrest. Its ectopic expression significantly promoted NE transdifferentiation in adenocarcinoma cells subjected to androgen deprivation treatment. Mechanistically, HP1α reduced expression of androgen receptor and RE1 silencing transcription factor and enriched the repressive trimethylated histone H3 at Lys9 mark on their respective gene promoters. These observations indicate a novel mechanism underlying NEPC development mediated by abnormally expressed heterochromatin genes, with HP1α as an early functional mediator and a potential therapeutic target for NEPC prevention and management.Significance: Heterochromatin proteins play a fundamental role in NEPC, illuminating new therapeutic targets for this aggressive disease. Cancer Res; 78(10); 2691-704. ©2018 AACR.
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Affiliation(s)
- Xinpei Ci
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Experimental Therapeutics, BC Cancer, Vancouver, British Columbia, Canada
| | - Jun Hao
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Experimental Therapeutics, BC Cancer, Vancouver, British Columbia, Canada
| | - Xin Dong
- Department of Experimental Therapeutics, BC Cancer, Vancouver, British Columbia, Canada
| | - Stephen Y Choi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Experimental Therapeutics, BC Cancer, Vancouver, British Columbia, Canada
| | - Hui Xue
- Department of Experimental Therapeutics, BC Cancer, Vancouver, British Columbia, Canada
| | - Rebecca Wu
- Department of Experimental Therapeutics, BC Cancer, Vancouver, British Columbia, Canada
| | - Sifeng Qu
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Experimental Therapeutics, BC Cancer, Vancouver, British Columbia, Canada
| | - Peter W Gout
- Department of Experimental Therapeutics, BC Cancer, Vancouver, British Columbia, Canada
| | - Fang Zhang
- Department of Experimental Therapeutics, BC Cancer, Vancouver, British Columbia, Canada
| | - Anne M Haegert
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ladan Fazli
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Francesco Crea
- School of Life, Health and Chemical Sciences, the Open University, Walton Hall, Milton Keynes, United Kingdom
| | - Christopher J Ong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Housheng H He
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Martin E Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Colin C Collins
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dong Lin
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Experimental Therapeutics, BC Cancer, Vancouver, British Columbia, Canada
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Experimental Therapeutics, BC Cancer, Vancouver, British Columbia, Canada
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Yan S, Wu G. Could ALDH2 *2 be the reason for low incidence and mortality of ovarian cancer for East Asia women? Oncotarget 2017; 9:12503-12512. [PMID: 29552329 PMCID: PMC5844765 DOI: 10.18632/oncotarget.23605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/16/2017] [Indexed: 12/15/2022] Open
Abstract
It is curious that East Asian women have a low incidence and mortality of ovarian cancer in various epidemiological studies. Although different explanations were given, they appear unsubstantial. We notice that East Asian population usually are inactive aldehyde dehydrogenase 2 mutation (ALDH2 * 2) carriers, and ALDH plays an important role in the resistance of ovarian cancer to chemotherapeutics, especially in ovarian cancer stem cells. Therefore, we hypothesize whether ALDH2 mutation is the major reason for low incidence and mortality of ovarian cancer in East Asian women, and use the evidence from literature, transcriptomic data with average 5-year overall survival to confirm our hypothesis.
