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Manoochehrabadi S, Talebi M, Pashaiefar H, Ghafouri-Fard S, Vaezi M, Omrani MD, Ahmadvand M. Upregulation of lnc-FOXD2-AS1, CDC45, and CDK1 in patients with primary non-M3 AML is associated with a worse prognosis. Blood Res 2024; 59:4. [PMID: 38485838 PMCID: PMC10903518 DOI: 10.1007/s44313-024-00002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/03/2024] [Indexed: 03/18/2024] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous hematologic malignancy with an unfavorable outcome. The present research aimed to identify novel biological targets for AML diagnosis and treatment. In this study, we performed an in-silico method to identify antisense RNAs (AS-RNAs) and their related co-expression genes. GSE68172 was selected from the AML database of the Gene Expression Omnibus and compared using the GEO2R tool to find DEGs. Antisense RNAs were selected from all the genes that had significant expression and a survival plot was drawn for them in the GEPIA database, FOXD2-AS1 was chosen for further investigation based on predetermined criteria (logFC ≥|1| and P < 0.05) and its noteworthy association between elevated expression level and a marked reduction in the overall survival (OS) in patients diagnosed with AML. The GEPIA database was utilized to investigate FOXD2-AS1-related co-expression and similar genes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and gene ontology (GO) function analysis of the mentioned gene lists were performed using the DAVID database. The protein-protein interaction (PPI) network was then constructed using the STRING database. Hub genes were screened using Cytoscape software. Pearson correlation analysis was conducted using the GEPIA database to explore the relationship between FOXD2-AS1 and the hub genes. The transcription of the selected coding and non-coding genes, including FOXD2-AS1, CDC45, CDC20, CDK1, and CCNB1, was validated in 150 samples, including 100 primary AML non-M3 blood samples and 50 granulocyte colony stimulating factor (G-CSF)-mobilized healthy donors, using quantitative Real-Time PCR (qRT-PCR). qRT-PCR results displayed significant upregulation of lnc-FOXD2-AS1, CDC45, and CDK1 in primary AML non-M3 blood samples compared to healthy blood samples (P = 0.0032, P = 0.0078, and P = 0.0117, respectively). The expression levels of CDC20 and CCNB1 were not statistically different between the two sets of samples (P = 0.8315 and P = 0.2788, respectively). We identified that AML patients with upregulation of FOXD2-AS1, CDK1, and CDC45 had shorter overall survival (OS) and Relapse-free survival (RFS) compared those with low expression of FOXD2-AS1, CDK1, and CDC45. Furthermore, the receiver operating characteristic (ROC) curve showed the potential biomarkers of lnc -FOXD2-AS1, CDC45, and CDK1 in primary AML non-M3 blood samples. This research proposed that the dysregulation of lnc-FOXD2-AS1, CDC45, and CDK1 can contribute to both disease state and diagnosis as well as treatment. The present study proposes the future evolution of the functional role of lnc-FOXD2-AS1, CDC45, and CDK1 in AML development.
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Affiliation(s)
- Saba Manoochehrabadi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Morteza Talebi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Pashaiefar
- Cell Therapy and Hematopoietic Stem Cell Transplantation Research Center, Hematology and Cell Therapy, Research Institute for Oncology, Tehran University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Vaezi
- Cell Therapy and Hematopoietic Stem Cell Transplantation Research Center, Hematology and Cell Therapy, Research Institute for Oncology, Tehran University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Ahmadvand
- Cell Therapy and Hematopoietic Stem Cell Transplantation Research Center, Hematology and Cell Therapy, Research Institute for Oncology, Tehran University of Medical Sciences, Tehran, Iran.
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Wang X, Chan S, Dai L, Xu Y, Yang Q, Wang M, Han Q, Chen J, Zuo X, Wang Z, Yang Y, Zhao H, Zhang G, Zhang H, Chen W. Identification of novel T cell proliferation patterns, potential biomarkers and therapeutic drugs in colorectal cancer. J Cancer 2024; 15:1234-1254. [PMID: 38356712 PMCID: PMC10861827 DOI: 10.7150/jca.91835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/23/2023] [Indexed: 02/16/2024] Open
Abstract
Background: T cells are crucial components of antitumor immunity. A list of genes associated with T cell proliferation was recently identified; however, the impact of T cell proliferation-related genes (TRGs) on the prognosis and therapeutic responses of patients with colorectal cancer (CRC) remains unclear. Methods: 33 TRG expression information and clinical information of patients with CRC gathered from multiple datasets were subjected to bioinformatic analysis. Consensus clustering was used to determine the molecular subtypes associated with T cell proliferation. Utilizing the Lasso-Cox regression, a predictive signature was created and verified in external cohorts. A tumor immune environment analysis was conducted, and potential biomarkers and therapeutic drugs were identified and confirmed via in vitro and in vivo studies. Results: CRC patients were separated into two TRG clusters, and differentially expressed genes (DEGs) were identified. Patient information was divided into three different gene clusters, and the determined molecular subtypes were linked to patient survival, immune cells, and immune functions. Prognosis-associated DEGs in the three gene clusters were used to evaluate the risk score, and a predictive signature was developed. The ability of the risk score to predict patient survival and treatment response has been successfully validated using multiple datasets. To discover more possible biomarkers for CRC, the weighted gene co-expression network analysis algorithm was utilized to screen key TRG variations between groups with high- and low-risk. CDK1, BATF, IL1RN, and ITM2A were screened out as key TRGs, and the expression of key TRGs was confirmed using real-time reverse transcription polymerase chain reaction. According to the key TRGs, 7,8-benzoflavone was identified as the most significant drug molecule, and MTT, colony formation, wound healing, transwell assays, and in vivo experiments indicated that 7,8-benzoflavone significantly suppressed the proliferation and migration of CRC cells. Conclusion: T cell proliferation-based molecular subtypes and predictive signatures can be utilized to anticipate patient results, immunological landscape, and treatment response in CRC. Novel biomarker candidates and potential therapeutic drugs for CRC were identified and verified using in vitro and in vivo tests.
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Affiliation(s)
- Xu Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, Anhui, China
| | - Shixin Chan
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, Anhui, China
| | - Longfei Dai
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, Anhui, China
| | - Yuanmin Xu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, Anhui, China
| | - Qi Yang
- Department of Gastroenterology, The First Affiliated Hospital of Wannan Medical College, Wuhu, 241000, China
| | - Ming Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, Anhui, China
| | - Qijun Han
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, Anhui, China
| | - Jiajie Chen
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, Anhui, China
| | - Xiaomin Zuo
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, Anhui, China
| | - Zhenglin Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, Anhui, China
| | - Yang Yang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, Anhui, China
| | - Hu Zhao
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, Anhui, China
| | - Guihong Zhang
- The Pathology Department of Anhui Medical University, Hefei 230032, Anhui, China
| | - Huabing Zhang
- Department of Biochemistry and Molecular Biology, Metabolic Disease Research Center, School of Basic Medicine, Anhui Medical University, Hefei 230032, Anhui, China
- The First Affiliated Chuzhou Hospital of Anhui Medical University, Chuzhou 239000, Anhui, China
| | - Wei Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, Anhui, China
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Guan L, Tang Y, Li G, Qin Z, Li S. Comprehensive Analysis of Role of Cyclin-Dependent Kinases Family Members in Colorectal Cancer. Front Oncol 2022; 12:921710. [PMID: 35814446 PMCID: PMC9258493 DOI: 10.3389/fonc.2022.921710] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/24/2022] [Indexed: 01/10/2023] Open
Abstract
Background Cyclin-dependent kinases (CDKs) are cell cycle regulators, and abnormal activation can accelerate tumor cell proliferation. However, The relation between CDKs dysregulation to colorectal cancer incidence and progression have not been examined in detail. Methods:Differences in CDKs expression between colorectal cancer and normal tissues, associations between expression and clinical prognosis, incidence and frequencies of CDKs gene mutations, and the influences of CDKs on tumor infiltration by immune cells were examined by analyses of Oncomine, Gene Expression Profiling Interactive Analysis, Kaplan-Meier plotter, cBioPortal, GeneMANIA, and TIMER databases. Results Colorectal cancer tissues showed enhanced expression levels of CDKs 1/2/4/5/6/8/12/13/19 but reduced CDK3 expression. CDK7 was highly expressed in some colorectal cancer tissues but downregulated in others. Expression levels of CDK1/3/4/7/8/10/11b/13/18/19/20 were correlated with clinical stage, and CDK 5/10/12/16 expression levels predicted prognosis and survival. Differential CDKs expression correlated with cell cycle progression, amino acid polypeptide modifications, and activation of other protein kinases. Expression levels of all CDKs except CDK16 were correlated with infiltration of CD4+T, CD8+T, B and Tregs cells. Conclusions CDK 1 and 4 could be used as diagnostic biomarkers for CRC. CDK 5/10/12/16 can be utilized as prognostic biomarkers.
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Affiliation(s)
- Liping Guan
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
- Henan International Joint Laboratory of Immunity and Targeted Therapy for Liver-Intestinal Tumors, Xinxiang Medical University, Xinxiang, China
| | - Yuanyuan Tang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Guanghua Li
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Zhao Qin
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Shaoshan Li
- Department of General Surgery of the Third Affiliated Hospital of Xinxiang Medical University, Xinxiang Medical University, Xinxiang, China
- *Correspondence: Shaoshan Li,
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Wei ZL, Zhou X, Lan CL, Huang HS, Liao XW, Mo ST, Wei YG, Peng T. Clinical implications and molecular mechanisms of Cyclin-dependent kinases 4 for patients with hepatocellular carcinoma. BMC Gastroenterol 2022; 22:77. [PMID: 35193513 PMCID: PMC8864914 DOI: 10.1186/s12876-022-02152-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/11/2022] [Indexed: 12/15/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) was frequently considered as a kind of malignant tumor with a poor prognosis. Cyclin-dependent kinases (CDK) 4 was considered to be cell-cycle-related CDK gene. In this study, we explored the clinical significance of CDK4 in HCC patients. Methods Data of HCC patients were obtained from The Cancer Genome Atlas database (TCGA) and the Gene Expression Omnibus (GEO) database. Kaplan–Meier analysis and Cox regression model were performed to calculate median survival time (MST) and the hazard ration (HR), respectively. The joint-effect analysis and prognostic risk score model were constructed to demonstrate significance of prognosis-related genes. The differential expression of prognostic genes was further validated using reverse transcription-quantitative PCR (RT-qPCR) of 58 pairs of HCC samples. Results CDK1 and CDK4 were considered prognostic genes in TCGA and GSE14520 cohort. The result of joint-effect model indicated patients in CDK1 and CDK4 low expression groups had a better prognosis in TCGA (adjusted HR = 0.491; adjusted P = 0.003) and GSE14520 cohort (adjusted HR = 0.431; adjusted P = 0.002). Regarding Kaplan–Meier analysis, high expression of CDK1 and CDK4 was related to poor prognosis in both the TCGA (P < 0.001 and = 0.001 for CDK1 and CDK4, respectively) and the GSE14520 cohort (P = 0.006 and = 0.033 for CDK1 and CDK4, respectively). However, only CDK4 (P = 0.042) was validated in RT-qPCR experiment, while CDK1 (P = 0.075) was not. Conclusion HCC patients with high CDK4 expression have poor prognosis, and CDK4 could be a potential candidate diagnostic biomarker for HCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12876-022-02152-w.
