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Wang Z, Chao Z, Wang Q, Zou F, Song T, Xu L, Ning J, Cheng F. EXO1/P53/SREBP1 axis-regulated lipid metabolism promotes prostate cancer progression. J Transl Med 2024; 22:104. [PMID: 38279172 PMCID: PMC10811948 DOI: 10.1186/s12967-023-04822-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/20/2023] [Indexed: 01/28/2024] Open
Abstract
Prostate cancer (PCa) is one of the most common malignant tumors affecting the male genitourinary system. However, there is currently a lack of effective treatments for patients with advanced prostate cancer, which significantly impacts men's overall health. Exonuclease 1 (EXO1), a protein with mismatch repair and recombination functions, has been found to play a vital role in various diseases. In our study, we discovered that EXO1 acts as a novel biomarker of PCa, which promotes prostate cancer progression by regulating lipid metabolism reprogramming in prostate cancer cells. Mechanistically, EXO1 promotes the expression of SREBP1 by inhibiting the P53 signaling pathway. In summary, our findings suggest that EXO1 regulated intracellular lipid reprogramming through the P53/SREBP1 axis, thus promoting PCa progression. The result could potentially lead to new insights and therapeutic targets for diagnosing and treating PCa.
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Affiliation(s)
- Zefeng Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Zheng Chao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qi Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fan Zou
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Tianbao Song
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Lizhe Xu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jinzhuo Ning
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
| | - Fan Cheng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
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2
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Jacquet E, Chuffart F, Vitte AL, Nika E, Mousseau M, Khochbin S, Rousseaux S, Bourova-Flin E. Aberrant activation of five embryonic stem cell-specific genes robustly predicts a high risk of relapse in breast cancers. BMC Genomics 2023; 24:463. [PMID: 37592220 PMCID: PMC10436393 DOI: 10.1186/s12864-023-09571-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/09/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND In breast cancer, as in all cancers, genetic and epigenetic deregulations can result in out-of-context expressions of a set of normally silent tissue-specific genes. The activation of some of these genes in various cancers empowers tumours cells with new properties and drives enhanced proliferation and metastatic activity, leading to a poor survival prognosis. RESULTS In this work, we undertook an unprecedented systematic and unbiased analysis of out-of-context activations of a specific set of tissue-specific genes from testis, placenta and embryonic stem cells, not expressed in normal breast tissue as a source of novel prognostic biomarkers. To this end, we combined a strict machine learning framework of transcriptomic data analysis, and successfully created a new robust tool, validated in several independent datasets, which is able to identify patients with a high risk of relapse. This unbiased approach allowed us to identify a panel of five biomarkers, DNMT3B, EXO1, MCM10, CENPF and CENPE, that are robustly and significantly associated with disease-free survival prognosis in breast cancer. Based on these findings, we created a new Gene Expression Classifier (GEC) that stratifies patients. Additionally, thanks to the identified GEC, we were able to paint the specific molecular portraits of the particularly aggressive tumours, which show characteristics of male germ cells, with a particular metabolic gene signature, associated with an enrichment in pro-metastatic and pro-proliferation gene expression. CONCLUSIONS The GEC classifier is able to reliably identify patients with a high risk of relapse at early stages of the disease. We especially recommend to use the GEC tool for patients with the luminal-A molecular subtype of breast cancer, generally considered of a favourable disease-free survival prognosis, to detect the fraction of patients undergoing a high risk of relapse.
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Affiliation(s)
- Emmanuelle Jacquet
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, EpiMed, Institute for Advanced Biosciences, Grenoble, France
- Université Grenoble Alpes, CHU Grenoble Alpes, Medical Oncology Unit, Cancer and Blood Diseases Department, Grenoble, France
| | - Florent Chuffart
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, EpiMed, Institute for Advanced Biosciences, Grenoble, France
| | - Anne-Laure Vitte
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, EpiMed, Institute for Advanced Biosciences, Grenoble, France
| | - Eleni Nika
- Université Grenoble Alpes, CHU Grenoble Alpes, Department of Pathology, Grenoble, France
| | - Mireille Mousseau
- Université Grenoble Alpes, CHU Grenoble Alpes, Medical Oncology Unit, Cancer and Blood Diseases Department, Grenoble, France
- Université Grenoble Alpes, INSERM U1039, Bioclinical Radiopharmaceuticals, Grenoble, France
| | - Saadi Khochbin
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, EpiMed, Institute for Advanced Biosciences, Grenoble, France
| | - Sophie Rousseaux
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, EpiMed, Institute for Advanced Biosciences, Grenoble, France
| | - Ekaterina Bourova-Flin
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, EpiMed, Institute for Advanced Biosciences, Grenoble, France.
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3
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Arumugam P, Ramesh V, Sampathkumar B, Perumalsamy H, Balusamy SR, Suganya K, Balraj S, Nachimuthu SK, Sundaravadivelu S. Integrative transcriptome analysis of triple negative breast cancer profiles for identification of druggable targets. J Biomol Struct Dyn 2023; 41:12106-12119. [PMID: 36617953 DOI: 10.1080/07391102.2022.2164795] [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: 11/30/2021] [Accepted: 12/29/2022] [Indexed: 01/10/2023]
Abstract
As triple negative breast cancer (TNBC) lacks a specific target, exploration of abnormally expressed genes during the progression of TNBC is important for a better understanding of tumorigenesis and to find a specific target. We intended to figure out genes associated with TNBC, which can provide unique insights into gene dysregulation in TNBC while also pointing to new possible therapeutic targets for TNBC. A meta-analysis of multiple TNBC mRNA profiles was performed to identify consistently differentially expressed genes (CDGs). The pathways involved in modulating these genes were analyzed by MsigDB, and the interaction map was constructed. These CDGs were evaluated for their expression in cell lines, and drugs that could modulate the expression of CDGs were obtained using the connectivity map. CDGs were docked with doxorubicin and anethole, which is a phytocompound. The expression of selected CDGs was analyzed in MDA-MB-231 cells after treatment with doxorubicin and anethole. We found 45 CDGs, out of which 36 were upregulated and 9 were downregulated. MDA-MB-231 cell line was found to have high expression of CDGs, and drug that could modulate the expression of CDGs was doxorubicin. Docking results revealed that anethole and doxorubicin had good interaction with the CDGs especially with the genes AURKA, CDC6, DEPDC1, KIF23, KPNA2, MELK, CTNNB1, FLI1 and E2F1. Gene expression studies of the selected CDGs showed that the synergistic effect of anethole and doxorubicin effectively downregulated the expression. The CDGs identified from multiple cohorts have clinical significance and may be effectively exploited in the targeted therapy for TNBC.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Poornima Arumugam
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education For Women, Coimbatore, Tamil Nadu, India
| | - Vignesh Ramesh
- International Center for Clinical Research, Friedrich Alexander University, Erlangen-Nurnberb, Germany
| | - Banupriya Sampathkumar
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education For Women, Coimbatore, Tamil Nadu, India
| | - Haribalan Perumalsamy
- Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin, Republic of Korea
| | | | - Kanagaraj Suganya
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education For Women, Coimbatore, Tamil Nadu, India
| | - Sudha Balraj
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education For Women, Coimbatore, Tamil Nadu, India
| | | | - Sumathi Sundaravadivelu
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education For Women, Coimbatore, Tamil Nadu, India
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4
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Maurer-Morelli CV, de Vasconcellos JF, Bruxel EM, Rocha CS, do Canto AM, Tedeschi H, Yasuda CL, Cendes F, Lopes-Cendes I. Gene expression profile suggests different mechanisms underlying sporadic and familial mesial temporal lobe epilepsy. Exp Biol Med (Maywood) 2022; 247:2233-2250. [PMID: 36259630 PMCID: PMC9899983 DOI: 10.1177/15353702221126666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Most patients with pharmacoresistant mesial temporal lobe epilepsy (MTLE) have hippocampal sclerosis on the postoperative histopathological examination. Although most patients with MTLE do not refer to a family history of the disease, familial forms of MTLE have been reported. We studied surgical specimens from patients with MTLE who had epilepsy surgery for medically intractable seizures. We assessed and compared gene expression profiles of the tissue lesion found in patients with familial MTLE (n = 3) and sporadic MTLE (n = 5). In addition, we used data from control hippocampi obtained from a public database (n = 7). We obtained expression profiles using the Human Genome U133 Plus 2.0 (Affymetrix) microarray platform. Overall, the molecular profile identified in familial MTLE differed from that in sporadic MTLE. In the tissue of patients with familial MTLE, we found an over-representation of the biological pathways related to protein response, mRNA processing, and synaptic plasticity and function. In sporadic MTLE, the gene expression profile suggests that the inflammatory response is highly activated. In addition, we found enrichment of gene sets involved in inflammatory cytokines and mediators and chemokine receptor pathways in both groups. However, in sporadic MTLE, we also found enrichment of epidermal growth factor signaling, prostaglandin synthesis and regulation, and microglia pathogen phagocytosis pathways. Furthermore, based on the gene expression signatures, we identified different potential compounds to treat patients with familial and sporadic MTLE. To our knowledge, this is the first study assessing the mRNA profile in surgical tissue obtained from patients with familial MTLE and comparing it with sporadic MTLE. Our results clearly show that, despite phenotypic similarities, both forms of MTLE present distinct molecular signatures, thus suggesting different underlying molecular mechanisms that may require distinct therapeutic approaches.
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Affiliation(s)
- Claudia V Maurer-Morelli
- Department of Translational Medicine,
School of Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-888,
Brazil,Brazilian Institute of Neuroscience and
Neurotechnology (BRAINN), Campinas 13083-888, Brazil
| | - Jaira F de Vasconcellos
- Department of Translational Medicine,
School of Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-888,
Brazil,Department of Biology, James Madison
University, Harrisonburg, VA 22807, USA
| | - Estela M Bruxel
- Department of Translational Medicine,
School of Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-888,
Brazil,Brazilian Institute of Neuroscience and
Neurotechnology (BRAINN), Campinas 13083-888, Brazil
| | - Cristiane S Rocha
- Department of Translational Medicine,
School of Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-888,
Brazil,Brazilian Institute of Neuroscience and
Neurotechnology (BRAINN), Campinas 13083-888, Brazil
| | - Amanda M do Canto
- Department of Translational Medicine,
School of Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-888,
Brazil,Brazilian Institute of Neuroscience and
Neurotechnology (BRAINN), Campinas 13083-888, Brazil
| | - Helder Tedeschi
- Department of Neurology, School of
Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-887, Brazil
| | - Clarissa L Yasuda
- Brazilian Institute of Neuroscience and
Neurotechnology (BRAINN), Campinas 13083-888, Brazil,Department of Neurology, School of
Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-887, Brazil
| | - Fernando Cendes
- Brazilian Institute of Neuroscience and
Neurotechnology (BRAINN), Campinas 13083-888, Brazil,Department of Neurology, School of
Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-887, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine,
School of Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-888,
Brazil,Brazilian Institute of Neuroscience and
Neurotechnology (BRAINN), Campinas 13083-888, Brazil,Iscia Lopes-Cendes.
