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Lin G, Gao Z, Wu S, Zheng J, Guo X, Zheng X, Chen R. scRNA-seq revealed high stemness epithelial malignant cell clusters and prognostic models of lung adenocarcinoma. Sci Rep 2024; 14:3709. [PMID: 38355636 PMCID: PMC10867035 DOI: 10.1038/s41598-024-54135-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the sole causes of death in lung cancer patients. This study combined with single-cell RNA-seq analysis to identify tumor stem-related prognostic models to predict the prognosis of lung adenocarcinoma, chemotherapy agents, and immunotherapy efficacy. mRNA expression-based stemness index (mRNAsi) was determined by One Class Linear Regression (OCLR). Differentially expressed genes (DEGs) were detected by limma package. Single-cell RNA-seq analysis in GSE123902 dataset was performed using Seurat package. Weighted Co-Expression Network Analysis (WGCNA) was built by rms package. Cell differentiation ability was determined by CytoTRACE. Cell communication analysis was performed by CellCall and CellChat package. Prognosis model was constructed by 10 machine learning and 101 combinations. Drug predictive analysis was conducted by pRRophetic package. Immune microenvironment landscape was determined by ESTIMATE, MCP-Counter, ssGSEA analysis. Tumor samples have higher mRNAsi, and the high mRNAsi group presents a worse prognosis. Turquoise module was highly correlated with mRNAsi in TCGA-LUAD dataset. scRNA analysis showed that 22 epithelial cell clusters were obtained, and higher CSCs malignant epithelial cells have more complex cellular communication with other cells and presented dedifferentiation phenomenon. Cellular senescence and Hippo signaling pathway are the major difference pathways between high- and low CSCs malignant epithelial cells. The pseudo-temporal analysis shows that cluster1, 2, high CSC epithelial cells, are concentrated at the end of the differentiation trajectory. Finally, 13 genes were obtained by intersecting genes in turquoise module, Top200 genes in hdWGCNA, DEGs in high- and low- mRNAsi group as well as DEGs in tumor samples vs. normal group. Among 101 prognostic models, average c-index (0.71) was highest in CoxBoost + RSF model. The high-risk group samples had immunosuppressive status, higher tumor malignancy and low benefit from immunotherapy. This work found that malignant tumors and malignant epithelial cells have high CSC characteristics, and identified a model that could predict the prognosis, immune microenvironment, and immunotherapy of LUAD, based on CSC-related genes. These results provided reference value for the clinical diagnosis and treatment of LUAD.
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Affiliation(s)
- GuoYong Lin
- Department of Respiratory and Critical Illness Medicine, The First Hospital of Putian, Putian, 351100, China
| | - ZhiSen Gao
- Department of Respiratory and Critical Illness Medicine, The First Hospital of Putian, Putian, 351100, China
| | - Shun Wu
- Department of Respiratory and Critical Illness Medicine, The First Hospital of Putian, Putian, 351100, China
| | - JianPing Zheng
- Department of Respiratory and Critical Illness Medicine, The First Hospital of Putian, Putian, 351100, China
| | - XiangQiong Guo
- Department of Respiratory and Critical Illness Medicine, The First Hospital of Putian, Putian, 351100, China
| | - XiaoHong Zheng
- Department of Respiratory and Critical Illness Medicine, The First Hospital of Putian, Putian, 351100, China
| | - RunNan Chen
- Department of Respiratory and Critical Illness Medicine, The First Hospital of Putian, Putian, 351100, China.
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Young JJ, Park HJ, Kim M, Par-Young J, Bartlett H, Kim HS, Unlu S, Osmani L, Shin MS, Bucala R, van Dyck CH, Allore H, Mecca AP, You S, Kang I. Aging gene signature of memory CD8 + T cells is associated with neurocognitive functioning in Alzheimer's disease. Immun Ageing 2023; 20:71. [PMID: 38042785 PMCID: PMC10693128 DOI: 10.1186/s12979-023-00396-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/20/2023] [Indexed: 12/04/2023]
Abstract
BACKGROUND Memory CD8+ T cells expand with age. We previously demonstrated an age-associated expansion of effector memory (EM) CD8+ T cells expressing low levels of IL-7 receptor alpha (IL-7Rαlow) and the presence of its gene signature (i.e., IL-7Rαlow aging genes) in peripheral blood of older adults without Alzheimer's disease (AD). Considering age as the strongest risk factor for AD and the recent finding of EM CD8+ T cell expansion, mostly IL-7Rαlow cells, in AD, we investigated whether subjects with AD have alterations in IL-7Rαlow aging gene signature, especially in relation to genes possibly associated with AD and disease severity. RESULTS We identified a set of 29 candidate genes (i.e., putative AD genes) which could be differentially expressed in peripheral blood of patients with AD through the systematic search of publicly available datasets. Of the 29 putative AD genes, 9 genes (31%) were IL-7Rαlow aging genes (P < 0.001), suggesting the possible implication of IL-7Rαlow aging genes in AD. These findings were validated by RT-qPCR analysis of 40 genes, including 29 putative AD genes, additional 9 top IL-7R⍺low aging but not the putative AD genes, and 2 inflammatory control genes in peripheral blood of cognitively normal persons (CN, 38 subjects) and patients with AD (40 mild cognitive impairment and 43 dementia subjects). The RT-qPCR results showed 8 differentially expressed genes between AD and CN groups; five (62.5%) of which were top IL-7Rαlow aging genes (FGFBP2, GZMH, NUAK1, PRSS23, TGFBR3) not previously reported to be altered in AD. Unbiased clustering analysis revealed 3 clusters of dementia patients with distinct expression levels of the 40 analyzed genes, including IL-7Rαlow aging genes, which were associated with neurocognitive function as determined by MoCA, CDRsob and neuropsychological testing. CONCLUSIONS We report differential expression of "normal" aging genes associated with IL-7Rαlow EM CD8+ T cells in peripheral blood of patients with AD, and the significance of such gene expression in clustering subjects with dementia due to AD into groups with different levels of cognitive functioning. These results provide a platform for studies investigating the possible implications of age-related immune changes, including those associated with CD8+ T cells, in AD.
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Affiliation(s)
- Juan Joseph Young
- Department of Psychiatry, Yale School of Medicine, 300 Cedar Street, New Haven, CT, 06520, USA
| | - Hong-Jai Park
- Department of Psychiatry, Yale School of Medicine, 300 Cedar Street, New Haven, CT, 06520, USA
| | - Minhyung Kim
- Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jennefer Par-Young
- Department of Psychiatry, Yale School of Medicine, 300 Cedar Street, New Haven, CT, 06520, USA
| | - Hugh Bartlett
- Department of Psychiatry, Yale School of Medicine, 300 Cedar Street, New Haven, CT, 06520, USA
- Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Hye Sun Kim
- Yale School of Public Health, New Haven, CT, USA
| | - Serhan Unlu
- Department of Psychiatry, Yale School of Medicine, 300 Cedar Street, New Haven, CT, 06520, USA
- Cleveland Clinic Fairview Hospital, Cleveland, OH, USA
| | - Lais Osmani
- Department of Psychiatry, Yale School of Medicine, 300 Cedar Street, New Haven, CT, 06520, USA
| | - Min Sun Shin
- Department of Psychiatry, Yale School of Medicine, 300 Cedar Street, New Haven, CT, 06520, USA
| | - Richard Bucala
- Department of Psychiatry, Yale School of Medicine, 300 Cedar Street, New Haven, CT, 06520, USA
| | - Christopher H van Dyck
- Department of Psychiatry, Yale School of Medicine, 300 Cedar Street, New Haven, CT, 06520, USA
| | - Heather Allore
- Department of Psychiatry, Yale School of Medicine, 300 Cedar Street, New Haven, CT, 06520, USA
- Yale School of Public Health, New Haven, CT, USA
| | - Adam P Mecca
- Department of Psychiatry, Yale School of Medicine, 300 Cedar Street, New Haven, CT, 06520, USA
| | - Sungyong You
- Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Insoo Kang
- Department of Psychiatry, Yale School of Medicine, 300 Cedar Street, New Haven, CT, 06520, USA.
