1
|
Pan T, He Y, Chen H, Pei J, Li Y, Zeng R, Xia J, Zuo Y, Qin L, Chen S, Xiao L, Zhou H. Identification and Validation of a Prognostic Gene Signature for Diffuse Large B-Cell Lymphoma Based on Tumor Microenvironment-Related Genes. Front Oncol 2021; 11:614211. [PMID: 33692952 PMCID: PMC7938316 DOI: 10.3389/fonc.2021.614211] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/05/2021] [Indexed: 12/14/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is an extremely heterogeneous tumor entity, which makes prognostic prediction challenging. The tumor microenvironment (TME) has a crucial role in fostering and restraining tumor development. Consequently, we performed a systematic investigation of the TME and genetic factors associated with DLBCL to identify prognostic biomarkers for DLBCL. Data for a total of 1,084 DLBCL patients from the Gene Expression Omnibus database were included in this study, and patients were divided into a training group, an internal validation group, and two external validation groups. We calculated the abundance of immune–stromal components of DLBCL and found that they were related to tumor prognosis and progression. Then, differentially expressed genes were obtained based on immune and stromal scores, and prognostic TME‐related genes were further identified using a protein–protein interaction network and univariate Cox regression analysis. These genes were analyzed by the least absolute shrinkage and selection operator Cox regression model to establish a seven-gene signature, comprising TIMP2, QKI, LCP2, LAMP2, ITGAM, CSF3R, and AAK1. The signature was shown to have critical prognostic value in the training and validation sets and was also confirmed to be an independent prognostic factor. Subgroup analysis also indicated the robust prognostic ability of the signature. A nomogram integrating the seven-gene signature and components of the International Prognostic Index was shown to have value for prognostic prediction. Gene set enrichment analysis between risk groups demonstrated that immune-related pathways were enriched in the low-risk group. In conclusion, a novel and reliable TME relevant gene signature was proposed and shown to be capable of predicting the survival of DLBCL patients at high risk of poor survival.
Collapse
Affiliation(s)
- Tao Pan
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yizi He
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Huan Chen
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Junfei Pei
- Department of Gastrointestinal Surgery, First Hospital of Jilin University, Changchun, Jilin, China
| | - Yajun Li
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Ruolan Zeng
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiliang Xia
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, Hengyang School of Medicine, University of South China, Hengyang, China
| | - Yilang Zuo
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Liping Qin
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Siwei Chen
- Department of Histology and Embryology of School of Basic Medical Science, Central South University, Changsha, China
| | - Ling Xiao
- Department of Histology and Embryology of School of Basic Medical Science, Central South University, Changsha, China
| | - Hui Zhou
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| |
Collapse
|
2
|
Zhang S, Hu Z, Lan Y, Long J, Wang Y, Chen X, Xu X, Zeng Z, Ouyang Y. Prognostic significance of survival-associated alternative splicing events in gastric cancer. Aging (Albany NY) 2020; 12:21923-21941. [PMID: 33186122 PMCID: PMC7695385 DOI: 10.18632/aging.104013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/17/2020] [Indexed: 04/13/2023]
Abstract
Alternative splicing events are a major source of transcript and protein diversity in eukaryotes. Aberrant alternative splicing events have been increasingly reported in various cancers, including gastric cancer. To further explore the prognostic significance of alternative splicing events in gastric cancer patients, a comprehensive and systematic investigation was conducted by integrating alternative splicing event data and clinical information. Univariate Cox regression analysis identified 1383 alternative splicing events to be significantly associated with the overall survival of gastric cancer patients. Then, least absolute shrinkage and selection operator (LASSO) and multivariate Cox analyses were performed for the development of prognostic signatures. The final prognostic signature based on all seven types of alternative splicing events can act as an independent prognostic indicator after multivariate adjustment of several clinical parameters. Furthermore, the correlation and function analysis identified CELF2, BAG2, RBFOX2, PTBP2 and QKI as hub splicing factors, and the focal adhesion signaling pathway was most significantly correlated with survival-associated alternative splicing events. The results of this study may establish a foundation for further research investigating the underlying mechanism of alternative splicing events in the progression of gastric cancer.
