1651
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1652
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Hasan N, Ahuja N. The Emerging Roles of ATP-Dependent Chromatin Remodeling Complexes in Pancreatic Cancer. Cancers (Basel) 2019; 11:E1859. [PMID: 31769422 PMCID: PMC6966483 DOI: 10.3390/cancers11121859] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/08/2023] Open
Abstract
Pancreatic cancer is an aggressive cancer with low survival rates. Genetic and epigenetic dysregulation has been associated with the initiation and progression of pancreatic tumors. Multiple studies have pointed to the involvement of aberrant chromatin modifications in driving tumor behavior. ATP-dependent chromatin remodeling complexes regulate chromatin structure and have critical roles in stem cell maintenance, development, and cancer. Frequent mutations and chromosomal aberrations in the genes associated with subunits of the ATP-dependent chromatin remodeling complexes have been detected in different cancer types. In this review, we summarize the current literature on the genomic alterations and mechanistic studies of the ATP-dependent chromatin remodeling complexes in pancreatic cancer. Our review is focused on the four main subfamilies: SWItch/sucrose non-fermentable (SWI/SNF), imitation SWI (ISWI), chromodomain-helicase DNA-binding protein (CHD), and INOsitol-requiring mutant 80 (INO80). Finally, we discuss potential novel treatment options that use small molecules to target these complexes.
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Affiliation(s)
| | - Nita Ahuja
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06520, USA;
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1653
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Chun YJ, Choi JW, Hong MH, Jung D, Son H, Cho EK, Min YJ, Kim SW, Park K, Lee SS, Kim S, Kim HR, Cho BC. Molecular characterization of lung adenocarcinoma from Korean patients using next generation sequencing. PLoS One 2019; 14:e0224379. [PMID: 31765373 PMCID: PMC6876835 DOI: 10.1371/journal.pone.0224379] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 10/13/2019] [Indexed: 02/07/2023] Open
Abstract
The treatment of Lung adenocarcinoma (LUAD) could benefit from the incorporation of precision medicine. This study was to identify cancer-related genetic alterations by next generation sequencing (NGS) in resected LUAD samples from Korean patients and to determine their associations with clinical features. A total of 201 tumors and their matched peripheral blood samples were analyzed using targeted sequencing via the Illumina HiSeq 2500 platform of 242 genes with a median depth of coverage greater than 500X. One hundred ninety-two tumors were amenable to data analysis. EGFR was the most frequently mutated gene, occurring in 106 (55%) patients, followed by TP53 (n = 67, 35%) and KRAS (n = 11, 6%). EGFR mutations were strongly increased in patients that were female and never-smokers. Smokers had a significantly higher tumor mutational burden (TMB) than never-smokers (average 4.84 non-synonymous mutations/megabase [mt/Mb] vs. 2.84 mt/Mb, p = 0.019). Somatic mutations of APC, CTNNB1, and AMER1 in the WNT signaling pathway were highly associated with shortened disease-free survival (DFS) compared to others (median DFS of 89 vs. 27 months, p = 0.018). Patients with low TMB, annotated as less than 2 mt/Mb, had longer DFS than those with high TMB (p = 0.041). A higher frequency of EGFR mutations and a lower of KRAS mutations were observed in Korean LUAD patients. Profiles of 242 genes mapped in this study were compared with whole exome sequencing genetic profiles generated in The Cancer Genome Atlas Lung Adenocarcinoma. NGS-based diagnostics can provide clinically relevant information such as mutations or TMB from readily available formalin-fixed paraffin-embedded tissue.
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Affiliation(s)
- You Jin Chun
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Woo Choi
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Korea
| | - Min Hee Hong
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Dongmin Jung
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Hyeonju Son
- Department of Biomedical Systems Informatics, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Kyung Cho
- Division of Hematology-Oncology, Department of Internal Medicine, Gachon Medical School, Gil Medical Center, Incheon, Korea
| | - Young Joo Min
- Division of Hematology and Oncology, Department of Internal Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, Korea
| | - Sang-We Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Keunchil Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sung Sook Lee
- Department of Hematology-Oncology, Inje University Haeundae Paik Hospital, Busan, Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Hye Ryun Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Byoung Chul Cho
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
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1654
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Inder S, Bates M, Ni Labhrai N, McDermott N, Schneider J, Erdmann G, Jamerson T, Belle VA, Prina-Mello A, Thirion P, Manecksha PR, Cormican D, Finn S, Lynch T, Marignol L. Multiplex profiling identifies clinically relevant signalling proteins in an isogenic prostate cancer model of radioresistance. Sci Rep 2019; 9:17325. [PMID: 31758038 PMCID: PMC6874565 DOI: 10.1038/s41598-019-53799-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 11/04/2019] [Indexed: 12/22/2022] Open
Abstract
The exact biological mechanism governing the radioresistant phenotype of prostate tumours at a high risk of recurrence despite the delivery of advanced radiotherapy protocols remains unclear. This study analysed the protein expression profiles of a previously generated isogenic 22Rv1 prostate cancer model of radioresistance using DigiWest multiplex protein profiling for a selection of 90 signalling proteins. Comparative analysis of the profiles identified a substantial change in the expression of 43 proteins. Differential PARP-1, AR, p53, Notch-3 and YB-1 protein levels were independently validated using Western Blotting. Pharmacological targeting of these proteins was associated with a mild but significant radiosensitisation effect at 4Gy. This study supports the clinical relevance of isogenic in vitro models of radioresistance and clarifies the molecular radiation response of prostate cancer cells.
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Affiliation(s)
- S Inder
- Translational Radiobiology and Molecular oncology, Applied Radiation Therapy Trinity, Trinity Translational Medicine Institute (TTMI), Trinity College Dublin, Dublin, Ireland
- Department of Urology, St James's Hospital, Dublin, Ireland
| | - M Bates
- Translational Radiobiology and Molecular oncology, Applied Radiation Therapy Trinity, Trinity Translational Medicine Institute (TTMI), Trinity College Dublin, Dublin, Ireland
| | - N Ni Labhrai
- Translational Radiobiology and Molecular oncology, Applied Radiation Therapy Trinity, Trinity Translational Medicine Institute (TTMI), Trinity College Dublin, Dublin, Ireland
| | - N McDermott
- Translational Radiobiology and Molecular oncology, Applied Radiation Therapy Trinity, Trinity Translational Medicine Institute (TTMI), Trinity College Dublin, Dublin, Ireland
| | | | - G Erdmann
- NMI TT Pharmaservices, Berlin, Germany
| | - T Jamerson
- Department of International Health, Mount Sinai School of Medicine, New York, USA
| | - V A Belle
- Department of International Health, Mount Sinai School of Medicine, New York, USA
| | - A Prina-Mello
- Laboratory for Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute (TTMI), AMBER centre at CRANN Institute, Trinity College Dublin, Dublin, Ireland
- Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - P Thirion
- St Luke's Radiation Oncology Network, St James's Hospital, Dublin, Ireland
| | - P R Manecksha
- Department of Urology, St James's Hospital, Dublin, Ireland
- Department of Surgery, Trinity College Dublin, Dublin, Ireland
| | - D Cormican
- Department of Histopathology, St James's Hospital, Dublin, Ireland
| | - S Finn
- Department of Histopathology, St James's Hospital, Dublin, Ireland
| | - T Lynch
- Department of Urology, St James's Hospital, Dublin, Ireland
| | - L Marignol
- Translational Radiobiology and Molecular oncology, Applied Radiation Therapy Trinity, Trinity Translational Medicine Institute (TTMI), Trinity College Dublin, Dublin, Ireland.
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1655
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Distinct co-acquired alterations and genomic evolution during TKI treatment in non-small-cell lung cancer patients with or without acquired T790M mutation. Oncogene 2019; 39:1846-1859. [DOI: 10.1038/s41388-019-1104-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/29/2019] [Accepted: 11/05/2019] [Indexed: 12/17/2022]
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1656
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Guo J, Wang M, Wang JP, Wu CX. Ubiquitin-conjugating enzyme E2T knockdown suppresses hepatocellular tumorigenesis via inducing cell cycle arrest and apoptosis. World J Gastroenterol 2019; 25:6386-6403. [PMID: 31798276 PMCID: PMC6881511 DOI: 10.3748/wjg.v25.i43.6386] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is now the most common primary liver malignancy worldwide, and multiple risk factors attribute to the occurrence and development of HCC. Recently, increasing studies suggest that ubiquitin-conjugating enzyme E2T (UBE2T) serves as a promising prognostic factor in human cancers, although the molecular mechanism of UBE2T in HCC remains unclear.
AIM To investigate the clinical relevance and role of UBE2T in HCC development.
METHODS UBE2T expression in HCC tissues from the TCGA database and its association with patient survival were analyzed. A lentivirus-mediated strategy was used to knock down UBE2T in HCC cells. qRT-PCR and Western blot assays were performed to check the effect of UBE2T silencing in HCC cells. Cell growth in vitro and in vivo was analyzed by multiparametric high-content screening and the xenograft tumorigenicity assay, respectively. Cell cycle distribution and apoptosis were determined by flow cytometry. The genes regulated by UBE2T were profiled by microarray assay.
RESULTS UBE2T was overexpressed in HCC tissues compared with paired and non-paired normal tissues. High expression of UBE2T predicted a poor overall survival in HCC patients. In vitro, lentivirus-mediated UBE2T knockdown significantly reduced the viability of both SMMC-7721 and BEL-7404 cells. In vivo, the xenograft tumorigenesis of SMMC-7721 cells was largely attenuated by UBE2T silencing. The cell cycle was arrested at G1/S phase in SMMC-7721 and BEL-7404 cells with UBE2T knockdown. Furthermore, apoptosis was increased by UBE2T knockdown. At the molecular level, numerous genes were dysregulated after UBE2T silencing, including IL-1B, FOSL1, PTGS2, and BMP6.
CONCLUSION UBE2T plays an important role in cell cycle progression, apoptosis, and HCC development.
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Affiliation(s)
- Jian Guo
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, Shanxi Province, China
- Department of General Surgery, Shanxi Provincial People’s Hospital, the Affiliated People’s Hospital of Shanxi Medical University, Taiyuan 030012, Shanxi Province, China
| | - Mu Wang
- Department of Neurology, Shanxi Provincial People’s Hospital, the Affiliated People’s Hospital of Shanxi Medical University, Taiyuan 030012, Shanxi Province, China
| | - Jun-Ping Wang
- Department of Gastroenterology, Shanxi Provincial People’s Hospital, the Affiliated People’s Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi Province, China
| | - Chang-Xin Wu
- The Institutes of Biomedical Sciences, Shanxi University, Taiyuan 03006, Shanxi Province, China
- Key Laboratory of Molecular Biology and Biochemistry of Ministry of Education, Shanxi University, Taiyuan 030006, Shanxi Province, China
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1657
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Myc/Max dependent intronic long antisense noncoding RNA, EVA1A-AS, suppresses the expression of Myc/Max dependent anti-proliferating gene EVA1A in a U2 dependent manner. Sci Rep 2019; 9:17319. [PMID: 31754186 PMCID: PMC6872820 DOI: 10.1038/s41598-019-53944-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/22/2019] [Indexed: 01/26/2023] Open
Abstract
The Myc gene has been implicated in the pathogenesis of most types of human cancerous tumors. Myc/Max activates large numbers of pro-tumor genes; however it also induces anti-proliferation genes. When anti-proliferation genes are activated by Myc, cancer cells can only survive if they are downregulated. Hepatocellular carcinoma (HCC) specific intronic long noncoding antisense (lnc-AS) RNA, the EVA1A-AS gene, is located within the second intron (I2) of the EVA1A gene (EVA-1 homolog A) that encodes an anti-proliferation factor. Indeed, EVA1A, but not EVA1A-AS, is expressed in normal liver. Depletion of EVA1A-AS suppressed cell proliferation of HepG2 cells by upregulation of EVA1A. Overexpression of EVA1A caused cell death at the G2/M phase via microtubule catastrophe. Furthermore, suppressed EVA1A expression levels are negatively correlated with differentiation grade in 365 primary HCCs, while EVA1A-AS expression levels are positively correlated with patient survival. Notably, both EVA1A and EVA1A-AS were activated by the Myc/Max complex. Eva1A-AS is transcribed in the opposite direction near the 3′splice site of EVA1A I2. The second intron did not splice out in a U2 dependent manner and EVA1A mRNA is not exported. Thus, the Myc/Max dependent anti-proliferating gene, EVA1A, is controlled by Myc/Max dependent anti-sense noncoding RNA for HCC survival.