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Affiliation(s)
- Zhong-Liu Wei
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xin Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Chen-Lu Lan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hua-Sheng Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xi-Wen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Shu-Tian Mo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yong-Guang Wei
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
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Core Circadian Clock Proteins as Biomarkers of Progression in Colorectal Cancer. Biomedicines 2021; 9:biomedicines9080967. [PMID: 34440171 PMCID: PMC8391187 DOI: 10.3390/biomedicines9080967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/23/2021] [Accepted: 07/31/2021] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common tumours in developed countries. Although its incidence and mortality rates have decreased, its prognosis has not changed, and a high percentage of patients with CRC develop relapse (metachronous metastasis, MM, or local recurrence, LR) during their disease. The identification of these patients is very important for their correct management, but the lack of prognostic markers makes it difficult. Given the connection between circadian disruption and cancer development and progression, we aimed to analyse the prognostic significance of core circadian proteins in CRC. We measured the expression of PER1-3, CRY1-2, BMAL1 and NR1D2 in a cohort of CRC patients by immunohistochemistry (IHC) and analysed their prognostic potential in this disease. A low expression of PER2 and BMAL1 was significantly associated with metastasis at the moment of disease diagnosis, whereas a high expression of CRY1 appeared as an independent prognostic factor of MM development. A high expression of NR1D2 appeared as an independent prognostic factor of LR development after disease diagnosis. Moreover, patients with a low expression of BMAL1 and a high expression of CRY1 showed lower OS and DFS at five years. Although these markers need to be validated in larger and different ethnic cohorts, the simplicity of IHC makes these proteins candidates for personalizing CRC treatment.
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Hossain MJ, Chowdhury UN, Islam MB, Uddin S, Ahmed MB, Quinn JMW, Moni MA. Machine learning and network-based models to identify genetic risk factors to the progression and survival of colorectal cancer. Comput Biol Med 2021; 135:104539. [PMID: 34153790 DOI: 10.1016/j.compbiomed.2021.104539] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/12/2021] [Accepted: 05/26/2021] [Indexed: 01/04/2023]
Abstract
Colorectal cancer (CRC) is one of the most common and lethal malignant lesions. Determining how the identified risk factors drive the formation and development of CRC could be an essential means for effective therapeutic development. Aiming this, we investigated how the altered gene expression resulting from exposure to putative CRC risk factors contribute to prognostic biomarker identification. Differentially expressed genes (DEGs) were first identified for CRC and other eight risk factors. Gene set enrichment analysis (GSEA) through the molecular pathway and gene ontology (GO), as well as protein-protein interaction (PPI) network, were then conducted to predict the functions of these DEGs. Our identified genes were explored through the dbGaP and OMIM databases to compare with the already identified and known prognostic CRC biomarkers. The survival time of CRC patients was also examined using a Cox Proportional Hazard regression-based prognostic model by integrating transcriptome data from The Cancer Genome Atlas (TCGA). In this study, PPI analysis identified 4 sub-networks and 8 hub genes that may be potential therapeutic targets, including CXCL8, ICAM1, SOD2, CXCL2, CCL20, OIP5, BUB1, ASPM and IL1RN. We also identified seven signature genes (PRR5.ARHGAP8, CA7, NEDD4L, GFR2, ARHGAP8, SMTN, OIP5) in independent analysis and among which PRR5. ARHGAP8 was found in both multivariate analyses and in analyses that combined gene expression and clinical information. This approach provides both mechanistic information and, when combined with predictive clinical information, good evidence that the identified genes are significant biomarkers of processes involved in CRC progression and survival.
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Affiliation(s)
- Md Jakir Hossain
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Utpala Nanda Chowdhury
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - M Babul Islam
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Shahadat Uddin
- Complex Systems Research Group & Project Management Program, Faculty of Engineering, The University of Sydney, NSW, 2006, Australia
| | - Mohammad Boshir Ahmed
- School of Material Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Julian M W Quinn
- Healthy Ageing Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Mohammad Ali Moni
- Healthy Ageing Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia; WHO Collaborating Centre on eHealth, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, NSW, 2052, Australia.
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Fadaka AO, Samantha Sibuyi NR, Bakare OO, Klein A, Madiehe AM, Meyer M. Expression of cyclin-dependent kinases and their clinical significance with immune infiltrates could predict prognosis in colorectal cancer. ACTA ACUST UNITED AC 2021; 29:e00602. [PMID: 33732631 PMCID: PMC7937668 DOI: 10.1016/j.btre.2021.e00602] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/26/2021] [Accepted: 02/20/2021] [Indexed: 12/15/2022]
Abstract
The expression and prognostic values of AURKA and RB1 may also be significant to CRC diagnosis than previously studies. The association of CDKs with immune infiltrates may serve as target molecules for immunotherapy in CRC. The expression of CDK is significant among CRC subtypes and therefore, it can be inferred as a potential biomarker in the cancer subtype. An increase in tumor purity was positively correlated with the expression of CDK-1 in COAD due to CD4+ cells and CDK-4 in COAD and READ resulting from a fraction of immune cells.
Introduction Colorectal cancer (CRC) is one of the most cancer-related mortalities worldwide and remains a major public health issue. Despite several attempts to develop promising therapies for CRC, its survival rate decreases with metastasis. Cyclin-dependent kinases (CDKs) are a family of protein kinases with various regulatory activities including cell cycle, mRNA expression, transcription, and differentiation. Aside from their role in cell proliferation when mutated, abnormal expression of these genes has been reported in some human cancer subtypes. This study explored the roles and therapeutic potentials of CDK 1 and 4 as prognostic biomarkers in CRC. Methods Bioinformatics analyses were carried out to demonstrate the expression and prognostic values of CDK-1 and CDK-4 with immune infiltrate in CRC. Discussion CDK levels in CRC were remarkably higher than those in normal tissues (p < 0.05), and overexpression in CRC tissues was significantly related to nodal metastatic status (p < 0.05) and histological subtypes. Kaplan-Meier analyses showed that patients with CRC who exhibited CDK-1 overexpression had worse overall survival (OS) as against patients with CDK-4 overexpression. The alteration observed was a mutation while the mutation hotspots include E163* and R24A/C/H/L respectively for CDK-1 and CDK-4 on the Pkinase domain. Of the associated genes, AURKA and RB1 were predominantly altered. Furthermore, CDK-4 is positively correlated with tumor purity in both COAD and READ while CDK-1is only positively correlated in COAD. CDK-1 overexpression was significantly associated with poor prognosis as opposed to CDK-4. Conclusion The expression and prognostic values of AURKA and RB1 may also be significant to CRC diagnosis. CDKs together with the co-expressed genes and their association with immune infiltrates may serve as target molecules for immunotherapy in CRC.
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Affiliation(s)
- Adewale Oluwaseun Fadaka
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Nicole Remaliah Samantha Sibuyi
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Olalekan Olanrewaju Bakare
- Bioinformatics Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Bellville, 7535, Cape Town, South Africa
| | - Ashwil Klein
- Plant Omics Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Bellville, 7535, Cape Town, South Africa
| | - Abram Madimabe Madiehe
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa.,Nanobiotechnology Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Mervin Meyer
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
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Meng H, Liu J, Qiu J, Nie S, Jiang Y, Wan Y, Cheng W. Identification of Key Genes in Association with Progression and Prognosis in Cervical Squamous Cell Carcinoma. DNA Cell Biol 2020; 39:848-863. [PMID: 32202912 DOI: 10.1089/dna.2019.5202] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cervical cancer remains a primary cause of female death in developing countries, but its prognosis can be greatly improved if patients are diagnosed earlier. In the present study, we screened the common differentially expressed genes (DEGs) of cervical squamous cell carcinoma (CESC) from dataset GSE7803, Gene Expression Omnibus, and The Cancer Genome Atlas databases. An integrated bioinformatics analysis was performed based on these DEGs for their enrichment in functions and pathways, interaction network, prognostic signature, and candidate molecular drugs. As a result, 164 (114 upregulated and 47 downregulated) DEGs of CESC were identified for further investigation. We then conducted the gene ontology term enrichment and Kyoto Encyclopedia of Genes and Genomes Pathway analyses to reveal the underlying functions and pathways of these DEGs. In the protein-protein interaction network, hub module and hub genes were identified. Five genes of significant prognostic value-DSG2, ITM2A, CENPM, RIBC2, and MEIS2-were identified by prognostic signature analysis and used to construct a risk linear model. Further validation and investigation suggested DSG2 might be a key gene in CESC prognosis. We then identified two candidate small molecules (trichostatin A and tanespimycin) against CESC. Further validation and exploration of these hub genes are warranted for future prospect in clinical applications.
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Affiliation(s)
- Huangyang Meng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiangnan Qiu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Sipei Nie
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yi Jiang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yicong Wan
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wenjun Cheng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Deb B, Puttamallesh VN, Gondkar K, Thiery JP, Gowda H, Kumar P. Phosphoproteomic Profiling Identifies Aberrant Activation of Integrin Signaling in Aggressive Non-Type Bladder Carcinoma. J Clin Med 2019; 8:E703. [PMID: 31108958 PMCID: PMC6572125 DOI: 10.3390/jcm8050703] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 12/16/2022] Open
Abstract
Bladder carcinoma is highly heterogeneous and its complex molecular landscape; thus, poses a significant challenge for resolving an effective treatment in metastatic tumors. We computed the epithelial-mesenchymal transition (EMT) scores of three bladder carcinoma subtypes-luminal, basal, and non-type. The EMT score of the non-type indicated a "mesenchymal-like" phenotype, which correlates with a relatively more aggressive form of carcinoma, typified by an increased migration and invasion. To identify the altered signaling pathways potentially regulating this EMT phenotype in bladder cancer cell lines, we utilized liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based phosphoproteomic approach. Bioinformatics analyses were carried out to determine the activated pathways, networks, and functions in bladder carcinoma cell lines. A total of 3125 proteins were identified, with 289 signature proteins noted to be differentially phosphorylated (p ≤ 0.05) in the non-type cell lines. The integrin pathway was significantly enriched and five major proteins (TLN1, CTTN, CRKL, ZYX and BCAR3) regulating cell motility and invasion were hyperphosphorylated. Our study reveals GSK3A/B and CDK1 as promising druggable targets for the non-type molecular subtype, which could improve the treatment outcomes for aggressive bladder carcinoma.
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Affiliation(s)
- Barnali Deb
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.