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Affiliation(s)
- Shaomin Yan
- Bioscience and Technology Research Center, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, China
| | - Guang Wu
- Bioscience and Technology Research Center, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, China
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Eriksson M, Hååg P, Brzozowska B, Lipka M, Lisowska H, Lewensohn R, Wojcik A, Viktorsson K, Lundholm L. Analysis of Chromatin Opening in Heterochromatic Non-Small Cell Lung Cancer Tumor-Initiating Cells in Relation to DNA-Damaging Antitumor Treatment. Int J Radiat Oncol Biol Phys 2017; 100:174-187. [PMID: 29107335 DOI: 10.1016/j.ijrobp.2017.09.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 08/31/2017] [Accepted: 09/14/2017] [Indexed: 01/09/2023]
Abstract
PURPOSE We previously reported that sphere-forming non-small cell lung cancer (NSCLC) tumor-initiating cells (TICs) have an altered activation of DNA damage response- and repair proteins and are refractory to DNA-damaging treatments. We analyzed whether chromatin organization plays a role in the observed refractoriness. METHODS AND MATERIALS Bulk cells and TICs from the NSCLC H23 and H1299 cell lines were examined using cell viability, clonogenic survival, Western blot, short interfering RNA analysis, and micronucleus assay. RESULTS NSCLC TICs displayed elevated heterochromatin markers trimethylated lysine 9 of histone H3 and heterochromatin protein 1γ relative to bulk cells and reduced cell viability upon histone deacetylase inhibition (HDACi). Vorinostat and trichostatin A increased the euchromatin markers acetylated lysine 9/14 of histone H3 and lysine 8 of histone H4, and HDACi pretreatment increased the phosphorylation of the DNA damage response proteins ataxia telangiectasia mutated and DNA-dependent protein kinase, catalytic subunit, upon irradiation in TICs. HDACi sensitized TICs to cisplatin and to some extent to ionizing irradiation. The protectiveness of a dense chromatin structure was indicated by an enhanced frequency of micronuclei in TICs following irradiation, after knockdown of heterochromatin protein 1γ. CONCLUSIONS Although confirmatory studies in additional NSCLC model systems and with respect to analyses of other DNA damage response proteins are needed, our data point toward a heterochromatic structure of NSCLC TICs, such that HDACi can sensitize TICs to DNA damage.
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Affiliation(s)
- Mina Eriksson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Petra Hååg
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Beata Brzozowska
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; Biomedical Physics Division, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Poland
| | - Magdalena Lipka
- Department of Radiobiology and Immunology, Institute of Biology, Jan Kochanowski University, Kielce, Poland
| | - Halina Lisowska
- Department of Radiobiology and Immunology, Institute of Biology, Jan Kochanowski University, Kielce, Poland
| | - Rolf Lewensohn
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Andrzej Wojcik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; Department of Radiobiology and Immunology, Institute of Biology, Jan Kochanowski University, Kielce, Poland
| | | | - Lovisa Lundholm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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Cross-Kingdom Regulation of Putative miRNAs Derived from Happy Tree in Cancer Pathway: A Systems Biology Approach. Int J Mol Sci 2017; 18:ijms18061191. [PMID: 28587194 PMCID: PMC5486014 DOI: 10.3390/ijms18061191] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/17/2017] [Accepted: 05/27/2017] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are well-known key regulators of gene expression primarily at the post-transcriptional level. Plant-derived miRNAs may pass through the gastrointestinal tract, entering into the body fluid and regulate the expression of endogenous mRNAs. Camptotheca acuminata, a highly important medicinal plant known for its anti-cancer potential was selected to investigate cross-kingdom regulatory mechanism and involvement of miRNAs derived from this plant in cancer-associated pathways through in silico systems biology approach. In this study, total 33 highly stable putative novel miRNAs were predicted from the publically available 53,294 ESTs of C. acuminata, out of which 14 miRNAs were found to be regulating 152 target genes in human. Functional enrichment, gene-disease associations and network analysis of these target genes were carried out and the results revealed their association with prominent types of cancers like breast cancer, leukemia and lung cancer. Pathways like focal adhesion, regulation of lipolysis in adipocytes and mTOR signaling pathways were found significantly associated with the target genes. The regulatory network analysis showed the association of some important hub proteins like GSK3B, NUMB, PEG3, ITGA2 and DLG2 with cancer-associated pathways. Based on the analysis results, it can be suggested that the ingestion of the C. acuminata miRNAs may have a functional impact on tumorigenesis in a cross-kingdom way and may affect the physiological condition at genetic level. Thus, the predicted miRNAs seem to hold potentially significant role in cancer pathway regulation and therefore, may be further validated using in vivo experiments for a better insight into their mechanism of epigenetic action of miRNA.