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Jiang J, Wang Y, Liu D, Wang X, Zhu Y, Tong J, Chen E, Xue L, Zhao N, Liang T, Zheng C. Selinexor Synergistically Promotes the Antileukemia Activity of Venetoclax in Acute Myeloid Leukemia by Inhibiting Glycolytic Function and Downregulating the Expression of DNA Replication Genes. Immunotargets Ther 2023; 12:135-147. [PMID: 38026089 PMCID: PMC10680489 DOI: 10.2147/itt.s429402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The BCL-2 inhibitor venetoclax has been widely used in the treatment of acute myeloid leukemia (AML); however, AML patients treated with venetoclax gradually develop resistance. The exportin-1 (XPO1) inhibitor selinexor can synergistically promote the antileukemia activity of venetoclax, but the mechanism remains unclear. Methods and Results Annexin V/7-aminoactinomycin D assays were used to examine the effects of a combination of venetoclax and selinexor (VEN+SEL) on AML cell lines and primary AML cells. RNA sequencing and oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) determinations by a Seahorse XF analyzer were employed to investigate the molecular mechanism of the toxicity of the VEN+SEL combination to AML cells. The cytotoxicity of NK cell combined with VEN+SEL combination was assessed in vitro using flow cytometry. VEN+SEL enhanced the apoptosis of AML cells (KG-1A and THP-1) and primary AML samples in vitro. The ECAR and OCR results demonstrated that the VEN+SEL combination significantly inhibited glycolytic function. RNA sequencing of THP-1 cells demonstrated that DNA replication-related genes were downregulated after treatment with the VEN+SEL combination. Conclusion This study indicated that selinexor can synergistically enhance the antileukemia activity of venetoclax in AML cells in vitro by inhibiting glycolytic function and downregulating DNA replication-related genes. Based on our experimental data, combining selinexor with venetoclax is an appropriate advanced treatment option for AML patients.
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Affiliation(s)
- Jiqian Jiang
- Department of Hematology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Yan Wang
- Department of Hematology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Dan Liu
- Department of Hematology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Xiaoyu Wang
- Department of Hematology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Yingqiao Zhu
- Department of Hematology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Juan Tong
- Department of Hematology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Erling Chen
- Department of Hematology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Lei Xue
- Department of Hematology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Na Zhao
- Department of Hematology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Tingting Liang
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Changcheng Zheng
- Department of Hematology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
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Young J, Park HJ, Kim M, Par-Young J, Bartlett H, Kim HS, Unlu S, Osmani L, Shin MS, Bucala R, van Dyck C, Allore H, Mecca A, You S, Kang I. Aging gene signature of IL-7 receptor alpha low effector memory CD8 + T cells is associated with neurocognitive functioning in Alzheimer's disease. RESEARCH SQUARE 2023:rs.3.rs-2736771. [PMID: 37066364 PMCID: PMC10104241 DOI: 10.21203/rs.3.rs-2736771/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
CD45RA+ effector memory (EM) CD8+ T cell expansion was reported in Alzheimer's disease (AD). Such cells are IL-7 receptor alpha (IL-7Rα)low EM CD8+ T cells, which expand with age and have a unique aging gene signature (i.e., IL-7Rαlow aging genes). Here we investigated whether IL-7Rαlow aging genes and previously reported AD and memory (ADM) genes overlapped with clinical significance in AD patients. RT-qPCR analysis of 40 genes, including 29 ADM, 9 top IL-7Ralow aging and 2 control genes, showed 8 differentially expressed genes between AD and cognitively normal groups; five (62.5%) of which were top IL-7Rαlow aging genes. Over-representation analysis revealed that these genes were highly present in molecular and biological pathways associated with AD. Distinct expression levels of these genes were associated with neuropsychological testing performance in 3 subgroups of dementia participants. Our findings support the possible implication of the IL-7Rαlow aging gene signature with AD.
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Wu X, Liu Y, Wang W, Crimmings K, Williams A, Mager J, Cui W. Early embryonic lethality of mice lacking POLD2. Mol Reprod Dev 2023; 90:98-108. [PMID: 36528861 PMCID: PMC9974775 DOI: 10.1002/mrd.23663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/09/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
As a highly conserved DNA polymerase (Pol), Pol δ plays crucial roles in chromosomal DNA synthesis and various DNA repair pathways. However, the function of POLD2, the second small subunit of DNA Pol δ (p50 subunit), has not been characterized in vivo during mammalian development. Here, we report for the first time, the essential role of subunit POLD2 during early murine embryogenesis. Although Pold2 mutant mouse embryos exhibit normal morphology at E3.5 blastocyst stage, they cannot be recovered at gastrulation stages. Outgrowth assays reveal that mutant blastocysts cannot hatch from the zona pellucida, indicating impaired blastocyst function. Notably, these phenotypes can be recapitulated by small interfering RNA (siRNA)-mediated knockdown, which also exhibit slowed cellular proliferation together with skewed primitive endoderm and epiblast allocation during the second cell lineage specification. In summary, our study demonstrates that POLD2 is essential for the earliest steps of mammalian development, and the retarded proliferation and embryogenesis may also alter the following cell lineage specifications in the mouse blastocyst embryos.
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Affiliation(s)
- Xiaoqing Wu
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Fuyang Normal University, Fuyang, Anhui, China
| | - Yong Liu
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Fuyang Normal University, Fuyang, Anhui, China
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Wenying Wang
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Fuyang Normal University, Fuyang, Anhui, China
| | - Kate Crimmings
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Andrea Williams
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Wei Cui
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
- Animal Models Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA
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Huo X, Guo T, Wang K, Yao B, Li D, Li H, Chen W, Wang L, Wu Z. Methylation-based reclassification and risk stratification of skull-base chordomas. Front Oncol 2022; 12:960005. [PMID: 36439461 PMCID: PMC9691996 DOI: 10.3389/fonc.2022.960005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/11/2022] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Skull-base chordomas are rare malignant bone cancers originating from the remnant of the notochord. Survival is variable, and clinical or molecular factors cannot reliably predict their outcomes. This study therefore identified epigenetic subtypes that defined new chordoma epigenetic profiles and their corresponding characteristics. METHODS Methylation profiles of 46 chordoma-resected neoplasms between 2008 and 2014, along with clinical information, were collected. K-means consensus clustering and principal component analysis were used to identify and validate the clusters. Single-sample gene set enrichment analysis, methylCIBERSORT algorithm, and copy number analysis were used to identify the characteristics of the clusters. RESULTS Unsupervised clustering analysis confirmed two clusters with a progression-free survival difference. Gene set enrichment analysis indicated that the early and late estrogen response pathways and the hypoxia pathway were activated whereas the inflammatory and interferon gamma responses were suppressed. Forty-six potential therapeutic targets corresponding to differentially methylated sites were identified from chordoma patients. Subgroups with a worse outcome were characterized by low immune cell infiltration, higher tumor purity, and higher stemness indices. Moreover, copy number amplifications mostly occurred in cluster 1 tumors and the high-risk group. Additionally, the presence of a CCNE1 deletion was exclusively found in the group of chordoma patients with better outcome, whereas RB1 and CDKN2A/2B deletions were mainly found in the group of chordoma patients with worse outcome. CONCLUSIONS Chordoma prognostic epigenetic subtypes were identified, and their corresponding characteristics were found to be variable.