- Manipal Academy of Higher Education, Madhav Nagar, Manipal 576104, India.
| | - Vinuth N Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India.
| | - Kirti Gondkar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India.
| | - Jean P Thiery
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine NUS Yong Loo Lin School of Medicine, Singapore 117597, Singapore.
- Comprehensive Cancer Center, Institut Gustave Roussy, 114 Rue Edouard Vaillant, 94800 Villejuif, France.
- CNRS UMR 7057, Matter and Complex Systems, Université Paris Diderot, 10 rue Alice Domon et Léonie Duquet Paris, 75205 Paris, France.
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.
- Manipal Academy of Higher Education, Madhav Nagar, Manipal 576104, India.
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Zhang Y, Zhang Z, Wang D, Xu J, Li Y, Wang H, Li J, Mo S, Zhang Y, Lin Y, Fan X, Li E, Huang J, Fan H, Yi Y. Multidimensional Integration Analysis of Autophagy-related Modules in Colorectal Cancer. LETT ORG CHEM 2019; 16:340-346. [DOI: 10.2174/1570178615666180914113224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/30/2018] [Accepted: 09/05/2018] [Indexed: 11/22/2022]
Abstract
Colorectal cancer (CRC) is a common malignant tumor of the digestive tract occurring in the colon, which mainly divided into adenocarcinoma, mucinous adenocarcinoma, and undifferentiated carcinoma. However, autophagy is related to the occurrence and development of various kinds of human diseases such as cancer. There is little research on the relationship between CRC and autophagy. Hence, we performed multidimensional integration analysis to systematically explore potential relationship between autophagy and CRC. Based on gene expression datasets of colon adenocarcinoma (COAD) and protein-protein interactions (PPIs), we first identified 12 autophagy-related modules in COAD using WGCNA. Then, 9 module pairs which with significantly crosstalk were deciphered, a total of 6 functional modules. Autophagy-related genes in these modules were closely related with CRC, emphasizing that the important role of autophagy-related genes in CRC, including PPP2CA and EIF4E, etc. In addition to, by integrating transcription factor (TF)-target and RNA-associated interactions, a regulation network was constructed, in which 42 TFs (including SMAD3 and TP53, etc.) and 20 miRNAs (including miR-20 and miR-30a, etc.) were identified as pivot regulators. Pivot TFs were mainly involved in cell cycle, cell proliferation and pathways in cancer. And pivot miRNAs were demonstrated associated with CRC. It suggests that these pivot regulators might be have an effect on the development of CRC by regulating autophagy. In a word, our results suggested that multidimensional integration strategy provides a novel approach to discover potential relationships between autophagy and CRC, and further improves our understanding of autophagy and tumor in human.
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Affiliation(s)
- Yang Zhang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Zheng Zhang
- Department of Physical Education, Nanjing Audit University, Nanjing, China
| | - Dong Wang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Jianzhen Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area and Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - Yanhui Li
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Peking University Health Science Center, Beijing, China
| | - Hong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shaowen Mo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yuncong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yunqing Lin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiuzhao Fan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Enmin Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area and Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Huihui Fan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ying Yi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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11
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Coleman OI, Lobner EM, Bierwirth S, Sorbie A, Waldschmitt N, Rath E, Berger E, Lagkouvardos I, Clavel T, McCoy KD, Weber A, Heikenwalder M, Janssen KP, Haller D. Activated ATF6 Induces Intestinal Dysbiosis and Innate Immune Response to Promote Colorectal Tumorigenesis. Gastroenterology 2018; 155:1539-1552.e12. [PMID: 30063920 DOI: 10.1053/j.gastro.2018.07.028] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/12/2018] [Accepted: 07/25/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Activating transcription factor 6 (ATF6) regulates endoplasmic reticulum stress. We studied whether ATF6 contributes to the development of colorectal cancer (CRC) using tissue from patients and transgenic mice. METHODS We analyzed data from 541 patients with CRC in The Cancer Genome Atlas database for genetic variants and aberrant expression levels of unfolded protein response genes. Findings were validated in a cohort of 83 patients with CRC in Germany. We generated mice with intestinal epithelial cell-specific expression of the active form of Atf6 (nATF6IEC) from 2 alleles (homozygous), mice with expression of nATF6IEC from 1 allele (heterozygous), and nATF6IECfl/fl mice (controls). All nATF6IEC mice were housed under either specific-pathogen-free or germ-free conditions. Cecal microbiota from homozygous nATF6IEC mice or control mice was transferred into homozygous nATF6IEC mice or control mice. nATF6IEC mice were crossed with mice with disruptions in the myeloid differentiation primary response gene 88 and toll-like receptor adaptor molecule 1 gene (Myd88/Trif-knockout mice). Intestinal tissues were collected from mice and analyzed by histology, immunohistochemistry, immunoblots, gene expression profiling of unfolded protein response and inflammatory genes, array-based comparative genome hybridization, and 16S ribosomal RNA gene sequencing. RESULTS Increased expression of ATF6 was associated with reduced disease-free survival times of patients with CRC. Homozygous nATF6IEC mice developed spontaneous colon adenomas at 12 weeks of age. Compared with controls, homozygous nATF6IEC mice had changes in the profile of their cecal microbiota, increased proliferation of intestinal epithelial cells, and loss of the mucus barrier-all preceding tumor formation. These mice had increased penetration of bacteria into the inner mucus layer and activation of signal transducer and activator of transcription 3, yet inflammation was not observed at the pretumor or tumor stages. Administration of antibiotics to homozygous nATF6IEC mice greatly reduced tumor incidence, and germ-free housing completely prevented tumorigenesis. Analysis of nATF6IEC MyD88/TRIF-knockout mice showed that tumor initiation and growth required MyD88/TRIF-dependent activation of signal transducer and activator of transcription 3. Transplantation of cecal microbiota from nATF6IEC mice and control mice, collected before tumor formation, caused tumor formation in ex-germ-free nATF6IEC mice. CONCLUSIONS In patients with CRC, ATF6 was associated with reduced time of disease-free survival. In studies of nATF6IEC mice, we found sustained intestinal activation of ATF6 in the colon to promote dysbiosis and microbiota-dependent tumorigenesis.
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Affiliation(s)
- Olivia I Coleman
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Elena M Lobner
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Sandra Bierwirth
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Adam Sorbie
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Nadine Waldschmitt
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Eva Rath
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Emanuel Berger
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Ilias Lagkouvardos
- ZIEL -Institute for Food & Health, Technische Universität München, Germany
| | - Thomas Clavel
- ZIEL -Institute for Food & Health, Technische Universität München, Germany
| | - Kathleen D McCoy
- Department of Physiology and Pharmacology, University of Calgary, Canada
| | - Achim Weber
- Institute of Pathology, University Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, München, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany; ZIEL -Institute for Food & Health, Technische Universität München, Germany.
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12
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Sperlich A, Balmert A, Doll D, Bauer S, Franke F, Keller G, Wilhelm D, Mur A, Respondek M, Friess H, Nitsche U, Janssen KP. Genetic and immunological biomarkers predict metastatic disease recurrence in stage III colon cancer. BMC Cancer 2018; 18:998. [PMID: 30340556 PMCID: PMC6194664 DOI: 10.1186/s12885-018-4940-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/11/2018] [Indexed: 02/08/2023] Open
Abstract
Background Even though the post-operative outcome varies greatly among patients with nodal positive colon cancer (UICC stage III), personalized prediction of systemic disease recurrence is currently insufficient. We investigated in a retrospective setting whether genetic and immunological biomarkers can be applied for stratification of distant metastasis occurrence risk. Methods Eighty four patients with complete resection (R0) of stage III colon cancer from two clinical centres were analysed for genetic biomarkers: microsatellite instability, oncogenic mutations in KRAS exon2 and BRAF exon15, expression of osteopontin and the metastasis-associated genes SASH1 and MACC1. Tumor-infiltrating CD3 and CD8 positive T-cells were quantified by immunocytochemistry. Results were correlated with outcome and response to 5-FU based adjuvant chemotherapy, using Cox’s proportional hazard models and integrative two-step cluster analysis. Results Distant metastasis risk was significantly correlated with oncogenic KRAS mutations (p = 0.015), expression of SASH1 (p = 0.016), and the density of CD8-positive T-cells (p = 0.007) in Kaplan-Meier analysis. Upon multivariate Cox-regression analysis, KRAS mutation (p = 0.008) and density of CD8-positive TILs (p = 0.009) were retained as prognostic parameters for metachronous distant metastasis. Integrative two-step cluster analysis was used to combine all genetic markers, allowing stratification of patient subgroups. Post-operative distant metastasis risk ranged from 31% (low-risk) to 41% (intermediate), and 57% (high-risk) (p = 0.032). Increased expression of osteopontin (p = 0.019) and low density of CD8-positive T-cells (p = 0.043) were significantly associated with unfavourable response to 5-FU. Conclusions Integrative biomarker analysis allows stratification of stage III colon cancer patients for the risk of metastatic disease recurrence and may indicate response to 5-FU. Thus, biomarker analysis might facilitate the use of adjuvant therapy for high risk patients. Electronic supplementary material The online version of this article (10.1186/s12885-018-4940-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andreas Sperlich
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Alexander Balmert
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Dietrich Doll
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany.,Darmzentrum Vechta, St. Marienhospital, Marienstraße 6-8, 49377, Vechta, Germany
| | - Sabine Bauer
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Fabian Franke
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Gisela Keller
- Institute of Pathology, Technical University of Munich, Trogerstr. 18, 81675, Munich, Germany
| | - Dirk Wilhelm
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Anna Mur
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Michael Respondek
- St. Marienhospital, Praxis für Pathologie Vechta, Marienstr. 11, 49377, Vechta, Germany
| | - Helmut Friess
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Ulrich Nitsche
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany.
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13
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Aberrantly Expressed Genes and miRNAs in Slow Transit Constipation Based on RNA-Seq Analysis. BIOMED RESEARCH INTERNATIONAL 2018; 2018:2617432. [PMID: 30186855 PMCID: PMC6112260 DOI: 10.1155/2018/2617432] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/26/2018] [Accepted: 07/18/2018] [Indexed: 02/06/2023]
Abstract
Background This study aims to identify the key genes and miRNAs in slow transit constipation (STC). Methods MRNA and miRNA expression profiling were obtained. Differentially expressed genes (DEGs) and miRNAs were identified followed by the regulatory network construction. Functional annotation analysis and protein-protein interaction (PPI) network were conducted. The electronic validation was performed. Results Hsa-miR-2116-3p, hsa-miR-3622a-5p, hsa-miR-424-5p, and hsa-miR-1273-3p covered most DEGs. HLA-DRB1, HLA-DRB5, C3, and ICAM were significantly involved in staphylococcus aureus infection. The PPI network generated several hub proteins including ZBTB16, FBN1, CCNF, and CDK1. Electronic validation of HLA-DRB1, PTGDR, MKI67, BIRC5, CCNF, and CDK1 was consistent with the RNA-sequencing analysis. Conclusion Our study might be helpful in understanding the pathology of STC at the molecular level.