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1658
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Bogusławska J, Popławski P, Alseekh S, Koblowska M, Iwanicka-Nowicka R, Rybicka B, Kędzierska H, Głuchowska K, Hanusek K, Tański Z, Fernie AR, Piekiełko-Witkowska A. MicroRNA-Mediated Metabolic Reprograming in Renal Cancer. Cancers (Basel) 2019; 11:cancers11121825. [PMID: 31756931 PMCID: PMC6966432 DOI: 10.3390/cancers11121825] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/15/2019] [Indexed: 02/07/2023] Open
Abstract
Metabolic reprogramming is one of the hallmarks of renal cell cancer (RCC). We hypothesized that altered metabolism of RCC cells results from dysregulation of microRNAs targeting metabolically relevant genes. Combined large-scale transcriptomic and metabolic analysis of RCC patients tissue samples revealed a group of microRNAs that contribute to metabolic reprogramming in RCC. miRNAs expressions correlated with their predicted target genes and with gas chromatography-mass spectrometry (GC-MS) metabolome profiles of RCC tumors. Assays performed in RCC-derived cell lines showed that miR-146a-5p and miR-155-5p targeted genes of PPP (the pentose phosphate pathway) (G6PD and TKT), the TCA (tricarboxylic acid cycle) cycle (SUCLG2), and arginine metabolism (GATM), respectively. miR-106b-5p and miR-122-5p regulated the NFAT5 osmoregulatory transcription factor. Altered expressions of G6PD, TKT, SUCLG2, GATM, miR-106b-5p, miR-155-5p, and miR-342-3p correlated with poor survival of RCC patients. miR-106b-5p, miR-146a-5p, and miR-342-3p stimulated proliferation of RCC cells. The analysis involving >6000 patients revealed that miR-34a-5p, miR-106b-5p, miR-146a-5p, and miR-155-5p are PanCancer metabomiRs possibly involved in global regulation of cancer metabolism. In conclusion, we found that microRNAs upregulated in renal cancer contribute to disturbed expression of key genes involved in the regulation of RCC metabolome. miR-146a-5p and miR-155-5p emerge as a key “metabomiRs” that target genes of crucial metabolic pathways (PPP (the pentose phosphate pathway), TCA cycle, and arginine metabolism).
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Affiliation(s)
- Joanna Bogusławska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland; (J.B.); (P.P.); (B.R.); (H.K.); (K.G.); (K.H.)
| | - Piotr Popławski
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland; (J.B.); (P.P.); (B.R.); (H.K.); (K.G.); (K.H.)
| | - Saleh Alseekh
- Max-Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (S.A.); (A.R.F.)
- Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Marta Koblowska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland; (M.K.); (R.I.-N.)
- Laboratory for Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Roksana Iwanicka-Nowicka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland; (M.K.); (R.I.-N.)
- Laboratory for Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Beata Rybicka
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland; (J.B.); (P.P.); (B.R.); (H.K.); (K.G.); (K.H.)
| | - Hanna Kędzierska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland; (J.B.); (P.P.); (B.R.); (H.K.); (K.G.); (K.H.)
| | - Katarzyna Głuchowska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland; (J.B.); (P.P.); (B.R.); (H.K.); (K.G.); (K.H.)
| | - Karolina Hanusek
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland; (J.B.); (P.P.); (B.R.); (H.K.); (K.G.); (K.H.)
| | - Zbigniew Tański
- Masovian Specialist Hospital in Ostroleka, 07-410 Ostroleka, Poland;
| | - Alisdair R. Fernie
- Max-Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (S.A.); (A.R.F.)
- Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Agnieszka Piekiełko-Witkowska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland; (J.B.); (P.P.); (B.R.); (H.K.); (K.G.); (K.H.)
- Correspondence: ; Tel.: +48-22-5693810
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1659
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Guven-Maiorov E, Tsai CJ, Nussinov R. Oncoviruses Can Drive Cancer by Rewiring Signaling Pathways Through Interface Mimicry. Front Oncol 2019; 9:1236. [PMID: 31803618 PMCID: PMC6872517 DOI: 10.3389/fonc.2019.01236] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/28/2019] [Indexed: 01/17/2023] Open
Abstract
Oncoviruses rewire host pathways to subvert host immunity and promote their survival and proliferation. However, exactly how is challenging to understand. Here, by employing the first and to date only interface-based host-microbe interaction (HMI) prediction method, we explore a pivotal strategy oncoviruses use to drive cancer: mimicking binding surfaces-interfaces-of human proteins. We show that oncoviruses can target key human network proteins and transform cells by acquisition of cancer hallmarks. Experimental large-scale mapping of HMIs is difficult and individual HMIs do not permit in-depth grasp of tumorigenic virulence mechanisms. Our computational approach is tractable and 3D structural HMI models can help elucidate pathogenesis mechanisms and facilitate drug design. We observe that many host proteins are unique targets for certain oncoviruses, whereas others are common to several, suggesting similar infectious strategies. A rough estimation of our false discovery rate based on the tissue expression of oncovirus-targeted human proteins is 25%.
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Affiliation(s)
- Emine Guven-Maiorov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
- Department of Human Genetics and Molecular Medicine, Sackler Institute of Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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1660
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Reynolds IS, O'Connell E, Fichtner M, McNamara DA, Kay EW, Prehn JHM, Furney SJ, Burke JP. Mucinous adenocarcinoma of the colon and rectum: A genomic analysis. J Surg Oncol 2019; 120:1427-1435. [PMID: 31729037 DOI: 10.1002/jso.25764] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND OBJECTIVES Mucinous adenocarcinoma is a distinct subtype of colorectal cancer (CRC) with a worse prognosis when compared with non-mucinous adenocarcinoma. The aim of this study was to compare somatic mutations and copy number alteration (CNA) between mucinous and non-mucinous CRC. METHODS Data from The Cancer Genome Atlas-colon adenocarcinoma and rectum adenocarcinoma projects were utilized. Mucinous and non-mucinous CRC were compared with regard to microsatellite status, overall mutation rate, the most frequently mutated genes, mutations in genes coding for mismatch repair (MMR) proteins and genes coding for mucin glycoproteins. CNA analysis and pathway analysis was undertaken. RESULTS Mucinous CRC was more likely to be microsatellite instability-high (MSI-H) and hypermutated. When corrected for microsatellite status the single-nucleotide variation and insertion-deletion rate was similar between the two cohorts. Mucinous adenocarcinoma was more likely to have mutations in genes coding for MMR proteins and mucin glycoproteins. Pathway analysis revealed further differences between the two histological subtypes in the cell cycle, RTK-RAS, transforming growth factor-β, and TP53 pathways. CONCLUSIONS Mucinous CRC has some distinct genomic aberrations when compared with non-mucinous adenocarcinoma, many of which are driven by the increased frequency of MSI-H tumors. These genomic aberrations may play an important part in the difference seen in response to treatment and prognosis in mucinous adenocarcinoma.
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Affiliation(s)
- Ian S Reynolds
- Department of Colorectal Surgery, Beaumont Hospital, Dublin, Ireland.,Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Emer O'Connell
- Department of Colorectal Surgery, Beaumont Hospital, Dublin, Ireland.,Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Michael Fichtner
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Deborah A McNamara
- Department of Colorectal Surgery, Beaumont Hospital, Dublin, Ireland.,Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Elaine W Kay
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.,Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Simon J Furney
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.,Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland.,Genomic Oncology Research Group, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - John P Burke
- Department of Colorectal Surgery, Beaumont Hospital, Dublin, Ireland
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1661
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Montero J, Gstalder C, Kim DJ, Sadowicz D, Miles W, Manos M, Cidado JR, Paul Secrist J, Tron AE, Flaherty K, Stephen Hodi F, Yoon CH, Letai A, Fisher DE, Haq R. Destabilization of NOXA mRNA as a common resistance mechanism to targeted therapies. Nat Commun 2019; 10:5157. [PMID: 31727958 PMCID: PMC6856172 DOI: 10.1038/s41467-019-12477-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 08/06/2019] [Indexed: 12/15/2022] Open
Abstract
Most targeted cancer therapies fail to achieve complete tumor regressions or attain durable remissions. To understand why these treatments fail to induce robust cytotoxic responses despite appropriately targeting oncogenic drivers, here we systematically interrogated the dependence of cancer cells on the BCL-2 family of apoptotic proteins after drug treatment. We observe that multiple targeted therapies, including BRAF or EGFR inhibitors, rapidly deplete the pro-apoptotic factor NOXA, thus creating a dependence on the anti-apoptotic protein MCL-1. This adaptation requires a pathway leading to destabilization of the NOXA mRNA transcript. We find that interruption of this mechanism of anti-apoptotic adaptive resistance dramatically increases cytotoxic responses in cell lines and a murine melanoma model. These results identify NOXA mRNA destabilization/MCL-1 adaptation as a non-genomic mechanism that limits apoptotic responses, suggesting that sequencing of MCL-1 inhibitors with targeted therapies could overcome such widespread and clinically important resistance. MAPK-targeted therapies fail to achieve complete remission. Here, the authors show that anti-apoptosis resistance is acquired in these targeted therapies through the mRNA destabilization of NOXA which leads to dependence on MCL-1, and that sequential combination of MCL-1 inhibition with targeted therapies overcomes this resistance.
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Affiliation(s)
- Joan Montero
- Division of Hematologic Neoplasia/Malignancies, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, 02115, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, 02115, MA, USA.,Institute for Bioengineering of Catalonia, C/Baldiri Reixac 15-21, Ed. Hèlix 3ª planta · 08028, Barcelona, Spain
| | - Cécile Gstalder
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, 02115, MA, USA.,Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, 02115, MA, USA
| | - Daniel J Kim
- Department of Dermatology and Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, 44 Fruit Street, Boston, MA, 02114, USA
| | - Dorota Sadowicz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, 02115, MA, USA.,Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, 02115, MA, USA
| | - Wayne Miles
- Department of Molecular Genetics, The Ohio State University, 820 Biomedical Research Tower 460 West 12th Avenue, Columbus, 43210, OH, USA
| | - Michael Manos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, 02115, MA, USA
| | - Justin R Cidado
- Bioscience, Oncology IMED Biotech Unit, AstraZeneca, 35 Gatehouse Dr, Waltham, Boston, 02451, MA, USA
| | - J Paul Secrist
- Bioscience, Oncology IMED Biotech Unit, AstraZeneca, 35 Gatehouse Dr, Waltham, Boston, 02451, MA, USA.,LifeMine Therapeutics, 100 Acorn Park Drive, 6th Floor Cambridge, Cambridge, MA, 02140, USA
| | - Adriana E Tron
- Bioscience, Oncology IMED Biotech Unit, AstraZeneca, 35 Gatehouse Dr, Waltham, Boston, 02451, MA, USA
| | - Keith Flaherty
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Harvard Medical School, 44 Fruit Street, Boston, MA, 02114, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, 02115, MA, USA
| | - Charles H Yoon
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, 02115, USA
| | - Anthony Letai
- Division of Hematologic Neoplasia/Malignancies, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, 02115, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, 02115, MA, USA
| | - David E Fisher
- Department of Dermatology and Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, 44 Fruit Street, Boston, MA, 02114, USA. .,Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Harvard Medical School, 44 Fruit Street, Boston, MA, 02114, USA.
| | - Rizwan Haq
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, 02115, MA, USA. .,Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, 02115, MA, USA.
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1662
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Pan-Cancer Landscape of Aberrant DNA Methylation across Human Tumors. Cell Rep 2019; 25:1066-1080.e8. [PMID: 30355485 DOI: 10.1016/j.celrep.2018.09.082] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 08/29/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022] Open
Abstract
The discovery of cancer-associated alterations has primarily focused on genetic variants. Nonetheless, altered epigenomes contribute to deregulate transcription and promote oncogenic pathways. Here, we designed an algorithmic approach (RESET) to identify aberrant DNA methylation and associated cis-transcriptional changes across >6,000 human tumors. Tumors exhibiting mutations of chromatin remodeling factors and Wnt signaling displayed DNA methylation instability, characterized by numerous hyper- and hypo-methylated loci. Most silenced and enhanced genes coalesced in specific pathways including apoptosis, DNA repair, and cell metabolism. Cancer-germline antigens (CG) were frequently epigenomically enhanced and their expression correlated with response to anti-PD-1, but not anti-CTLA4, in skin melanoma. Finally, we demonstrated the potential of our approach to explore DNA methylation changes in pediatric tumors, which frequently lack genetic drivers and exhibit epigenomic modifications. Our results provide a pan-cancer map of aberrant DNA methylation to inform functional and therapeutic studies.