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Affiliation(s)
- Xulei Huo
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Tengxian Guo
- Department of Neurosurgery, Beijing Fengtai Hospital, Beijing, China
| | - Ke Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Bohan Yao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Da Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Huan Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Wei Chen
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Liang Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Zhen Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
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Zhang Z. POLD2 is activated by E2F1 to promote triple-negative breast cancer proliferation. Front Oncol 2022; 12:981329. [PMID: 36119494 PMCID: PMC9479206 DOI: 10.3389/fonc.2022.981329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly malignant breast cancer subtype with a poor prognosis. Improved insight into the molecular biology basis of TNBC progression is urgently needed. Herein, we reported that POLD2 was highly expressed in TNBC and patients with high POLD2 expression in their tumors had poor clinical outcomes. In functional studies, knockdown of POLD2 inhibited the proliferation of TNBC. Mechanistically, we revealed that transcription factor E2F1 directly bound to the promoter of POLD2 and regulated its expression in TNBC cells, which in turn contributed to the proliferation of TNBC. Additionally, rescue experiments validated that E2F1-mediated cell proliferation in TNBC was dependent on POLD2. Taken together, our results elucidated a novel mechanism of the E2F1-POLD2 axis in TNBC proliferation, and POLD2 may be a potential therapeutic target for TNBC treatment.
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Cong F, Long J, Liu J, Deng Z, Yan B, Liang C, Huang X, Liu J, Tang W. An integrative analysis revealing POLD2 as a tumor suppressive immune protein and prognostic biomarker in pan-cancer. Front Genet 2022; 13:877468. [PMID: 36081989 PMCID: PMC9447486 DOI: 10.3389/fgene.2022.877468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/22/2022] [Indexed: 11/15/2022] Open
Abstract
Introduction: POLD2 is an indispensable subunit of DNA polymerase δ, which is responsible for the synthesis of the backward accompanying strand in eukaryotic organisms. Current studies have found an association between POLD2 and the development of a variety of cancers. However, its value in cancer immunotherapy has not been fully established. Methods: POLD2 expression was analyzed using RNA expression and clinical data from TCGA and GTEx databases. The prognostic impact of POLD2 on tumor patients was analyzed using clinical survival data from TCGA. Gene enrichment analysis was performed using the R package “cluster analyzer” to explore the role of POLD2. We used the TIMER2 database to analyze the relationship between immune cell infiltration and POLD2 expression in TCGA. We downloaded relevant data from TCGA and analyzed the relationship between POLD2 and immune checkpoints, immunosuppressive genes, immune activating genes, chemokines and chemokine receptors. Results: POLD2 was significantly overexpressed in most tumors compared to normal tissue. High POLD2 expression was significantly associated with advanced tumor stage, significantly shorter overall survival and progression-free survival. Also, we found that POLD2 expression correlated strongly with immunomodulatory genes, and significantly negatively with most immune checkpoints (PD-L1, CTLA4, TIM3, and CD28). Pathway enrichment analysis suggests that low expression of POLD2 promotes immune regulation-related pathways and high expression promotes metabolic and DNA repair-related pathways. Furthermore, tumor microenvironment analysis suggests that high POLD2 expression inhibits infiltration of CD8+ T cells and CD4+ memory T cells. Discussion: In conclusion, POLD2 may be a molecular biomarker for pan-cancer prognosis and immunotherapy. It may serve as a potential target for new insights in human tumor prognosis prediction and immunotherapy assessment.
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Affiliation(s)
- Fengyun Cong
- Division of Colorectal and Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Department of Gastroenteroanal Surgery, The First People’s Hospital of Nanning, Nanning, China
| | - Junxian Long
- Division of Colorectal and Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Department of Gastroenteroanal Surgery, The First People’s Hospital of Nanning, Nanning, China
| | - Jun Liu
- Division of Colorectal and Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Zhixiang Deng
- Division of Colorectal and Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Binli Yan
- Division of Colorectal and Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Cao Liang
- Division of Colorectal and Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xiaoliang Huang
- Division of Colorectal and Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Jinxin Liu
- Department of Gastroenteroanal Surgery, The First People’s Hospital of Nanning, Nanning, China
- *Correspondence: Jinxin Liu, ; Weizhong Tang,
| | - Weizhong Tang
- Division of Colorectal and Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- *Correspondence: Jinxin Liu, ; Weizhong Tang,
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Wang Q, Zhang S, Xu Q, Liang J, Zhang P, Huang W, Lin Z, Zheng S, Gu S, Yan J. The Mechanism and Prognostic Value of DNA Polymerase δ Subunits in Hepatocellular Carcinoma: Implications for Precision Therapy. Int J Gen Med 2022; 15:1365-1380. [PMID: 35173474 PMCID: PMC8841512 DOI: 10.2147/ijgm.s347162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/25/2022] [Indexed: 02/05/2023] Open
Abstract
PURPOSE Polymerase δ (POLD) proteins is a pivotal B-family DNA polymerase in the process of genome replication and repair and are comprised of POLD1-4. The predictive value of POLDs in hepatocellular carcinoma (HCC) has not been evaluated until now. PATIENTS AND METHODS A total of 369 hepatocellular carcinoma samples and 50 adjacent normal samples were enrolled from the TCGA-LIHC database, and the GSE10186 database was also used. Transcription, methylation and genetic alteration status of HCC patients were evaluated by GEPIA, Kaplan-Meier plotter, cBioPortal, MethHC, MethSurv. SurvExpress was employed to generate the overall prognosis prediction signature of POLDs. POLDs coexpressed genes were explored and enriched in potential pathways. K-M curves were generated to compare the different survival results in different groups, while ROC curves were used to validate the efficiency of the POLD signature. RESULTS All four POLD subunits were highly expressed in HCC tumor tissues. POLD1-3 and increased mRNA levels were also positively associated with advanced tumor stage and OS prognosis. Methylation in the promoter of POLDs affects mRNA expression and OS, especially for some specific CpG sites. Meanwhile, POLDs could preferably predict the prognosis for patients who suffered from a high gene mutation burden. We evaluated the combined prognostic predictive value of four POLD subunits in both the TCGA-LIHC and GSE10186 databases and recognized the statistically significant HR of the high-risk group, along with the reliable predictive value. The coexpressed gene sets and annotation results showed that the POLD coexpressed genes were mostly associated with DNA repair and cell cycle regulation pathways. CONCLUSION POLD is an essential predictive factor for the prognosis of HCC. The united signature could precisely identify unfavorable clinical outcome of HCC.