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5
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Shi Q, Yao XY, Wang HY, Li YJ, Zhang XX, Sun C. Breast cancer-associated SNP rs72755295 is a cis-regulatory variation for human EXO1. Genet Mol Biol 2022; 45:e20210420. [PMID: 36255267 PMCID: PMC9631386 DOI: 10.1590/1678-4685-gmb-2021-0420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 08/07/2022] [Indexed: 11/04/2022] Open
Abstract
Breast cancer is the most common malignant tumor in women. A previous genome-wide association study reports that rs72755295, a SNP locating at intron of EXO1 (exonuclease 1), is associated with breast cancer. Due to the complete linkage disequilibrium between rs72755295 and rs4149909, a nonsynonymous mutation for EXO1, rs4149909 is supposed to be the causal SNP. Since EXO1 is overexpressed in breast carcinoma samples, we hypothesized that the genetic variations in this locus might confer breast cancer risk by regulating EXO1 expression. To substantiate this, a functional genomics study was performed. The dual luciferase assay indicated that G of rs72755295 presents significantly higher relative enhancer activity than A, thus verifying that this SNP can influence gene expression in breast cell. Through chromosome conformation capture it was disclosed that the enhancer containing rs72755295 can interact with the EXO1 promoter. RNA-seq analysis indicated that EXO1 expression is dependent on the rs72755295 genotype. By chromatin immunoprecipitation, the transcription factor PAX6 (paired box 6) was recognized to bind the region spanning rs72755295. In electrophoretic mobility shift assay, G of rs72755295 displays obviously higher binding affinity with nuclear protein than A. Our results indicated that rs72755295 is a cis-regulatory variation for EXO1 and might confer breast cancer risk besides rs4149909.
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Affiliation(s)
- Qiang Shi
- Shaanxi Normal University, College of Life Sciences, Xi'an, Shaanxi, P.R. China
| | - Xing-Yuan Yao
- Shaanxi Normal University, College of Life Sciences, Xi'an, Shaanxi, P.R. China
| | - Hong-Yan Wang
- Shaanxi Normal University, College of Life Sciences, Xi'an, Shaanxi, P.R. China
| | - Ya-Jie Li
- Shaanxi Normal University, College of Life Sciences, Xi'an, Shaanxi, P.R. China
| | - Xin-Xin Zhang
- Shaanxi Normal University, College of Life Sciences, Xi'an, Shaanxi, P.R. China
| | - Chang Sun
- Shaanxi Normal University, College of Life Sciences, Xi'an, Shaanxi, P.R. China
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6
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Ma J, Jin J, Lu H, Zhang J, Li Y, Cai X. Exonuclease 1 is a Potential Diagnostic and Prognostic Biomarker in Hepatocellular Carcinoma. Front Mol Biosci 2022; 9:889414. [PMID: 35769911 PMCID: PMC9234278 DOI: 10.3389/fmolb.2022.889414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) represents a global health challenge. Effective biomarkers are required for an early diagnosis to improve the survival rates of HCC patients. Exonuclease 1 (EXO1) plays a significant role in the DNA repair and recombination mechanisms. This study aimed to investigate the diagnostic and prognostic roles of EXO1 in HCC. Methods: We analyzed the EXO1 expression levels in various cancers including HCC from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. RNA sequencing data were analyzed using the R packages to determine differentially expressed genes (DEGs) between high- and low-EXO1 expressing HCC tissues from the TCGA–LIHC database. A Spearman’s correlation analysis was performed to determine the association between EXO1 expression and immune cell infiltration, and immune checkpoint genes and TP53. MethSurv and CBioPortal databases were used to evaluate the DNA methylation changes and genetic alterations in the EXO1 gene. A logistic regression analysis was performed to determine the association between EXO1 expression and the clinicopathological characteristics of the HCC patients. The diagnostic and prognostic predictive values of EXO1 were evaluated using the Kaplan–Meier (K-M) survival curves, diagnostic receiver operating characteristic (ROC) curves, nomogram model, and Cox regression analysis. Results: EXO1 expression levels were significantly higher in the tumor tissues and serums of HCC patients compared to the corresponding controls. The DEGs associated with EXO1 were significantly enriched in the cell proliferation pathways. EXO1 expression levels significantly correlated with immune cell infiltration, immune checkpoint genes, and TP53 in the HCC tissues. The DNA methylation status in five CpG islands of the EXO1 gene was associated with the prognosis of HCC. EXO1 expression levels in the HCC tissues were associated with the tumor grades, alpha-fetoprotein (AFP) levels, and the tumor stages. Cox regression analysis showed that EXO1 was a potential independent risk factor for the overall survival (OS) and disease-specific survival (DSS) of HCC patients. ROC curve analysis showed that EXO1 expression levels accurately distinguished HCC tissues from the adjacent normal liver tissues. Conclusion: Our study demonstrated that EXO1 was a potential diagnostic and prognostic biomarker, and a promising therapeutic target in HCC.
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7
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Bhalla S, Melnekoff DT, Aleman A, Leshchenko V, Restrepo P, Keats J, Onel K, Sawyer JR, Madduri D, Richter J, Richard S, Chari A, Cho HJ, Dudley JT, Jagannath S, Laganà A, Parekh S. Patient similarity network of newly diagnosed multiple myeloma identifies patient subgroups with distinct genetic features and clinical implications. SCIENCE ADVANCES 2021; 7:eabg9551. [PMID: 34788103 PMCID: PMC8598000 DOI: 10.1126/sciadv.abg9551] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 09/29/2021] [Indexed: 05/04/2023]
Abstract
The remarkable genetic heterogeneity of multiple myeloma poses a substantial challenge for proper prognostication and clinical management of patients. Here, we introduce MM-PSN, the first multiomics patient similarity network of myeloma. MM-PSN enabled accurate dissection of the genetic and molecular landscape of the disease and determined 12 distinct subgroups defined by five data types generated from genomic and transcriptomic profiling of 655 patients. MM-PSN identified patient subgroups not previously described defined by specific patterns of alterations, enriched for specific gene vulnerabilities, and associated with potential therapeutic options. Our analysis revealed that co-occurrence of t(4;14) and 1q gain identified patients at significantly higher risk of relapse and shorter survival as compared to t(4;14) as a single lesion. Furthermore, our results show that 1q gain is the most important single lesion conferring high risk of relapse and that it can improve on the current International Staging Systems (ISS and R-ISS).
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Affiliation(s)
- Sherry Bhalla
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David T. Melnekoff
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo Aleman
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Violetta Leshchenko
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paula Restrepo
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan Keats
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Kenan Onel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatric Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey R. Sawyer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Deepu Madduri
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joshua Richter
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shambavi Richard
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ajai Chari
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hearn Jay Cho
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Sundar Jagannath
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alessandro Laganà
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samir Parekh
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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8
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Bisht K, Walker B, Kumar SK, Spicka I, Moreau P, Martin T, Costa LJ, Richter J, Fukao T, Macé S, van de Velde H. Chromosomal 1q21 abnormalities in multiple myeloma: a review of translational, clinical research, and therapeutic strategies. Expert Rev Hematol 2021; 14:1099-1114. [PMID: 34551651 DOI: 10.1080/17474086.2021.1983427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Multiple myeloma (MM) remains an incurable disease with a median overall survival of approximately 5 years. Gain or amplification of 1q21 (1q21+) occurs in around 40% of patients with MM and generally portends a poor prognosis. Patients with MM who harbor 1q21+ are at increased risk of drug resistance, disease progression, and death. New pharmacotherapies with novel modes of action are required to overcome the negative prognostic impact of 1q21+. Areas covered: This review discusses the detection, biology, prognosis, and therapeutic targeting of 1q21+ in newly diagnosed and relapsed MM. Patients with MM and 1q21+ tend to present with higher tumor burden, greater end-organ damage, and more co-occurring high-risk cytogenetic abnormalities than patients without 1q21+. The chromosomal rearrangements associated with 1q21+ result in dysregulation of genes involved in oncogenesis. Identification and characterization of the 1q21+ molecular targets are needed to inform on prognosis and treatment strategy. Clinical trial data are emerging that addition of isatuximab to combination therapies may improve outcomes in patients with 1q21+ MM. Expert opinion: In the next 5 years, the results of ongoing research and trials are likely to focus on the therapeutic impact and treatment decisions associated with 1q21+ in MM.