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14
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Zhang Y, Xia Q, Lin J. Identification of the potential oncogenes in glioblastoma based on bioinformatic analysis and elucidation of the underlying mechanisms. Oncol Rep 2018; 40:715-725. [PMID: 29901201 PMCID: PMC6072298 DOI: 10.3892/or.2018.6483] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/31/2018] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma (GBM) is a common malignant tumour in the human brain, but its molecular mechanisms have not been systematically evaluated. The aim of this study was to identify potential key oncogenes associated with the progression of GBM and to elucidate their mechanisms. The gene expression profile of GSE50161, selected from the Gene Expression Omnibus database, was analysed to find cancer-associated genes and gene functions in GBM. In total, 486 differentially expressed genes, including 128 upregulated genes, were identified. The function and pathway enrichment of these genes were analysed through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. Survival analysis for three selected partially upregulated genes, CDK1, CCNB1 and CDC20, showed that their high expression was significantly associated with poor survival in GBM. CDK1 was selected for validation of its function and molecular mechanism in GBM. This gene was significantly overexpressed in GBM cancer tissues and cells compared with normal control cells. In addition, knockdown of CDK1 clearly inhibited GBM cell proliferation. Notably, we demonstrated that CDK1 was involved in the Akt signalling pathway, where it promotes the process involved in GBM malignancy.
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Affiliation(s)
- Yong Zhang
- Department of Neurosurgery, The People's Hospital of Guizhou Provincial, Guiyang, Guizhou 550002, P.R. China
| | - Qiming Xia
- Department of Neurosurgery, The People's Hospital of Guizhou Provincial, Guiyang, Guizhou 550002, P.R. China
| | - Jun Lin
- Department of Neurosurgery, The People's Hospital of Guizhou Provincial, Guiyang, Guizhou 550002, P.R. China
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15
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Prognostic and predictive values of CDK1 and MAD2L1 in lung adenocarcinoma. Oncotarget 2018; 7:85235-85243. [PMID: 27835911 PMCID: PMC5356732 DOI: 10.18632/oncotarget.13252] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/28/2016] [Indexed: 12/17/2022] Open
Abstract
Lung cancer remains as the leading cause of cancer-related death worldwide, and lung adenocarcinoma (LUAD) is the most common histological subtype. This study aims to investigate biomarkers associated with cancer progression and prognosis of LUAD. We integrated expression profiles of 668 lung cancer patients in five datasets from the Gene Expression Omnibus (GEO) and identified a panel of differentially expressed genes (DEGs). Function enrichment analysis highlighted that these genes were closely associated with the carcinogenesis of LUAD, such as cell cycle, ECM-receptor interaction and p53 signaling pathway. Cyclin-dependent kinase 1 (CDK1) and MAD2 mitotic arrest deficient-like 1 (MAD2L1), two critical mitotic checkpoint genes, were selected for further study. Elevated expression of CDK1 and MAD2L1 was validated in an independent LUAD cohort. Kaplan-Meier analysis revealed that CDK1 and MAD2L1 expression was negatively correlated with both overall survival (OS) and relapse-free survival (RFS). In conclusion, CDK1 and MAD2L1 were adverse prognostic biomarkers for LUAD whose increased expression could render patients with LUAD a high risk of cancer recurrence and poor survival, suggesting that they might be applied as potential targets for LUAD treatment.
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16
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Mills CC, Kolb EA, Sampson VB. Recent Advances of Cell-Cycle Inhibitor Therapies for Pediatric Cancer. Cancer Res 2017; 77:6489-6498. [PMID: 29097609 DOI: 10.1158/0008-5472.can-17-2066] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/24/2017] [Accepted: 09/19/2017] [Indexed: 12/21/2022]
Abstract
This review describes the pivotal roles of cell-cycle and checkpoint regulators and discusses development of specific cell-cycle inhibitors for therapeutic use for pediatric cancer. The mechanism of action as well as the safety and tolerability of drugs in pediatric patients, including compounds that target CDK4/CDK6 (palbociclib, ribociclib, and abemaciclib), aurora kinases (AT9283 and MLN8237), Wee1 kinase (MK-1775), KSP (ispinesib), and tubulin (taxanes, vinca alkaloids), are presented. The design of mechanism-based combinations that exploit the cross-talk of signals activated by cell-cycle arrest, as well as pediatric-focused drug development, are critical for the advancement of drugs for rare childhood diseases. Cancer Res; 77(23); 6489-98. ©2017 AACR.
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Affiliation(s)
| | - E A Kolb
- Nemours Center for Cancer and Blood Disorders, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Valerie B Sampson
- Nemours Center for Cancer and Blood Disorders, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware.
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17
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Kistner L, Doll D, Holtorf A, Nitsche U, Janssen KP. Interferon-inducible CXC-chemokines are crucial immune modulators and survival predictors in colorectal cancer. Oncotarget 2017; 8:89998-90012. [PMID: 29163806 PMCID: PMC5685727 DOI: 10.18632/oncotarget.21286] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 08/26/2017] [Indexed: 12/22/2022] Open
Abstract
Tumor-infiltrating T-cells are strongly associated with prognosis in colorectal cancer, but the mechanisms governing intratumoral lymphocyte recruitment are unclear. We investigated the clinical relevance and functional contribution of interferon-regulated CXC-chemokines CXCL9, CXCL10, and CXCL11, described as T-cells attractants. Their expression was significantly elevated in tumors as compared to normal colon in 163 patients with colon cancer, represented an independent positive predictor of post-operative survival, and was highly significantly correlated with the presence of tumor-infiltrating cytotoxic CD8+ T-cells and CD4+ TH1-effector cells. The regulation of chemokine expression was investigated in established cell lines and in tissue explants from resected tumor specimen (n=22). All colorectal cancer cell lines tested, as well as stroma or endothelial cells, produced CXC-chemokines in response to cytokine stimulation. Moreover, resected tumor explants could be stimulated to produce CXC-chemokines, even in cases with initially low CXC-levels. Lastly, a causative role of chemokine expression was evaluated with an orthotopic mouse model, based on isogenic rectal CT26 cancer cells, engineered to express CXCL10. The orthotopic model demonstrated a protective and anti-metastatic role of intratumoral CXCL10 expression, mediated mainly by adaptive immunity.
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Affiliation(s)
- Larissa Kistner
- Department of Surgery, Klinikum rechts der Isar, TUM, Munich, Germany
| | - Dietrich Doll
- Department of Surgery, Klinikum rechts der Isar, TUM, Munich, Germany.,Current/Present Address: St. Marienhospital Vechta, Vechta, Germany
| | - Anne Holtorf
- Department of Surgery, Klinikum rechts der Isar, TUM, Munich, Germany
| | - Ulrich Nitsche
- Department of Surgery, Klinikum rechts der Isar, TUM, Munich, Germany
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18
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Liu R, Zhang W, Liu ZQ, Zhou HH. Associating transcriptional modules with colon cancer survival through weighted gene co-expression network analysis. BMC Genomics 2017; 18:361. [PMID: 28486948 PMCID: PMC5424422 DOI: 10.1186/s12864-017-3761-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 05/03/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Colon cancer (CC) is a heterogeneous disease influenced by complex gene networks. As such, the relationship between networks and CC should be elucidated to obtain further insights into tumour biology. RESULTS Weighted gene co-expression network analysis, a powerful technique used to extract co-expressed gene networks from mRNA expressions, was conducted to identify 11 co-regulated modules in a discovery dataset with 461 patients. A transcriptional module enriched in cell cycle processes was correlated with the recurrence-free survival of the CC patients in the discovery (HR = 0.59; 95% CI = 0.42-0.81) and validation (HR = 0.51; 95% CI = 0.25-1.05) datasets. The prognostic potential of the hub gene Centromere Protein-A (CENPA) was also identified and the upregulation of this gene was associated with good survival. Another cell cycle phase-related gene module was correlated with the survival of the patients with a KRAS mutation CC subtype. The downregulation of several genes, including those found in this co-expression module, such as cyclin-dependent kinase 1 (CDK1), was associated with poor survival. CONCLUSION Network-based approaches may facilitate the discovery of biomarkers for the prognosis of a subset of patients with stage II or III CC, these approaches may also help direct personalised therapies.
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Affiliation(s)
- Rong Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008 People’s Republic of China
- Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078 People’s Republic of China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008 People’s Republic of China
- Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078 People’s Republic of China
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008 People’s Republic of China
- Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078 People’s Republic of China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008 People’s Republic of China
- Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078 People’s Republic of China
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19
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Waks Z, Weissbrod O, Carmeli B, Norel R, Utro F, Goldschmidt Y. Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins. Sci Rep 2016; 6:38988. [PMID: 28008934 PMCID: PMC5180091 DOI: 10.1038/srep38988] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/07/2016] [Indexed: 12/18/2022] Open
Abstract
Compiling a comprehensive list of cancer driver genes is imperative for oncology diagnostics and drug development. While driver genes are typically discovered by analysis of tumor genomes, infrequently mutated driver genes often evade detection due to limited sample sizes. Here, we address sample size limitations by integrating tumor genomics data with a wide spectrum of gene-specific properties to search for rare drivers, functionally classify them, and detect features characteristic of driver genes. We show that our approach, CAnceR geNe similarity-based Annotator and Finder (CARNAF), enables detection of potentially novel drivers that eluded over a dozen pan-cancer/multi-tumor type studies. In particular, feature analysis reveals a highly concentrated pool of known and putative tumor suppressors among the <1% of genes that encode very large, chromatin-regulating proteins. Thus, our study highlights the need for deeper characterization of very large, epigenetic regulators in the context of cancer causality.