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Affiliation(s)
- Qing Wang
- Department of Biliary-Pancreatic Minimally Invasive Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, People’s Republic of China
| | - Song Zhang
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, People’s Republic of China
| | - Qiaodong Xu
- Department of Biliary-Pancreatic Minimally Invasive Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, People’s Republic of China
| | - Jiahong Liang
- Department of Biliary-Pancreatic Minimally Invasive Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, People’s Republic of China
| | - Peidong Zhang
- Department of Biliary-Pancreatic Minimally Invasive Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, People’s Republic of China
| | - Wenlong Huang
- Department of Biliary-Pancreatic Minimally Invasive Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, People’s Republic of China
| | - Zhihuan Lin
- Department of Biliary-Pancreatic Minimally Invasive Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, People’s Republic of China
| | - Shaodong Zheng
- Department of Biliary-Pancreatic Minimally Invasive Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, People’s Republic of China
| | - Songgang Gu
- Department of Biliary-Pancreatic Minimally Invasive Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, People’s Republic of China
| | - Jiang Yan
- Department of Biliary-Pancreatic Minimally Invasive Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, People’s Republic of China
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Hombach A, Barden M, Hannappel L, Chmielewski M, Rappl G, Sachinidis A, Abken H. IL12 integrated into the CAR exodomain converts CD8 + T cells to poly-functional NK-like cells with superior killing of antigen-loss tumors. Mol Ther 2022; 30:593-605. [PMID: 34678512 PMCID: PMC8821972 DOI: 10.1016/j.ymthe.2021.10.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 08/30/2021] [Accepted: 10/10/2021] [Indexed: 02/04/2023] Open
Abstract
Chimeric antigen receptor (CAR)-redirected T cell therapy often fails to control tumors in the long term due to selecting cancer cells that downregulated or lost CAR targeted antigen. To reprogram the functional capacities specifically of engineered CAR T cells, we inserted IL12 into the extracellular moiety of a CD28-ζ CAR; both the CAR endodomain and IL12 were functionally active, as indicated by antigen-redirected effector functions and STAT4 phosphorylation, respectively. The IL12-CAR reprogrammed CD8+ T cells toward a so far not recognized natural killer (NK) cell-like signature and a CD94+CD56+CD62Lhigh phenotype closely similar, but not identical, to NK and cytokine induced killer (CIK) cells. In contrast to conventional CAR T cells, IL12-CAR T cells acquired antigen-independent, human leukocyte antigen E (HLA-E) restricted cytotoxic capacities eliminating antigen-negative cancer cells in addition to eliminating cancer cells with CAR cognate antigen. Simultaneous signaling through both the CAR endodomain and IL12 were required for inducing maximal NK-like cytotoxicity; adding IL12 to conventional CAR T cells was not sufficient. Antigen-negative tumors were attacked by IL12-CAR T cells, but not by conventional CAR T cells. Overall, we present a prototype of a new family of CARs that augments tumor recognition and elimination through expanded functional capacities by an appropriate cytokine integrated into the CAR exodomain.
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Affiliation(s)
- Andreas Hombach
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany,Department I Internal Medicine, University Hospital Cologne, 50931 Cologne, Germany
| | - Markus Barden
- RCI, Regensburg Center for Interventional Immunology, Department Genetic Immunotherapy, and University Hospital Regensburg, 93053 Regensburg, Germany
| | - Lisa Hannappel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Markus Chmielewski
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany,Department I Internal Medicine, University Hospital Cologne, 50931 Cologne, Germany
| | - Gunter Rappl
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Agapios Sachinidis
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany,University of Cologne, Faculty of Medicine and Center for Physiology, University Hospital Cologne, 50931 Cologne, Germany
| | - Hinrich Abken
- RCI, Regensburg Center for Interventional Immunology, Department Genetic Immunotherapy, and University Hospital Regensburg, 93053 Regensburg, Germany,Corresponding author: Hinrich Abken, RCI, Regensburg Center for Interventional Immunology, Department Genetic Immunotherapy, and University Hospital Regensburg, 93053 Regensburg, Germany.
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11
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Liu B, Liu Z, Feng C, Li C, Zhang H, Li Z, Tu C, He S. Identification of cuproptosis-related lncRNA prognostic signature for osteosarcoma. Front Endocrinol (Lausanne) 2022; 13:987942. [PMID: 36313774 PMCID: PMC9606239 DOI: 10.3389/fendo.2022.987942] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/12/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Copper is an indispensably mineral element involved in various metabolic processes and functions in the active sites of many metalloproteins. Copper dysregulation is associated with cancers such as osteosarcoma (OS), the most common primary bone malignancy with invasiveness and metastasis. However, the causality between cuproptosis and OS remains elusive. We aim to identify cuproptosis-related long non-coding RNAs (lncRNAs) for osteosarcomatous prognosis, immune microenvironment response, and immunotherapy. METHODS The Person correlation and differential expression analysis were used to identify differentially expressed cuproptosis-related lncRNAs (CRLs). The univariate, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analysis were performed to construct the CRL signature. The Kaplan-Meier (K-M) survival analysis, receiver operating characteristic (ROC) curve, internal validation, independent prognostic analysis, and nomograph were used to evaluate the prognostic value. The functional enrichment, tumor microenvironment, immunotherapy and chemotherapy response between the two distinct groups were further explored using a series of algorithms. The expression of signature CRLs was verified by real-time quantitative polymerase chain reaction (RT-qPCR) in OS cell lines. RESULTS A novel CRL signature consisting of four CRLs were successfully identified. The K-M survival analysis indicated that the OS patients in the low-risk groups had a better prognosis than that in the high-risk group. Then, the ROC curve and subgroup survival analysis confirmed the prognostic evaluation performance of the signature. Equally, the independent prognostic analysis demonstrated that the CRL signature was an independently predicted factor for OS. Friends analysis determined the hub genes that played a critical role in differentially expressed genes between two distinct risk groups. In addition, the risk score was related to immunity status, immunotherapy response, and chemotherapeutic drug sensitivity. Finally, the expression of these signature CRLs detected by RT-qPCR was consistent with the bioinformatic analysis results. CONCLUSION In summary, our study confirmed that the novel CRL signature could effectively evaluate prognosis, tumor immune microenvironment, and immunotherapy response in OS. It may benefit for clinical decision-making and provide new insights for personalized therapeutics.
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Affiliation(s)
- Binfeng Liu
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhongyue Liu
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chengyao Feng
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chenbei Li
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Haixia Zhang
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhihong Li
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chao Tu
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Chao Tu, ; Shasha He,
| | - Shasha He
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Chao Tu, ; Shasha He,
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12
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Zheng T, Sun M, Liu L, Lan Y, Wang L, Lin F. GPR116 overexpression correlates with poor prognosis in gastric cancer. Medicine (Baltimore) 2021; 100:e28059. [PMID: 35049225 PMCID: PMC9191289 DOI: 10.1097/md.0000000000028059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/10/2021] [Indexed: 12/18/2022] Open
Abstract
The G protein-coupled receptor 116 (GPR116) is an adhesion subtype of the G protein-coupled receptor family and has been reported to be involved in tumorigenesis and cancer progression. Moreover, it has been shown to predict poor prognosis in breast and colorectal cancers. However, little is known about the role of GPR116 in gastric cancer (GC). In this study, we aimed to investigate the expression and clinical prognostic significance of GPR116 in GC.The mRNA expression levels of GPR116 in GC were analyzed using Gene Expression Omnibus and UALCAN databases, and GPR116 protein expression in GC tissues was detected using immunohistochemistry. The relationship between GPR116 expression and prognosis in patients with GC was analyzed and further validated using the Kaplan-Meier Plotter database. The correlation between GPR116 and the differentially expressed genes identified was analyzed using the LinkedOmics database. Gene set enrichment analysis was performed using WebGestalt. The results revealed that GPR116 expression was significantly upregulated in GC tissues, which was positively correlated with tumor node metastasis (TNM) staging and tumor invasion. Prognostic analysis suggested that high GPR116 expression contributed to poor overall survival in GC patients. Multivariate Cox analysis indicated that GPR116 overexpression was an independent prognostic indicator in patients with GC (HR = 1.855, 95% CI 1.021-3.370, P = .043). Enrichment analysis showed that GPR116 co-expression genes were mainly involved in extracellular matrix-receptor interaction, focal adhesion, cell adhesion, PI3K-Akt signaling, DNA replication, and cell cycle pathways. In conclusion, GPR116 was highly expressed in GC tissues and associated with poor prognosis in patients with GC, Thus GPR116 may be a novel prognostic marker and a potential therapeutic target for GC treatment.