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Affiliation(s)
- Kamlesh Bisht
- Oncology Therapeutic Area, Sanofi Research and Development, Cambridge, MA, USA
| | - Brian Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA
| | - Shaji K Kumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ivan Spicka
- First Department of Medicine, Department of Hematology, First Faculty of Medicine, Charles University and General Hospital, Prague, Czech Republic
| | - Philippe Moreau
- Department of Hematology, University Hospital of Nantes, Nantes, France
| | - Tom Martin
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Luciano J Costa
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joshua Richter
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Taro Fukao
- Oncology Therapeutic Area, Sanofi Research and Development, Cambridge, MA, USA
| | - Sandrine Macé
- Sanofi Research and Development, Sanofi, Vitry-Sur-Seine, France
| | - Helgi van de Velde
- Oncology Therapeutic Area, Sanofi Research and Development, Cambridge, MA, USA
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9
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Huang S, Chen Y, Pan L, Fei C, Wang N, Chu F, Peng D, Duan X, Wang Y. Exploration of the Potential Mechanism of Tao Hong Si Wu Decoction for the Treatment of Breast Cancer Based on Network Pharmacology and In Vitro Experimental Verification. Front Oncol 2021; 11:731522. [PMID: 34513708 PMCID: PMC8427760 DOI: 10.3389/fonc.2021.731522] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/09/2021] [Indexed: 12/26/2022] Open
Abstract
Background Tao Hong Si Wu Decoction (THSWD) is a well-known traditional Chinese medicine used clinically alone or combined with drugs to treat breast cancer. However, there has been no study to date on the underlying mechanisms of its therapeutic effects. Objectives To explore the potential mechanism of THSWD for the treatment of breast cancer using network pharmacology and experimental research. Methods The active ingredients of THSWD were screened according to Lipinski's rule of five based on the 107 ingredients of THSWD identified by UPLC-Q-TOF-MSE. The targets of THSWD and breast cancer from multiple databases were collected, and a Compound-Target-Pathway network based on protein-protein interaction (PPI) was constructed. Gene ontology (GO) analysis and KEGG pathway analysis were performed via the DAVID server. Molecular docking studies verified the selected key ingredients and key targets. The results of network pharmacology were verified by in vitro experiments. Including the effects of THSWD drug-containing rat serum (THSWD serum) on cell proliferation, and on the targets HRAS, MAPK1, AKT1, GRB2, and MAPK14 were assayed by RT-qPCR and Western blot assays. Results In total, 27 active ingredients including 8 core components, were obtained from 107 ingredients and 218 THSWD target genes for the treatment of breast cancer were identified. THSWD is active in the treatment of breast cancer by targeting Ras, FoxO, PI3K-Akt and other signaling pathways. MCF-7 and MDA-MB-231 cell proliferation was inhibited by THSWD serum in a time and concentration dependent manner. THSWD could regulated the RNA and protein expression of core targets HRAS, MAPK1, AKT1, GRB2, and MAPK14 for treatment of breast cancer. Conclusion The results of network pharmacology study showed that THSWD is active against breast cancer by intervening with multiple targets and pathways. Luteolin, kaempferol, senkyunolide E, and other 8 compounds may be the core active ingredients of THSWD in the treatment of breast cancer. THSWD treatment of breast cancer may be related to targeting Ras, FoxO, PI3K-Akt, and other signal pathways associated with the core targets HRAS, MAPK1, AKT1, GRB2, and MAPK14.
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Affiliation(s)
- Shi Huang
- The First Affiliated Hospital of Anhui University of Chinese Medicinee, Hefei, China.,College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Yan Chen
- The First Affiliated Hospital of Anhui University of Chinese Medicinee, Hefei, China.,College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Lingyu Pan
- The First Affiliated Hospital of Anhui University of Chinese Medicinee, Hefei, China
| | - Changyi Fei
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Ni Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Furui Chu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Daiyin Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Xianchun Duan
- The First Affiliated Hospital of Anhui University of Chinese Medicinee, Hefei, China
| | - Yongzhong Wang
- The First Affiliated Hospital of Anhui University of Chinese Medicinee, Hefei, China
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10
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Mwapagha LM, Chibanga V, Shipanga H, Parker MI. New insights from Whole Genome Sequencing: BCLAF1 deletion as a structural variant that predisposes cells towards cellular transformation. Oncol Rep 2021; 46:229. [PMID: 34490482 DOI: 10.3892/or.2021.8180] [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: 03/16/2021] [Accepted: 07/16/2021] [Indexed: 11/06/2022] Open
Abstract
Cancer arises from a multi‑step cellular transformation process where some mutations may be inherited, while others are acquired during the process of malignant transformation. Aberrations in the BCL2 associated transcription factor 1 (BCLAF1) gene have previously been identified in patients with cancer and the aim of the present study was to identify structural variants (SVs) and the effects of BCLAF1 gene silencing on cell transformation. Whole‑genome sequencing was performed on DNA isolated from tumour biopsies with a histologically confirmed diagnosis of oesophageal squamous cell carcinoma (OSCC). Paired‑end sequencing was performed on the Illumina HiSeq2000, with 300 bp reads. Reads were aligned to the Homo sapiens reference genome (NCBI37) using ELAND and CASAVA software. SVs reported from the alignment were collated with gene loci, using the variant effect predictor of Ensembl. The affected genes were subsequently cross‑checked against the Genetic Association Database for disease and cancer associations. BCLAF1 deletion was identified as a noteworthy SV that could be associated with OSCC. Transient small interfering RNA‑mediated knockdown of BCLAF1 resulted in the altered expression of several downstream genes, including downregulation of the proapoptotic genes Caspase‑3 and BAX and the DNA damage repair genes exonuclease 1, ATR‑interacting protein and transcription regulator protein BACH1. BCLAF1 deficiency also attenuated P53 gene expression. Inhibition of BCLAF1 expression also resulted in increased colony formation. These results provide evidence that the abrogation of BCLAF1 expression results in the dysregulation of several cancer signalling pathways and abnormal cell proliferation.
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Affiliation(s)
- Lamech M Mwapagha
- Department of Integrative Biomedical Sciences, Division of Medical Biochemistry and Structural Biology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape 7925, South Africa
| | - Vimbaishe Chibanga
- Department of Integrative Biomedical Sciences, Division of Medical Biochemistry and Structural Biology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape 7925, South Africa
| | - Hendrina Shipanga
- Department of Integrative Biomedical Sciences, Division of Medical Biochemistry and Structural Biology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape 7925, South Africa
| | - M Iqbal Parker
- Department of Integrative Biomedical Sciences, Division of Medical Biochemistry and Structural Biology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape 7925, South Africa
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11
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Calcium channel blockers lercanidipine and amlodipine inhibit YY1/ERK/TGF-β mediated transcription and sensitize the gastric cancer cells to doxorubicin. Toxicol In Vitro 2021; 74:105152. [DOI: 10.1016/j.tiv.2021.105152] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 02/24/2021] [Accepted: 03/22/2021] [Indexed: 12/24/2022]
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12
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Cancer type-specific alterations in actin genes: Worth a closer look? INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 360:133-184. [PMID: 33962749 DOI: 10.1016/bs.ircmb.2021.02.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Actins form a strongly conserved family of proteins that are central to the functioning of the actin cytoskeleton partaking in natural processes such as cell division, adhesion, contraction and migration. These processes, however, also occur during the various phases of cancer progression. Yet, surprisingly, alterations in the six human actin genes in cancer studies have received little attention and the focus was mostly on deregulated expression levels of actins and even more so of actin-binding or regulatory proteins. Starting from the early mutation work in the 1980s, we propose based on reviewing literature and data from patient cancer genomes that alterations in actin genes are different in distinct cancer subtypes, suggesting some specificity. These actin gene alterations include (missense) mutations, gene fusions and copy number alterations (deletions and amplifications) and we illustrate their occurrence for a limited number of examples including actin mutations in lymphoid cancers and nonmelanoma skin cancer and actin gene copy number alterations for breast, prostate and liver cancers. A challenge in the future will be to further sort out the specificity per actin gene, alteration type and cancer subtype. Even more challenging is (experimentally) distinguishing between cause and consequence: which alterations are passengers and which are involved in tumor progression of particular cancer subtypes?
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13
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Privitera AP, Barresi V, Condorelli DF. Aberrations of Chromosomes 1 and 16 in Breast Cancer: A Framework for Cooperation of Transcriptionally Dysregulated Genes. Cancers (Basel) 2021; 13:1585. [PMID: 33808143 PMCID: PMC8037453 DOI: 10.3390/cancers13071585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Derivative chromosome der(1;16), isochromosome 1q, and deleted 16q-producing arm-level 1q-gain and/or 16q-loss-are recurrent cytogenetic abnormalities in breast cancer, but their exact role in determining the malignant phenotype is still largely unknown. We exploited The Cancer Genome Atlas (TCGA) data to generate and analyze groups of breast invasive carcinomas, called 1,16-chromogroups, that are characterized by a pattern of arm-level somatic copy number aberrations congruent with known cytogenetic aberrations of chromosome 1 and 16. Substantial differences were found among 1,16-chromogroups in terms of other chromosomal aberrations, aneuploidy scores, transcriptomic data, single-point mutations, histotypes, and molecular subtypes. Breast cancers with a co-occurrence of 1q-gain and 16q-loss can be distinguished in a "low aneuploidy score" group, congruent to der(1;16), and a "high aneuploidy score" group, congruent to the co-occurrence of isochromosome 1q and deleted 16q. Another three groups are formed by cancers showing separately 1q-gain or 16q-loss or no aberrations of 1q and 16q. Transcriptome comparisons among the 1,16-chromogroups, integrated with functional pathway analysis, suggested the cooperation of overexpressed 1q genes and underexpressed 16q genes in the genesis of both ductal and lobular carcinomas, thus highlighting the putative role of genes encoding gamma-secretase subunits (APH1A, PSEN2, and NCSTN) and Wnt enhanceosome components (BCL9 and PYGO2) in 1q, and the glycoprotein E-cadherin (CDH1), the E3 ubiquitin-protein ligase WWP2, the deubiquitinating enzyme CYLD, and the transcription factor CBFB in 16q. The analysis of 1,16-chromogroups is a strategy with far-reaching implications for the selection of cancer cell models and novel experimental therapies.
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Affiliation(s)
| | - Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Via S. Sofia 89-97, 95123 Catania, Italy;
| | - Daniele Filippo Condorelli
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Via S. Sofia 89-97, 95123 Catania, Italy;
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14
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Dass SA, Tan KL, Selva Rajan R, Mokhtar NF, Mohd Adzmi ER, Wan Abdul Rahman WF, Tengku Din TADAA, Balakrishnan V. Triple Negative Breast Cancer: A Review of Present and Future Diagnostic Modalities. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:62. [PMID: 33445543 PMCID: PMC7826673 DOI: 10.3390/medicina57010062] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive breast type of cancer with no expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor-2 (HER2). It is a highly metastasized, heterogeneous disease that accounts for 10-15% of total breast cancer cases with a poor prognosis and high relapse rate within five years after treatment compared to non-TNBC cases. The diagnostic and subtyping of TNBC tumors are essential to determine the treatment alternatives and establish personalized, targeted medications for every TNBC individual. Currently, TNBC is diagnosed via a two-step procedure of imaging and immunohistochemistry (IHC), which are operator-dependent and potentially time-consuming. Therefore, there is a crucial need for the development of rapid and advanced technologies to enhance the diagnostic efficiency of TNBC. This review discusses the overview of breast cancer with emphasis on TNBC subtypes and the current diagnostic approaches of TNBC along with its challenges. Most importantly, we have presented several promising strategies that can be utilized as future TNBC diagnostic modalities and simultaneously enhance the efficacy of TNBC diagnostic.