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1663
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Azarkhalili B, Saberi A, Chitsaz H, Sharifi-Zarchi A. DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome. Sci Rep 2019; 9:16526. [PMID: 31712594 PMCID: PMC6848155 DOI: 10.1038/s41598-019-52937-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 10/23/2019] [Indexed: 11/16/2022] Open
Abstract
Despite great advances, molecular cancer pathology is often limited to the use of a small number of biomarkers rather than the whole transcriptome, partly due to computational challenges. Here, we introduce a novel architecture of Deep Neural Networks (DNNs) that is capable of simultaneous inference of various properties of biological samples, through multi-task and transfer learning. It encodes the whole transcription profile into a strikingly low-dimensional latent vector of size 8, and then recovers mRNA and miRNA expression profiles, tissue and disease type from this vector. This latent space is significantly better than the original gene expression profiles for discriminating samples based on their tissue and disease. We employed this architecture on mRNA transcription profiles of 10750 clinical samples from 34 classes (one healthy and 33 different types of cancer) from 27 tissues. Our method significantly outperforms prior works and classical machine learning approaches in predicting tissue-of-origin, normal or disease state and cancer type of each sample. For tissues with more than one type of cancer, it reaches 99.4% accuracy in identifying the correct cancer subtype. We also show this system is very robust against noise and missing values. Collectively, our results highlight applications of artificial intelligence in molecular cancer pathology and oncological research. DeePathology is freely available at https://github.com/SharifBioinf/DeePathology.
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Affiliation(s)
- Behrooz Azarkhalili
- Department of Stem Cell Biology and Technology, Royan Institute, Tehran, Iran.,Department of Mathematics and Computer Science, Sharif University of Technology, Tehran, Iran
| | - Ali Saberi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Hamidreza Chitsaz
- Department of Computer Science, Colorado State University, Fort Collins, CO, USA
| | - Ali Sharifi-Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran.
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1664
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Crow J, Samuel G, Godwin AK. Beyond tumor mutational burden: potential and limitations in using exosomes to predict response to immunotherapy. Expert Rev Mol Diagn 2019; 19:1079-1088. [PMID: 31687863 DOI: 10.1080/14737159.2020.1688144] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Introduction: Immune checkpoint blockade (ICB) has ushered in a new era of cancer therapeutics. The standard for determining which patients might benefit from ICB-based therapies is through the assessment of tumor mutational burden using formalin-fixed paraffin-embedded (FFPE) tumor tissue samples; however, this strategy is imperfect. The discovery of exosomal PD-L1 has placed these nano-vesicles to the forefront of immunotherapy biomarker development. Exosomes and other extracellular vesicles contain proteins and nucleic acids specific to their cell of origin and their production is increased in disease state such as cancer and can be isolated from most types of liquid biopsy. Given this opportunity, a large-scale bioengineering effort has centered on developing technologies capable of isolating distinct subsets of exosomes and interrogating their content for biomarker discovery.Areas covered: This review investigates the current state of small extracellular vesicles (sEVs), focusing on exosomes, as they relate to biomarkers of IBC. We will discuss technologies being developed to both capture and evaluate exosomal cargo and as some of the challenges they face.Expert opinion: The advancement of microfluidic technologies, along with rapidly evolving methodologies in RNAseq and proteomics, are making the potential of utilizing exosomes as prognostic and diagnostic biomarkers of ICB into a likely reality.
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Affiliation(s)
- Jennifer Crow
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Glenson Samuel
- Division of Hematology Oncology, and Bone Marrow Transplant, The Children's Mercy Hospital, Kansas City, MO, USA
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA.,University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
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1665
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Desterke C, Chiappini F. Lipid Related Genes Altered in NASH Connect Inflammation in Liver Pathogenesis Progression to HCC: A Canonical Pathway. Int J Mol Sci 2019; 20:ijms20225594. [PMID: 31717414 PMCID: PMC6888337 DOI: 10.3390/ijms20225594] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 02/06/2023] Open
Abstract
Nonalcoholic steatohepatitis (NASH) is becoming a public health problem worldwide. While the number of research studies on NASH progression rises every year, sometime their findings are controversial. To identify the most important and commonly described findings related to NASH progression, we used an original bioinformatics, integrative, text-mining approach that combines PubMed database querying and available gene expression omnibus dataset. We have identified a signature of 25 genes that are commonly found to be dysregulated during steatosis progression to NASH and cancer. These genes are implicated in lipid metabolism, insulin resistance, inflammation, and cancer. They are functionally connected, forming the basis necessary for steatosis progression to NASH and further progression to hepatocellular carcinoma (HCC). We also show that five of the identified genes have genome alterations present in HCC patients. The patients with these genes associated to genome alteration are associated with a poor prognosis. In conclusion, using an integrative literature- and data-mining approach, we have identified and described a canonical pathway underlying progression of NASH. Other parameters (e.g., polymorphisms) can be added to this pathway that also contribute to the progression of the disease to cancer. This work improved our understanding of the molecular basis of NASH progression and will help to develop new therapeutic approaches.
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Affiliation(s)
| | - Franck Chiappini
- Laboratoire Croissance, Régénération, Réparation et Régénération Tissulaires (CRRET)/ EAC CNRS 7149, Univ Paris-Est Créteil (UPEC), F-94010 Créteil, France
- Correspondence: ; Tel.: +33-(0)1-45177080; Fax: +33-(0)1-45171816
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1666
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Integrative Analysis Reveals Comprehensive Altered Metabolic Genes Linking with Tumor Epigenetics Modification in Pan-Cancer. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6706354. [PMID: 31828117 PMCID: PMC6881592 DOI: 10.1155/2019/6706354] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/21/2019] [Accepted: 10/01/2019] [Indexed: 02/06/2023]
Abstract
Background Cancer cells undergo various rewiring of metabolism and dysfunction of epigenetic modification to support their biosynthetic needs. Although the major features of metabolic reprogramming have been elucidated, the global metabolic genes linking epigenetics were overlooked in pan-cancer. Objectives Identifying the critical metabolic signatures with differential expressions which contributes to the epigenetic alternations across cancer types is an urgent issue for providing the potential targets for cancer therapy. Method The differential gene expression and DNA methylation were analyzed by using the 5726 samples data from the Cancer Genome Atlas (TCGA). Results Firstly, we analyzed the differential expression of metabolic genes and found that cancer underwent overall metabolism reprogramming, which exhibited a similar expression trend with the data from the Gene Expression Omnibus (GEO) database. Secondly, the regulatory network of histone acetylation and DNA methylation according to altered expression of metabolism genes was summarized in our results. Then, the survival analysis showed that high expression of DNMT3B had a poorer overall survival in 5 cancer types. Integrative altered methylation and expression revealed specific genes influenced by DNMT3B through DNA methylation across cancers. These genes do not overlap across various cancer types and are involved in different function annotations depending on the tissues, which indicated DNMT3B might influence DNA methylation in tissue specificity. Conclusions Our research clarifies some key metabolic genes, ACLY, SLC2A1, KAT2A, and DNMT3B, which are most disordered and indirectly contribute to the dysfunction of histone acetylation and DNA methylation in cancer. We also found some potential genes in different cancer types influenced by DNMT3B. Our study highlights possible epigenetic disorders resulting from the deregulation of metabolic genes in pan-cancer and provides potential therapy in the clinical treatment of human cancer.
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1667
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Braicu C, Gulei D, Raduly L, Harangus A, Rusu A, Berindan-Neagoe I. Altered expression of miR-181 affects cell fate and targets drug resistance-related mechanisms. Mol Aspects Med 2019; 70:90-105. [PMID: 31703947 DOI: 10.1016/j.mam.2019.10.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/22/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) are non-coding transcripts which regulate genetic and epigenetic events by interfering with mRNA translation. miRNAs are involved in regulation of cell fate due to their ability of interfering with physiological or pathological processes. In this review paper, we evaluate the role of miR-181 family members as prognostic or diagnostic markers or therapeutic targets in malignant pathologies in connection with the main hallmarks of cancer that are modulated by the family. Also, we take over the dual role of this family in dependency with the tumour suppressor and oncogenic features presented in cell and cancer type specific manner. Restoration of the altered expression levels contributes to the activation of cell death pathways or to a reduction in the invasion and migration mechanism; moreover, the mechanism of drug resistance is also modulated by miR-181 sequences with important applications in therapeutic strategies for malignant cells sensitisation. Overall, the main miR-181 family regulatory mechanisms are presented in a cancer specific context, emphasizing the possible clinical application of this family in terms of novel diagnosis and therapy approaches.
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Affiliation(s)
- Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.
| | - Diana Gulei
- MedFuture Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Lajos Raduly
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Antonia Harangus
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania; "Leon Daniello" Pneumophtisiology Clinic, 6 Bogdan Petriceicu Hasdeu Street, 400332, Cluj-Napoca, Romania.
| | | | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania; MedFuture Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Cluj-Napoca, Romania.
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1668
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He J, Wink S, de Bont H, Le Dévédec S, Zhang Y, van de Water B. FRET biosensor-based kinase inhibitor screen for ERK and AKT activity reveals differential kinase dependencies for proliferation in TNBC cells. Biochem Pharmacol 2019; 169:113640. [DOI: 10.1016/j.bcp.2019.113640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/13/2019] [Indexed: 11/26/2022]
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1669
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Reiter JG, Baretti M, Gerold JM, Makohon-Moore AP, Daud A, Iacobuzio-Donahue CA, Azad NS, Kinzler KW, Nowak MA, Vogelstein B. An analysis of genetic heterogeneity in untreated cancers. Nat Rev Cancer 2019; 19:639-650. [PMID: 31455892 PMCID: PMC6816333 DOI: 10.1038/s41568-019-0185-x] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/23/2019] [Indexed: 12/12/2022]
Abstract
Genetic intratumoural heterogeneity is a natural consequence of imperfect DNA replication. Any two randomly selected cells, whether normal or cancerous, are therefore genetically different. Here, we review the different forms of genetic heterogeneity in cancer and re-analyse the extent of genetic heterogeneity within seven types of untreated epithelial cancers, with particular regard to its clinical relevance. We find that the homogeneity of predicted functional mutations in driver genes is the rule rather than the exception. In primary tumours with multiple samples, 97% of driver-gene mutations in 38 patients were homogeneous. Moreover, among metastases from the same primary tumour, 100% of the driver mutations in 17 patients were homogeneous. With a single biopsy of a primary tumour in 14 patients, the likelihood of missing a functional driver-gene mutation that was present in all metastases was 2.6%. Furthermore, all functional driver-gene mutations detected in these 14 primary tumours were present among all their metastases. Finally, we found that individual metastatic lesions responded concordantly to targeted therapies in 91% of 44 patients. These analyses indicate that the cells within the primary tumours that gave rise to metastases are genetically homogeneous with respect to functional driver-gene mutations, and we suggest that future efforts to develop combination therapies have the potential to be curative.