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Affiliation(s)
- Tian Zheng
- Shengli Clinical Medical College of Fujian Medical University, Department of Geriatric Medicine, Fujian Provincial Hospital, Fujian Provincial Center for Geriatrics, Fuzhou, Fujian, China
| | - Mingyao Sun
- Department of Clinical nutrition, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Lanzai Liu
- Gastrointestinal Endoscopy Center, Fujian Provincial Hospital South Branch, Fuzhou, Fujian, China
| | - Yanfen Lan
- Department of Radiology, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Lihua Wang
- Shengli Clinical Medical College of Fujian Medical University, Department of Geriatric Medicine, Fujian Provincial Hospital, Fujian Provincial Center for Geriatrics, Fuzhou, Fujian, China
| | - Fan Lin
- Shengli Clinical Medical College of Fujian Medical University, Department of Geriatric Medicine, Fujian Provincial Hospital, Fujian Provincial Center for Geriatrics, Fuzhou, Fujian, China
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13
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Shiiba M, Yamagami H, Sudo T, Tomokuni Y, Kashiwabara D, Kirita T, Kusukawa J, Komiya M, Tei K, Kitagawa Y, Imai Y, Kawamata H, Bukawa H, Satomura K, Oki H, Shinozuka K, Sugihara K, Sugiura T, Sekine J, Yokoe H, Saito K, Tanzawa H. Development of prediction models for the sensitivity of oral squamous cell carcinomas to preoperative S-1 administration. Heliyon 2020; 6:e04601. [PMID: 32793829 PMCID: PMC7408317 DOI: 10.1016/j.heliyon.2020.e04601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/18/2020] [Accepted: 07/28/2020] [Indexed: 11/29/2022] Open
Abstract
S-1 is an anticancer agent that is comprised of tegafur, gimeracil, and oteracil potassium, and is widely used in various carcinomas including oral squamous cell carcinoma (OSCC). Although an established prediction tool is not available, we aimed to develop prediction models for the sensitivity of primary OSCC cases to the preoperative administration of S-1. We performed DNA microarray analysis of 95 cases with OSCC. Using global gene expression data and the clinical data, we developed two different prediction models, namely, model 1 that comprised the complete response (CR) + the partial response (PR) versus stable disease (SD) + progressive disease (PD), and model 2 that comprised responders versus non-responders. Twelve and 18 genes were designated as feature genes (FGs) in models 1 and 2, respectively, and, of these, six genes were common to both models. The sensitivity was 96.3%, the specificity was 91.2%, and the accuracy was 92.6% for model 1, and the sensitivity was 95.6%, the specificity was 85.2%, and the accuracy was 92.6% for model 2. These models were validated using receiver operating characteristic analysis, and the areas under the curves were 0.967 and 0.949 in models 1 and 2, respectively. The data led to the development of models that can reliably predict the sensitivity of patients with OSCC to the preoperative administration of S-1. The mechanism that regulates S-1 sensitivity remains unclear; however, the prediction models developed provide hope that further functional investigations into the FGs will lead to a greater understanding of drug resistance.
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Affiliation(s)
- Masashi Shiiba
- Department of Medical Oncology, Graduate School of Medicine, Chiba University, Japan.,Department of Oral Science, Graduate School of Medicine, Chiba University, Japan.,Division of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Japan
| | | | | | | | | | - Tadaaki Kirita
- Department of Oral and Maxillofacial Surgery, Nara Medical University, Japan
| | - Jingo Kusukawa
- Department of Dental and Oral Medical Center, Kurume University School of Medicine, Japan
| | - Masamichi Komiya
- Department of Oral Surgery, Nihon University School of Dentistry at Matsudo, Japan.,Division of Dental and Oral Surgery, Nihon University Itabashi Hospital, Japan
| | - Kanchu Tei
- Department of Oral and Maxillofacial Surgery, Graduate School of Dental Medicine, Hokkaido University, Japan
| | - Yoshimasa Kitagawa
- Department of Oral Diagnosis and Medicine, Graduate School of Dental Medicine, Hokkaido University, Japan
| | - Yutaka Imai
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, Japan
| | - Hitoshi Kawamata
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, Japan
| | - Hiroki Bukawa
- Department of Oral and Maxillofacial Surgery, University of Tsukuba, Japan
| | - Kazuhito Satomura
- Department of Oral Medicine and Stomatology, School of Dental Medicine, Tsurumi University, Japan
| | - Hidero Oki
- Department of Maxillofacial Surgery, Nihon University School of Dentistry, Japan
| | - Keiji Shinozuka
- Department of Maxillofacial Surgery, Nihon University School of Dentistry, Japan
| | - Kazumasa Sugihara
- Maxillofacial Diagnostic and Surgical Sciences, Department of Oral and Maxillofacial Rehabilitation, Course of Developmental Therapeutics, Kagoshima University Graduate School of Medical and Dental Sciences, Japan
| | - Tsuyoshi Sugiura
- Maxillofacial Diagnostic and Surgical Sciences, Department of Oral and Maxillofacial Rehabilitation, Course of Developmental Therapeutics, Kagoshima University Graduate School of Medical and Dental Sciences, Japan
| | - Joji Sekine
- Department of Oral and Maxillofacial Surgery, Shimane University Faculty of Medicine, Japan
| | - Hidetaka Yokoe
- Department of Dentistry and Oral Surgery, National Defense Medical College, Japan
| | - Kengo Saito
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, Japan
| | - Hideki Tanzawa
- Department of Oral Science, Graduate School of Medicine, Chiba University, Japan.,Division of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Japan
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14
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Xu Q, Hu C, Zhu Y, Wang K, Lal B, Li L, Tang J, Wei S, Huang G, Xia S, Lv S, Laterra J, Jiang Y, Li Y. ShRNA-based POLD2 expression knockdown sensitizes glioblastoma to DNA-Damaging therapeutics. Cancer Lett 2020; 482:126-135. [PMID: 31954770 DOI: 10.1016/j.canlet.2020.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 10/25/2022]
Abstract
Glioblastoma (GBM) has limited therapeutic options. DNA repair mechanisms contribute GBM cells to escape therapies and re-establish tumor growth. Multiple studies have shown that POLD2 plays a critical role in DNA replication, DNA repair and genomic stability. We demonstrate for the first time that POLD2 is highly expressed in human glioma specimens and that expression correlates with poor patient survival. siRNA or shRNA POLD2 inhibited GBM cell proliferation, cell cycle progression, invasiveness, sensitized GBM cells to chemo/radiation-induced cell death and reversed the cytoprotective effects of EGFR signaling. Conversely, forced POLD2 expression was found to induce GBM cell proliferation, colony formation, invasiveness and chemo/radiation resistance. POLD2 expression associated with stem-like cell subsets (CD133+ and SSEA-1+ cells) and positively correlated with Sox2 expression in clinical specimens. Its expression was induced by Sox2 and inhibited by the forced differentiation of GBM neurospheres. shRNA-POLD2 modestly inhibited GBM neurosphere-derived orthotopic xenografts growth, when combined with radiation, dramatically inhibited xenograft growth in a cooperative fashion. These novel findings identify POLD2 as a new potential therapeutic target for enhancing GBM response to current standard of care therapeutics.