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Affiliation(s)
- Sylvia Annabel Dass
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Penang 11800, Malaysia; (S.A.D.); (K.L.T.); (R.S.R.)
| | - Kim Liu Tan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Penang 11800, Malaysia; (S.A.D.); (K.L.T.); (R.S.R.)
| | - Rehasri Selva Rajan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Penang 11800, Malaysia; (S.A.D.); (K.L.T.); (R.S.R.)
| | - Noor Fatmawati Mokhtar
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia; (N.F.M.); (E.R.M.A.)
| | - Elis Rosliza Mohd Adzmi
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia; (N.F.M.); (E.R.M.A.)
| | - Wan Faiziah Wan Abdul Rahman
- Department of Pathology, School of Medical Sciences, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia;
- Breast Cancer Awareness & Research Unit, Hospital Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia;
| | - Tengku Ahmad Damitri Al-Astani Tengku Din
- Breast Cancer Awareness & Research Unit, Hospital Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia;
- Chemical Pathology Department, School of Medical Sciences, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Venugopal Balakrishnan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Penang 11800, Malaysia; (S.A.D.); (K.L.T.); (R.S.R.)
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15
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Development of a cell-based pathway modulator screening system to screen the targeted cancer therapeutic candidates. Hum Cell 2021; 34:445-456. [PMID: 33405176 DOI: 10.1007/s13577-020-00476-x] [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: 08/13/2020] [Accepted: 12/17/2020] [Indexed: 10/22/2022]
Abstract
To overcome the issues of poor prognosis and to tackle the non-responsiveness to various chemotherapeutics; it is necessary to develop targeted cancer therapeutic agents. Also, it is being necessary to understand the molecular targets of the drug candidates and drugs in the context of cellular signaling pathways, to make progress towards the development of targeted cancer therapeutics. Towards addressing these, we have established a cell-based and pathway-focused drug screening system for the pathways such as MYC, E2F, WNT, ERK, NRF1/2, HIF1α, p53, YY1 and NFκB. These signaling pathways are highly dysregulated in many cancers, including gastric cancer. The developed firefly luciferase assay-based screening system in gastric cancer lineage is suitable for the screening of the massive panel of drugs, drug candidates, small molecule inhibitors, chemicals and alternate drug formulations. The developed stable cell lines have been demonstrated for their pathway activity reporting features using the corresponding pathway-specific modulators. A proof-of-concept medium throughput screening focusing on YY1 signaling pathway also revealed the connection between calcium channel blockers and YY1 signaling. The developed signaling pathway screening assay cells are valuable resource and will serve as the screening platform for screening the drug libraries towards the development of targeted cancer therapeutics.
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16
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Liu J, Zhang J. Elevated EXO1 expression is associated with breast carcinogenesis and poor prognosis. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:135. [PMID: 33569437 PMCID: PMC7867906 DOI: 10.21037/atm-20-7922] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Breast cancer is the most common cancer and leading cause of cancer mortality in women worldwide. Exonuclease 1 (EXO1), a protein with 5' to 3' exonuclease and RNase H activity, could be involved in mismatch repair and recombination. This study aims to investigate the prognostic value of EXO1 in breast cancer and explore the association between EXO1 expression and breast carcinogenesis. Methods The data of 1,215 breast cancer susceptibility gene (BRCA) samples were obtained from The Cancer Genome Atlas (TCGA). Real-time quantitative polymerase chain reaction (RT-qPCR) further verified the elevated mRNA expression level of EXO1 in human BRCA cells MDA-MB231 compared with that in human breast epithelial cells MCF-10A. EXO1 copy number was proved to be correlated with its expression level. Besides, Kaplan-Meier analysis, differentially expressed genes and function enrichment analysis were performed. Results Analysis of data from The Cancer Genome Atlas (TCGA) revealed that the EXO1 expression level in breast cancer tissues was significantly increased. Real-time quantitative polymerase chain reaction (RT-qPCR) supported the elevated mRNA expression level of EXO1 in human breast cancer cells MDA-MB231 compared with that in human breast epithelial cells MCF-10A. EXO1 copy number was shown to be correlated with its expression level. Kaplan-Meier analysis showed that elevated EXO1 was an indicator of poor breast cancer prognosis. Furthermore, differentially expressed genes and function enrichment analysis indicated that the cell cycle pathway and cardiac muscle contraction pathway were activated and inhibited respectively in breast cancer samples with high EXO1 expression. Conclusions Therefore, this study shows that elevated EXO1 expression is associated with carcinogenesis and poor prognosis in breast cancer, and might be a biomarker for breast cancer treatment.
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Affiliation(s)
- Jingjing Liu
- 3rd Department of Breast Cancer, China Tianjin Breast Cancer Prevention, Treatment and Research Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy of Ministry of Education, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Jin Zhang
- 3rd Department of Breast Cancer, China Tianjin Breast Cancer Prevention, Treatment and Research Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy of Ministry of Education, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
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17
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Sertic S, Quadri R, Lazzaro F, Muzi-Falconi M. EXO1: A tightly regulated nuclease. DNA Repair (Amst) 2020; 93:102929. [DOI: 10.1016/j.dnarep.2020.102929] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Fan J, Zhao Y, Yuan H, Yang J, Li T, He Z, Wu X, Luo C. Phospholipase C-ε regulates bladder cancer cells via ATM/EXO1. Am J Cancer Res 2020; 10:2319-2336. [PMID: 32905533 PMCID: PMC7471350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023] Open
Abstract
Whole human genome microarray was performed to identify the potential molecular mechanisms associated with phospholipase C epsilon (PLCε). Gene Ontology, Kyoto Encyclopedia of Genes, and Genomes pathway analysis revealed that differentially expressed genes were significantly enriched in DNA repair-related pathways. Gene expression of PLCε, exonuclease 1 (EXO1), and ATM serine/threonine kinase (ATM) was significantly higher in 72 bladder cancer (BCa) tissue samples than in 24 samples of adjacent nonneoplastic tissue. The protein levels of PLCε and EXO1 showed appositive correlation in clinical bladder samples. Subsequent experiments showed that PLCε expression facilitated DNA repair in BCa by regulating ATM/EXO1 signaling. Additionally, we found that microRNA-145 is an antagonist of PLCε in T24 cells by directly targeting the 3'untranslated region of PLCε mRNA. Notably, microRNA-145 overexpression significantly increased the sensitivity to cisplatin, consistent with its PLCε silencing effect in BCa cells. Taken together, these findings reveal a novel physiological role for PLCε in DNA repair-related pathways with significant implications for the understanding of BCa biology.
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Affiliation(s)
- Jiaxin Fan
- Key Laboratory of Diagnostics Medicine Designated by The Ministry of Education, Chongqing Medical UniversityChongqing, China
| | - Yan Zhao
- Key Laboratory of Diagnostics Medicine Designated by The Ministry of Education, Chongqing Medical UniversityChongqing, China
- Department Blood of Transfusion, Affiliated Hospital of Jining Medical UniversityShandong, China
| | - Hongling Yuan
- Key Laboratory of Diagnostics Medicine Designated by The Ministry of Education, Chongqing Medical UniversityChongqing, China
| | - Jinxiao Yang
- Key Laboratory of Diagnostics Medicine Designated by The Ministry of Education, Chongqing Medical UniversityChongqing, China
| | - Ting Li
- Key Laboratory of Diagnostics Medicine Designated by The Ministry of Education, Chongqing Medical UniversityChongqing, China
| | - Zhenting He
- Key Laboratory of Diagnostics Medicine Designated by The Ministry of Education, Chongqing Medical UniversityChongqing, China
| | - Xiaohou Wu
- Department of Urology, First Affiliated Hospital of Chongqing Medical UniversityChongqing, China
| | - Chunli Luo
- Key Laboratory of Diagnostics Medicine Designated by The Ministry of Education, Chongqing Medical UniversityChongqing, China
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Transcriptome Signature Reversion as a Method to Reposition Drugs Against Cancer for Precision Oncology. ACTA ACUST UNITED AC 2020; 25:116-120. [PMID: 30896533 DOI: 10.1097/ppo.0000000000000370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Transcriptome signature reversion (TSR) has been hypothesized as a promising method for discovery and use of existing noncancer drugs as potential drugs in the treatment of cancer (i.e., drug repositioning, drug repurposing). The TSR assumes that drugs with the ability to revert the gene expression associated with a diseased state back to its healthy state are potentially therapeutic candidates for that disease. This article reviews methodology of TSR and critically discusses key TSR studies. In addition, potential conceptual and computational improvements of this novel methodology are discussed as well as its current and possible future application in precision oncology trials.
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20
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Yang G, Dong K, Zhang Z, Zhang E, Liang B, Chen X, Huang Z. EXO1 Plays a Carcinogenic Role in Hepatocellular Carcinoma and is related to the regulation of FOXP3. J Cancer 2020; 11:4917-4932. [PMID: 32626539 PMCID: PMC7330697 DOI: 10.7150/jca.40673] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 05/29/2020] [Indexed: 12/21/2022] Open
Abstract
Exonuclease 1 (EXO1), a member of the RAD2 nuclease family, was first described as possessing 5' to 3' nuclease activity and 5' structure-specific endonuclease activity. Here, we show that EXO1 is significantly upregulated in HCC tumor tissues and that high EXO1 expression is significantly correlated with liver cirrhosis. We further demonstrate that EXO1 knockdown decreases proliferation and colony forming abilities of HCC cells in vitro and tumorigenicity in vivo, as well as decreases migration and invasive capabilities of HCC cells. Alternatively, EXO1 overexpression significantly increases the proliferation, colony forming ability, and migration and invasive capabilities of HCC cells in vitro. Additionally, we truncated a region upstream of the transcription start site (TSS) of EXO1 and used the region with the strongest transcriptional activity to predict that the transcription factor FOXP3 can bind to the EXO1 promoter. Bioinformatics analysis found that FOXP3 was positively correlated with EXO1 and luciferase reporter assays and RT-PCR confirmed that FOXP3 could enhance the transcriptional activity of EXO1. CCK-8 assays showed that depletion of FOXP3 further reduces cell proliferation ability after knocking down of EXO1 in vitro. Taken together, our findings indicate that EXO1 acts as an oncogene in HCC and its expression level is related to FOXP3 activity.