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Affiliation(s)
- Johannes G Reiter
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, USA.
| | - Marina Baretti
- The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jeffrey M Gerold
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA, USA
| | - Alvin P Makohon-Moore
- The David M. Rubenstein Center for Pancreatic Cancer Research, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adil Daud
- University of California, San Francisco, San Francisco, CA, USA
| | - Christine A Iacobuzio-Donahue
- The David M. Rubenstein Center for Pancreatic Cancer Research, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nilofer S Azad
- The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth W Kinzler
- The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Martin A Nowak
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Mathematics, Harvard University, Cambridge, MA, USA.
| | - Bert Vogelstein
- The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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1670
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Zhou CY, Gong LY, Liao R, Weng NN, Feng YY, Dong YP, Zhu H, Zhao YQ, Zhang YY, Zhu Q, Han SX. Evaluation of the target genes of arsenic trioxide in pancreatic cancer by bioinformatics analysis. Oncol Lett 2019; 18:5163-5172. [PMID: 31612027 PMCID: PMC6781497 DOI: 10.3892/ol.2019.10889] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/07/2019] [Indexed: 02/05/2023] Open
Abstract
The aim of the present study was to evaluate the potential network of arsenic trioxide (ATO) target genes in pancreatic cancer. The DrugBank, STITCH, cBioPortal, Kaplan-Meier plotter and Oncomine websites were used to analyze the association of ATO and its target genes with pancreatic cancer. Initially, 19 ATO target genes were identified, along with their associated protein-protein interaction networks and Kyoto Encyclopedia of Genes and Genomes pathways. ATO was found to be associated with multiple types of cancer, and the most common solid cancer was pancreatic cancer. A total of 6 ATO target genes (namely AKT1, CCND1, CDKN2A, IKBKB, MAPK1 and MAPK3) were found to be associated with pancreatic cancer. Next, the mutation information of the 6 ATO target genes in pancreatic cancer was collected. A total of 20 ATO interacting genes were identified, which were mainly involved in hepatitis B, prostate cancer, pathways in cancer, glioma and chronic myeloid leukemia. Finally, the genes CCND1 and MAPK1 were detected to be prognostic factors in patients with pancreatic cancer. In conclusion, bioinformatics analysis may help elucidate the molecular mechanisms underlying the involvement of ATO in pancreatic cancer, enabling more effective treatment of this disease.
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Affiliation(s)
- Cong-Ya Zhou
- Department of Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Liu-Yun Gong
- Department of Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Rong Liao
- Department of Abdominal Oncology, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ning-Na Weng
- Department of Abdominal Oncology, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yao-Yue Feng
- Department of Abdominal Oncology, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yi-Ping Dong
- Department of Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Hong Zhu
- Department of Abdominal Oncology, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ya-Qin Zhao
- Department of Abdominal Oncology, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yuan-Yuan Zhang
- Department of Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Qing Zhu
- Department of Abdominal Oncology, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Su-Xia Han
- Department of Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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1671
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Kanev GK, de Graaf C, de Esch IJP, Leurs R, Würdinger T, Westerman BA, Kooistra AJ. The Landscape of Atypical and Eukaryotic Protein Kinases. Trends Pharmacol Sci 2019; 40:818-832. [PMID: 31677919 DOI: 10.1016/j.tips.2019.09.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 02/07/2023]
Abstract
Kinases are attractive anticancer targets due to their central role in the growth, survival, and therapy resistance of tumor cells. This review explores the two primary kinase classes, the eukaryotic protein kinases (ePKs) and the atypical protein kinases (aPKs), and provides a structure-centered comparison of their sequences, structures, hydrophobic spines, mutation and SNP hotspots, and inhibitor interaction patterns. Despite the limited sequence similarity between these two classes, atypical kinases commonly share the archetypical kinase fold but lack conserved eukaryotic kinase motifs and possess altered hydrophobic spines. Furthermore, atypical kinase inhibitors explore only a limited number of binding modes both inside and outside the orthosteric binding site. The distribution of genetic variations in both classes shows multiple ways they can interfere with kinase inhibitor binding. This multilayered review provides a research framework bridging the eukaryotic and atypical kinase classes.
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Affiliation(s)
- Georgi K Kanev
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands; Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Rob Leurs
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Thomas Würdinger
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Bart A Westerman
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
| | - Albert J Kooistra
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.
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1672
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Wen Y, Zhang S, Yang J, Guo D. Identification of driver genes regulating immune cell infiltration in cervical cancer by multiple omics integration. Biomed Pharmacother 2019; 120:109546. [PMID: 31675687 DOI: 10.1016/j.biopha.2019.109546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 12/24/2022] Open
Abstract
Cervical cancer (CC) is one of the most common cancers in women. However, copy number alteration (CNA)-driven dysregulated genes and their functions in CC are still rarely investigated. In the present study, we conducted integrative analysis of CNA and gene expression data from The Cancer Genome Atlas (TCGA) cervical cancer to identify dysregulated genes triggered by CNAs. The integration of copy number status and RNA expression revealed 763 amplified and 1,391 deleted genes significantly dysregulated by the CNAs (P-value < 1e-8). Among these CNA genes, five driver genes, including PI3KCA, PI3KCB, DVL3, WWTR1, and ERBB2, exhibited a strong association with immune cell infiltration, suggesting that the pathways that they participate in may be involved in regulating immune cell infiltration. Moreover, we also observed that the genes of immunotherapeutic targets were abundantly expressed in the wild-type samples, suggesting that immunotherapy based on these immunotherapeutic targets may be applied to wild-type samples. In addition, the two CNA driver genes, DVL3 and ERBB2, might be sensitive and resistant biomarkers for examining the tumor's response to chemoradiotherapy, respectively. Particularly, the expression of ERBB2 was also observed to be higher in responders of chemotherapy than non-responders. Furthermore, a subset of CNA genes was identified to predict the prognosis of cervical cancer. In summary, our systematic data analysis of these CNA genes not only improved our understanding of the veiled mechanism behind immune cell infiltration, but also provided the potential clinical application of these CNA genes in cervical cancer.
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Affiliation(s)
- Yanqi Wen
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, 430060, China
| | - Silin Zhang
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, 430060, China
| | - Jing Yang
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, 430060, China.
| | - Duanying Guo
- Longgang District People's Hospital of Shenzhen, Shenzhen, China.
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1673
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Hallin J, Engstrom LD, Hargis L, Calinisan A, Aranda R, Briere DM, Sudhakar N, Bowcut V, Baer BR, Ballard JA, Burkard MR, Fell JB, Fischer JP, Vigers GP, Xue Y, Gatto S, Fernandez-Banet J, Pavlicek A, Velastagui K, Chao RC, Barton J, Pierobon M, Baldelli E, Patricoin EF, Cassidy DP, Marx MA, Rybkin II, Johnson ML, Ou SHI, Lito P, Papadopoulos KP, Jänne PA, Olson P, Christensen JG. The KRAS G12C Inhibitor MRTX849 Provides Insight toward Therapeutic Susceptibility of KRAS-Mutant Cancers in Mouse Models and Patients. Cancer Discov 2019; 10:54-71. [PMID: 31658955 DOI: 10.1158/2159-8290.cd-19-1167] [Citation(s) in RCA: 768] [Impact Index Per Article: 153.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 10/18/2019] [Accepted: 10/18/2019] [Indexed: 11/16/2022]
Abstract
Despite decades of research, efforts to directly target KRAS have been challenging. MRTX849 was identified as a potent, selective, and covalent KRASG12C inhibitor that exhibits favorable drug-like properties, selectively modifies mutant cysteine 12 in GDP-bound KRASG12C, and inhibits KRAS-dependent signaling. MRTX849 demonstrated pronounced tumor regression in 17 of 26 (65%) KRASG12C-positive cell line- and patient-derived xenograft models from multiple tumor types, and objective responses have been observed in patients with KRASG12C-positive lung and colon adenocarcinomas. Comprehensive pharmacodynamic and pharmacogenomic profiling in sensitive and partially resistant nonclinical models identified mechanisms implicated in limiting antitumor activity including KRAS nucleotide cycling and pathways that induce feedback reactivation and/or bypass KRAS dependence. These factors included activation of receptor tyrosine kinases (RTK), bypass of KRAS dependence, and genetic dysregulation of cell cycle. Combinations of MRTX849 with agents that target RTKs, mTOR, or cell cycle demonstrated enhanced response and marked tumor regression in several tumor models, including MRTX849-refractory models. SIGNIFICANCE: The discovery of MRTX849 provides a long-awaited opportunity to selectively target KRASG12C in patients. The in-depth characterization of MRTX849 activity, elucidation of response and resistance mechanisms, and identification of effective combinations provide new insight toward KRAS dependence and the rational development of this class of agents.See related commentary by Klempner and Hata, p. 20.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Jill Hallin
- Mirati Therapeutics, Inc., San Diego, California
| | | | | | | | - Ruth Aranda
- Mirati Therapeutics, Inc., San Diego, California
| | | | | | | | | | | | | | | | | | | | - Yaohua Xue
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sole Gatto
- Monoceros Biosystems LLC, San Diego, California
| | | | | | | | | | | | | | | | | | | | | | | | - Melissa L Johnson
- Sarah Cannon Research Institute Tennessee Oncology, Nashville, Tennessee
| | - Sai-Hong Ignatius Ou
- University of California, Irvine, Chao Family Comprehensive Cancer Center, Orange, California
| | - Piro Lito
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Pasi A Jänne
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Peter Olson
- Mirati Therapeutics, Inc., San Diego, California
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1674
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Chokchaitaweesuk C, Kobayashi T, Izumikawa T, Itano N. Enhanced hexosamine metabolism drives metabolic and signaling networks involving hyaluronan production and O-GlcNAcylation to exacerbate breast cancer. Cell Death Dis 2019; 10:803. [PMID: 31645543 PMCID: PMC6811536 DOI: 10.1038/s41419-019-2034-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 09/20/2019] [Accepted: 10/04/2019] [Indexed: 02/08/2023]
Abstract
The hexosamine biosynthetic pathway (HBP) metabolically regulates dynamic cellular events by linking nutrient availability to numerous signaling networks. Significant alterations in the HBP are often associated with cancer pathogenesis. In this study, we investigated the molecular events underlying cancer pathogenesis associated with enhanced HBP flux. Multidimensional analysis of microarray datasets demonstrated up-regulation of genes encoding HBP enzymes in clinical breast cancers and revealed that co-expression of hyaluronan synthase 2 (HAS2) and glutamine:fructose-6-phosphate amidotransferase (GFAT), a rate-limiting enzyme of the HBP, was strongly correlated with a poor prognosis in advanced cancer patients. Consistently with the clinical data, comparative analyses of distinct breast cancer mouse models demonstrated enhancement of the HBP gene expression in primary carcinoma cells, with elevation of Has2 expression and hyaluronan production in aggressive breast cancer cells. The silencing of GFAT reduced CD44high/CD24low cancer stem cell (CSC)-like subpopulations, aldehyde dehydrogenase-positive cell populations, and mammosphere size, which were further diminished by gene targeting of Has2. Has2 gene disruption reduced the in vivo growth of aggressive cancer cells and attenuated pro-tumorigenic Akt/GSK3β/β-catenin signaling and cisplatin resistance. Overall protein O-GlcNAcylation was also elevated in association with HBP enhancement in aggressive cancer cells, and the modification exhibited overlapping but distinct roles from the hyaluronan signal in the regulation of CSC-like features. The current data therefore demonstrate that enhanced hexosamine metabolism drives pro-tumorigenic signaling pathways involving hyaluronan and O-GlcNAcylation in aggressive breast cancer.
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Affiliation(s)
| | - Takashi Kobayashi
- Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Tomomi Izumikawa
- Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
- College of Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Ritsumeikan University, Shiga, 525-8577, Japan
| | - Naoki Itano
- Division of Life Sciences, Kyoto Sangyo University Graduate School, Kyoto, 603-8555, Japan.
- Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan.
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1675
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Pfaff P, Samarasinghe KTG, Crews CM, Carreira EM. Reversible Spatiotemporal Control of Induced Protein Degradation by Bistable PhotoPROTACs. ACS CENTRAL SCIENCE 2019; 5:1682-1690. [PMID: 31660436 PMCID: PMC6813558 DOI: 10.1021/acscentsci.9b00713] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 05/09/2023]
Abstract
Off-tissue effects are persistent issues of modern inhibition-based therapies. By merging the strategies of photopharmacology and small-molecule degraders, we introduce a novel concept for persistent spatiotemporal control of induced protein degradation that potentially prevents off-tissue toxicity. Building on the successful principle of bifunctional all-small-molecule Proteolysis Targeting Chimeras (PROTACs), we designed photoswitchable PROTACs (photoPROTACs) by including ortho-F4-azobenzene linkers between both warhead ligands. This highly bistable yet photoswitchable structural component leads to reversible control over the topological distance between both ligands. The azo-cis-isomer is observed to be inactive because the distance defined by the linker is prohibitively short to permit complex formation between the protein binding partners. By contrast, the azo-trans-isomer is active since it can engage both protein partners to form the necessary and productive ternary complex. Importantly, due to the bistable nature of the ortho-F4-azobenzene moiety employed, the photostationary state of the photoPROTAC is persistent, with no need for continuous irradiation. This technique offers reversible on/off switching of protein degradation that is compatible with an intracellular environment and, therefore, could be useful in experimental exploration of biological signaling pathways-such as those crucial for oncogenic signal transduction. Additionally, this strategy may be suitable for therapeutic intervention to address a variety of diseases. By enabling reversible activation and deactivation of protein degradation, photoPROTACs offer advantages over conventional photocaging strategies that irreversibly release active agents.