Collapse
Affiliation(s)
- Shichao Zhang
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, Guizhou, P.R. China
| | - Zuquan Hu
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, Guizhou, P.R. China
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of China, Guiyang 550025, Guizhou, P.R. China
| | - Yingwu Lan
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, Guizhou, P.R. China
| | - Jinhua Long
- Affiliated Tumor Hospital, Guizhou Medical University, Guiyang 550025, Guizhou, P.R. China
| | - Yun Wang
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, Guizhou, P.R. China
| | - Xiaowen Chen
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, Guizhou, P.R. China
| | - Xiaofeng Xu
- The Clinical Laboratory of Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Zhu Zeng
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, Guizhou, P.R. China
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of China, Guiyang 550025, Guizhou, P.R. China
| | - Yan Ouyang
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, Guizhou, P.R. China
| |
Collapse
|
3
|
Abshire ET, Hughes KL, Diao R, Pearce S, Gopalakrishna S, Trievel RC, Rorbach J, Freddolino PL, Goldstrohm AC. Differential processing and localization of human Nocturnin controls metabolism of mRNA and nicotinamide adenine dinucleotide cofactors. J Biol Chem 2020; 295:15112-15133. [PMID: 32839274 PMCID: PMC7606674 DOI: 10.1074/jbc.ra120.012618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 08/06/2020] [Indexed: 01/02/2023] Open
Abstract
Nocturnin (NOCT) is a eukaryotic enzyme that belongs to a superfamily of exoribonucleases, endonucleases, and phosphatases. In this study, we analyze the expression, processing, localization, and cellular functions of human NOCT. We find that NOCT protein is differentially expressed and processed in a cell and tissue type-specific manner to control its localization to the cytoplasm or mitochondrial exterior or interior. The N terminus of NOCT is necessary and sufficient to confer import and processing in the mitochondria. We measured the impact of cytoplasmic NOCT on the transcriptome and observed that it affects mRNA levels of hundreds of genes that are significantly enriched in osteoblast, neuronal, and mitochondrial functions. Recent biochemical data indicate that NOCT dephosphorylates NADP(H) metabolites, and thus we measured the effect of NOCT on these cofactors in cells. We find that NOCT increases NAD(H) and decreases NADP(H) levels in a manner dependent on its intracellular localization. Collectively, our data indicate that NOCT can regulate levels of both mRNAs and NADP(H) cofactors in a manner specified by its location in cells.
Collapse
Affiliation(s)
- Elizabeth T Abshire
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA; Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Kelsey L Hughes
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rucheng Diao
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Sarah Pearce
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institute, Solna, Sweden; Max Planck Institute Biology of Ageing - Karolinska Institute Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Shreekara Gopalakrishna
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institute, Solna, Sweden
| | - Raymond C Trievel
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institute, Solna, Sweden; Max Planck Institute Biology of Ageing - Karolinska Institute Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Aaron C Goldstrohm
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.
| |
Collapse
|
4
|
Wang X, Guo J, Che X, Jia R. PCBP1 inhibits the expression of oncogenic STAT3 isoform by targeting alternative splicing of STAT3 exon 23. Int J Biol Sci 2019; 15:1177-1186. [PMID: 31223278 PMCID: PMC6567812 DOI: 10.7150/ijbs.33103] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/28/2019] [Indexed: 01/27/2023] Open
Abstract
STAT3 plays very important roles in the initiation and development of tumors. Despite of extensive studies in repressing its activation and function via multiple ways, so far, there are few effective therapeutic methods to inhibit STAT3 in the clinic. STAT3 has two isoforms generated by alternative splicing of exon 23. STAT3α is the longer isoform and encodes the full-length oncogenic STAT3α protein. STAT3β is shorter and encodes the truncated and tumor-suppressive STAT3β protein. It remains unknown how the alternative splicing of STAT3 exon 23 is regulated. Here, we discovered that there is an exonic splicing suppressor (ESS) in exon 23. Importantly, splicing factor PCBP1 binds to this ESS. Overexpression of PCBP1 significantly reduced the proportion of STAT3α /STAT3β isoforms and the expression of STAT3α protein. Moreover, increased PCBP1 inhibited the growth of oral squamous cell carcinoma and breast cancer cells, and the expression of STAT3 target genes. Our results demonstrated that PCBP1 is the key splicing factor that promotes the switch from oncogenic isoform STAT3α to tumor-suppressive isoform STAT3β. Our results pave the way for finding new anti-STAT3 methods for cancer treatment.