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Phosphoproteomics Reveals HMGA1, a CK2 Substrate, as a Drug-Resistant Target in Non-Small Cell Lung Cancer. Sci Rep 2017; 7:44021. [PMID: 28290473 PMCID: PMC5349541 DOI: 10.1038/srep44021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 02/03/2017] [Indexed: 12/13/2022] Open
Abstract
Although EGFR tyrosine kinase inhibitors (TKIs) have demonstrated good efficacy in non-small-cell lung cancer (NSCLC) patients harboring EGFR mutations, most patients develop intrinsic and acquired resistance. We quantitatively profiled the phosphoproteome and proteome of drug-sensitive and drug-resistant NSCLC cells under gefitinib treatment. The construction of a dose-dependent responsive kinase-substrate network of 1548 phosphoproteins and 3834 proteins revealed CK2-centric modules as the dominant core network for the potential gefitinib resistance-associated proteins. CK2 knockdown decreased cell survival in gefitinib-resistant NSCLCs. Using motif analysis to identify the CK2 core sub-network, we verified that elevated phosphorylation level of a CK2 substrate, HMGA1 was a critical node contributing to EGFR-TKI resistance in NSCLC cell. Both HMGA1 knockdown or mutation of the CK2 phosphorylation site, S102, of HMGA1 reinforced the efficacy of gefitinib in resistant NSCLC cells through reactivation of the downstream signaling of EGFR. Our results delineate the TKI resistance-associated kinase-substrate network, suggesting a potential therapeutic strategy for overcoming TKI-induced resistance in NSCLC.
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37
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Gene Co-Expression Network Analysis Unraveling Transcriptional Regulation of High-Altitude Adaptation of Tibetan Pig. PLoS One 2016; 11:e0168161. [PMID: 27936142 PMCID: PMC5148111 DOI: 10.1371/journal.pone.0168161] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/27/2016] [Indexed: 02/08/2023] Open
Abstract
Tibetan pigs have survived at high altitude for millennia and they have a suite of adaptive features to tolerate the hypoxic environment. However, the molecular mechanisms underlying the regulation of hypoxia-adaptive phenotypes have not been completely elucidated. In this study, we analyzed differentially expressed genes (DEGs), biological pathways and constructed co-expression regulation networks using whole-transcriptome microarrays from lung tissues of Tibetan and Duroc pigs both at high and low altitude. A total of 3,066 DEGs were identified and this list was over-represented for the ontology terms including metabolic process, catalytic activity, and KEGG pathway including metabolic pathway and PI3K-Akt signaling pathway. The regulatory (RIF) and phenotypic (PIF) impact factor analysis identified several known and several potentially novel regulators of hypoxia adaption, including: IKBKG, KLF6 and RBPJ (RIF1), SF3B1, EFEMP1, HOXB6 and ATF6 (RIF2). These findings provide new details of the regulatory architecture of hypoxia-adaptive genes and also insight into which genes may undergo epigenetic modification for further study in the high-altitude adaptation.
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Le Rhun E, Duhamel M, Wisztorski M, Gimeno JP, Zairi F, Escande F, Reyns N, Kobeissy F, Maurage CA, Salzet M, Fournier I. Evaluation of non-supervised MALDI mass spectrometry imaging combined with microproteomics for glioma grade III classification. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:875-890. [PMID: 27890679 DOI: 10.1016/j.bbapap.2016.11.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 11/17/2016] [Accepted: 11/20/2016] [Indexed: 10/20/2022]
Abstract
An integrated diagnosis using molecular features is recommended in the 2016 World Health Organization (WHO) classification. Our aim was to explore non-targeted molecular classification using MALDI mass spectrometry imaging (MALDI MSI) associated to microproteomics in order to classify anaplastic glioma by integration of clinical data. We used fresh-frozen tissue sections to perform MALDI MSI of proteins based on their digestion peptides after in-situ trypsin digestion of the tissue sections and matrix deposition by micro-spraying. The generated 70μm spatial resolution image datasets were further processed by individual or global segmentation in order to cluster the tissues according to their molecular protein signature. The clustering gives 3 main distinct groups. Within the tissues the ROIs (regions of interest) defined by these groups were used for microproteomics by micro-extraction of the tryptic peptides after on-tissue enzymatic digestion. More than 2500 proteins including 22 alternative proteins (AltProt) are identified by the Shotgun microproteomics. Statistical analysis on the basis of the label free quantification of the proteins shows a similar classification to the MALDI MSI segmentation into 3 groups. Functional analysis performed on each group reveals sub-networks related to neoplasia for group 1, glioma with inflammation for group 2 and neurogenesis for group 3. This demonstrates the interest on these new non-targeted large molecular data combining both MALDI MSI and microproteomics data, for tumor classification. This analysis provides new insights into grade III glioma organization. This specific information could allow a more accurate classification of the biopsies according to the prognosis and the identification of potential new targeted therapeutic options. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Emilie Le Rhun
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Lille University Hospital, Neuro-Oncology, Department of Neurosurgery, F-59000 Lille, France; Breast Unit, Department of Medical Oncology, Oscar Lambret Center, Lille, France.