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Affiliation(s)
- Guang Yang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Keshuai Dong
- Department of Hepatobiliary and Laparoscopic Surgery, Renmin Hospital, Wuhan University, Hubei Key Laboratory of Digestive System Disease, Wuhan, China
| | - Zunyi Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Erlei Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Binyong Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyong Huang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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21
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Chen W, Liao L, Lai H, Yi X, Wang D. Identification of core biomarkers associated with pathogenesis and prognostic outcomes of laryngeal squamous-cell cancer using bioinformatics analysis. Eur Arch Otorhinolaryngol 2020; 277:1397-1408. [PMID: 32067095 DOI: 10.1007/s00405-020-05856-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/06/2020] [Indexed: 12/20/2022]
Abstract
PURPOSE Despite advances in the treatment of laryngeal squamous-cell carcinoma (LSCC), the survival rate of LSCC remains poor. Thereby, it is urgent to identify novel diagnostic and prognostic biomarkers for LSCC. The study aimed to identify potential core genes associated with the pathogenesis and prognosis of LSCC. METHODS Differentially expressed genes between LSCC and normal laryngeal tissue samples were screened by an integrated analysis of data from GEO and TCGA databases. Core genes related to the pathogenesis and prognosis of LSCC were identified by employing protein-protein interaction network and Cox proportional hazards model analyses. RESULTS Ten hub genes (AURKA, AURKB, CDC45, KIF2C, NDC80, EXO1, TYMS, RAD51AP1, ITGA3, and UBE2T) that might be highly related to the pathogenesis of LSCC were identified. An eight-gene prognostic signature consisted of ZG16B, STATH, RTN4R, MSRA, CBX8, SLC5A1, EFNB1 and CNTFR was constructed with a good performance in predicting overall survivals. CONCLUSION Our findings might shed some new light on the pathogenesis of LSCC and help identify new therapeutic targets of LSCC.
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Affiliation(s)
- Wei Chen
- Department of Otolaryngology, Fujian Medical University Union Hospital, 29# Xinquan Road, Fujian, 350001, Fuzhou, China
| | - Lianming Liao
- Department of Laboratory Medicine, Fujian Medical University Union Hospital, Fujian, 350001, Fuzhou, China
| | - Haichun Lai
- Department of Otolaryngology, Fujian Medical University Union Hospital, 29# Xinquan Road, Fujian, 350001, Fuzhou, China
| | - Xuehan Yi
- Department of Otolaryngology, Fujian Medical University Union Hospital, 29# Xinquan Road, Fujian, 350001, Fuzhou, China
| | - Desheng Wang
- Department of Otolaryngology, Fujian Medical University Union Hospital, 29# Xinquan Road, Fujian, 350001, Fuzhou, China.
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Gao Y, Kim S, Lee YI, Lee J. Cellular Stress-Modulating Drugs Can Potentially Be Identified by in Silico Screening with Connectivity Map (CMap). Int J Mol Sci 2019; 20:ijms20225601. [PMID: 31717493 PMCID: PMC6888006 DOI: 10.3390/ijms20225601] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/27/2022] Open
Abstract
Accompanied by increased life span, aging-associated diseases, such as metabolic diseases and cancers, have become serious health threats. Recent studies have documented that aging-associated diseases are caused by prolonged cellular stresses such as endoplasmic reticulum (ER) stress, mitochondrial stress, and oxidative stress. Thus, ameliorating cellular stresses could be an effective approach to treat aging-associated diseases and, more importantly, to prevent such diseases from happening. However, cellular stresses and their molecular responses within the cell are typically mediated by a variety of factors encompassing different signaling pathways. Therefore, a target-based drug discovery method currently being used widely (reverse pharmacology) may not be adequate to uncover novel drugs targeting cellular stresses and related diseases. The connectivity map (CMap) is an online pharmacogenomic database cataloging gene expression data from cultured cells treated individually with various chemicals, including a variety of phytochemicals. Moreover, by querying through CMap, researchers may screen registered chemicals in silico and obtain the likelihood of drugs showing a similar gene expression profile with desired and chemopreventive conditions. Thus, CMap is an effective genome-based tool to discover novel chemopreventive drugs.
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Affiliation(s)
- Yurong Gao
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea; (Y.G.); (S.K.)
| | - Sungwoo Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea; (Y.G.); (S.K.)
| | - Yun-Il Lee
- Well Aging Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
- Correspondence: (Y.-I.L.); (J.L.)
| | - Jaemin Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea; (Y.G.); (S.K.)
- Correspondence: (Y.-I.L.); (J.L.)
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23
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Luo F, Wang YZ, Lin D, Li J, Yang K. Exonuclease 1 expression is associated with clinical progression, metastasis, and survival prognosis of prostate cancer. J Cell Biochem 2019; 120:11383-11389. [PMID: 30775798 DOI: 10.1002/jcb.28415] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/16/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
Prostate cancer (PCa) is the most prevalent malignancy and the second leading cause of cancer-related deaths in the male population in western countries, and we explored the association between exonuclease 1 (EXO1) expression and clinical progression, metastasis (Met), and survival prognosis of PCa. EXO1 expression of high/low-metastatic patient-derived xenografts model was investigated and clinical correlation and prognosis outcomes were validated. EXO1 in high-metastatic models was significantly increased compared with low-metastatic lines. In memorial sloan-kettering cancer center (MSKCC) cohort, EXO1 expression positively correlated with PCa Met, and patients with high EXO1 had poor biochemical recurrence-free survival in primary PCa cohort. Validation in The Cancer Genome Atlas primary cohort indicated EXO1 expression was significantly associated with lymph node Met and disease-free survival. The overexpression of EXO1 is significantly associated with PCa poor survival outcome, and is a promising biomarker for PCa, especially for primary PCa. A prospective study is clearly needed to validate these findings.
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Affiliation(s)
- Fei Luo
- Department of Urology, Tianjin Union Medical Center, Tianjin, China.,The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Yu-Zhuo Wang
- The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Dong Lin
- The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jian Li
- Department of Urology, Tianjin Union Medical Center, Tianjin, China
| | - Kuo Yang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin, China
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24
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Chen J, Wang Z, Shen X, Cui X, Guo Y. Identification of novel biomarkers and small molecule drugs in human colorectal cancer by microarray and bioinformatics analysis. Mol Genet Genomic Med 2019; 7:e00713. [PMID: 31087508 PMCID: PMC6625111 DOI: 10.1002/mgg3.713] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/01/2019] [Accepted: 04/15/2019] [Indexed: 12/15/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common malignant tumors. In the present study, the expression profile of human multistage colorectal mucosa tissues, including healthy, adenoma, and adenocarcinoma samples was downloaded to identify critical genes and potential drugs in CRC. Methods Expression profiles, GSE33113 and GSE44076, were integrated using bioinformatics methods. Differentially expressed genes (DEGs) were analyzed by R language. Functional enrichment analyses of the DEGs were performed using the Database for Annotation, visualization, and integrated discovery (DAVID) database. Then, the search tool for the retrieval of interacting genes (STRING) database and Cytoscape were used to construct a protein–protein interaction (PPI) network and identify hub genes. Subsequently, survival analysis was performed among the key genes using Gene Expression Profiling Interactive Analysis (GEPIA). Connectivity Map (CMap) was used to query potential drugs for CRC. Results A total of 428 upregulated genes and 751 downregulated genes in CRC were identified. The functional changes of these DEGs were mainly associated with cell cycle, oocyte meiosis, DNA replication, p53 signaling pathway, and progesterone‐mediated oocyte maturation. A PPI network was identified by STRING with 482 nodes and 2,368 edges. Survival analysis revealed that high mRNA expression of AURKA, CCNB1, CCNF, and EXO1 was significantly associated with longer overall survival. Moreover, CMap predicted a panel of small molecules as possible adjuvant drugs to treat CRC. Conclusion Our study found key dysregulated genes involved in CRC and potential drugs to combat it, which may provide novel insights and potential biomarkers for prognosis, as well as providing new CRC treatments.
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Affiliation(s)
- Juan Chen
- Laboratory Medicine Center, People's Hospital of Hai'an County, Nantong, P. R. China
| | - Ziheng Wang
- Department of Clinical Biobank, Nantong University Affiliated Hospital, Nantong, P. R. China.,Department of Medicine, Nantong University Xinling college, Nantong, P.R. China
| | - Xianjuan Shen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, P. R. China
| | - Xiaopeng Cui
- Department of general surgery, Affiliated Hospital of Nantong University, Nantong, P. R. China
| | - Yuehua Guo
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, P. R. China
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25
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Goeppert B, Toth R, Singer S, Albrecht T, Lipka DB, Lutsik P, Brocks D, Baehr M, Muecke O, Assenov Y, Gu L, Endris V, Stenzinger A, Mehrabi A, Schirmacher P, Plass C, Weichenhan D, Roessler S. Integrative Analysis Defines Distinct Prognostic Subgroups of Intrahepatic Cholangiocarcinoma. Hepatology 2019; 69:2091-2106. [PMID: 30615206 PMCID: PMC6594081 DOI: 10.1002/hep.30493] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 01/03/2019] [Indexed: 12/11/2022]
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is the second most common primary liver cancer. It is defined by cholangiocytic differentiation and has poor prognosis. Recently, epigenetic processes have been shown to play an important role in cholangiocarcinogenesis. We performed an integrative analysis on 52 iCCAs using both genetic and epigenetic data with a specific focus on DNA methylation components. We found recurrent isocitrate dehydrogenase 1 (IDH1) and IDH2 (28%) gene mutations, recurrent arm-length copy number alterations (CNAs), and focal alterations such as deletion of 3p21 or amplification of 12q15, which affect BRCA1 Associated Protein 1, polybromo 1, and mouse double minute 2 homolog. DNA methylome analysis revealed excessive hypermethylation of iCCA, affecting primarily the bivalent genomic regions marked with both active and repressive histone modifications. Integrative clustering of genetic and epigenetic data identified four iCCA subgroups with prognostic relevance further designated as IDH, high (H), medium (M), and low (L) alteration groups. The IDH group consisted of all samples with IDH1 or IDH2 mutations and showed, together with the H group, a highly disrupted genome, characterized by frequent deletions of chromosome arms 3p and 6q. Both groups showed excessive hypermethylation with distinct patterns. The M group showed intermediate characteristics regarding both genetic and epigenetic marks, whereas the L group exhibited few methylation changes and mutations and a lack of CNAs. Methylation-based latent component analysis of cell-type composition identified differences among these four groups. Prognosis of the H and M groups was significantly worse than that of the L group. Conclusion: Using an integrative genomic and epigenomic analysis approach, we identified four major iCCA subgroups with widespread genomic and epigenomic differences and prognostic implications. Furthermore, our data suggest differences in the cell-of-origin of the iCCA subtypes.