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Affiliation(s)
- Qingfu Xu
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, 510623, PR China; Department of Neurosurgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, PR China; Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Chengchen Hu
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Yan Zhu
- Department of Ultrasonography, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, 510623, PR China; Department of Obstetrics and Gynecology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, PR China
| | - Kimberly Wang
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA
| | - Bachuchu Lal
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA
| | - Lichao Li
- Department of Neurosurgery, The First Hospital of Lanzhou University, Lanzhou, Gansu, 730000, PR China
| | - Junhai Tang
- Department of Neurosurgery, Third Military Medical University, Chongqing, 400037, PR China
| | - Shuang Wei
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA
| | - Guohao Huang
- Department of Neurosurgery, Third Military Medical University, Chongqing, 400037, PR China
| | - Shuli Xia
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Shengqing Lv
- Department of Neurosurgery, Third Military Medical University, Chongqing, 400037, PR China
| | - John Laterra
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA; Department of Oncology, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA; Department of Neuroscience, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Yugang Jiang
- Department of Neurosurgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, PR China
| | - Yunqing Li
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA.
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15
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Gao Y, Yang H, Fang R, Zhang Y, Goode EL, Cui Y. Testing Mediation Effects in High-Dimensional Epigenetic Studies. Front Genet 2019; 10:1195. [PMID: 31824577 PMCID: PMC6883258 DOI: 10.3389/fgene.2019.01195] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 10/29/2019] [Indexed: 12/24/2022] Open
Abstract
Mediation analysis has been a powerful tool to identify factors mediating the association between exposure variables and outcomes. It has been applied to various genomic applications with the hope to gain novel insights into the underlying mechanism of various diseases. Given the high-dimensional nature of epigenetic data, recent effort on epigenetic mediation analysis is to first reduce the data dimension by applying high-dimensional variable selection techniques, then conducting testing in a low dimensional setup. In this paper, we propose to assess the mediation effect by adopting a high-dimensional testing procedure which can produce unbiased estimates of the regression coefficients and can properly handle correlations between variables. When the data dimension is ultra-high, we first reduce the data dimension from ultra-high to high by adopting a sure independence screening (SIS) method. We apply the method to two high-dimensional epigenetic studies: one is to assess how DNA methylations mediate the association between alcohol consumption and epithelial ovarian cancer (EOC) status; the other one is to assess how methylation signatures mediate the association between childhood maltreatment and post-traumatic stress disorder (PTSD) in adulthood. We compare the performance of the method with its counterpart via simulation studies. Our method can be applied to other high-dimensional mediation studies where high-dimensional mediation variables are collected.
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Affiliation(s)
- Yuzhao Gao
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Haitao Yang
- Division of Health Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Ruiling Fang
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Yanbo Zhang
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Ellen L Goode
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, United States
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, United States
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16
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He W, Fu L, Yan Q, Zhou Q, Yuan K, Chen L, Han Y. Gene set enrichment analysis and meta-analysis identified 12 key genes regulating and controlling the prognosis of lung adenocarcinoma. Oncol Lett 2019; 17:5608-5618. [PMID: 31186783 PMCID: PMC6507356 DOI: 10.3892/ol.2019.10236] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 03/01/2019] [Indexed: 12/14/2022] Open
Abstract
The aim of the present study was to analyze lung adenocarcinoma-associated microarray data and identify potentially crucial genes. The gene expression profiles were downloaded from the Gene Expression Omnibus database and 6 datasets, of which 2 were discarded and 4 were retained, were preprocessed using packages in the R computing language. Subsequently, Gene Set Enrichment Analysis (GSEA) and meta-analysis was used to screen the common pathways and differentially expressed genes at the transcriptional level. The genes detected from GSEA through The Cancer Genome Atlas databases were subsequently examined, and the crucial genes by survival data were identified. Pathways of the crucial genes were obtained using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway of the online website Database for Annotation, Visualization and Integrated Discovery (DAVID) tool, and the pathways of crucial genes that were upregulated or downregulated were matched using the Venn method to identify the common crucial pathways. Furthermore, on the basis of the common crucial pathways, key genes that are closely associated with the development and progression of lung adenocarcinoma were identified with the KEGG pathway of DAVID. Additional information was obtained through Gene Ontology annotation. A total of two key pathways, including cell cycle and DNA replication, as well as 12 key genes [DNA polymerase δ subunit 2, DNA replication licensing factor MCM4, MCM6, mitotic checkpoint serine/threonine-protein kinase BUB1, BUB1β, mitotic spindle assembly checkpoint protein MAD2A, dual specificity protein kinase TTK, M-phase inducer phosphatase 1, cell division control protein 45 homolog, cyclin-dependent kinase inhibitor 1C, pituitary tumor-transforming gene 1 protein and polo-like kinase 1] were identified. These key pathways and genes may be studied in future studies involving gene transfection/knockdown, which may provide insights into the prognosis of lung adenocarcinoma. Additional studies are required to confirm their biological function.
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Affiliation(s)
- Wenwu He
- Department of Thoracic Surgery, Sichuan Cancer Hospital and Research Institute, Chengdu, Sichuan 610041, P.R. China
| | - Liangmin Fu
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Qunlun Yan
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Qiuxi Zhou
- Department of Respiratory Medicine, Nanchong Central Hospital, Nanchong, Sichuan 637000, P.R. China
| | - Kun Yuan
- Department of Anesthesiology, North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Linxin Chen
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Yongtao Han
- Department of Thoracic Surgery, Sichuan Cancer Hospital and Research Institute, Chengdu, Sichuan 610041, P.R. China
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17
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Givechian KB, Garner C, Garban H, Rabizadeh S, Soon-Shiong P. CAD/POLD2 gene expression is associated with poor overall survival and chemoresistance in bladder urothelial carcinoma. Oncotarget 2018; 9:29743-29752. [PMID: 30038717 PMCID: PMC6049856 DOI: 10.18632/oncotarget.25701] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/13/2018] [Indexed: 12/13/2022] Open
Abstract
Somatic mutations in DNA repair genes have been clinically associated with chemosensitivity, although few studies have interrogated the nucleotide synthesis pathways that supply DNA repair processes. Previous work suggests that bladder urothelial carcinoma is uniquely enriched for mutations in nucleotide excision repair genes, and that these mutations are associated with response to platinum-based therapy and favorable survival. Conversely, the de novo pyrimidine synthesis pathway has recently emerged as a putative clinical target. This anabolic process is thought to supply DNA repair processes such as nucleotide excision repair; that is, DNA repair enzymes may require a sufficient nucleotide supply available to reverse the intended genotoxic damage of systemic chemotherapy in rapidly proliferating cancer cells. Therefore, we explored the prognostic complementarity between de novo pyrimidine synthesis and nucleotide excision repair expression in a total of 570 bladder urothelial carcinoma patients. Ultimately, we show that the de novo pyrimidine synthesis gene CAD is associated with poor survival (P = 0.008) and is co-altered with the nucleotide excision repair gene POLD2. High expression of POLD2 was also associated with poor overall survival (P = 0.019) and was significantly correlated with CAD expression in pre-treatment patient tumor samples (P = 2.44e-4). Expression of each gene was associated with cisplatin-based therapy resistance, and accordingly, CADhighPOLD2high patients were associated with worse survival than CADhighPOLD2low and CADlowPOLD2high patients. Together, these biomarkers could help elucidate mechanisms of chemoresistance to further personalize therapeutic strategies in bladder urothelial carcinoma.