| | - Marie Duhamel
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Maxence Wisztorski
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Jean-Pascal Gimeno
- ONCOLille, Maison Régionale de la Recherche Clinique, F-59000 Lille, France.
| | - Fahed Zairi
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Lille University Hospital, Department of Neurosurgery, F-59000 Lille, France.
| | - Fabienne Escande
- Lille University Hospital, Pôle Pathologie Biologique, Service Anatomie Pathologique, F-59000 Lille, France.
| | - Nicolas Reyns
- Lille University Hospital, Department of Neurosurgery, F-59000 Lille, France.
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Lebanon; Department of Psychiatry, Center of Neuroproteomics and Biomarkers Research, University of Florida, Gainesville, FL, USA.
| | - Claude-Alain Maurage
- Lille University Hospital, Pôle Pathologie Biologique, Service Anatomie Pathologique, F-59000 Lille, France.
| | - Michel Salzet
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Isabelle Fournier
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
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Hsu CL, Chung FH, Chen CH, Hsu TT, Liu SM, Chung DS, Hsu YF, Chen CL, Ma N, Lee HC. Genotypes of cancer stem cells characterized by epithelial-to-mesenchymal transition and proliferation related functions. Sci Rep 2016; 6:32523. [PMID: 27597445 PMCID: PMC5011650 DOI: 10.1038/srep32523] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/08/2016] [Indexed: 12/13/2022] Open
Abstract
Cancer stem cells (CSCs), or cancer cells with stem cell-like properties, generally exhibit drug resistance and have highly potent cancer inducing capabilities. Genome-wide expression data collected at public repositories over the last few years provide excellent material for studies that can lead to insights concerning the molecular and functional characteristics of CSCs. Here, we conducted functional genomic studies of CSC based on fourteen PCA-screened high quality public CSC whole genome gene expression datasets and, as control, four high quality non-stem-like cancer cell and non-cancerous stem cell datasets from the Gene Expression Omnibus database. A total of 6,002 molecular signatures were taken from the Molecular Signatures Database and used to characterize the datasets, which, under two-way hierarchical clustering, formed three genotypes. Type 1, consisting of mainly glia CSCs, had significantly enhanced proliferation, and significantly suppressed epithelial-mesenchymal transition (EMT), related functions. Type 2, mainly breast CSCs, had significantly enhanced EMT, but not proliferation, related functions. Type 3, composed of ovarian, prostate, and colon CSCs, had significantly suppressed proliferation related functions and mixed expressions on EMT related functions.