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Affiliation(s)
- Benjamin Goeppert
- Institute of PathologyUniversity Clinic of HeidelbergHeidelbergGermany,Liver Cancer Center HeidelbergHeidelbergGermany
| | - Reka Toth
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - Stephan Singer
- Institute of PathologyUniversity Clinic of HeidelbergHeidelbergGermany,Institute of PathologyErnst‐Moritz‐Arndt UniversityGreifswaldGermany
| | - Thomas Albrecht
- Institute of PathologyUniversity Clinic of HeidelbergHeidelbergGermany
| | - Daniel B. Lipka
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - Pavlo Lutsik
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - David Brocks
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - Marion Baehr
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - Oliver Muecke
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - Yassen Assenov
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - Lei Gu
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany,Boston Children's HospitalBostonMA
| | - Volker Endris
- Institute of PathologyUniversity Clinic of HeidelbergHeidelbergGermany
| | | | - Arianeb Mehrabi
- Liver Cancer Center HeidelbergHeidelbergGermany,Department of General Visceral and Transplantation SurgeryUniversity Hospital HeidelbergHeidelbergGermany
| | - Peter Schirmacher
- Institute of PathologyUniversity Clinic of HeidelbergHeidelbergGermany,Liver Cancer Center HeidelbergHeidelbergGermany,German Consortium for Translational Cancer ResearchHeidelbergGermany
| | - Christoph Plass
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany,German Consortium for Translational Cancer ResearchHeidelbergGermany
| | - Dieter Weichenhan
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - Stephanie Roessler
- Institute of PathologyUniversity Clinic of HeidelbergHeidelbergGermany,Liver Cancer Center HeidelbergHeidelbergGermany
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26
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Ca 2+-Stimulated AMPK-Dependent Phosphorylation of Exo1 Protects Stressed Replication Forks from Aberrant Resection. Mol Cell 2019; 74:1123-1137.e6. [PMID: 31053472 DOI: 10.1016/j.molcel.2019.04.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 02/04/2019] [Accepted: 03/29/2019] [Indexed: 12/22/2022]
Abstract
Abnormal processing of stressed replication forks by nucleases can cause fork collapse, genomic instability, and cell death. Despite its importance, it is poorly understood how the cell properly controls nucleases to prevent detrimental fork processing. Here, we report a signaling pathway that controls the activity of exonuclease Exo1 to prevent aberrant fork resection during replication stress. Our results indicate that replication stress elevates intracellular Ca2+ concentration ([Ca2+]i), leading to activation of CaMKK2 and the downstream kinase 5' AMP-activated protein kinase (AMPK). Following activation, AMPK directly phosphorylates Exo1 at serine 746 to promote 14-3-3 binding and inhibit Exo1 recruitment to stressed replication forks, thereby avoiding unscheduled fork resection. Disruption of this signaling pathway results in excessive ssDNA, chromosomal instability, and hypersensitivity to replication stress inducers. These findings reveal a link between [Ca2+]i and the replication stress response as well as a function of the Ca2+-CaMKK2-AMPK signaling axis in safeguarding fork structure to maintain genome stability.
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27
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Human Exonuclease 1 (EXO1) Regulatory Functions in DNA Replication with Putative Roles in Cancer. Int J Mol Sci 2018; 20:ijms20010074. [PMID: 30585186 PMCID: PMC6337416 DOI: 10.3390/ijms20010074] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/12/2018] [Accepted: 12/19/2018] [Indexed: 12/11/2022] Open
Abstract
Human exonuclease 1 (EXO1), a 5'→3' exonuclease, contributes to the regulation of the cell cycle checkpoints, replication fork maintenance, and post replicative DNA repair pathways. These processes are required for the resolution of stalled or blocked DNA replication that can lead to replication stress and potential collapse of the replication fork. Failure to restart the DNA replication process can result in double-strand breaks, cell-cycle arrest, cell death, or cellular transformation. In this review, we summarize the involvement of EXO1 in the replication, DNA repair pathways, cell cycle checkpoints, and the link between EXO1 and cancer.
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28
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A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. Cell 2017; 171:1437-1452.e17. [PMID: 29195078 DOI: 10.1016/j.cell.2017.10.049] [Citation(s) in RCA: 1713] [Impact Index Per Article: 244.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/25/2017] [Accepted: 10/27/2017] [Indexed: 12/16/2022]
Abstract
We previously piloted the concept of a Connectivity Map (CMap), whereby genes, drugs, and disease states are connected by virtue of common gene-expression signatures. Here, we report more than a 1,000-fold scale-up of the CMap as part of the NIH LINCS Consortium, made possible by a new, low-cost, high-throughput reduced representation expression profiling method that we term L1000. We show that L1000 is highly reproducible, comparable to RNA sequencing, and suitable for computational inference of the expression levels of 81% of non-measured transcripts. We further show that the expanded CMap can be used to discover mechanism of action of small molecules, functionally annotate genetic variants of disease genes, and inform clinical trials. The 1.3 million L1000 profiles described here, as well as tools for their analysis, are available at https://clue.io.
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29
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Novel pan PI3K inhibitor-induced apoptosis in APL cells correlates with suppression of telomerase: An emerging mechanism of action of BKM120. Int J Biochem Cell Biol 2017; 91:1-8. [DOI: 10.1016/j.biocel.2017.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/30/2017] [Accepted: 08/14/2017] [Indexed: 12/21/2022]
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30
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Depreeuw J, Stelloo E, Osse EM, Creutzberg CL, Nout RA, Moisse M, Garcia-Dios DA, Dewaele M, Willekens K, Marine JC, Matias-Guiu X, Amant F, Lambrechts D, Bosse T. Amplification of 1q32.1 Refines the Molecular Classification of Endometrial Carcinoma. Clin Cancer Res 2017; 23:7232-7241. [PMID: 28939739 DOI: 10.1158/1078-0432.ccr-17-0566] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 07/13/2017] [Accepted: 09/15/2017] [Indexed: 01/02/2023]
Abstract
Purpose: Molecular classification of endometrial cancer identified distinct molecular subgroups. However, the largest subset of endometrial cancers remains poorly characterized and is referred to as the "nonspecific molecular profile" (NSMP) subgroup. Here, we aimed at refining the classification of this subgroup by profiling somatic copy-number aberrations (SCNAs).Experimental Design: SCNAs were analyzed in 141 endometrial cancers using whole-genome SNP arrays and pooled with 361 endometrial cancers from The Cancer Genome Atlas. Genomic Identification of Significant Targets in Cancer (GISTIC) identified statistically enriched SCNAs and penalized Cox regression assessed survival effects. The prognostic significance of relevant SCNAs was validated using multiplex ligation-dependent probe amplification in 840 endometrial cancers from the PORTEC-1/2 trials. Copy-number status of genes was correlated with gene expression to identify potential cancer drivers. One plausible oncogene was validated in vitro using antisense oligonucleotide-based strategy.Results: SCNAs affecting chromosome 1q32.1 significantly correlated with worse relapse-free survival (RFS) in the NSMP subgroup (HR, 2.12; 95% CI, 1.26-3.59; P = 0.005). This effect was replicated in NSMP endometrial cancers from PORTEC-1/2 (HR, 2.34; 95% CI, 1.17-4.70; P = 0.017). A new molecular classification including the 1q32.1 amplification improved risk prediction of recurrence. MDM4 gene expression strongly correlated with 1q32.1 amplification. Silencing MDM4 inhibited cell growth in cell lines carrying 1q32.1 amplification, but not in those without MDM4 amplification. Vice versa, increasing MDM4 expression in nonamplified cell lines stimulated cell proliferation.Conclusions: 1q32.1 amplification was identified as a prognostic marker for poorly characterized NSMP endometrial cancers, refining the molecular classification of this subgroup. We functionally validated MDM4 as a potential oncogenic driver in the 1q32.1 region. Clin Cancer Res; 23(23); 7232-41. ©2017 AACR.
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Affiliation(s)
- Jeroen Depreeuw
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, KU Leuven (University of Leuven), University Hospitals Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Laboratory for Translational Genetics, Leuven, Belgium.,VIB, VIB Center for Cancer Biology, Laboratory for Translational Genetics, Leuven, Belgium
| | - Ellen Stelloo
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Elisabeth M Osse
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Carien L Creutzberg
- Department of Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Remi A Nout
- Department of Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Matthieu Moisse
- Department of Human Genetics, KU Leuven, Laboratory for Translational Genetics, Leuven, Belgium.,VIB, VIB Center for Cancer Biology, Laboratory for Translational Genetics, Leuven, Belgium
| | - Diego A Garcia-Dios
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, KU Leuven (University of Leuven), University Hospitals Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Laboratory for Translational Genetics, Leuven, Belgium.,VIB, VIB Center for Cancer Biology, Laboratory for Translational Genetics, Leuven, Belgium
| | - Michael Dewaele
- Department of Oncology, KU Leuven, Laboratory for Molecular Cancer Biology, Leuven, Belgium.,VIB, VIB Center for Cancer Biology, Laboratory for Molecular Cancer Biology, Leuven, Belgium
| | - Karen Willekens
- Department of Oncology, KU Leuven, Laboratory for Molecular Cancer Biology, Leuven, Belgium.,VIB, VIB Center for Cancer Biology, Laboratory for Molecular Cancer Biology, Leuven, Belgium
| | - Jean-Christophe Marine
- Department of Oncology, KU Leuven, Laboratory for Molecular Cancer Biology, Leuven, Belgium.,VIB, VIB Center for Cancer Biology, Laboratory for Molecular Cancer Biology, Leuven, Belgium
| | - Xavier Matias-Guiu
- Pathology and Molecular Genetics, Institut de Recerca Biomedica de Lleida, Lleida, Spain
| | - Frédéric Amant
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, KU Leuven (University of Leuven), University Hospitals Leuven, Leuven, Belgium.,Center for Gynaecologic Oncology Amsterdam (CGOA), Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Diether Lambrechts
- Department of Human Genetics, KU Leuven, Laboratory for Translational Genetics, Leuven, Belgium.,VIB, VIB Center for Cancer Biology, Laboratory for Translational Genetics, Leuven, Belgium
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
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31
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Gopal R, Selvarasu K, Pandian PP, Ganesan K. Integrative transcriptome analysis of liver cancer profiles identifies upstream regulators and clinical significance of ACSM3 gene expression. Cell Oncol (Dordr) 2017; 40:219-233. [PMID: 28390038 DOI: 10.1007/s13402-017-0321-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2017] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is one of the most common human malignancies. It has frequently been associated with metabolic perturbations and liver damages. Various members of the family of acyl-CoA synthetases are known to be involved in the production of bioactive fatty acids, and altered expression of its encoding genes has been found to be involved in metabolic perturbations. For the development of novel diagnostic and therapeutic HCC options, a fundamental understanding of the mechanisms associated with the deregulation of candidate genes involved in metabolic perturbation is required. METHODS A meta-analysis of multiple HCC mRNA profiles was performed to identify consistently deregulated genes. Expression of the acyl-CoA synthetase medium chain family member 3 (ACSM3) gene was subsequently assessed in different HCC tumor stages and correlated with various clinicopathological features. Transcription regulation, survival and pathway-associated features of the ACSM3 gene were investigated using integrative functional genomic and molecular cell biological methods. RESULTS We found that expression of the ACSM3 gene was significantly reduced in HCC tissues and was frequently downregulated in patients exhibiting high alpha-fetoprotein (AFP) levels, high alanine aminotransferase (ALT) levels, multiple nodules and large tumors. Loss of ACSM3 expression was found to correlate with advanced HCC stages and a poor survival. In addition, HNF4α was found to positively regulate the expression of the ACSM3 gene, while PPARγ was found to transcriptionally repress it. Downregulation of ACSM3 expression was perceived upon activation of the TGFβ, WNT, AKT and MYC signalling pathways. In addition, we found that ACSM3 expression correlates with fatty acid oxidation in HCC. CONCLUSION Our data provide evidence for a differential expression and regulation of the ACSM3 gene in HCC, and may lay a foundation for therapeutically targeting fatty acid metabolism in these tumors.