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Affiliation(s)
- Zeev Waks
- Machine Learning for Healthcare and Life Sciences, IBM Research - Haifa, Mount Carmel Campus, Israel
| | - Omer Weissbrod
- Machine Learning for Healthcare and Life Sciences, IBM Research - Haifa, Mount Carmel Campus, Israel
| | - Boaz Carmeli
- Machine Learning for Healthcare and Life Sciences, IBM Research - Haifa, Mount Carmel Campus, Israel
| | - Raquel Norel
- Computational Biology Center, IBM T. J. Watson Research, Yorktown Heights, NY 10598, USA
| | - Filippo Utro
- Computational Biology Center, IBM T. J. Watson Research, Yorktown Heights, NY 10598, USA
| | - Yaara Goldschmidt
- Machine Learning for Healthcare and Life Sciences, IBM Research - Haifa, Mount Carmel Campus, Israel
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20
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Xue X, Ramakrishnan SK, Weisz K, Triner D, Xie L, Attili D, Pant A, Győrffy B, Zhan M, Carter-Su C, Hardiman KM, Wang TD, Dame MK, Varani J, Brenner D, Fearon ER, Shah YM. Iron Uptake via DMT1 Integrates Cell Cycle with JAK-STAT3 Signaling to Promote Colorectal Tumorigenesis. Cell Metab 2016; 24:447-461. [PMID: 27546461 PMCID: PMC5023486 DOI: 10.1016/j.cmet.2016.07.015] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 06/07/2016] [Accepted: 07/20/2016] [Indexed: 12/31/2022]
Abstract
Dietary iron intake and systemic iron balance are implicated in colorectal cancer (CRC) development, but the means by which iron contributes to CRC are unclear. Gene expression and functional studies demonstrated that the cellular iron importer, divalent metal transporter 1 (DMT1), is highly expressed in CRC through hypoxia-inducible factor 2α-dependent transcription. Colon-specific Dmt1 disruption resulted in a tumor-selective inhibitory effect of proliferation in mouse colon tumor models. Proteomic and genomic analyses identified an iron-regulated signaling axis mediated by cyclin-dependent kinase 1 (CDK1), JAK1, and STAT3 in CRC progression. A pharmacological inhibitor of DMT1 antagonized the ability of iron to promote tumor growth in a CRC mouse model and a patient-derived CRC enteroid orthotopic model. Our studies implicate a growth-promoting signaling network instigated by elevated intracellular iron levels in tumorigenesis, offering molecular insights into how a key dietary component may contribute to CRC.
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Affiliation(s)
- Xiang Xue
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sadeesh K Ramakrishnan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kevin Weisz
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel Triner
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Liwei Xie
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Durga Attili
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Asha Pant
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest 1117, Hungary; 2nd Department of Pediatrics, Semmelweis University, Budapest 1085, Hungary
| | - Mingkun Zhan
- Department of Plastic Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, China
| | - Christin Carter-Su
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karin M Hardiman
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas D Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael K Dame
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - James Varani
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dean Brenner
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eric R Fearon
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yatrik M Shah
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
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Identification of Phosphorylated Cyclin-Dependent Kinase 1 Associated with Colorectal Cancer Survival Using Label-Free Quantitative Analyses. PLoS One 2016; 11:e0158844. [PMID: 27383761 PMCID: PMC4934865 DOI: 10.1371/journal.pone.0158844] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 06/22/2016] [Indexed: 01/16/2023] Open
Abstract
Colorectal cancer is the most common form of cancer in the world, and the five-year survival rate is estimated to be almost 90% in the early stages. Therefore, the identification of potential biomarkers to assess the prognosis of early stage colorectal cancer patients is critical for further clinical treatment. Dysregulated tyrosine phosphorylation has been found in several diseases that play a significant regulator of signaling in cellular pathways. In this study, this strategy was used to characterize the tyrosine phosphoproteome of colorectal cell lines with different progression abilities (SW480 and SW620). We identified a total of 280 phosphotyrosine (pTyr) peptides comprising 287 pTyr sites from 261 proteins. Label-free quantitative analysis revealed the differential level of a total of 103 pTyr peptides between SW480 and SW620 cells. We showed that cyclin-dependent kinase I (CDK1) pTyr15 level in SW480 cells was 3.3-fold greater than in SW620 cells, and these data corresponded with the label-free mass spectrometry-based proteomic quantification analysis. High level CDK1 pTyr15 was associated with prolonged disease-free survival for stage II colorectal cancer patients (n = 79). Taken together, our results suggest that the CDK1 pTyr15 protein is a potential indicator of the progression of colorectal cancer.
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22
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Geyer PE, Maak M, Nitsche U, Perl M, Novotny A, Slotta-Huspenina J, Dransart E, Holtorf A, Johannes L, Janssen KP. Gastric Adenocarcinomas Express the Glycosphingolipid Gb3/CD77: Targeting of Gastric Cancer Cells with Shiga Toxin B-Subunit. Mol Cancer Ther 2016; 15:1008-17. [PMID: 26826119 DOI: 10.1158/1535-7163.mct-15-0633] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 01/15/2016] [Indexed: 11/16/2022]
Abstract
The B-subunit of the bacterial Shiga toxin (STxB), which is nontoxic and has low immunogenicity, can be used for tumor targeting of breast, colon, and pancreatic cancer. Here, we tested whether human gastric cancers, which are among the most aggressive tumor entities, express the cellular receptor of Shiga toxin, the glycosphingolipid globotriaosylceramide (Gb3/CD77). The majority of cases showed an extensive staining for Gb3 (36/50 cases, 72%), as evidenced on tissue sections of surgically resected specimen. Gb3 expression was detected independent of type (diffuse/intestinal), and was negatively correlated to increasing tumor-node-metastasis stages (P = 0.0385), as well as with markers for senescence. Gb3 expression in nondiseased gastric mucosa was restricted to chief and parietal cells at the bottom of the gastric glands, and was not elevated in endoscopic samples of gastritis (n = 10). Gb3 expression in established cell lines of gastric carcinoma was heterogeneous, with 6 of 10 lines being positive, evidenced by flow cytometry. STxB was taken up rapidly by live Gb3-positive gastric cancer cells, following the intracellular retrograde transport route, avoiding lysosomes and rapidly reaching the Golgi apparatus and the endoplasmic reticulum. Treatment of the Gb3-expressing gastric carcinoma cell line St3051 with STxB coupled to SN38, the active metabolite of the topoisomerase type I inhibitor irinotecan, resulted in >100-fold increased cytotoxicity, as compared with irinotecan alone. No cytotoxicity was observed on gastric cancer cell lines lacking Gb3 expression, demonstrating receptor specificity of the STxB-SN38 compound. Thus, STxB is a highly specific transport vehicle for cytotoxic agents in gastric carcinoma. Mol Cancer Ther; 15(5); 1008-17. ©2016 AACR.
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Affiliation(s)
- Philipp Emanuel Geyer
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Matthias Maak
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Ulrich Nitsche
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Markus Perl
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Alexander Novotny
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Julia Slotta-Huspenina
- Institute of Pathology and Pathological Anatomy, Technische Universität München, Munich, Germany
| | - Estelle Dransart
- Endocytic Trafficking and Intracellular Delivery team, Institut Curie, Paris, France. CNRS UMR3666, Paris, France. INSERM U1143, Paris, France
| | - Anne Holtorf
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Ludger Johannes
- Endocytic Trafficking and Intracellular Delivery team, Institut Curie, Paris, France. CNRS UMR3666, Paris, France. INSERM U1143, Paris, France
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
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23
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Loregger A, Grandl M, Mejías-Luque R, Allgäuer M, Degenhart K, Haselmann V, Oikonomou C, Hatzis P, Janssen KP, Nitsche U, Gradl D, van den Broek O, Destree O, Ulm K, Neumaier M, Kalali B, Jung A, Varela I, Schmid RM, Rad R, Busch DH, Gerhard M. The E3 ligase RNF43 inhibits Wnt signaling downstream of mutated β-catenin by sequestering TCF4 to the nuclear membrane. Sci Signal 2015; 8:ra90. [PMID: 26350900 DOI: 10.1126/scisignal.aac6757] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Given its fundamental role in development and cancer, the Wnt-β-catenin signaling pathway is tightly controlled at multiple levels. RING finger protein 43 (RNF43) is an E3 ubiquitin ligase originally found in stem cells and proposed to inhibit Wnt signaling by interacting with the Wnt receptors of the Frizzled family. We detected endogenous RNF43 in the nucleus of human intestinal crypt and colon cancer cells. We found that RNF43 physically interacted with T cell factor 4 (TCF4) in cells and tethered TCF4 to the nuclear membrane, thus silencing TCF4 transcriptional activity even in the presence of constitutively active mutants of β-catenin. This inhibitory mechanism was disrupted by the expression of RNF43 bearing mutations found in human gastrointestinal tumors, and transactivation of the Wnt pathway was observed in various cells and in Xenopus embryos when the RING domain of RNF43 was mutated. Our findings indicate that RNF43 inhibits the Wnt pathway downstream of oncogenic mutations that activate the pathway. Mimicking or enhancing this inhibitory activity of RNF43 may be useful to treat cancers arising from aberrant activation of the Wnt pathway.
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Affiliation(s)
- Anke Loregger
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich 81675, Germany
| | - Martina Grandl
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich 81675, Germany
| | - Raquel Mejías-Luque
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich 81675, Germany
| | - Michael Allgäuer
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich 81675, Germany. Medical Department II, Technische Universität München, Munich 81675, Germany
| | - Kathrin Degenhart
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich 81675, Germany
| | - Verena Haselmann
- Institute for Clinical Chemistry, University Medical Centre Mannheim, Mannheim 68167, Germany
| | - Christina Oikonomou
- Division of Molecular Biology and Genetics, Biomedical Sciences Research Center "Alexander Fleming," Vari 16672, Greece
| | - Pantelis Hatzis
- Division of Molecular Biology and Genetics, Biomedical Sciences Research Center "Alexander Fleming," Vari 16672, Greece
| | - Klaus-Peter Janssen
- Department of Surgery, Technische Universität München, Munich 81675, Germany
| | - Ulrich Nitsche
- Department of Surgery, Technische Universität München, Munich 81675, Germany
| | - Dietmar Gradl
- Zoologisches Institut II, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | | | | | - Kurt Ulm
- Institute of Medical Statistics and Epidemiology, Technische Universität München, Munich 81675, Germany
| | - Michael Neumaier
- Institute for Clinical Chemistry, University Medical Centre Mannheim, Mannheim 68167, Germany
| | - Behnam Kalali
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich 81675, Germany
| | - Andreas Jung
- Institute of Pathology, University of Munich, Munich 80337, Germany
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria, Santander 39011, Spain
| | - Roland M Schmid
- Medical Department II, Technische Universität München, Munich 81675, Germany
| | - Roland Rad
- Medical Department II, Technische Universität München, Munich 81675, Germany
| | - Dirk H Busch
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich 81675, Germany
| | - Markus Gerhard
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich 81675, Germany.
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24
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The expression of CDK1 is associated with proliferation and can be a prognostic factor in epithelial ovarian cancer. Tumour Biol 2015; 36:4939-48. [PMID: 25910705 DOI: 10.1007/s13277-015-3141-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 01/19/2015] [Indexed: 12/11/2022] Open
Abstract
Overexpression of cyclin-dependent kinase 1 (CDK1) has been noted to correlation with several human cancers. However, the effects of CDK1 on ovarian cancer development remain unclear. The aim of this study was to examine the effect of CDK1 and related mechanism in the proliferation and resistance to chemotherapeutic drugs of epithelial ovarian cancer (EOC). Immunohistochemical analysis was performed in 119 human ovarian cancer samples, and the data were correlated with clinicopathologic features. Furthermore, Western blot analysis was performed for CDK1 in EOC samples and cell lines to evaluate their protein levels and molecular interaction. Kaplan-Meier survival analysis showed that strong expression of CDK1 exhibited a significant correlation with poor prognosis in human EOC (P = 0.02). Meanwhile, we found that knockdown CDK1 by shCDK1 promoted the apoptosis rate and increased the sensitivity to chemotherapy drugs. Thus, CDK1 might serve as a prognostic marker, and it might be of great value for experimental therapies in EOC.