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Affiliation(s)
- Patrick Pfaff
- Department
of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Kusal T. G. Samarasinghe
- Department
of Molecular, Cell, and Developmental Biology, Yale University, 260
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Department
of Molecular, Cell, and Developmental Biology, Yale University, 260
Whitney Avenue, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Department
of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Erick M. Carreira
- Department
of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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1676
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Interval breast cancer is associated with other types of tumors. Nat Commun 2019; 10:4648. [PMID: 31641120 PMCID: PMC6805891 DOI: 10.1038/s41467-019-12652-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 09/20/2019] [Indexed: 12/23/2022] Open
Abstract
Breast cancer (BC) patients diagnosed between two screenings (interval cancers) are more likely than screen-detected patients to carry rare deleterious mutations in cancer genes potentially leading to increased risk for other non-breast cancer (non-BC) tumors. In this study, we include 14,846 women diagnosed with BC of which 1,772 are interval and 13,074 screen-detected. Compared to women with screen-detected cancers, interval breast cancer patients are more likely to have a non-BC tumor before (Odds ratio (OR): 1.43 [1.19–1.70], P = 9.4 x 10−5) and after (OR: 1.28 [1.14–1.44], P = 4.70 x 10−5) breast cancer diagnosis, are more likely to report a family history of non-BC tumors and have a lower genetic risk score based on common variants for non-BC tumors. In conclusion, interval breast cancer is associated with other tumors and common cancer variants are unlikely to be responsible for this association. These findings could have implications for future screening and prevention programs. Interval cancer patients are more likely to carry rare gene mutations than screen-detected breast cancer patients. Here, the authors report that interval cancer patients are more likely cancer survivors and are at a greater risk of developing other non-breast tumors.
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1677
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Tutuncuoglu B, Krogan NJ. Mapping genetic interactions in cancer: a road to rational combination therapies. Genome Med 2019; 11:62. [PMID: 31640753 PMCID: PMC6805649 DOI: 10.1186/s13073-019-0680-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/16/2019] [Indexed: 01/08/2023] Open
Abstract
The discovery of synthetic lethal interactions between poly (ADP-ribose) polymerase (PARP) inhibitors and BRCA genes, which are involved in homologous recombination, led to the approval of PARP inhibition as a monotherapy for patients with BRCA1/2-mutated breast or ovarian cancer. Studies following the initial observation of synthetic lethality demonstrated that the reach of PARP inhibitors is well beyond just BRCA1/2 mutants. Insights into the mechanisms of action of anticancer drugs are fundamental for the development of targeted monotherapies or rational combination treatments that will synergize to promote cancer cell death and overcome mechanisms of resistance. The development of targeted therapeutic agents is premised on mapping the physical and functional dependencies of mutated genes in cancer. An important part of this effort is the systematic screening of genetic interactions in a variety of cancer types. Until recently, genetic-interaction screens have relied either on the pairwise perturbations of two genes or on the perturbation of genes of interest combined with inhibition by commonly used anticancer drugs. Here, we summarize recent advances in mapping genetic interactions using targeted, genome-wide, and high-throughput genetic screens, and we discuss the therapeutic insights obtained through such screens. We further focus on factors that should be considered in order to develop a robust analysis pipeline. Finally, we discuss the integration of functional interaction data with orthogonal methods and suggest that such approaches will increase the reach of genetic-interaction screens for the development of rational combination therapies.
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Affiliation(s)
- Beril Tutuncuoglu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 16th Street, Mission Bay Campus, San Francisco, CA, 94158-2140, USA.,The J. David Gladstone Institutes, Owens Street, San Francisco, CA, 94158, USA.,Quantitative Biosciences Institute, University of California, San Francisco, 4th Street, San Francisco, CA, 94158, USA.,Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 16th Street, Mission Bay Campus, San Francisco, CA, 94158-2140, USA. .,The J. David Gladstone Institutes, Owens Street, San Francisco, CA, 94158, USA. .,Quantitative Biosciences Institute, University of California, San Francisco, 4th Street, San Francisco, CA, 94158, USA. .,Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA.
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1678
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Braicu C, Buse M, Busuioc C, Drula R, Gulei D, Raduly L, Rusu A, Irimie A, Atanasov AG, Slaby O, Ionescu C, Berindan-Neagoe I. A Comprehensive Review on MAPK: A Promising Therapeutic Target in Cancer. Cancers (Basel) 2019; 11:cancers11101618. [PMID: 31652660 PMCID: PMC6827047 DOI: 10.3390/cancers11101618] [Citation(s) in RCA: 504] [Impact Index Per Article: 100.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/13/2019] [Accepted: 10/16/2019] [Indexed: 02/07/2023] Open
Abstract
The mitogen-activated protein kinase (MAPK) pathway is an important bridge in the switch from extracellular signals to intracellular responses. Alterations of signaling cascades are found in various diseases, including cancer, as a result of genetic and epigenetic changes. Numerous studies focused on both the homeostatic and the pathologic conduct of MAPK signaling; however, there is still much to be deciphered in terms of regulation and action models in both preclinical and clinical research. MAPK has implications in the response to cancer therapy, particularly the activation of the compensatory pathways in response to experimental MAPK inhibition. The present paper discusses new insights into MAPK as a complex cell signaling pathway with roles in the sustenance of cellular normal conduit, response to cancer therapy, and activation of compensatory pathways. Unfortunately, most MAPK inhibitors trigger resistance due to the activation of compensatory feed-back loops in tumor cells and tumor microenvironment components. Therefore, novel combinatorial therapies have to be implemented for cancer management in order to restrict the possibility of alternative pathway activation, as a perspective for developing novel therapies based on integration in translational studies.
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Affiliation(s)
- Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Mihail Buse
- MEDFUTURE-Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Constantin Busuioc
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Rares Drula
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Diana Gulei
- MEDFUTURE-Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Lajos Raduly
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | | | - Alexandru Irimie
- Department of Surgery, The Oncology Institute "Prof. Dr. Ion Chiricuta", 40015 Cluj-Napoca, Romania.
- Department of Surgical Oncology and Gynecological Oncology, Iuliu Hatieganu University of Medicine and Pharmacy, 40015 Cluj-Napoca, Romania.
| | - Atanas G Atanasov
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzebiec, 05-552 Magdalenka, Poland.
- Institute of Neurobiology, Bulgarian Academy of Sciences, 23 Acad. G. Bonchev str., 1113 Sofia, Bulgaria.
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, 601 77 Brno, Czech Republic.
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, 601 77 Brno, Czech Republic.
| | - Calin Ionescu
- th Surgical Department, Municipal Hospital, 400139, Cluj-Napoca, Romania.
- Department of Surgery, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- MEDFUTURE-Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Department of Functional Genomics and Experimental Pathology, The Oncology Institute Prof. Dr. Ion Chiricuta, Republicii 34 Street, 400015 Cluj-Napoca, Romania.
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1679
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Yun MR, Choi HM, Lee YW, Joo HS, Park CW, Choi JW, Kim DH, Kang HN, Pyo KH, Shin EJ, Shim HS, Soo RA, Yang JCH, Lee SS, Chang H, Kim MH, Hong MH, Kim HR, Cho BC. Targeting YAP to overcome acquired resistance to ALK inhibitors in ALK-rearranged lung cancer. EMBO Mol Med 2019; 11:e10581. [PMID: 31633304 PMCID: PMC6895608 DOI: 10.15252/emmm.201910581] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022] Open
Abstract
Clinical benefit of ALK tyrosine kinase inhibitors (ALK‐TKIs) in ALK‐rearranged lung cancer has been limited by the inevitable development of acquired resistance, and bypass‐molecular resistance mechanisms remain poorly understood. We investigated a novel therapeutic target through screening FDA‐approved drugs in ALK‐TKI‐resistant models. Cerivastatin, the rate‐limiting enzyme inhibitor of the mevalonate pathway, showed anti‐cancer activity against ALK‐TKI resistance in vitro/in vivo, accompanied by cytoplasmic retention and subsequent inactivation of transcriptional co‐regulator YAP. The marked induction of YAP‐targeted oncogenes (EGFR, AXL, CYR61, and TGFβR2) in resistant cells was abolished by cerivastatin. YAP silencing suppressed tumor growth in resistant cells, patient‐derived xenografts, and EML4‐ALK transgenic mice, whereas YAP overexpression decreased the responsiveness of parental cells to ALK inhibitor. In matched patient samples before/after ALK inhibitor treatment, nuclear accumulation of YAP was mainly detected in post‐treatment samples. High expression of YAP in pretreatment samples was correlated with poor response to ALK‐TKIs. Our findings highlight a crucial role of YAP in ALK‐TKI resistance and provide a rationale for targeting YAP as a potential treatment option for ALK‐rearranged patients with acquired resistance to ALK inhibitors.
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Affiliation(s)
- Mi Ran Yun
- JEUK Institute for Cancer Research, JEUK Co., Ltd., Gumi-City, Korea.,Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Hun Mi Choi
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - You Won Lee
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Hyeong Seok Joo
- JEUK Institute for Cancer Research, JEUK Co., Ltd., Gumi-City, Korea
| | - Chae Won Park
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Woo Choi
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Korea.,Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Dong Hwi Kim
- JEUK Institute for Cancer Research, JEUK Co., Ltd., Gumi-City, Korea
| | - Han Na Kang
- JEUK Institute for Cancer Research, JEUK Co., Ltd., Gumi-City, Korea.,Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Kyoung-Ho Pyo
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Joo Shin
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Ross A Soo
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore
| | - James Chih-Hsin Yang
- Graduate Institute of Oncology, National Taiwan University, Taipei, Taiwan.,Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Sung Sook Lee
- Department of Hematology-Oncology, Inje University Haeundae Paik Hospital, Busan, Korea
| | - Hyun Chang
- International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea
| | - Min Hwan Kim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Min Hee Hong
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Hye Ryun Kim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Byoung Chul Cho
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
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1680
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Feng L, Li J, Li F, Li H, Bei S, Zhang X, Yang Z. Long noncoding RNA VCAN-AS1 contributes to the progression of gastric cancer via regulating p53 expression. J Cell Physiol 2019; 235:4388-4398. [PMID: 31637706 DOI: 10.1002/jcp.29315] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 09/30/2019] [Indexed: 12/30/2022]
Abstract
Gastric cancer (GC) is one of the most frequent malignancies worldwide. Long noncoding RNAs (lncRNAs) are found to be largely implicated in various cancers, including GC. However, the function of lncRNA VCAN antisense RNA 1 (VCAN-AS1) in GC remains unclear. Herein, we observed a low level of VCAN-AS1 in normal gastric tissues through NCBI and UCSC, and that VCAN-AS1 upregulation in GC tissues was related to poor prognosis by TCGA. Furthermore, VCAN-AS1 was found markedly enhanced in GC tissues and cell lines, while its upregulation was related with clinical outcomes of GC patients. Besides this, silencing VCAN-AS1 represses cell proliferation, migration, and invasion but enhances apoptosis. More important, we discovered that VCAN-AS1 expression was negatively correlated with wild-type p53 levels in GC tissues and that p53 was negatively modulated by VCAN-AS1 in GC cells. Furthermore, p53 suppression reversed the repression of VCAN-AS1 silence on the biological processes of AGS cells. Intriguingly, we identified that both VCAN-AS1 and TP53 can bind with eIF4A3, one of the core proteins in the exon junction complex. Also, we confirmed that VCAN-AS1 negatively regulates TP53 expression by competitively binding with eIF4A3. Our findings disclosed that VCAN-AS1 contributes to GC progression through interacting with eIF4A3 to downregulate TP53 expression, indicating that VCAN-AS1 is a novel therapeutic strategy for GC treatment.