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Affiliation(s)
- Ramani Gopal
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | - Karthikeyan Selvarasu
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | - Ponmathi Panneer Pandian
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | - Kumaresan Ganesan
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India.
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32
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Singchat W, Hitakomate E, Rerkarmnuaychoke B, Suntronpong A, Fu B, Bodhisuwan W, Peyachoknagul S, Yang F, Koontongkaew S, Srikulnath K. Genomic Alteration in Head and Neck Squamous Cell Carcinoma (HNSCC) Cell Lines Inferred from Karyotyping, Molecular Cytogenetics, and Array Comparative Genomic Hybridization. PLoS One 2016; 11:e0160901. [PMID: 27501229 PMCID: PMC4976893 DOI: 10.1371/journal.pone.0160901] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 07/26/2016] [Indexed: 02/06/2023] Open
Abstract
Genomic alteration in head and neck squamous cell carcinoma (HNSCC) was studied in two cell line pairs (HN30-HN31 and HN4-HN12) using conventional C-banding, multiplex fluorescence in situ hybridization (M-FISH), and array comparative genomic hybridization (array CGH). HN30 and HN4 were derived from primary lesions in the pharynx and base of tongue, respectively, and HN31 and HN12 were derived from lymph-node metastatic lesions belonging to the same patients. Gain of chromosome 1, 7, and 11 were shared in almost all cell lines. Hierarchical clustering revealed that HN31 was closely related to HN4, which shared eight chromosome alteration cases. Large C-positive heterochromatins were found in the centromeric region of chromosome 9 in HN31 and HN4, which suggests complex structural amplification of the repetitive sequence. Array CGH revealed amplification of 7p22.3p11.2, 8q11.23q12.1, and 14q32.33 in all cell lines involved with tumorigenesis and inflammation genes. The amplification of 2p21 (SIX3), 11p15.5 (H19), and 11q21q22.3 (MAML2, PGR, TRPC6, and MMP family) regions, and deletion of 9p23 (PTPRD) and 16q23.1 (WWOX) regions were identified in HN31 and HN12. Interestingly, partial loss of PTPRD (9p23) and WWOX (16q23.1) genes was identified in HN31 and HN12, and the level of gene expression tended to be the down-regulation of PTPRD, with no detectable expression of the WWOX gene. This suggests that the scarcity of PTPRD and WWOX genes might have played an important role in progression of HNSCC, and could be considered as a target for cancer therapy or a biomarker in molecular pathology.
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Affiliation(s)
- Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Ekarat Hitakomate
- Faculty of Dentistry, Thammasart University, Pathum Thani, 12121, Thailand
| | - Budsaba Rerkarmnuaychoke
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Beiyuan Fu
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Winai Bodhisuwan
- Department of Statistics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.,Center of Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Thailand (CASTNAR, NRU-KU, Thailand)
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | | | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.,Center of Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Thailand (CASTNAR, NRU-KU, Thailand)
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33
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Keijzers G, Liu D, Rasmussen LJ. Exonuclease 1 and its versatile roles in DNA repair. Crit Rev Biochem Mol Biol 2016; 51:440-451. [PMID: 27494243 DOI: 10.1080/10409238.2016.1215407] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Exonuclease 1 (EXO1) is a multifunctional 5' → 3' exonuclease and a DNA structure-specific DNA endonuclease. EXO1 plays roles in DNA replication, DNA mismatch repair (MMR) and DNA double-stranded break repair (DSBR) in lower and higher eukaryotes and contributes to meiosis, immunoglobulin maturation, and micro-mediated end-joining in higher eukaryotes. In human cells, EXO1 is also thought to play a role in telomere maintenance. Mutations in the human EXO1 gene correlate with increased susceptibility to some cancers. This review summarizes recent studies on the enzymatic functions and biological roles of EXO1, its possible protective role against cancer and aging, and regulation of EXO1 by posttranslational modification.
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Affiliation(s)
- Guido Keijzers
- a Department of Cellular and Molecular Medicine , Center for Healthy Aging, University of Copenhagen , Copenhagen , Denmark
| | - Dekang Liu
- a Department of Cellular and Molecular Medicine , Center for Healthy Aging, University of Copenhagen , Copenhagen , Denmark
| | - Lene Juel Rasmussen
- a Department of Cellular and Molecular Medicine , Center for Healthy Aging, University of Copenhagen , Copenhagen , Denmark
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Ramesh V, Ganesan K. Integrative functional genomic analysis unveils the differing dysregulated metabolic processes across hepatocellular carcinoma stages. Gene 2016; 588:19-29. [PMID: 27107678 DOI: 10.1016/j.gene.2016.04.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 04/17/2016] [Accepted: 04/18/2016] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is a highly heterogeneous disease and the development of targeted therapeutics is still at an early stage. The 'omics' based genome-wide profiling comprising the transcriptome, miRNome and proteome are highly useful in identifying the deregulated molecular processes involved in hepatocarcinogenesis. One of the end products and processes of the central dogma being the metabolites and metabolic processes mediate the cellular functions. In recent years, metabolomics based investigations have revealed the major deregulated metabolic processes involved in carcinogenesis. However, the integrative analysis of the holistic metabolic processes with genomics is at an early stage. Since the gene-sets are highly useful in assessing the biological processes and pathways, we made an attempt to infer the deregulated cellular metabolic processes involved in HCC by employing metabolism associated gene-set enrichment analysis. Further, the metabolic process enrichment scores were integrated with the transcriptome profiles of HCC. Integrative analysis shows three distinct metabolic deregulations: i) hepatocyte function related molecular processes involving lipid/fatty acid/bile acid synthesis, ii) inflammatory processes with cytokine, sphingolipid & chondriotin sulphate metabolism and iii) enriched nucleotide metabolic process involving purine/pyrimidine & glucose mediated catabolic process, in hepatocarcinogenesis. The three distinct metabolic processes were found to occur both in tumor and liver cancer cell line profiles. Unsupervised hierarchical clustering of the metabolic processes along with clinical sample information has identified two major clusters based on AFP (alpha-fetoprotein) and metastasis. The study reveals the three major regulatory processes involved in HCC stages.
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Affiliation(s)
- Vignesh Ramesh
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, India
| | - Kumaresan Ganesan
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, India.
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Samadder P, Aithal R, Belan O, Krejci L. Cancer TARGETases: DSB repair as a pharmacological target. Pharmacol Ther 2016; 161:111-131. [PMID: 26899499 DOI: 10.1016/j.pharmthera.2016.02.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cancer is a disease attributed to the accumulation of DNA damages due to incapacitation of DNA repair pathways resulting in genomic instability and a mutator phenotype. Among the DNA lesions, double stranded breaks (DSBs) are the most toxic forms of DNA damage which may arise as a result of extrinsic DNA damaging agents or intrinsic replication stress in fast proliferating cancer cells. Accurate repair of DSBs is therefore paramount to the cell survival, and several classes of proteins such as kinases, nucleases, helicases or core recombinational proteins have pre-defined jobs in precise execution of DSB repair pathways. On one hand, the proper functioning of these proteins ensures maintenance of genomic stability in normal cells, and on the other hand results in resistance to various drugs employed in cancer therapy and therefore presents a suitable opportunity for therapeutic targeting. Higher relapse and resistance in cancer patients due to non-specific, cytotoxic therapies is an alarming situation and it is becoming more evident to employ personalized treatment based on the genetic landscape of the cancer cells. For the success of personalized treatment, it is of immense importance to identify more suitable targetable proteins in DSB repair pathways and also to explore new synthetic lethal interactions with these pathways. Here we review the various alternative approaches to target the various protein classes termed as cancer TARGETases in DSB repair pathway to obtain more beneficial and selective therapy.
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Affiliation(s)
- Pounami Samadder
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, 60200 Brno, Czech Republic
| | - Rakesh Aithal
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; Department of Biology, Masaryk University, 62500 Brno, Czech Republic
| | - Ondrej Belan
- Department of Biology, Masaryk University, 62500 Brno, Czech Republic
| | - Lumir Krejci
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, 60200 Brno, Czech Republic; Department of Biology, Masaryk University, 62500 Brno, Czech Republic.