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Affiliation(s)
- Chueh-Lin Hsu
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan
| | - Feng-Hsiang Chung
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan
| | - Chih-Hao Chen
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan
| | - Tzu-Ting Hsu
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan
| | - Szu-Mam Liu
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan
| | - Dao-Sheng Chung
- Department of Radiation Oncology, Landseed Hospital, Taoyuan, 324, Taiwan
| | - Ya-Fen Hsu
- Department of Surgery, Landseed Hospital, Taoyuan, 324, Taiwan
| | - Chien-Lung Chen
- Department of Nephrology, Landseed Hospital, Taoyuan, 324, Taiwan
| | - Nianhan Ma
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan
| | - Hoong-Chien Lee
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan.,Department of Physics, Chung Yuan Christian University, Zhongli, 32023, Taiwan.,Center for Dynamical Biomarkers and Translational Medicine, National Central University, Zhongli, 32001, Taiwan
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40
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Lee WJ, Kim SC, Yoon JH, Yoon SJ, Lim J, Kim YS, Kwon SW, Park JH. Meta-Analysis of Tumor Stem-Like Breast Cancer Cells Using Gene Set and Network Analysis. PLoS One 2016; 11:e0148818. [PMID: 26870956 PMCID: PMC4752453 DOI: 10.1371/journal.pone.0148818] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/22/2016] [Indexed: 12/24/2022] Open
Abstract
Generally, cancer stem cells have epithelial-to-mesenchymal-transition characteristics and other aggressive properties that cause metastasis. However, there have been no confident markers for the identification of cancer stem cells and comparative methods examining adherent and sphere cells are widely used to investigate mechanism underlying cancer stem cells, because sphere cells have been known to maintain cancer stem cell characteristics. In this study, we conducted a meta-analysis that combined gene expression profiles from several studies that utilized tumorsphere technology to investigate tumor stem-like breast cancer cells. We used our own gene expression profiles along with the three different gene expression profiles from the Gene Expression Omnibus, which we combined using the ComBat method, and obtained significant gene sets using the gene set analysis of our datasets and the combined dataset. This experiment focused on four gene sets such as cytokine-cytokine receptor interaction that demonstrated significance in both datasets. Our observations demonstrated that among the genes of four significant gene sets, six genes were consistently up-regulated and satisfied the p-value of < 0.05, and our network analysis showed high connectivity in five genes. From these results, we established CXCR4, CXCL1 and HMGCS1, the intersecting genes of the datasets with high connectivity and p-value of < 0.05, as significant genes in the identification of cancer stem cells. Additional experiment using quantitative reverse transcription-polymerase chain reaction showed significant up-regulation in MCF-7 derived sphere cells and confirmed the importance of these three genes. Taken together, using meta-analysis that combines gene set and network analysis, we suggested CXCR4, CXCL1 and HMGCS1 as candidates involved in tumor stem-like breast cancer cells. Distinct from other meta-analysis, by using gene set analysis, we selected possible markers which can explain the biological mechanisms and suggested network analysis as an additional criterion for selecting candidates.
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Affiliation(s)
- Won Jun Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang Cheol Kim
- Department of Biomedical Informatics, Center for Genome Science, National Institute of Health, KCDC, Choongchung-Buk-do, 28159, Republic of Korea
| | - Jung-Ho Yoon
- Department of Biochemistry and Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Sang Jun Yoon
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Johan Lim
- Department of Statistics, Seoul National University, Seoul, 08826, Republic of Korea
| | - You-Sun Kim
- Department of Biochemistry and Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Sung Won Kwon
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jeong Hill Park
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- * E-mail:
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Vad-Nielsen J, Nielsen AL. Beyond the histone tale: HP1α deregulation in breast cancer epigenetics. Cancer Biol Ther 2015; 16:189-200. [PMID: 25588111 DOI: 10.1080/15384047.2014.1001277] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Heterochromatin protein 1α (HP1α) encoded from the CBX5-gene is an evolutionary conserved protein that binds histone H3 di- or tri-methylated at position lysine 9 (H3K9me2/3), a hallmark for heterochromatin, and has an essential role in forming higher order chromatin structures. HP1α has diverse functions in heterochromatin formation, gene regulation, and mitotic progression, and forms complex networks of gene, RNA, and protein interactions. Emerging evidence has shown that HP1α serves a unique biological role in breast cancer related processes and in particular for epigenetic control mechanisms involved in aberrant cell proliferation and metastasis. However, how HP1α deregulation plays dual mechanistic functions for cancer cell proliferation and metastasis suppression and the underlying cellular mechanisms are not yet comprehensively described. In this paper we provide an overview of the role of HP1α as a new sight of epigenetics in proliferation and metastasis of human breast cancer. This highlights the importance of addressing HP1α in breast cancer diagnostics and therapeutics.