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Affiliation(s)
- Li Feng
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Jian Li
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Fan Li
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Huanqin Li
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Songhua Bei
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Xiaohong Zhang
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Zhen Yang
- Surgical Department, Minhang Hospital, Fudan University, Shanghai, China
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1681
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Zhang X, Wang Y. Identification of hub genes and key pathways associated with the progression of gynecological cancer. Oncol Lett 2019; 18:6516-6524. [PMID: 31788113 PMCID: PMC6865827 DOI: 10.3892/ol.2019.11004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 06/05/2019] [Indexed: 12/20/2022] Open
Abstract
Gynecological cancer is the leading cause of cancer mortality in women. However, the mechanisms underlying gynecological cancer progression have remained largely unclear. In the present study, 799 dysregulated genes were identified in ovarian serous cystadenocarcinoma (OV), 488 dysregulated genes in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), and 621 dysregulated genes in uterine corpus endometrial carcinoma (UCEC). Bioinformatics analysis revealed that mRNA splicing and cell proliferation-associated biological processes served important roles in OV progression. Metabolism-associated biological processes played important roles in CESC progression, and protein phosphorylation and small GTPase-mediated signal transduction served important roles in UCEC progression. The present study also constructed OV, CESC and UCEC progression-associated protein-protein interaction networks to reveal the associations among these genes. Furthermore, Kaplan-Meier curve analysis showed that progression-related genes were associated with the duration of overall survival. Finally, NARS2 and TPT1 in OV, SMYD2, EGLN1, TNFRSF10D, FUT11, SYTL3, MMP8 and EREG in CESC, and SLC5A1, TXN, KDM4B, TXNDC11, HSDL2, COX16, MGAT4A, DAGLA, ELOVL7, THRB and PCOLCE2 in UCEC were identified as hub genes in cancer progression. Therefore, this study may assist in the identification of novel mechanisms underlying cancer progression and new biomarkers for gynecological cancer prognosis and therapy.
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Affiliation(s)
- Xi Zhang
- Department of Gynecology, Changning Maternity and Infant Health Hospital, Shanghai 200051, P.R. China
| | - Yudong Wang
- Department of Gynecology, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
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1682
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Emergence of allosteric drug-resistance mutations: new challenges for allosteric drug discovery. Drug Discov Today 2019; 25:177-184. [PMID: 31634592 DOI: 10.1016/j.drudis.2019.10.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/28/2019] [Accepted: 10/11/2019] [Indexed: 01/31/2023]
Abstract
Allosteric drugs have several significant advantages over traditional orthosteric drugs, encompassing higher selectivity and lower toxicity. Although allosteric drugs have potential advantages as therapeutic agents to treat human diseases, allosteric drug-resistance mutations still occur, rendering these drugs ineffective. Here, we review the emergence of allosteric drug-resistance mutations with an emphasis on examples covering clinically important therapeutic targets, including Breakpoint cluster region-Abelson tyrosine kinase (Bcr-Abl), Akt kinase [also called Protein Kinase B (PKB)], isocitrate dehydrogenase (IDH), MAPK/ERK kinase (MEK), and SRC homology 2 domain-containing phosphatase 2 (SHP2). We also discuss challenges associated with tackling allosteric drug resistance and the possible strategies to overcome this issue.
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1683
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Qiao K, Ning S, Wan L, Wu H, Wang Q, Zhang X, Xu S, Pang D. LINC00673 is activated by YY1 and promotes the proliferation of breast cancer cells via the miR-515-5p/MARK4/Hippo signaling pathway. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:418. [PMID: 31623640 PMCID: PMC6796384 DOI: 10.1186/s13046-019-1421-7] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023]
Abstract
Background An increasing number of studies have shown that long noncoding RNAs (lncRNAs) play essential roles in tumor initiation and progression. LncRNAs act as tumor promoters or suppressors by targeting specific genes via epigenetic modifications and competing endogenous RNA (ceRNA) mechanisms. In this study, we explored the function and detailed mechanisms of long intergenic nonprotein coding RNA 673 (LINC00673) in breast cancer progression. Methods Quantitative real-time PCR (qRT-PCR) was used to examine the expression of LINC00673 in breast cancer tissues and in adjacent normal tissues. Gain-of-function and loss-of function experiments were conducted to investigate the biological functions of LINC00673 in vitro and in vivo. We also explored the potential role of LINC00673 as a therapeutic target using antisense oligonucleotide (ASO) in vivo. RNA sequencing (RNA-seq), dual-luciferase reporter assays, chromatin immunoprecipitation (ChIP) assay, and rescue experiments were performed to uncover the detailed mechanism of LINC00673 in promoting breast cancer progression. Results In the present study, LINC00673 displayed a trend of remarkably increased expression in breast cancer tissues and was associated with poor prognosis in breast cancer patients. Importantly, LINC00673 depletion inhibited breast cancer cell proliferation by inhibiting the cell cycle and increasing apoptosis. Furthermore, ASO therapy targeting LINC00673 substantially suppressed breast cancer cell proliferation in vivo. Mechanistically, LINC00673 was found to act as a ceRNA by sponging miR-515-5p to regulate MARK4 expression, thus inhibiting the Hippo signaling pathway. Finally, ChIP assay showed that the transcription factor Yin Yang 1 (YY1) could bind to the LINC00673 promoter and increase its transcription in cis. Conclusions YY1-activated LINC00673 may exert an oncogenic function by acting as a sponge for miR-515-5p to upregulate the MARK4 and then inhibit Hippo signaling pathway, and may serve as a potential therapeutic target.
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Affiliation(s)
- Kun Qiao
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150086, China
| | - Shipeng Ning
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150086, China
| | - Lin Wan
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150086, China
| | - Hao Wu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150086, China
| | - Qin Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150086, China
| | - Xingda Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150086, China
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150086, China.
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150086, China. .,Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin, 150086, China.
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1684
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Baloghova N, Lidak T, Cermak L. Ubiquitin Ligases Involved in the Regulation of Wnt, TGF-β, and Notch Signaling Pathways and Their Roles in Mouse Development and Homeostasis. Genes (Basel) 2019; 10:genes10100815. [PMID: 31623112 PMCID: PMC6826584 DOI: 10.3390/genes10100815] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 10/02/2019] [Accepted: 10/13/2019] [Indexed: 12/20/2022] Open
Abstract
The Wnt, TGF-β, and Notch signaling pathways are essential for the regulation of cellular polarity, differentiation, proliferation, and migration. Differential activation and mutual crosstalk of these pathways during animal development are crucial instructive forces in the initiation of the body axis and the development of organs and tissues. Due to the ability to initiate cell proliferation, these pathways are vulnerable to somatic mutations selectively producing cells, which ultimately slip through cellular and organismal checkpoints and develop into cancer. The architecture of the Wnt, TGF-β, and Notch signaling pathways is simple. The transmembrane receptor, activated by the extracellular stimulus, induces nuclear translocation of the transcription factor, which subsequently changes the expression of target genes. Nevertheless, these pathways are regulated by a myriad of factors involved in various feedback mechanisms or crosstalk. The most prominent group of regulators is the ubiquitin-proteasome system (UPS). To open the door to UPS-based therapeutic manipulations, a thorough understanding of these regulations at a molecular level and rigorous confirmation in vivo are required. In this quest, mouse models are exceptional and, thanks to the progress in genetic engineering, also an accessible tool. Here, we reviewed the current understanding of how the UPS regulates the Wnt, TGF-β, and Notch pathways and we summarized the knowledge gained from related mouse models.
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Affiliation(s)
- Nikol Baloghova
- Laboratory of Cancer Biology, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 42 Vestec, Czech Republic.
| | - Tomas Lidak
- Laboratory of Cancer Biology, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 42 Vestec, Czech Republic.
| | - Lukas Cermak
- Laboratory of Cancer Biology, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 42 Vestec, Czech Republic.
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1685
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Ahmed F. Integrated Network Analysis Reveals FOXM1 and MYBL2 as Key Regulators of Cell Proliferation in Non-small Cell Lung Cancer. Front Oncol 2019; 9:1011. [PMID: 31681566 PMCID: PMC6804573 DOI: 10.3389/fonc.2019.01011] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/20/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Loss of control on cell division is an important factor for the development of non-small cell lung cancer (NSCLC), however, its molecular mechanism and gene regulatory network are not clearly understood. This study utilized the systems bioinformatics approach to reveal the “driver-network” involve in tumorigenic processes in NSCLC. Methods: A meta-analysis of gene expression data of NSCLC was integrated with protein-protein interaction (PPI) data to construct an NSCLC network. MCODE and iRegulone were used to identify the local clusters and its upstream transcription regulators involve in NSCLC. Pair-wise gene expression correlation was performed using GEPIA. The survival analysis was performed by the Kaplan-Meier plot. Results: This study identified a local “driver-network” with highest MCODE score having 26 up-regulated genes involved in the process of cell proliferation in NSCLC. Interestingly, the “driver-network” is under the regulation of TFs FOXM1 and MYBL2 as well as miRNAs. Furthermore, the overexpression of member genes in “driver-network” and the TFs are associated with poor overall survival (OS) in NSCLC patients. Conclusion: This study identified a local “driver-network” and its upstream regulators responsible for the cell proliferation in NSCLC, which could be promising biomarkers and therapeutic targets for NSCLC treatment.
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Affiliation(s)
- Firoz Ahmed
- Department of Biochemistry, University of Jeddah, Jeddah, Saudi Arabia.,University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah, Saudi Arabia
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1686
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Zhou G, Zhu Z, Li L, Ding J. Resibufogenin inhibits ovarian clear cell carcinoma (OCCC) growth in vivo, and migration of OCCC cells in vitro, by down-regulating the PI3K/AKT and actin cytoskeleton signaling pathways. Am J Transl Res 2019; 11:6290-6303. [PMID: 31737183 PMCID: PMC6834496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 05/31/2019] [Indexed: 06/10/2023]
Abstract
Patients diagnosed with ovarian clear cell carcinoma (OCCC), a rare histologic subtype of ovarian cancer, often experience poor prognosis owing to the chemoresistance of their disease. Thus, there is an urgent need to identify new therapeutic options for these patients. A drug screen of 172 traditional Chinese herbs identified resibufogenin as a compound that inhibited the growth of cultured OCCC cells. Resibufogenin, a bioactive compound originally isolated from toad venom, is used in traditional Chinese medicine to treat several malignancies. The current study examined the impact of resibufogenin treatment on proliferation, migration, and invasion of ES-2 and TOV-21G OCCC cells in vitro. Flow cytometric analyses were employed to determine if resibufogenin affects apoptosis in OCCC cells. Additionally, the ability of resibufogenin to inhibit tumor growth in vivo was evaluated in murine xenograft models. RNA sequencing, quantitative polymerase chain reactions (qPCR), immunohistochemical assays, and western blotting were used to identify and verify cellular pathways potentially targeted by resibufogenin. Resibufogenin inhibited proliferation, migration, and invasion of OCCC cells, and induced apoptosis in them. Resibufogenin also suppressed the growth of xenograft tumors, which consequently showed lower Ki-67 and higher terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) expression. We observed down-regulation of (a) PI3K and AKT in the PI3K/AKT signaling pathway, and (b) MDM2 and myosin in the actin cytoskeleton pathway upon resibufogenin treatment. Thus, resibufogenin inhibits growth and migration of OCCC cells in vitro and suppresses OCCC growth in vivo through the PI3K/AKT and actin cytoskeleton signaling pathways.