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25
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Aleem E, Arceci RJ. Targeting cell cycle regulators in hematologic malignancies. Front Cell Dev Biol 2015; 3:16. [PMID: 25914884 PMCID: PMC4390903 DOI: 10.3389/fcell.2015.00016] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/25/2015] [Indexed: 12/20/2022] Open
Abstract
Hematologic malignancies represent the fourth most frequently diagnosed cancer in economically developed countries. In hematologic malignancies normal hematopoiesis is interrupted by uncontrolled growth of a genetically altered stem or progenitor cell (HSPC) that maintains its ability of self-renewal. Cyclin-dependent kinases (CDKs) not only regulate the mammalian cell cycle, but also influence other vital cellular processes, such as stem cell renewal, differentiation, transcription, epigenetic regulation, apoptosis, and DNA repair. Chromosomal translocations, amplification, overexpression and altered CDK activities have been described in different types of human cancer, which have made them attractive targets for pharmacological inhibition. Mouse models deficient for one or more CDKs have significantly contributed to our current understanding of the physiological functions of CDKs, as well as their roles in human cancer. The present review focuses on selected cell cycle kinases with recent emerging key functions in hematopoiesis and in hematopoietic malignancies, such as CDK6 and its role in MLL-rearranged leukemia and acute lymphocytic leukemia, CDK1 and its regulator WEE-1 in acute myeloid leukemia (AML), and cyclin C/CDK8/CDK19 complexes in T-cell acute lymphocytic leukemia. The knowledge gained from gene knockout experiments in mice of these kinases is also summarized. An overview of compounds targeting these kinases, which are currently in clinical development in various solid tumors and hematopoietic malignances, is presented. These include the CDK4/CDK6 inhibitors (palbociclib, LEE011, LY2835219), pan-CDK inhibitors that target CDK1 (dinaciclib, flavopiridol, AT7519, TG02, P276-00, terampeprocol and RGB 286638) as well as the WEE-1 kinase inhibitor, MK-1775. The advantage of combination therapy of cell cycle inhibitors with conventional chemotherapeutic agents used in the treatment of AML, such as cytarabine, is discussed.
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Affiliation(s)
- Eiman Aleem
- Department of Child Health, The Ronald A. Matricaria Institute of Molecular Medicine at Phoenix Children's Hospital, University of Arizona College of Medicine-Phoenix Phoenix, AZ, USA ; Department of Zoology, Faculty of Science, Alexandria University Alexandria, Egypt
| | - Robert J Arceci
- Department of Child Health, The Ronald A. Matricaria Institute of Molecular Medicine at Phoenix Children's Hospital, University of Arizona College of Medicine-Phoenix Phoenix, AZ, USA
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26
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Mikhail S, Albanese C, Pishvaian MJ. Cyclin-dependent kinase inhibitors and the treatment of gastrointestinal cancers. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:1185-97. [PMID: 25747534 DOI: 10.1016/j.ajpath.2015.01.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/23/2014] [Accepted: 01/13/2015] [Indexed: 01/14/2023]
Abstract
The cell cycle is a highly conserved and tightly regulated biological system that controls cellular proliferation and differentiation. The cell cycle regulatory proteins, which include the cyclins, the cyclin-dependent kinases (CDKs), and the CDK inhibitors, are critical for the proper temporal and spatial regulation of cellular proliferation. Conversely, alterations in cell cycle regulatory proteins, leading to the loss of normal cell-cycle control, are a hallmark of many cancers, including gastrointestinal cancers. Accordingly, overexpression of CDKs and cyclins and by contrast loss of CDK inhibitors, are all linked to gastrointestinal cancers and are often associated with less favorable prognoses and outcomes. Because of the importance that the cell cycle regulatory proteins play in tumorigenesis, currently there is a broad spectrum of cell-cycle inhibitors under development that, as a group, hold promise as effective cancer treatments. In support of this approach to cancer treatment, the growing availability of molecular diagnostics techniques may help in identifying patients who have driving abnormalities in the cell-cycle machinery and are thus more likely to respond to cell-cycle inhibitors. In this review, we discuss the prevalence of cell-cycle abnormalities in patients with gastrointestinal cancers and provide a preclinical and clinical overview of new agents that target cell-cycle abnormalities with a special emphasis on gastrointestinal cancers.
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Affiliation(s)
- Sameh Mikhail
- James Cancer Hospital and Solove Research Institute, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Christopher Albanese
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia; Department of Pathology, Georgetown University Medical Center, Washington, District of Columbia.
| | - Michael J Pishvaian
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
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27
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Sung WW, Lin YM, Wu PR, Yen HH, Lai HW, Su TC, Huang RH, Wen CK, Chen CY, Chen CJ, Yeh KT. High nuclear/cytoplasmic ratio of Cdk1 expression predicts poor prognosis in colorectal cancer patients. BMC Cancer 2014; 14:951. [PMID: 25511643 PMCID: PMC4302138 DOI: 10.1186/1471-2407-14-951] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/11/2014] [Indexed: 11/30/2022] Open
Abstract
Background Cdk1 (cyclin-dependent kinase 1) is critical regulator of the G2-M checkpoint. Cyclin-dependent kinase pathways are considered possible targets for cancer treatment; however, the prognostic role of Cdk1 in colorectal cancer is still controversial. Therefore, we attempted to determine the impact of Cdk1 on the clinical outcome of colorectal cancer patients to further identify its role in colorectal cancer. Methods Cdk1 immunoreactivity was analyzed by immunohistochemistry (IHC) in 164 cancer specimens from primary colorectal cancer patients. The medium follow-up time after surgery was 3.7 years (range: 0.01 to 13.10 years). The prognostic value of Cdk1 on overall survival was determined by Kaplan-Meier analysis and Cox proportional hazard models. Results All samples displayed detectable Cdk1 expression with predominant location in the cytoplasm and nucleus. A high Cdk1 nuclear/cytoplasmic (N/C) expression ratio was correlated with poor overall survival (5-year survival rate: 26.3% vs 46.9%, N/C ratio ≥1.5 vs N/C ratio <1.5, log-rank p = 0.027). Accordingly, a Cdk1 N/C expression ratio ≥1.5 was identified as an independent risk factor by multivariate analysis (hazard ratio = 1.712, P = 0.039). Conclusions We suggest that Cdk1 N/C expression ratio determined by IHC staining could be an independent prognostic marker for colorectal cancer. Electronic supplementary material The online version of this article (doi:10.1186/1471-2407-14-951) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Chih-Jung Chen
- School of Medicine, Chung Shan Medical University, Taichuang, Taiwan.
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28
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Benard A, Goossens-Beumer IJ, van Hoesel AQ, Horati H, de Graaf W, Putter H, Zeestraten ECM, Liefers GJ, van de Velde CJH, Kuppen PJK. Nuclear expression of histone deacetylases and their histone modifications predicts clinical outcome in colorectal cancer. Histopathology 2014; 66:270-82. [PMID: 25307864 DOI: 10.1111/his.12534] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/14/2014] [Indexed: 12/17/2022]
Abstract
AIMS Epigenetic changes are of crucial importance in cancer development and are potentially reversible; they are therefore targets of interest for anti-cancer therapy. The aim of this study was to investigate the clinical prognostic value of the histone deacetylases SIRT1, HDAC1 and HDAC2 and the histone modifications H4K16Ac and H3K56Ac in colorectal cancer. METHODS AND RESULTS The epigenetic markers were immunohistochemically stained on tissue microarrays containing colorectal tumours (n = 254) and normal colorectal tissues (n = 50). Nuclear expression was assessed on the semi-automated Ariol system. Multivariate trend survival analyses of the combined markers showed better patient survival and less tumour recurrence when more markers showed high nuclear expression. For the combination of the histone deacetylases and H3K56Ac, the hazard ratio (HR) for overall survival (OS) was 0.82 [95% confidence interval (CI) 0.72-0.94; P = 0.005] and the HR for distant recurrence-free survival (DRFS) was 0.77 (95% CI 0.64-0.92; P = 0.003) per additional marker showing high expression. Similarly, for the combination of histone deactylases and H4K16Ac, HRs of 0.86 (95% CI 0.76-0.97; P = 0.01) for OS and 0.79 (95% CI 0.68-0.93; P = 0.006) for DRFS were observed per additional marker showing high expression. CONCLUSIONS The studied epigenetic markers showed clinical prognostic value in colorectal cancer, both as individual markers and when combined into multimarker analyses. These results indicate that epigenetic mechanisms play an important role in colorectal carcinogenesis.
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Affiliation(s)
- Anne Benard
- Department of Surgical Oncology, Leiden University Medical Centre, Leiden, The Netherlands
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29
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Goossens-Beumer IJ, Derr RS, Buermans HPJ, Goeman JJ, Böhringer S, Morreau H, Nitsche U, Janssen KP, van de Velde CJH, Kuppen PJK. MicroRNA classifier and nomogram for metastasis prediction in colon cancer. Cancer Epidemiol Biomarkers Prev 2014; 24:187-97. [PMID: 25315964 DOI: 10.1158/1055-9965.epi-14-0544-t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Colon cancer prognosis and treatment are currently based on a classification system still showing large heterogeneity in clinical outcome, especially in TNM stages II and III. Prognostic biomarkers for metastasis risk are warranted as development of distant recurrent disease mainly accounts for the high lethality rates of colon cancer. miRNAs have been proposed as potential biomarkers for cancer. Furthermore, a verified standard for normalization of the amount of input material in PCR-based relative quantification of miRNA expression is lacking. METHODS A selection of frozen tumor specimens from two independent patient cohorts with TNM stage II-III microsatellite stable primary adenocarcinomas was used for laser capture microdissection. Next-generation sequencing was performed on small RNAs isolated from colorectal tumors from the Dutch cohort (N = 50). Differential expression analysis, comparing in metastasized and nonmetastasized tumors, identified prognostic miRNAs. Validation was performed on colon tumors from the German cohort (N = 43) using quantitative PCR (qPCR). RESULTS miR25-3p and miR339-5p were identified and validated as independent prognostic markers and used to construct a multivariate nomogram for metastasis risk prediction. The nomogram showed good probability prediction in validation. In addition, we recommend combination of miR16-5p and miR26a-5p as standard for normalization in qPCR of colon cancer tissue-derived miRNA expression. CONCLUSIONS In this international study, we identified and validated a miRNA classifier in primary cancers, and propose a nomogram capable of predicting metastasis risk in microsatellite stable TNM stage II-III colon cancer. IMPACT In conjunction with TNM staging, by means of a nomogram, this miRNA classifier may allow for personalized treatment decisions based on individual tumor characteristics.