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Key Words
- CBX, chromobox homolog
- CD, chromo domain
- CSC, cancer stem cells
- CSD, cromo shadow domain
- CTE, C-terminal extension
- DNMT, DNA-methyltransferase
- EMT, epithelial-to-mesenchymal transition
- HDMT, histone demethylase
- HMT, histone methyltransferase
- HP1, heterochromatin protein 1
- NTE, N-terminal extension
- PEV, position effect variegation
- SOMU, sumoylation
- TGS, transcriptional gene silencing
- TSS, transcriptional start site
- bp, base pair
- breast-cancer, metastasis
- chromatin
- epigenetics
- histone-modifications
- invasion
- mitosis
- proliferation
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Allegra A, Alonci A, Penna G, Innao V, Gerace D, Rotondo F, Musolino C. The cancer stem cell hypothesis: a guide to potential molecular targets. Cancer Invest 2014; 32:470-95. [PMID: 25254602 DOI: 10.3109/07357907.2014.958231] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Common cancer theories hold that tumor is an uncontrolled somatic cell proliferation caused by the progressive addition of random mutations in critical genes that control cell growth. Nevertheless, various contradictions related to the mutation theory have been reported previously. These events may be elucidated by the persistence of residual tumor cells, called Cancer Stem Cells (CSCs) responsible for tumorigenesis, tumor maintenance, tumor spread, and tumor relapse. Herein, we summarize the current understanding of CSCs, with a focus on the possibility to identify specific markers of CSCs, and discuss the clinical application of targeting CSCs for cancer treatment.
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Banerji CRS, Miranda-Saavedra D, Severini S, Widschwendter M, Enver T, Zhou JX, Teschendorff AE. Cellular network entropy as the energy potential in Waddington's differentiation landscape. Sci Rep 2013; 3:3039. [PMID: 24154593 PMCID: PMC3807110 DOI: 10.1038/srep03039] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 10/08/2013] [Indexed: 02/08/2023] Open
Abstract
Differentiation is a key cellular process in normal tissue development that is significantly altered in cancer. Although molecular signatures characterising pluripotency and multipotency exist, there is, as yet, no single quantitative mark of a cellular sample's position in the global differentiation hierarchy. Here we adopt a systems view and consider the sample's network entropy, a measure of signaling pathway promiscuity, computable from a sample's genome-wide expression profile. We demonstrate that network entropy provides a quantitative, in-silico, readout of the average undifferentiated state of the profiled cells, recapitulating the known hierarchy of pluripotent, multipotent and differentiated cell types. Network entropy further exhibits dynamic changes in time course differentiation data, and in line with a sample's differentiation stage. In disease, network entropy predicts a higher level of cellular plasticity in cancer stem cell populations compared to ordinary cancer cells. Importantly, network entropy also allows identification of key differentiation pathways. Our results are consistent with the view that pluripotency is a statistical property defined at the cellular population level, correlating with intra-sample heterogeneity, and driven by the degree of signaling promiscuity in cells. In summary, network entropy provides a quantitative measure of a cell's undifferentiated state, defining its elevation in Waddington's landscape.
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Affiliation(s)
- Christopher R. S. Banerji
- Statistical Cancer Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London WC1E6BT United Kingdom
| | - Diego Miranda-Saavedra
- Bioinformatics and Genomics Laboratory, World Premier International (WPI) Immunology Frontier Research Center (IFReC), Osaka University, Osaka, Japan
| | - Simone Severini
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London WC1E6BT United Kingdom
- Department of Computer Science, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Martin Widschwendter
- Department of Women's Cancer, University College London, London WC1E 6BT, United Kingdom
| | - Tariq Enver
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom
| | - Joseph X. Zhou
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109-5234, USA
| | - Andrew E. Teschendorff
- Statistical Cancer Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London WC1E6BT United Kingdom
- CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, 320 Yue Yang Road, Shanghai 200031, China
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Ovarian and breast cancer spheres are similar in transcriptomic features and sensitive to fenretinide. BIOMED RESEARCH INTERNATIONAL 2013; 2013:510905. [PMID: 24222909 PMCID: PMC3816214 DOI: 10.1155/2013/510905] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 08/16/2013] [Accepted: 08/18/2013] [Indexed: 01/06/2023]
Abstract
Cancer stem cells (CSCs) are resistant to chemotherapy and are ability to regenerate cancer cell populations, thus attracting much attention in cancer research. In this report, we first demonstrated that sphere cells from ovarian cancer cell line A2780 shared many features of CSCs, such as resistance to cisplatin and able to initiate tumors in an efficient manner. Then, we conducted cDNA microarray analysis on spheres from ovarian A2780 cells, and from breast MCF7 and SUM159 cells, and found that molecular pathways underlying spheres from these cancer cell lines were similar to a large extent, suggesting that similar mechanisms are involved in the genesis of CSCs in both ovarian and breast cancer types. In addition, we showed that spheres from these cancer types were highly sensitive to fenretinide, a stimulus of oxidative stress-mediated apoptosis in cancer cells. Thus, our results not only provide important insights into mechanisms underlying CSCs in ovarian and breast cancer, but also lead to the development of more sophisticated protocols of cancer therapy in near future.