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Affiliation(s)
- Guannan Zhou
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan UniversityShanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related DiseasesShanghai 200011, China
| | - Zhongyi Zhu
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan UniversityShanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related DiseasesShanghai 200011, China
| | - Lihua Li
- Department of Cell Biology, Taizhou University1139 Shifu Road Jiaojiang District, Taizhou, China
| | - Jingxin Ding
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan UniversityShanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related DiseasesShanghai 200011, China
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1687
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Ohshima K, Fujiya K, Nagashima T, Ohnami S, Hatakeyama K, Urakami K, Naruoka A, Watanabe Y, Moromizato S, Shimoda Y, Ohnami S, Serizawa M, Akiyama Y, Kusuhara M, Mochizuki T, Sugino T, Shiomi A, Tsubosa Y, Uesaka K, Terashima M, Yamaguchi K. Driver gene alterations and activated signaling pathways toward malignant progression of gastrointestinal stromal tumors. Cancer Sci 2019; 110:3821-3833. [PMID: 31553483 PMCID: PMC6890443 DOI: 10.1111/cas.14202] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/17/2019] [Accepted: 09/22/2019] [Indexed: 12/28/2022] Open
Abstract
Mutually exclusive KIT and PDGFRA mutations are considered to be the earliest events in gastrointestinal stromal tumors (GIST), but insufficient for their malignant progression. Herein, we aimed to identify driver genes and signaling pathways relevant to GIST progression. We investigated genetic profiles of 707 driver genes, including mutations, gene fusions, copy number gain or loss, and gene expression for 65 clinical specimens of surgically dissected GIST, consisting of six metastatic tumors and 59 primary tumors from stomach, small intestine, rectum, and esophagus. Genetic alterations included oncogenic mutations and amplification‐dependent expression enhancement for oncogenes (OG), and loss of heterozygosity (LOH) and expression reduction for tumor suppressor genes (TSG). We assigned activated OG and inactivated TSG to 27 signaling pathways, the activation of which was compared between malignant GIST (metastasis and high‐risk GIST) and less malignant GIST (low‐ and very low‐risk GIST). Integrative molecular profiling indicated that a greater incidence of genetic alterations of driver genes was detected in malignant GIST (96%, 22 of 23) than in less malignant GIST (73%, 24 of 33). Malignant GIST samples groups showed mutations, LOH, and aberrant expression dominantly in driver genes associated with signaling pathways of PI3K (PIK3CA, AKT1, and PTEN) and the cell cycle (RB1, CDK4, and CDKN1B). Additionally, we identified potential PI3K‐related genes, the expression of which was upregulated (SNAI1 and TPX2) or downregulated (BANK1) in malignant GIST. Based on our observations, we propose that inhibition of PI3K pathway signals might potentially be an effective therapeutic strategy against malignant progression of GIST.
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Affiliation(s)
- Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Keiichi Fujiya
- Division of Gastric Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,SRL, Inc., Tokyo, Japan
| | - Sumiko Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Keiichi Hatakeyama
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,Region Resources Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Akane Naruoka
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yuko Watanabe
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Sachi Moromizato
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,SRL, Inc., Tokyo, Japan
| | - Shumpei Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Masakuni Serizawa
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Masatoshi Kusuhara
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,Region Resources Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Tohru Mochizuki
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Akio Shiomi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Yasuhiro Tsubosa
- Division of Esophageal Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Katsuhiko Uesaka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Masanori Terashima
- Division of Gastric Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center Hospital and Research Institute, Shizuoka, Japan
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1688
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Li ZX, Zheng ZQ, Wei ZH, Zhang LL, Li F, Lin L, Liu RQ, Huang XD, Lv JW, Chen FP, He XJ, Guan JL, Kou J, Ma J, Zhou GQ, Sun Y. Comprehensive characterization of the alternative splicing landscape in head and neck squamous cell carcinoma reveals novel events associated with tumorigenesis and the immune microenvironment. Am J Cancer Res 2019; 9:7648-7665. [PMID: 31695792 PMCID: PMC6831462 DOI: 10.7150/thno.36585] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 09/04/2019] [Indexed: 12/18/2022] Open
Abstract
Alternative splicing (AS) has emerged as a key event in tumor development and microenvironment formation. However, comprehensive analysis of AS and its clinical significance in head and neck squamous cell carcinoma (HNSC) is urgently required. Methods: Genome-wide profiling of AS events using RNA-Seq data from The Cancer Genome Atlas (TCGA) program was performed in a cohort of 464 patients with HNSC. Cancer-associated AS events (CASEs) were identified between paired HNSC and adjacent normal tissues and evaluated in functional enrichment analysis. Splicing networks and prognostic models were constructed using bioinformatics tools. Unsupervised clustering of the CASEs identified was conducted and associations with clinical, molecular and immune features were analyzed. Results: We detected a total of 32,309 AS events and identified 473 CASEs in HNSC; among these, 91 were validated in an independent cohort (n = 15). Functional protein domains were frequently altered, especially by CASEs affecting cancer drivers, such as PCSK5. CASE parent genes were significantly enriched in pathways related to HNSC and the tumor immune microenvironment, such as the viral carcinogenesis (FDR < 0.001), Human Papillomavirus infection (FDR < 0.001), chemokine (FDR < 0.001) and T cell receptor (FDR < 0.001) signaling pathways. CASEs enriched in immune-related pathways were closely associated with immune cell infiltration and cytolytic activity. AS regulatory networks suggested a significant association between splicing factor (SF) expression and CASEs and might be regulated by SF methylation. Eighteen CASEs were identified as independent prognostic factors for overall and disease-free survival. Unsupervised clustering analysis revealed distinct correlations between AS-based clusters and prognosis, molecular characteristics and immune features. Immunogenic features and immune subgroups cooperatively depict the immune features of AS-based clusters. Conclusion: This comprehensive genome-wide analysis of the AS landscape in HNSC revealed novel AS events related to carcinogenesis and immune microenvironment, with implications for prognosis and therapeutic responses.
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1689
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Liu R, Shuai Y, Luo J, Zhang Z. SEMA3C Promotes Cervical Cancer Growth and Is Associated With Poor Prognosis. Front Oncol 2019; 9:1035. [PMID: 31649890 PMCID: PMC6794562 DOI: 10.3389/fonc.2019.01035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 09/24/2019] [Indexed: 12/24/2022] Open
Abstract
Introduction: Aberrant activation of Semaphorin3C(SEMA3C) is widespread in human cancers. We aimed to analyze SEMA3C expression in cervical cancer and investigate the role of SEMA3C in cervical cancer and its underlying mechanism, which is important for exploring new therapeutic targets and prognostic factors. Materials and Methods: The expression of SEMA3C was examined in paraffin-embedded cervical cancer specimens. In vivo and in vitro assays were performed to validate the effect of SEMA3C on cervical cancer cell proliferation and p-ERK pathway activation. Gene Set Enrichment Analysis (GSEA) was performed using The Cancer Genome Atlas (TCGA) data set. Results: SEMA3C expression was associated with poor survival in both the TCGA cohort and our cohort. Silencing of SEMA3C suppressed cervical cancer cell proliferation, colony formation ability, and the activation of the p-ERK signaling pathway in vitro. SEMA3C depletion inhibited tumor growth in vitro. GSEA also showed that the epithelial mesenchymal transition (EMT), TGFβ signaling pathway, angiogenesis, and extracellular matrix (ECM) receptor interactions are associated with a high SEMA3C expression phenotype. Conclusion: SEMA3C is correlated with poor prognosis of cervical cancer patients and promotes tumor growth via the activation of the p-ERK pathway.
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Affiliation(s)
- Ruoyan Liu
- Department of Gynecologic Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Yanjie Shuai
- Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Department of Maxillofacial and Otorhinolaryngology Oncology and Department of Head and Neck Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Jingtao Luo
- Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Department of Maxillofacial and Otorhinolaryngology Oncology and Department of Head and Neck Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Ze Zhang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Department of Maxillofacial and Otorhinolaryngology Oncology and Department of Head and Neck Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
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1690
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Duan R, Gao L, Xu H, Song K, Hu Y, Wang H, Dong Y, Zhang C, Jia S. CEPICS: A Comparison and Evaluation Platform for Integration Methods in Cancer Subtyping. Front Genet 2019; 10:966. [PMID: 31649733 PMCID: PMC6792302 DOI: 10.3389/fgene.2019.00966] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 09/10/2019] [Indexed: 11/17/2022] Open
Abstract
Cancer subtypes can improve our understanding of cancer, and suggest more precise treatment for patients. Multi-omics molecular data can characterize cancers at different levels. Up to now, many computational methods that integrate multi-omics data for cancer subtyping have been proposed. However, there are no consistent criteria to evaluate the integration methods due to the lack of gold standards (e.g., the number of subtypes in a specific cancer). Since comprehensive evaluation and comparison between different methods serves as a useful tool or guideline for users to select an optimal method for their own purpose, we develop a scalable platform, CEPICS, for comprehensively evaluating and comparing multi-omics data integration methods in cancer subtyping. Given a user-specified maximum number of subtypes, k-max, CEPICS provides (1) cancer subtyping results using up to five built-in state-of-the-art integration methods under the number of subtypes from two to k-max, (2) a report including the evaluation of each user-selected method and comparisons across them using clustering performance metrics and clinical survival analysis, and (3) an overall analysis of subtyping results by different methods representing a robust cancer subtype prediction for samples. Furthermore, users can upload subtyping results of their own methods to compare with the built-in methods. CEPICS is implemented as an R package and is freely available at https://github.com/GaoLabXDU/CEPICS.
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Affiliation(s)
- Ran Duan
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Han Xu
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Kuo Song
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Yuxuan Hu
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Hongda Wang
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Yongqiang Dong
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Chenxing Zhang
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Songwei Jia
- School of Computer Science and Technology, Xidian University, Xi'an, China
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1691
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Liu Y. Clinicopathological correlation of immune response in human cancers. Oncotarget 2019; 10:5859-5870. [PMID: 31645905 PMCID: PMC6791389 DOI: 10.18632/oncotarget.27231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/24/2019] [Indexed: 11/25/2022] Open
Abstract
Background: The clinicopathologic association of tumor immune response is largely unknown. We systematically investigated this matter in human cancers. Results: Different cancer types exhibited distinct immune gene profiling. Four cancer types exhibited a significant and positive correlation of immune response with patient age. Significant but inconsistent correlation of immune response was observed with gender, surgical stage, and TNM stage in a small number of cancer types. In contrast, the histological grade appears to have much stronger and more consistent association with immune response as compared to the other clinicopathologic factors. Specifically, patients with high grade had significantly higher immune responses than those with low grade in 5 out of 12 analyzed cancer types. In addition, both histological and molecular classifications had a significant and strong association with tumor immune response. Methods: t-distributed stochastic neighbor embedding was used to assess similarity of immune gene profiling in human cancers. The Mann-Whitney or Kruskal-Wallis test was, respectively, used to compare the tumor immune response in two or more groups that were stratified by patient clinicopathological characteristics, such as gender, grade, stage (including surgical and TNM stage), histology, and molecular subtypes. Spearman correlation with student’s t-test was used to examine the association of patient age with immune response. Multiple tests with the Benjamini-Hochberg correction also were performed. Conclusions: Tumor grade should be taken into account in selection of patient candidates for immunotherapy. Prospective verification is needed before use of the findings for clinical practice.
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Affiliation(s)
- Yuexin Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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1692
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Zhang Z, Lee JH, Ruan H, Ye Y, Krakowiak J, Hu Q, Xiang Y, Gong J, Zhou B, Wang L, Lin C, Diao L, Mills GB, Li W, Han L. Transcriptional landscape and clinical utility of enhancer RNAs for eRNA-targeted therapy in cancer. Nat Commun 2019; 10:4562. [PMID: 31594934 PMCID: PMC6783481 DOI: 10.1038/s41467-019-12543-5] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 09/16/2019] [Indexed: 12/19/2022] Open
Abstract
Enhancer RNA (eRNA) is a type of noncoding RNA transcribed from the enhancer. Although critical roles of eRNA in gene transcription control have been increasingly realized, the systemic landscape and potential function of eRNAs in cancer remains largely unexplored. Here, we report the integration of multi-omics and pharmacogenomics data across large-scale patient samples and cancer cell lines. We observe a cancer-/lineage-specificity of eRNAs, which may be largely driven by tissue-specific TFs. eRNAs are involved in multiple cancer signaling pathways through putatively regulating their target genes, including clinically actionable genes and immune checkpoints. They may also affect drug response by within-pathway or cross-pathway means. We characterize the oncogenic potential and therapeutic liability of one eRNA, NET1e, supporting the clinical feasibility of eRNA-targeted therapy. We identify a panel of clinically relevant eRNAs and developed a user-friendly data portal. Our study reveals the transcriptional landscape and clinical utility of eRNAs in cancer.