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36
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Dürrbaum M, Storchová Z. Effects of aneuploidy on gene expression: implications for cancer. FEBS J 2015; 283:791-802. [DOI: 10.1111/febs.13591] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/02/2015] [Accepted: 11/05/2015] [Indexed: 01/23/2023]
Affiliation(s)
- Milena Dürrbaum
- Group Maintenance of Genome Stability; Max Planck Institute of Biochemistry; Martinsried Germany
- Center for Integrated Protein Science Munich; Ludwig-Maximilian-University Munich; Germany
| | - Zuzana Storchová
- Group Maintenance of Genome Stability; Max Planck Institute of Biochemistry; Martinsried Germany
- Center for Integrated Protein Science Munich; Ludwig-Maximilian-University Munich; Germany
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Bologna S, Altmannova V, Valtorta E, Koenig C, Liberali P, Gentili C, Anrather D, Ammerer G, Pelkmans L, Krejci L, Ferrari S. Sumoylation regulates EXO1 stability and processing of DNA damage. Cell Cycle 2015; 14:2439-50. [PMID: 26083678 DOI: 10.1080/15384101.2015.1060381] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
DNA double-strand break repair by the error-free pathway of homologous recombination (HR) requires the concerted action of several factors. Among these, EXO1 and DNA2/BLM are responsible for the extensive resection of DNA ends to produce 3'-overhangs, which are essential intermediates for downstream steps of HR. Here we show that EXO1 is a SUMO target and that sumoylation affects EXO1 ubiquitylation and protein stability. We identify an UBC9-PIAS1/PIAS4-dependent mechanism controlling human EXO1 sumoylation in vivo and demonstrate conservation of this mechanism in yeast by the Ubc9-Siz1/Siz2 using an in vitro reconstituted system. Furthermore, we show physical interaction between EXO1 and the de-sumoylating enzyme SENP6 both in vitro and in vivo, promoting EXO1 stability. Finally, we identify the major sites of sumoylation in EXO1 and show that ectopic expression of a sumoylation-deficient form of EXO1 rescues the DNA damage-induced chromosomal aberrations observed upon wt-EXO1 expression. Thus, our study identifies a novel layer of regulation of EXO1, making the pathways that regulate its function an ideal target for therapeutic intervention.
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Affiliation(s)
- Serena Bologna
- a Institute of Molecular Cancer Research; University of Zurich ; Zurich , Switzerland
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Park SJ, Kong HK, Kim YS, Lee YS, Park JH. Inhibition of S-adenosylhomocysteine hydrolase decreases cell mobility and cell proliferation through cell cycle arrest. Am J Cancer Res 2015; 5:2127-2138. [PMID: 26328244 PMCID: PMC4548325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/11/2015] [Indexed: 06/04/2023] Open
Abstract
S-adenosylhomocysteine hydrolase (AHCY) hydrolyzes S-adenosylhomocysteine to adenosine and l-homocysteine, and it is already known that inhibition of AHCY decreased cell proliferation by G2/M arrest in MCF7 cells. However, the previous study has not indicated what mechanism the cell cycle arrest is induced by. In this study, we aimed to investigate the different cell cycle mechanisms in both p53 wild-typed MCF7 and p53 mutant-typed MCF7-ADR by suppressing AHCY. We extensively proved that AHCY knockdown has an anti-proliferative effect by using the WST-1 assay, BrdU assay, and cell cytometry analysis and an anti-invasive, migration effect by wound-healing assay and trans-well analysis. Our study showed that down-regulation of AHCY effectively suppressed cell proliferation by regulating the MEK/ERK signaling pathway and through cell cycle arrests. The cell cycle arrest occurred at the G2/M checkpoint by inhibiting degradation of cyclinB1 and phosphorylation of CDC2 in MCF7 cells and at the G1 phase by inhibiting cyclinD1 and CDK6 in MCF7-ADR cells. Finally, we determined that AHCY regulates the expression of ATM kinase that phosphorylates p53 and affects to arrest of G2/M phase in MCF7 cells. The findings of this study significantly suggest that AHCY is an important regulator of cell proliferation through different mechanism in between MCF7 and MCF7-ADR cells as p53 status.
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Affiliation(s)
- Sae Jeong Park
- Department of Biological Science, Sookmyung Women's University Seoul, Korea
| | - Hyun Kyung Kong
- Department of Biological Science, Sookmyung Women's University Seoul, Korea
| | - Ye Sol Kim
- Department of Biological Science, Sookmyung Women's University Seoul, Korea
| | - Yeon Seon Lee
- Department of Biological Science, Sookmyung Women's University Seoul, Korea
| | - Jong Hoon Park
- Department of Biological Science, Sookmyung Women's University Seoul, Korea
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Abstract
Cancer cells differ from normal healthy cells in multiple aspects ranging from altered cellular signaling through metabolic changes to aberrant chromosome content, so called aneuploidy. The large-scale changes in copy numbers of chromosomes or large chromosomal regions due to aneuploidy alter significantly the gene expression, as several hundreds of genes are gained or lost. Comparison of quantitative genome, transcriptome and proteome data enables dissection of the molecular causes that underlie the gene expression changes observed in cancer cells and provides a new perspective on the molecular consequences of aneuploidy. Here, we will map to what degree aneuploidy affects the expression of genes located on the affected chromosomes. We will also address the effects of aneuploidy on global gene expression in cancer cells as well as whether and how it may contribute to the physiology of cancer cells.
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Affiliation(s)
- Milena Dürrbaum
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Center for Integrated Protein Science Munich, Ludwig-Maximilian-University Munich, 80336, Munich, Germany
| | - Zuzana Storchová
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
- Center for Integrated Protein Science Munich, Ludwig-Maximilian-University Munich, 80336, Munich, Germany.
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Kenicer J, Spears M, Lyttle N, Taylor KJ, Liao L, Cunningham CA, Lambros M, MacKay A, Yao C, Reis-Filho J, Bartlett JMS. Molecular characterisation of isogenic taxane resistant cell lines identify novel drivers of drug resistance. BMC Cancer 2014; 14:762. [PMID: 25312014 PMCID: PMC4203938 DOI: 10.1186/1471-2407-14-762] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/02/2014] [Indexed: 01/29/2023] Open
Abstract
Background Taxanes such as paclitaxel and docetaxel are used successfully to treat breast cancer, usually in combination with other agents. They interfere with microtubules causing cell cycle arrest; however, the mechanisms underlying the clinical effects of taxanes are yet to be fully elucidated. Methods Isogenic paclitaxel resistant (PACR) MDA‒MB‒231, paclitaxel resistant ZR75‒1 and docetaxel resistant (DOCR) ZR75‒1 cell lines were generated by incrementally increasing taxane dose in native cell lines in vitro. We used aCGH analysis to identify mechanisms driving taxane resistance. Results Taxane resistant cell lines exhibited an 18-170 fold increased resistance to taxanes, with the ZR75-1 resistant cell lines also demonstrating cross resistance to anthracyclines. Paclitaxel treatment of native cells resulted in a G2/M block and a decrease in the G1 phase of the cell cycle. However, in the resistant cell lines, minimal changes were present. Functional network analysis revealed that the mitotic prometaphase was lost in the resistant cell lines. Conclusion This study established a model system for examining taxane resistance and demonstrated that both MDR and mitosis represent common mechanism of taxane resistance. Electronic supplementary material The online version of this article (doi:10.1186/1471-2407-14-762) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - John M S Bartlett
- Biomarkers and Companion Diagnostics, Edinburgh Cancer Research Centre, Crewe Road South, Edinburgh EH4 2XR, UK.
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Refinement of breast cancer risk prediction with concordant leading edge subsets from prognostic gene signatures. Breast Cancer Res Treat 2014; 147:353-70. [PMID: 25158930 DOI: 10.1007/s10549-014-3104-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/12/2014] [Indexed: 12/23/2022]
Abstract
Several prognostic signatures have been identified for breast cancer. However, these signatures vary extensively in their gene compositions, and the poor concordance of the risk groups defined by the prognostic signatures hinders their clinical applicability. Breast cancer risk prediction was refined with a novel approach to finding concordant genes from leading edge analysis of prognostic signatures. Each signature was split into two gene sets, which contained either up-regulated or down-regulated genes, and leading edge analysis was performed within each array study for all up-/down-regulated gene sets of the same signature from all training datasets. Consensus of leading edge subsets among all training microarrays was used to synthesize a predictive model, which was then tested in independent studies by partial least squares regression. Only a small portion of six prognostic signatures (Amsterdam, Rotterdam, Genomic Grade Index, Recurrence Score, and Hu306 and PAM50 of intrinsic subtypes) was significantly enriched in the leading edge analysis in five training datasets (n = 2,380), and that the concordant leading edge subsets (43 genes) could identify the core signature genes that account for the enrichment signals providing prognostic power across all assayed samples. The proposed concordant leading edge algorithm was able to discriminate high-risk from low-risk patients in terms of relapse-free or distant metastasis-free survival in all training samples (hazard ratios: 1.84-2.20) and in three out of four independent studies (hazard ratios: 3.91-8.31). In some studies, the concordant leading edge subset remained a significant prognostic factor independent of clinical ER, HER2, and lymph node status. The present study provides a statistical framework for identifying core consensus across microarray studies with leading edge analysis, and a breast cancer risk predictive model was established.
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Shi Y, Lu J, Zhou J, Tan X, He Y, Ding J, Tian Y, Wang L, Wang K. Long non-coding RNA Loc554202 regulates proliferation and migration in breast cancer cells. Biochem Biophys Res Commun 2014; 446:448-53. [PMID: 24631686 DOI: 10.1016/j.bbrc.2014.02.144] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 02/26/2014] [Indexed: 12/21/2022]
Abstract
Data derived from massive cloning and traditional sequencing methods have revealed that long non-coding RNAs (lncRNA) play important roles in the development and progression of cancer. Although many studies suggest that the lncRNAs have different cellular functions, many of them are not yet to be identified and characterized for the mechanism of their functions. To address this question, we assay the expression level of lncRNAs-Loc554202 in breast cancer tissues and find that Loc554202 is significantly increased compared with normal control, and associated with advanced pathologic stage and tumor size. Moreover, knockdown of Loc554202 decreased breast cancer cell proliferation, induced apoptosis and inhibits migration/invasion in vitro and impeded tumorigenesis in vivo. These data suggest an important role of Loc554202 in breast tumorigenesis.
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Affiliation(s)
- Yongguo Shi
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Jianwei Lu
- Cancer Hospital of Jiangsu Province, Nanjing, Jiangsu, PR China.
| | - Jing Zhou
- Department of Oncology, Taizhou People' Hospital, Taizhou, Jiangsu, PR China.
| | - Xueming Tan
- Department of Gastroenterology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Ye He
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Jie Ding
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Yun Tian
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Li Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Keming Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China.
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