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Affiliation(s)
| | | | - Hermes Garban
- NantBioscience, Inc. | NantWorks, Culver City, CA 90232, USA
| | - Shahrooz Rabizadeh
- NantOmics LLC, Culver City, CA 90232, USA
- NantBioscience, Inc. | NantWorks, Culver City, CA 90232, USA
| | - Patrick Soon-Shiong
- NantOmics LLC, Culver City, CA 90232, USA
- NantBioscience, Inc. | NantWorks, Culver City, CA 90232, USA
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18
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Taetzsch T, Brayman VL, Valdez G. FGF binding proteins (FGFBPs): Modulators of FGF signaling in the developing, adult, and stressed nervous system. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2983-2991. [PMID: 29902550 DOI: 10.1016/j.bbadis.2018.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/17/2018] [Accepted: 06/09/2018] [Indexed: 01/18/2023]
Abstract
Members of the fibroblast growth factor (FGF) family are involved in a variety of cellular processes. In the nervous system, they affect the differentiation and migration of neurons, the formation and maturation of synapses, and the repair of neuronal circuits following insults. Because of the varied yet critical functions of FGF ligands, their availability and activity must be tightly regulated for the nervous system, as well as other tissues, to properly develop and function in adulthood. In this regard, FGF binding proteins (FGFBPs) have emerged as strong candidates for modulating the actions of secreted FGFs in neural and non-neural tissues. Here, we will review the roles of FGFBPs in the peripheral and central nervous systems.
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Affiliation(s)
- Thomas Taetzsch
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA.
| | - Vanessa L Brayman
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA; Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA, USA.
| | - Gregorio Valdez
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA; Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
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Tambe M, Pruikkonen S, Mäki-Jouppila J, Chen P, Elgaaen BV, Straume AH, Huhtinen K, Cárpen O, Lønning PE, Davidson B, Hautaniemi S, Kallio MJ. Novel Mad2-targeting miR-493-3p controls mitotic fidelity and cancer cells' sensitivity to paclitaxel. Oncotarget 2017; 7:12267-85. [PMID: 26943585 PMCID: PMC4914283 DOI: 10.18632/oncotarget.7860] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/17/2016] [Indexed: 01/17/2023] Open
Abstract
The molecular pathways that contribute to the proliferation and drug response of cancer cells are highly complex and currently insufficiently characterized. We have identified a previously unknown microRNA-based mechanism that provides cancer cells means to stimulate tumorigenesis via increased genomic instability and, at the same time, evade the action of clinically utilized microtubule drugs. We demonstrate miR-493-3p to be a novel negative regulator of mitotic arrest deficient-2 (MAD2), an essential component of the spindle assembly checkpoint that monitors the fidelity of chromosome segregation. The microRNA targets the 3′ UTR of Mad2 mRNA thereby preventing translation of the Mad2 protein. In cancer cells, overexpression of miR-493-3p induced a premature mitotic exit that led to increased frequency of aneuploidy and cellular senescence in the progeny cells. Importantly, excess of the miR-493-3p conferred resistance of cancer cells to microtubule drugs. In human neoplasms, miR-493-3p and Mad2 expression alterations correlated with advanced ovarian cancer forms and high miR-493-3p levels were associated with reduced survival of ovarian and breast cancer patients with aggressive tumors, especially in the paclitaxel therapy arm. Our results suggest that intratumoral profiling of miR-493-3p and Mad2 levels can have diagnostic value in predicting the efficacy of taxane chemotherapy.
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Affiliation(s)
- Mahesh Tambe
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland.,Centre for Biotechnology, University of Turku, Turku, Finland.,Drug Research Doctoral Programme and FinPharma Doctoral Program Drug Discovery, Finland
| | - Sofia Pruikkonen
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland.,Centre for Biotechnology, University of Turku, Turku, Finland.,Turku Doctoral Program of Molecular Medicine, University of Turku, Turku, Finland
| | - Jenni Mäki-Jouppila
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland.,Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Turku, Finland.,Drug Research Doctoral Programme and FinPharma Doctoral Program Drug Discovery, Finland
| | - Ping Chen
- Research Programs Unit, Genome-Scale Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Bente Vilming Elgaaen
- Department of Gynecological Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway
| | - Anne Hege Straume
- Department of Clinical Science, University of Bergen and Department of Clinical Oncology, Haukeland University Hospital, Bergen, Norway
| | - Kaisa Huhtinen
- Department of Pathology, University of Turku and Turku University Hospital, Turku, Finland
| | - Olli Cárpen
- Department of Pathology, University of Turku and Turku University Hospital, Turku, Finland.,Auria Biobank, Turku, Finland
| | - Per Eystein Lønning
- Department of Clinical Science, University of Bergen and Department of Clinical Oncology, Haukeland University Hospital, Bergen, Norway
| | - Ben Davidson
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sampsa Hautaniemi
- Research Programs Unit, Genome-Scale Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Marko J Kallio
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland.,Centre for Biotechnology, University of Turku, Turku, Finland
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20
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Loke SY, Wong PTH, Ong WY. Global gene expression changes in the prefrontal cortex of rabbits with hypercholesterolemia and/or hypertension. Neurochem Int 2016; 102:33-56. [PMID: 27890723 DOI: 10.1016/j.neuint.2016.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 11/14/2016] [Accepted: 11/23/2016] [Indexed: 02/01/2023]
Abstract
Although many studies have identified a link between hypercholesterolemia or hypertension and cognitive deficits, till date, comprehensive gene expression analyses of the brain under these conditions is still lacking. The present study was carried out to elucidate differential gene expression changes in the prefrontal cortex (PFC) of New Zealand white rabbits exposed to hypercholesterolemia and/or hypertension with a view of identifying gene networks at risk. Microarray analyses of the PFC of hypercholesterolemic rabbits showed 850 differentially expressed genes (DEGs) in the cortex of hypercholesterolemic rabbits compared to controls, but only 5 DEGs in hypertensive rabbits compared to controls. Up-regulated genes in the PFC of hypercholesterolemic rabbits included CIDEC, ODF2, RNASEL, FSHR, CES3 and MAB21L3, and down-regulated genes included FAM184B, CUL3, LOC100351029, TMEM109, LOC100357097 and PFDN5. Comparison with our previous study on the middle cerebral artery (MCA) of the same rabbits showed many differentially expressed genes in common between the PFC and MCA, during hypercholesterolemia. Moreover, these genes tended to fall into the same functional networks, as revealed by IPA analyses, with many identical node molecules. These include: proteasome, insulin, Akt, ERK1/2, histone, IL12, interferon alpha and NFκB. Of these, PSMB4, PSMD4, PSMG1 were chosen as representatives of genes related to the proteasome for verification by quantitative RT-PCR. Results indicate significant downregulation of all three proteasome associated genes in the PFC. Immunostaining showed significantly increased number of Aβ labelled cells in layers III and V of the cortex after hypercholesterolemia and hypertension, which may be due to decreased proteasome activity and/or increased β- or γ-secretase activity. Knowledge of altered gene networks during hypercholesterolemia and/or hypertension could inform our understanding of the link between these conditions and cognitive deficits in vascular dementia or Alzheimer's disease.
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Affiliation(s)
- Sau-Yeen Loke
- Department of Anatomy, National University of Singapore, 119260, Singapore
| | - Peter Tsun-Hon Wong
- Department of Pharmacology, National University of Singapore, 119260, Singapore
| | - Wei-Yi Ong
- Department of Anatomy, National University of Singapore, 119260, Singapore; Neurobiology and Ageing Research Program, Life Sciences Institute, National University of Singapore, 119260, Singapore.