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Affiliation(s)
- Zhao Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Joo-Hyung Lee
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Hang Ruan
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Joanna Krakowiak
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Qingsong Hu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yu Xiang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jing Gong
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Bingying Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, PR China
| | - Li Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, PR China
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Center for Precision Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Center for Precision Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
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1693
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Park E, Rawson S, Li K, Kim BW, Ficarro SB, Pino GGD, Sharif H, Marto JA, Jeon H, Eck MJ. Architecture of autoinhibited and active BRAF-MEK1-14-3-3 complexes. Nature 2019; 575:545-550. [PMID: 31581174 PMCID: PMC7014971 DOI: 10.1038/s41586-019-1660-y] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 09/26/2019] [Indexed: 12/14/2022]
Abstract
RAF family kinases are RAS-activated switches that initiate signaling through the MAP kinase cascade to control cellular proliferation, differentiation and survival1–3. RAF activity is tightly regulated, and inappropriate activation is a frequent cause of cancer4–6. At present, the structural basis for RAF regulation is poorly understood. Here we describe autoinhibited and active state structures of full-length BRAF in complexes with MEK1 and a 14-3-3 dimer, determined using cryo electron microscopy (cryo-EM). A 4.1Å resolution cryo-EM reconstruction reveals an inactive BRAF/MEK1 complex restrained in a cradle formed by the 14-3-3 dimer, which binds the phosphorylated S365 and S729 sites that flank the BRAF kinase domain. The BRAF cysteine-rich domain (CRD) occupies a central position that stabilizes this assembly, but the adjacent RAS-binding domain (RBD) is poorly ordered and peripheral. The 14-3-3 cradle maintains autoinhibition by sequestering the membrane-binding CRD and blocking dimerization of the BRAF kinase domain. In the active state, these inhibitory interactions are released and a single 14-3-3 dimer rearranges to bridge the C-terminal pS729 binding sites of two BRAFs, driving formation of an active, back-to-back BRAF dimer. Our structural snapshots provide a foundation for understanding normal RAF regulation and its mutational disruption in cancer and developmental syndromes.
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Affiliation(s)
- Eunyoung Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Kunhua Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Byeong-Won Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gonzalo Gonzalez-Del Pino
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Humayun Sharif
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hyesung Jeon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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1694
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Seo J, Kim MH, Hong H, Cho H, Park S, Kim SK, Kim J. MK5 Regulates YAP Stability and Is a Molecular Target in YAP-Driven Cancers. Cancer Res 2019; 79:6139-6152. [DOI: 10.1158/0008-5472.can-19-1339] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/21/2019] [Accepted: 09/27/2019] [Indexed: 11/16/2022]
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1695
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Bacolla A, Ye Z, Ahmed Z, Tainer JA. Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:47-61. [PMID: 30880007 PMCID: PMC6745008 DOI: 10.1016/j.pbiomolbio.2019.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 02/01/2023]
Abstract
A hallmark of cancer is genomic instability, which can enable cancer cells to evade therapeutic strategies. Here we employed a computational approach to uncover mechanisms underlying cancer mutational burden by focusing upon relationships between 1) translocation breakpoints and the thousands of G4 DNA-forming sequences within retrotransposons impacting transcription and exemplifying probable non-B DNA structures and 2) transcriptome profiling and cancer mutations. We determined the location and number of G4 DNA-forming sequences in the Genome Reference Consortium Human Build 38 and found a total of 358,605 covering ∼13.4 million bases. By analyzing >97,000 unique translocation breakpoints from the Catalogue Of Somatic Mutations In Cancer (COSMIC), we found that breakpoints are overrepresented at G4 DNA-forming sequences within hominid-specific SVA retrotransposons, and generally occur in tumors with mutations in tumor suppressor genes, such as TP53. Furthermore, correlation analyses between mRNA levels and exome mutational loads from The Cancer Genome Atlas (TCGA) encompassing >450,000 gene-mutation regressions revealed strong positive and negative associations, which depended upon tissue of origin. The strongest positive correlations originated from genes not listed as cancer genes in COSMIC; yet, these show strong predictive power for survival in most tumor types by Kaplan-Meier estimation. Thus, correlation analyses of DNA structure and gene expression with mutation loads complement and extend more traditional approaches to elucidate processes shaping genomic instability in cancer. The combined results point to G4 DNA, activation of cell cycle/DNA repair pathways, and mitochondrial dysfunction as three major factors driving the accumulation of somatic mutations in cancer cells.
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Affiliation(s)
- Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - Zu Ye
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - Zamal Ahmed
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
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1696
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Dong S, Li W, Wang L, Hu J, Song Y, Zhang B, Ren X, Ji S, Li J, Xu P, Liang Y, Chen G, Lou JT, Yu W. Histone-Related Genes Are Hypermethylated in Lung Cancer and Hypermethylated HIST1H4F Could Serve as a Pan-Cancer Biomarker. Cancer Res 2019; 79:6101-6112. [PMID: 31575549 DOI: 10.1158/0008-5472.can-19-1019] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/24/2019] [Accepted: 09/27/2019] [Indexed: 11/16/2022]
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Cytologic examination is the current "gold standard" for lung cancer diagnosis, however, this has low sensitivity. Here, we identified a typical methylation signature of histone genes in lung cancer by whole-genome DNA methylation analysis, which was validated by The Cancer Genome Atlas (TCGA) lung cancer cohort (n = 907) and was further confirmed in 265 bronchoalveolar lavage fluid samples with specificity and sensitivity of 96.7% and 87.0%, respectively. More importantly, HIST1H4F was universally hypermethylated in all 17 tumor types from TCGA datasets (n = 7,344), which was further validated in nine different types of cancer (n = 243). These results demonstrate that HIST1H4F can function as a universal-cancer-only methylation (UCOM) marker, which may aid in understanding general tumorigenesis and improve screening for early cancer diagnosis. SIGNIFICANCE: These findings identify a new biomarker for cancer detection and show that hypermethylation of histone-related genes seems to persist across cancers.
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Affiliation(s)
- Shihua Dong
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Li
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lin Wang
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Hu
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuanlin Song
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Baolong Zhang
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoguang Ren
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shimeng Ji
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jin Li
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Peng Xu
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ying Liang
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gang Chen
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jia-Tao Lou
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
| | - Wenqiang Yu
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
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1697
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Chae H, Kim D, Yoo C, Kim KP, Jeong JH, Chang HM, Lee SS, Park DH, Song TJ, Hwang S, Kim KH, Song GW, Ahn CS, Lee JH, Hwang DW, Kim SC, Jang SJ, Hong SM, Kim TW, Ryoo BY. Therapeutic relevance of targeted sequencing in management of patients with advanced biliary tract cancer: DNA damage repair gene mutations as a predictive biomarker. Eur J Cancer 2019; 120:31-39. [DOI: 10.1016/j.ejca.2019.07.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/07/2019] [Accepted: 07/20/2019] [Indexed: 01/08/2023]
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1698
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Mendoza-Almanza G, Ortíz-Sánchez E, Rocha-Zavaleta L, Rivas-Santiago C, Esparza-Ibarra E, Olmos J. Cervical cancer stem cells and other leading factors associated with cervical cancer development. Oncol Lett 2019; 18:3423-3432. [PMID: 31516560 PMCID: PMC6733009 DOI: 10.3892/ol.2019.10718] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 06/06/2019] [Indexed: 02/07/2023] Open
Abstract
Cervical cancer (CC) is one of the leading causes of cancer-associated mortalities in women from developing countries. Similar to other types of cancer, CC is considered to be a multifactorial disease, involving socioeconomic, cultural, immunological and epigenetic factors, as well as persistent human papilloma virus (HPV) infection. It has been well established that cancer stem cells (CSCs) play an important role in defining tumor size, the speed of development and the level of regression following treatment; therefore, CSCs are associated with a poor prognosis. CSCs have been detected in many types of cancer, including leukemia, pancreatic, colon, esophagus, liver, prostate, breast, gastric and lung cancer. In cervical cancer, CSCs have been associated with resistance to normally used drugs such as cisplatin. The present review summarizes the strategies that high-risk HPV viruses (HPV-16 and HPV-18) have developed to transform normal epithelial cells into cancer cells, as well as the cellular pathways and studies associated with the identification of cervical cancer stem cell biomarkers. In this sense, the present review provides state of the art information regarding CC development.
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Affiliation(s)
- Gretel Mendoza-Almanza
- National Council for Science and Technology, Autonomous University of Zacatecas, Zacatecas 98060, Mexico
| | | | - Leticia Rocha-Zavaleta
- Institute of Biomedical Research, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - César Rivas-Santiago
- National Council for Science and Technology, Autonomous University of Zacatecas, Zacatecas 98060, Mexico
| | - Edgar Esparza-Ibarra
- Academic Unit of Biological Sciences, Autonomous University of Zacatecas, Zacatecas 98060, Mexico
| | - Jorge Olmos
- Department of Marine Biotechnology, Center for Scientific Research and Higher Education, Ensenada 22860, Mexico
- Correspondence to: Dr Jorge Olmos, Department of Marine Biotechnology, Center for Scientific Research and Higher Education, 3918 Carretera Ensenada-Tijuana, Ensenada 22860, Mexico, E-mail:
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1699
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Mumbauer S, Pascual J, Kolotuev I, Hamaratoglu F. Ferritin heavy chain protects the developing wing from reactive oxygen species and ferroptosis. PLoS Genet 2019; 15:e1008396. [PMID: 31568497 PMCID: PMC6786644 DOI: 10.1371/journal.pgen.1008396] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 10/10/2019] [Accepted: 09/02/2019] [Indexed: 01/06/2023] Open
Abstract
The interplay between signalling pathways and metabolism is crucial for tissue growth. Yet, it remains poorly understood. Here, we studied the consequences of modulating iron metabolism on the growth of Drosophila imaginal discs. We find that reducing the levels of the ferritin heavy chain in the larval wing discs leads to drastic growth defects, whereas light chain depletion causes only minor defects. Mutant cell clones for the heavy chain lack the ability to compete against Minute mutant cells. Reactive oxygen species (ROS) accumulate in wing discs with reduced heavy chain levels, causing severe mitochondrial defects and ferroptosis. Preventing ROS accumulation alleviates some of the growth defects. We propose that the increased expression of ferritin in hippo mutant cells may protect against ROS accumulation. Despite being vital, the role of metals in biology is often overlooked. Specifically, how iron storage contributes to development remains unclear. Here, we dissected the function of the cellular iron storage complex, Ferritin, during development of a model organ, the fly wing. We took a genetic approach to uncover the role of both the heavy and light chains of Ferritin. Targeting the heavy chain consistently produced drastic growth defects in larval discs and adult wings. Moreover, lower levels of the heavy chain led to formation of reactive oxygen species (ROS) and preventing ROS accumulation alleviated the accompanying growth defects. We also observed hallmarks of ferroptosis, an iron dependent non-apoptotic cell death, upon knockdown of the heavy chain. By contrast, reducing the levels of the light chain was tolerable. This is surprising because the individual components of Ferritin were thought to function exclusively as part of the complex. Yet, the heavy chain alone encompasses the ferroxidase center, which is essential for iron loading. All together, we propose that the Ferritin heavy chain functions as an antioxidant and protects the developing organs from ferroptosis.
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Affiliation(s)
- Simone Mumbauer
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Justine Pascual
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Irina Kolotuev
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Fisun Hamaratoglu
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
- * E-mail:
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1700
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FADD in Cancer: Mechanisms of Altered Expression and Function, and Clinical Implications. Cancers (Basel) 2019; 11:cancers11101462. [PMID: 31569512 PMCID: PMC6826683 DOI: 10.3390/cancers11101462] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 12/15/2022] Open
Abstract
FADD was initially described as an adaptor molecule for death receptor-mediated apoptosis, but subsequently it has been implicated in nonapoptotic cellular processes such as proliferation and cell cycle control. During the last decade, FADD has been shown to play a pivotal role in most of the signalosome complexes, such as the necroptosome and the inflammasome. Interestingly, various mechanisms involved in regulating FADD functions have been identified, essentially posttranslational modifications and secretion. All these aspects have been thoroughly addressed in previous reviews. However, FADD implication in cancer is complex, due to pleiotropic effects. It has been reported either as anti- or protumorigenic, depending on the cell type. Regulation of FADD expression in cancer is a complex issue since both overexpression and downregulation have been reported, but the mechanisms underlying such alterations have not been fully unveiled. Posttranslational modifications also constitute a relevant mechanism controlling FADD levels and functions in tumor cells. In this review, we aim to provide detailed, updated information on alterations leading to changes in FADD expression and function in cancer. The participation of FADD in various biological processes is recapitulated, with a mention of interesting novel functions recently proposed for FADD, such as regulation of gene expression and control of metabolic pathways. Finally, we gather all the available evidence regarding the clinical implications of FADD alterations in cancer, especially as it has been proposed as a potential biomarker with prognostic value.
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