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Affiliation(s)
| | - Remco S Derr
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Henk P J Buermans
- Department of Human Genetics/Leiden Genome Technology Center, Leiden University Medical Center, Leiden, the Netherlands
| | - Jelle J Goeman
- Biostatistics, Department for Health Evidence, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Stefan Böhringer
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ulrich Nitsche
- Department of Surgery, Klinikum rechts der Isar, Technical University München, Munich, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum rechts der Isar, Technical University München, Munich, Germany
| | | | - Peter J K Kuppen
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands.
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30
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Kubo H, Suzuki T, Matsushima T, Ishihara H, Uchino K, Suzuki S, Tada S, Yoshimura M, Kondo T. Cyclin-dependent kinase-specific activity predicts the prognosis of stage I and stage II non-small cell lung cancer. BMC Cancer 2014; 14:755. [PMID: 25301183 PMCID: PMC4198674 DOI: 10.1186/1471-2407-14-755] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 10/03/2014] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Lung cancer is one of the leading causes of cancer death worldwide. Even with complete resection, the prognosis of early-stage non-small cell lung cancer is poor due to local and distant recurrence, and it remains unclear which biomarkers are clinically useful for predicting recurrence or for determining the efficacy of chemotherapy. Recently, several lines of evidence have indicated that the enzymatic activity of cyclin-dependent kinases could be a clinically relevant prognostic marker for some cancers. We investigated whether the specific activity of cyclin-dependent kinases 1 and 2 could predict recurrence or death in early non-small cell lung cancer patients. METHODS Patients with newly diagnosed, pathologically confirmed non-small cell lung cancer were entered into this blinded cohort study. The activity of cyclin-dependent kinases was determined in 171 samples by the C2P® assay, and the results were subjected to statistical analysis with recurrence or death as a clinical outcome. RESULTS The Cox proportional hazards model revealed that the activity of cyclin-dependent kinase 1, but not 2, was a predictor of recurrence, independent of sex, age, and stage. By contrast, cyclin-dependent kinase 2 activity was a predictor of death, independent of sex and stage. CONCLUSION This study suggested the possible clinical use of cyclin-dependent kinase 1 as a predictor of recurrence and cyclin-dependent kinase 2 as a predictor of overall survival in early-stage non-small cell lung cancer. Thus, a combination of activity of cyclin-dependent kinases 1 and 2 is useful in decision-making regarding treatment strategies for non-small cell lung cancer after surgery.
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Affiliation(s)
- Hiroshi Kubo
- Department of Advanced Preventive Medicine for Infectious Disease, Tohoku University Graduate School of Medicine, 2-1 Seiryoumachi, Aobaku, Sendai 980-8575, Japan.
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31
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Combined analysis of biomarkers of proliferation and apoptosis in colon cancer: an immunohistochemistry-based study using tissue microarray. Int J Colorectal Dis 2014; 29:1043-52. [PMID: 24950792 DOI: 10.1007/s00384-014-1930-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/12/2014] [Indexed: 02/04/2023]
Abstract
BACKGROUND Disturbance of the balance between proliferation and apoptosis is an important hallmark of tumor development. The goal of this study was to develop a descriptive parameter that represents this imbalance and relate this parameter to clinical outcome in all four stages of colon cancer. MATERIAL AND METHODS The study population consisted of 285 stage I-IV colon cancer patients of which a tumor tissue microarray (TMA) was available. TMA sections were immunohistochemically stained and quantified for the presence of Ki67 and cleaved caspase-3 tumor expression. These results were used to develop the combined apoptosis proliferation (CAP) parameter and correlated to patient outcome. RESULTS The CAP parameter was significantly related to clinical outcome; patients with CAP ++ (high level of both apoptosis and proliferation) showed the best outcome perspectives (overall survival (OS), p = 0.004 and disease-free survival (DFS), p = 0.009). The effect of the CAP parameter was related to tumor microsatellite status and indirectly to tumor location, where left-sided tumors with CAP + - (high level of proliferation, low level of apoptosis) showed a worse prognosis (DFS p value 0.02) and right-sided tumors with CAP + - had a better prognosis (DFS p value 0.032). With stratified analyses, the CAP parameter remained significant in stage II tumors only. CONCLUSIONS The CAP parameter, representing outcome of the balance between the level of apoptosis and proliferation, can be used as a prognostic marker in colon cancer patients for both DFS and OS, particularly in left-sided, microsatellite stable tumors when tumor-node-metastasis (TNM) stage is taken into account.
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32
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Clinical prognostic value of combined analysis of Aldh1, Survivin, and EpCAM expression in colorectal cancer. Br J Cancer 2014; 110:2935-44. [PMID: 24786601 PMCID: PMC4056050 DOI: 10.1038/bjc.2014.226] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/28/2014] [Accepted: 04/08/2014] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Tumour aggressiveness might be related to the degree of main cancer hallmark acquirement of tumour cells, reflected by expression levels of specific biomarkers. We investigated the expression of Aldh1, Survivin, and EpCAM, together reflecting main cancer hallmarks, in relation to clinical outcome of colorectal cancer (CRC) patients. METHODS Immunohistochemistry was performed using a tumour tissue microarray of TNM (Tumour, Node, Metastasis)-stage I-IV CRC tissues. Single-marker expression or their combination was assessed for associations with the clinical outcome of CRC patients (N=309). RESULTS Increased expression of Aldh1 or Survivin, or decreased expression of EpCAM was each associated with poor clinical outcome, and was therefore identified as clinically unfavourable expression. Analyses of the combination of all three markers showed worse clinical outcome, specifically in colon cancer patients, with an increasing number of markers showing unfavourable expression. Hazard ratios ranged up to 8.3 for overall survival (P<0.001), 36.6 for disease-specific survival (P<0.001), and 27.1 for distant recurrence-free survival (P<0.001). CONCLUSIONS Our data identified combined expression levels of Aldh1, Survivin, and EpCAM as strong independent prognostic factors, with high hazard ratios, for survival and tumour recurrence in colon cancer patients, and therefore reflect tumour aggressiveness.
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Malinowsky K, Nitsche U, Janssen KP, Bader FG, Späth C, Drecoll E, Keller G, Höfler H, Slotta-Huspenina J, Becker KF. Activation of the PI3K/AKT pathway correlates with prognosis in stage II colon cancer. Br J Cancer 2014; 110:2081-9. [PMID: 24619078 PMCID: PMC3992486 DOI: 10.1038/bjc.2014.100] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 11/05/2013] [Accepted: 01/28/2014] [Indexed: 12/27/2022] Open
Abstract
Background: Patients with UICC/AJCC stage II colon cancer have a high 5-year overall survival rate after surgery. Nevertheless, a significant subgroup of patients develops tumour recurrence. Currently, there are no clinically established biomarkers available to identify this patient group. We applied reverse-phase protein arrays (RPPA) for phosphatidylinositide-3-kinase pathway activation mapping to stratify patients according to their risk of tumour recurrence after surgery. Methods: Full-length proteins were extracted from formalin-fixed, paraffin-embedded tissue samples of 118 patients who underwent curative resection. RPPA technology was used to analyse expression and/or phosphorylation levels of six major factors of the phosphatidylinositide-3-kinase pathway. Oncogenic mutations of KRAS and BRAF, and DNA microsatellite status, currently discussed as prognostic markers, were analysed in parallel. Results: Expression of phospho-AKT (HR=3.52; P=0.032), S6RP (HR=6.3; P=0.044), and phospho-4E-BP1 (HR=4.12; P=0.011) were prognostic factors for disease-free survival. None of the molecular genetic alterations were significantly associated with prognosis. Conclusions: Our data indicate that activation of the PI3K/AKT pathway evidenced on the protein level might be a valuable prognostic marker to stratify patients for their risk of tumour recurrence. Beside adjuvant chemotherapy targeting of upregulated PI3K/AKT signalling may be an attractive strategy for treatment of high-risk patients.
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Affiliation(s)
- K Malinowsky
- Department of Pathology, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - U Nitsche
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - K-P Janssen
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - F G Bader
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - C Späth
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - E Drecoll
- Department of Pathology, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - G Keller
- Department of Pathology, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - H Höfler
- 1] Department of Pathology, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany [2] Department of Pathology, Helmholtz-Centre Munich, Ingolstädter Landstrasse 1, 85764 Munich, Germany
| | - J Slotta-Huspenina
- Department of Pathology, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - K-F Becker
- Department of Pathology, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
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Wang SA, Hung CY, Chuang JY, Chang WC, Hsu TI, Hung JJ. Phosphorylation of p300 increases its protein degradation to enhance the lung cancer progression. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1135-49. [PMID: 24530506 DOI: 10.1016/j.bbamcr.2014.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 01/21/2014] [Accepted: 02/02/2014] [Indexed: 01/05/2023]
Abstract
p300 is a transcription cofactor for a number of nuclear proteins. Most studies of p300 have focused on the regulation of its function, which primarily includes its role as a transcription co-factor for a number of nuclear proteins. In this study, we found that p300 was highly phosphorylated and its level was decreased during mitosis and tumorigenesis. In vitro and in vivo experiments aimed showed that cyclin-dependent kinase 1 (CDK1) and ERK1/2 phosphorylated p300 on Ser1038 and Ser2039. Mutations of Ser1038 and Ser2039 increased p300 protein stability and levels. Inhibition of p300 degradation by blocking its phosphorylation decreased the proliferation and metastasis activity of lung cancer cells, indicating that p300 acts as a tumor suppressor in lung cancer tumorigenesis. Investigation of the molecular mechanism showed that blocking p300 phosphorylation disrupted chromatin condensation and the increased the acetylation of histone H3. Analysis of cell cycle progression in HA-p300-S2A-expressing cells by flow cytometry showed that the p300 mutants arrested the cells at S-phase or delayed the mitotic entry and exit. The expression of several important oncogenes, MMP-9, vimentin, β-catenin, N-cadherin and c-myc, was negatively regulated by p300. In conclusion, during lung tumorigenesis, a phosphorylation-mediated decrease in p300 level enhanced oncogene expression during interphase and decreased histone H3 acetylation during mitosis, which promoted lung cancer progression.
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Affiliation(s)
- Shao-An Wang
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng-Kung University, Tainan 701, Taiwan
| | - Chia-Yang Hung
- Institute of Basic Medical Sciences, College of Medicine, National Cheng-Kung University, Tainan 701, Taiwan
| | - Jian-Ying Chuang
- Neural Regenerative Medicine, College of Medical Sciences and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Wen-Chang Chang
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng-Kung University, Tainan 701, Taiwan; Department of Pharmacology, National Cheng-Kung University, Tainan 701, Taiwan; Institute of Basic Medical Sciences, College of Medicine, National Cheng-Kung University, Tainan 701, Taiwan; Center for Infectious Disease and Signal Transduction, National Cheng-Kung University, Tainan 701, Taiwan; Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Tsung-I Hsu
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng-Kung University, Tainan 701, Taiwan; Center for Infectious Disease and Signal Transduction, National Cheng-Kung University, Tainan 701, Taiwan
| | - Jan-Jong Hung
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng-Kung University, Tainan 701, Taiwan; Department of Pharmacology, National Cheng-Kung University, Tainan 701, Taiwan; Institute of Basic Medical Sciences, College of Medicine, National Cheng-Kung University, Tainan 701, Taiwan; Center for Infectious Disease and Signal Transduction, National Cheng-Kung University, Tainan 701, Taiwan; Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan.