Collapse
Affiliation(s)
- Xiaole Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, PR China
| | - Jihua Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, PR China.,Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, PR China
| | - Xiaoxuan Che
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, PR China
| | - Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, PR China
| |
Collapse
|
5
|
Neumeyer S, Popanda O, Edelmann D, Butterbach K, Toth C, Roth W, Bläker H, Jiang R, Herpel E, Jäkel C, Schmezer P, Jansen L, Alwers E, Benner A, Burwinkel B, Hoffmeister M, Brenner H, Chang-Claude J. Genome-wide DNA methylation differences according to oestrogen receptor beta status in colorectal cancer. Epigenetics 2019; 14:477-493. [PMID: 30931802 DOI: 10.1080/15592294.2019.1595998] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Involvement of sex hormones in colorectal cancer (CRC) development has been linked to oestrogen receptor β (ERβ). Expression of ERβ is found reduced in tumour tissue and inversely related to mortality. However, mechanisms are not well understood. Our study aimed to detect differentially methylated genes associated with ERβ expression, which could point to mechanisms by which ERβ could influence risk and prognosis of CRC. Epigenome-wide DNA methylation profiling was performed using Illumina HumanMethylation450k BeadChip arrays in two independent tumour sample sets of CRC patients recruited in 2003-2010 by the German DACHS study (discovery cohort n = 917, replication cohort n = 907). ERβ expression was measured using immunohistochemistry and scored as negative, moderate and high. Differentially methylated CpG sites and genomic regions were determined using limma in the R-package RnBeads. For the comparison of tumours with moderate/high ERβ versus negative expression, differentially methylated CpG sites were identified but not confirmed by replication. Comparing tumours of high with tumours of negative ERβ expression revealed 2,904 differentially methylated CpG sites of which 403 were replicated (FDR adjusted p-value<0.05). Replicated CpGs were annotated to genes such as CD36, HK1 or LRP5. A survival analysis indicates that 30 of the replicated CpGs are also associated with overall survival (FDR-adjusted p-value<0.05). The regional analysis identified 60 differentially methylated promotor regions. The epigenome-wide analysis identified both novel genes as well as genes already implicated in CRC. Follow-up mechanistic studies to better understand the regulatory role of ERβ could inform potential targets for improving treatment or prevention of CRC.
Collapse
Affiliation(s)
- Sonja Neumeyer
- a Division of Cancer Epidemiology , German Cancer Research Center , Heidelberg , Germany.,b Medical Faculty Heidelberg , Heidelberg University , Heidelberg , Germany
| | - Odilia Popanda
- c Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Dominic Edelmann
- d Division of Biostatistics , German Cancer Research Center , Heidelberg , Germany
| | - Katja Butterbach
- a Division of Cancer Epidemiology , German Cancer Research Center , Heidelberg , Germany.,e Division of Clinical Epidemiology and Aging Research , German Cancer Research Center , Heidelberg , Germany
| | - Csaba Toth
- f Institute of Pathology , Heidelberg University , Heidelberg , Germany
| | - Wilfried Roth
- g Institute of Pathology , Universitätsmedizin der Johannes Gutenberg-Universität Mainz , Mainz , Germany
| | - Hendrik Bläker
- h Institute of Pathology , Charité University Medicine , Berlin , Germany
| | - Ruijingfang Jiang
- a Division of Cancer Epidemiology , German Cancer Research Center , Heidelberg , Germany
| | - Esther Herpel
- f Institute of Pathology , Heidelberg University , Heidelberg , Germany.,i NCT Tissue Bank , National Center for Tumor Diseases (NCT) , Heidelberg , Germany
| | - Cornelia Jäkel
- c Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Peter Schmezer
- c Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Lina Jansen
- e Division of Clinical Epidemiology and Aging Research , German Cancer Research Center , Heidelberg , Germany
| | - Elizabeth Alwers
- e Division of Clinical Epidemiology and Aging Research , German Cancer Research Center , Heidelberg , Germany
| | - Axel Benner
- d Division of Biostatistics , German Cancer Research Center , Heidelberg , Germany
| | - Barbara Burwinkel
- j Division of Molecular Epidemiology , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,k Department of Gynecology and Obstetrics, Molecular Biology of Breast Cancer , University of Heidelberg , Heidelberg , Germany
| | - Michael Hoffmeister
- e Division of Clinical Epidemiology and Aging Research , German Cancer Research Center , Heidelberg , Germany
| | - Hermann Brenner
- e Division of Clinical Epidemiology and Aging Research , German Cancer Research Center , Heidelberg , Germany.,l Division of Preventive Oncology , German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) , Heidelberg , Germany.,m German Cancer Consortium (DKTK) , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Jenny Chang-Claude
- a Division of Cancer Epidemiology , German Cancer Research Center , Heidelberg , Germany.,n Cancer Epidemiology Group , University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| |
Collapse
|