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Corominas-Faja B, Oliveras-Ferraros C, Cuyàs E, Segura-Carretero A, Joven J, Martin-Castillo B, Barrajón-Catalán E, Micol V, Bosch-Barrera J, Menendez JA. Stem cell-like ALDH(bright) cellular states in EGFR-mutant non-small cell lung cancer: a novel mechanism of acquired resistance to erlotinib targetable with the natural polyphenol silibinin. Cell Cycle 2013; 12:3390-404. [PMID: 24047698 DOI: 10.4161/cc.26417] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The enrichment of cancer stem cell (CSC)-like cellular states has not previously been considered to be a causative mechanism in the generalized progression of EGFR-mutant non-small cell lung carcinomas (NSCLC) after an initial response to the EGFR tyrosine kinase inhibitor erlotinib. To explore this possibility, we utilized a pre-clinical model of acquired erlotinib resistance established by growing NSCLC cells containing a TKI-sensitizing EGFR exon 19 deletion (ΔE746-A750) in the continuous presence of high doses of erlotinib. Genome-wide analyses using Agilent 44K Whole Human Genome Arrays were evaluated via bioinformatics analyses through GSEA-based screening of the KEGG pathway database to identify the molecular circuitries that were over-represented in the transcriptomic signatures of erlotinib-refractory cells. The genomic spaces related to erlotinib resistance included a preponderance of cell cycle genes (E2F1, - 2, CDC2, -6) and DNA replication-related genes (MCM4, - 5, - 6, - 7), most of which are associated with early lung development and poor prognosis. In addition, metabolic genes such as ALDH1A3 (a candidate marker for lung cancer cells with CSC-like properties) were identified. Thus, we measured the proportion of erlotinib-resistant cells expressing very high levels of aldehyde dehydrogenase (ALDH) activity attributed to ALDH1/3 isoforms. Using flow cytometry and the ALDEFLUOR® reagent, we confirmed that erlotinib-refractory cell populations contained drastically higher percentages (> 4500%) of ALDH(bright) cells than the parental erlotinib-responsive cells. Notably, strong decreases in the percentages of ALDH(bright) cells were observed following incubation with silibinin, a bioactive flavonolignan that can circumvent erlotinib resistance in vivo. The number of lung cancer spheres was drastically suppressed by silibinin in a dose-dependent manner, thus confirming the ability of this agent to inhibit the self-renewal of erlotinib-refractory CSC-like cells. This report is the first to show that: (1) loss of responsiveness to erlotinib in EGFR-mutant NSCLC can be explained in terms of erlotinib-refractory ALDH(bright) cells, which have been shown to exhibit stem cell-like properties; and (2) erlotinib-refractory ALDH(bright) cells are sensitive to the natural agent silibinin. Our findings highlight the benefit of administration of silibinin in combination with EGFR TKIs to target CSCs and minimize the ability of tumor cells to escape cell death in EGFR-mutant NSCLC patients.
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Affiliation(s)
- Bruna Corominas-Faja
- Metabolism & Cancer Group; Translational Research Laboratory; Catalan Institute of Oncology; Girona, Catalonia, Spain; Girona Biomedical Research Institute (IDIBGI); Girona, Catalonia, Spain
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