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Zeestraten ECM, Reimers MS, Saadatmand S, Dekker JWT, Liefers GJ, van den Elsen PJ, van de Velde CJH, Kuppen PJK. Combined analysis of HLA class I, HLA-E and HLA-G predicts prognosis in colon cancer patients. Br J Cancer 2014; 110:459-68. [PMID: 24196788 PMCID: PMC3899753 DOI: 10.1038/bjc.2013.696] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Evasion of immune surveillance and suppression of the immune system are important hallmarks of tumour development in colon cancer. The goal of this study was to establish a tumour profile based on biomarkers that reflect a tumour's immune susceptibility status and to determine their relation to patient outcome. METHODS The study population consisted of 285 stage I-IV colon cancer patients of which a tissue micro array (TMA) was available. Sections were immunohistochemically stained for the presence of Foxp3+ cells and tumour expression of HLA Class I (HLA-A, -B, -C) and non-classical HLA-E and HLA-G. All markers were combined for further analyses, resulting in three tumour immune phenotypes: strong immune system tumour recognition, intermediate immune system tumour recognition and poor immune system tumour recognition. RESULTS Loss of HLA class I expression was significantly related to a better OS (P-value 0.005) and DFS (P-value 0.008). Patients with tumours who showed neither HLA class I nor HLA-E or -G expression (phenotype a) had a significant better OS and DFS (P-value <0.001 and 0.001, respectively) compared with phenotype b (OS HR: 4.7, 95% CI: 1.2-19.0, P=0.001) or c (OS HR: 8.2, 95% CI: 2.0-34.2, P=0.0001). Further, the tumour immune phenotype was an independent predictor for OS and DFS (P-value 0.009 and 0.013, respectively). CONCLUSION Tumours showing absence of HLA class I, HLA-E and HLA-G expressions were related to a better OS and DFS. By combining the expression status of several immune-related biomarkers, three tumour immune phenotypes were created that related to patient outcome. These immune phenotypes represented significant, independent, clinical prognostic profiles in colon cancer.
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Affiliation(s)
- E C M Zeestraten
- Department of Surgery, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - M S Reimers
- Department of Surgery, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - S Saadatmand
- Department of Surgery, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - J-W T Dekker
- Department of Surgery, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - G J Liefers
- Department of Surgery, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - P J van den Elsen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
- Department of Pathology, VU University Medical Center, de Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - C J H van de Velde
- Department of Surgery, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - P J K Kuppen
- Department of Surgery, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
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The prognostic value of apoptotic and proliferative markers in breast cancer. Breast Cancer Res Treat 2013; 142:323-39. [DOI: 10.1007/s10549-013-2748-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 10/21/2013] [Indexed: 11/26/2022]
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Affiliation(s)
- Niels Ødum
- Department of International Health, Immunology and Microbiology; Copenhagen University, Copenhagen, Denmark.
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Hedblom A, Laursen KB, Miftakhova R, Sarwar M, Anagnostaki L, Bredberg A, Mongan NP, Gudas LJ, Persson JL. CDK1 interacts with RARγ and plays an important role in treatment response of acute myeloid leukemia. Cell Cycle 2013; 12:1251-66. [PMID: 23518499 PMCID: PMC3674090 DOI: 10.4161/cc.24313] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 03/14/2013] [Indexed: 11/19/2022] Open
Abstract
Alterations in cell cycle pathways and retinoic acid signaling are implicated in leukemogenesis. However, little is known about the roles of cyclin-dependent kinases (CDKs) in treatment response of leukemia. In this study, we observed that CDK1 expression was significantly higher in bone marrow from 42 patients with acute myeloid leukemia (AML) at recurrence than that at first diagnosis (p = 0.04). AML patients had higher level of nuclear CDK1 in their leukemic blasts tended to have poorer clinical outcome compared with those with lower levels. We showed that CDK1 function is required for all-trans retinoic acid (ATRA) to achieve the optimal effect in U-937 human leukemic cells. CDK1 modulates the levels of P27(kip) and AKT phosphorylation in response to ATRA treatment. Further, we show, for the first time, that RARγ in concert with ATRA regulates protein levels of CDK1 and its subcellular localization. The regulation of the subcellular content of CDK1 and RARγ by ATRA is an important process for achieving an effective response in treatment of leukemia. RARγ and CDK1 form a reciprocal regulatory circuit in the nucleus and influence the function and protein stability of each other and the level of P27(kip) protein. In addition, expression of wee1 kinase and Cdc25A/C phosphatases also coincide with CDK1 expression and its subcellular localization in response to ATRA treatment. Our study reveals a novel mechanism by which CDK1 and RARγ coordinate with ATRA to influence cell cycle progression and cellular differentiation.
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Affiliation(s)
- Andreas Hedblom
- Department of Laboratory Medicine; Division of Experimental Cancer Research; Clinical Research Center; Lund University; Malmö, Sweden
| | | | - Regina Miftakhova
- Department of Laboratory Medicine; Division of Experimental Cancer Research; Clinical Research Center; Lund University; Malmö, Sweden
| | - Martuza Sarwar
- Department of Laboratory Medicine; Division of Experimental Cancer Research; Clinical Research Center; Lund University; Malmö, Sweden
| | - Lola Anagnostaki
- Department of Pathology; Lund University; Skåne University Hospital; Malmö, Sweden
| | - Anders Bredberg
- Department of Clinical Microbiology; Lund University; Skåne University Hospital; Malmö, Sweden
| | - Nigel P. Mongan
- Faculty of Medicine and Health Sciences; School of Veterinary Medicine and Sciences; University of Nottingham; Leicestershire, UK
| | - Lorraine J. Gudas
- Department of Pharmacology; Weill Cornell Medical College; New York, NY USA
| | - Jenny L. Persson
- Department of Laboratory Medicine; Division of Experimental Cancer Research; Clinical Research Center; Lund University; Malmö, Sweden
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Integrative marker analysis allows risk assessment for metastasis in stage II colon cancer. Ann Surg 2013; 256:763-71; discussion 771. [PMID: 23095620 DOI: 10.1097/sla.0b013e318272de87] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Individualized risk assessment in patients with UICC stage II colon cancer based on a panel of molecular genetic alterations. BACKGROUND Risk assessment in patients with colon cancer and localized disease (UICC stage II) is not sufficiently reliable. Development of metachronous metastasis is assumed to be governed largely by individual tumor genetics. METHODS Fresh frozen tissue from 232 patients (T3-4, N0, M0) with complete tumor resection and a median follow-up of 97 months was analyzed for microsatellite stability, KRAS exon 2, and BRAF exon 15 mutations. Gene expression of the WNT-pathway surrogate marker osteopontin and the metastasis-associated genes SASH1 and MACC1 was determined for 179 patients. The results were correlated with metachronous distant metastasis risk (n = 22 patients). RESULTS Mutations of KRAS were detected in 30% patients, mutations of BRAF in 15% patients, and microsatellite instability in 26% patients. Risk of recurrence was associated with KRAS mutation (P = 0.033), microsatellite stable tumors (P = 0.015), decreased expression of SASH1 (P = 0.049), and increased expression of MACC1 (P < 0.001). MACC1 was the only independent parameter for recurrence prediction (hazard ratio: 6.2; 95% confidence interval: 2.4-16; P < 0.001). Integrative 2-step cluster analysis allocated patients into 4 groups, according to their tumor genetics. KRAS mutation, BRAF wild type, microsatellite stability, and high MACC1 expression defined the group with the highest risk of recurrence (16%, 7 of 43), whereas BRAF wild type, microsatellite instability, and low MACC1 expression defined the group with the lowest risk (4%, 1 of 26). CONCLUSIONS MACC1 expression predicts development of metastases, outperforming microsatellite stability status, as well as KRAS/BRAF mutation status.
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Rath-Wolfson L, Bergman M, Ori Y, Goldman A, Ram E, Koren R, Salman H. Expression of cyclin E in stage III colorectal carcinoma. Oncol Lett 2012; 5:145-148. [PMID: 23255910 DOI: 10.3892/ol.2012.955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Accepted: 09/25/2012] [Indexed: 11/06/2022] Open
Abstract
Carcinogenesis is characterized by an abnormal regulation of the cell cycle. Regulators of the cell cycle such as cyclin E play an important role in neoplasia and may be correlated with prognosis. The clinical significance of the expression of cyclin E in stage III colorectal carcinoma has not yet been investigated. The expression of cyclin E was evaluated in 49 patients. Using a multivariate analysis, the expression of cyclin E in the tumor at diagnosis was compared with various clinicopathological variables, including age, gender, tumor site, tumor size, tumor differentiation and lymph node involvement. There were more node-positive cases in the cyclin E-negative group than in the cyclin E-positive group (P=0.003). However, there was no correlation between the degree of cyclin E expression and the clinical data. In conclusion, our data suggest that overexpression of cyclin E does not predict the clinical outcome in colorectal cancer stage III. Negative cyclin E staining may be associated with lymph node involvement.
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Affiliation(s)
- Lea Rath-Wolfson
- Departments of Pathology ; Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Israel
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Li GS, Yan DG, Zhang RY, Zhen YH, Ji QH, Cheng HY. Correlation between expression of CK20 mRNA in peripheral blood and clinicopathological features and prognosis in patients with colorectal cancer. Shijie Huaren Xiaohua Zazhi 2012; 20:1993-1997. [DOI: 10.11569/wcjd.v20.i21.1993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the clinical significance of cytokeratin 20 (CK20) mRNA expression in peripheral venous blood of patients with colorectal carcinoma.
METHODS: The expression of CK20 mRNA was detected by RT-PCR in peripheral venous blood samples from 20 healthy volunteers, 10 patients with colorectal polyps, and 61 patients with colorectal cancer.
RESULTS: The positive rate of CK20 mRNA in peripheral venous blood of patients with colorectal cancer was 41.0% (25/61). CK20 mRNA expression in peripheral venous blood was associated with TNM stage, local lymph node metastasis, distant metastasis, and depth of invasion (all P < 0.05). The expression of CK20 mRNA was not detected in peripheral venous blood of healthy volunteers and patients with colorectal polyps. Seventeen cases died during the follow-up period, of whom 10 had positive expression of CK20 in peripheral blood.
CONCLUSION: CK20 is a specific marker for blood micrometastasis of colorectal cancer. The expression of CK20 mRNA in the blood of patients with colorectal cancer is related with the invasion and metastasis of colorectal cancer. Detection of CK20 mRNA in peripheral blood seems to be of relevance for prognosis in colorectal cancer.
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