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21
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Wang X, Wang SS, Zhou L, Yu L, Zhang LM. A network-pathway based module identification for predicting the prognosis of ovarian cancer patients. J Ovarian Res 2016; 9:73. [PMID: 27806724 PMCID: PMC5093979 DOI: 10.1186/s13048-016-0285-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 10/25/2016] [Indexed: 12/19/2022] Open
Abstract
Background This study aimed to screen multiple genes biomarkers based on gene expression data for predicting the survival of ovarian cancer patients. Methods Two microarray data of ovarian cancer samples were collected from The Cancer Genome Atlas (TCGA) database. The data in the training set were used to construct Reactome functional interactions network, which then underwent Markov clustering, supervised principal components, Cox proportional hazard model to screen significantly prognosis related modules. The distinguishing ability of each module for survival was further evaluated by the testing set. Gene Ontology (GO) functional and pathway annotations were performed to identify the roles of genes in each module for ovarian cancer. Results The network based approach identified two 7-gene functional interaction modules (31: DCLRE1A, EXO1, KIAA0101, KIN, PCNA, POLD3, POLD2; 35: DKK3, FABP3, IRF1, AIM2, GBP1, GBP2, IRF2) that are associated with prognosis of ovarian cancer patients. These network modules are related to DNA repair, replication, immune and cytokine mediated signaling pathways. Conclusions The two 7-gene expression signatures may be accurate predictors of clinical outcome in patients with ovarian cancer and has the potential to develop new therapeutic strategies for ovarian cancer patients.
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Affiliation(s)
- Xin Wang
- Department of Gynaecology and Obstetrics, The 306 Hospital of PLA, Beijing, 100037, China
| | - Shan-Shan Wang
- Outpatient Pharmacy, Outpatient Department, NO.16 Chengzhuang Fengtai Distinct, Beijing, 100071, China
| | - Lin Zhou
- Department of Gynaecology and Obstetrics, The 306 Hospital of PLA, Beijing, 100037, China
| | - Li Yu
- Department of Gynaecology and Obstetrics, The 306 Hospital of PLA, Beijing, 100037, China
| | - Lan-Mei Zhang
- Department of Gynaecology and Obstetrics, The 306 Hospital of PLA, Beijing, 100037, China.
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22
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Lu J, Luan P, Zhang X, Xue S, Peng L, Mahbooband S, Sun X. Gonadal transcriptomic analysis of yellow catfish (Pelteobagrus fulvidraco): identification of sex-related genes and genetic markers. Physiol Genomics 2014; 46:798-807. [PMID: 25185028 DOI: 10.1152/physiolgenomics.00088.2014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Yellow catfish (Pelteobagrus fulvidraco) has been recognized as a vital freshwater aquaculture species in East and Southeast Asia. In addition to its commercial interest, it is also attracted much attention because of its value in studying sex-determination mechanisms. A comprehensive gonadal transcriptome analysis is believed to provide a resource for genome annotation, candidate gene identification, and molecular marker development. Herein, we performed a de novo assembly of yellow catfish gonad transcriptome by high-throughput Illumina sequencing. A total of 82,123 contigs were obtained, ranging from 351 to 21,268 bp, and N50 of 2,329 bp. Unigenes of 21,869 in total were identified. Of these, 229 and 1,188 genes were found to be specifically expressed in XY gonad tissue for 1 yr and 2 yr old yellow catfish, respectively; correspondingly, 51 and 40 genes were identified in XX gonad tissue at those two stages. Gene ontology and KEGG analysis were conducted and classified all contigs into different categories. A large number of unigenes involved in sex determination were identified, as well as microsatellites and SNP variants. The expression patterns of sex-related genes were then validated by quantitative real-time PCR (qRT-PCR) suggesting the high reliability of RNA-Seq results. In this study, the transcriptome of yellow catfish gonad was first sequenced, assembled, and characterized; it provides a valuable genomic resource for better understanding of yellow catfish sex determination as well as development of molecular markers, thereby assisting in the production of monosex yellow catfish for aquaculture.
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Affiliation(s)
- Jianguo Lu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Peoples Republic of China; School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China; National and Local United Engineering Lab for Freshwater Fish Breeding, Harbin, Peoples Republic of China
| | - Peixian Luan
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Peoples Republic of China; National and Local United Engineering Lab for Freshwater Fish Breeding, Harbin, Peoples Republic of China
| | - Xiaofeng Zhang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Peoples Republic of China; National and Local United Engineering Lab for Freshwater Fish Breeding, Harbin, Peoples Republic of China
| | - Shuqun Xue
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Peoples Republic of China; National and Local United Engineering Lab for Freshwater Fish Breeding, Harbin, Peoples Republic of China
| | - Lina Peng
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Peoples Republic of China; Harbin Normal University, Harbin, Peoples Republic of China; and
| | - Shahid Mahbooband
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Xiaowen Sun
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Peoples Republic of China; National and Local United Engineering Lab for Freshwater Fish Breeding, Harbin, Peoples Republic of China;
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BUB1 mRNA is significantly co-expressed with AURKA and AURKB mRNA in advanced-stage ovarian serous carcinoma. Virchows Arch 2014; 464:701-7. [PMID: 24756216 DOI: 10.1007/s00428-014-1577-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/19/2014] [Accepted: 03/26/2014] [Indexed: 12/20/2022]
Abstract
The objective of this study was to investigate the expression and clinical role of the spindle checkpoint kinase budding uninhibited by benzimidazole 1 (Bub1) in primary and metastatic advanced-stage ovarian serous carcinoma. BUB1 mRNA expression was analyzed in 178 tumors (88 effusions, 38 primary carcinomas, and 52 solid metastases) from 144 patients with advanced-stage disease using quantitative real-time polymerase chain reaction (PCR). Bub1 protein expression by Western blotting was studied in 63 carcinomas (30 effusions and 33 solid lesions). BUB1 mRNA expression at different anatomic sites was studied for association with clinicopathologic parameters, including chemotherapy resistance and survival. BUB1 mRNA was universally expressed in serous carcinomas, irrespective of anatomic site. BUB1 mRNA levels were uniformly low in six ovarian surface epithelium specimens analyzed for comparative purposes. Bub1 protein was expressed in 22/30 effusions and 28/33 solid lesions. BUB1 mRNA expression was significantly higher in chemo-naïve primary carcinomas and solid metastases compared to specimens obtained following neoadjuvant chemotherapy (p < 0.001) and was unrelated to chemotherapy exposure in effusions nor to chemoresponse or survival at any anatomic site. BUB1 mRNA levels in both effusions and solid lesions were strongly related to the mRNA levels of AURKA and AURKB previously studied in this cohort (p < 0.001 for both). Bub1 is widely expressed in primary and metastatic OC, suggesting a biological role in this cancer. BUB1 mRNA levels are lower following chemotherapy exposure in solid lesions, though its presence is unrelated to clinical behavior including response to chemotherapy and survival. BUB1 is co-expressed with AURKA and AURKB suggesting biological relationship between these spindle cell components.
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Vilming Elgaaen B, Olstad OK, Haug KBF, Brusletto B, Sandvik L, Staff AC, Gautvik KM, Davidson B. Global miRNA expression analysis of serous and clear cell ovarian carcinomas identifies differentially expressed miRNAs including miR-200c-3p as a prognostic marker. BMC Cancer 2014; 14:80. [PMID: 24512620 PMCID: PMC3928323 DOI: 10.1186/1471-2407-14-80] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 02/07/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Improved insight into the molecular characteristics of the different ovarian cancer subgroups is needed for developing a more individualized and optimized treatment regimen. The aim of this study was to a) identify differentially expressed miRNAs in high-grade serous ovarian carcinoma (HGSC), clear cell ovarian carcinoma (CCC) and ovarian surface epithelium (OSE), b) evaluate selected miRNAs for association with clinical parameters including survival and c) map miRNA-mRNA interactions. METHODS Differences in miRNA expression between HGSC, CCC and OSE were analyzed by global miRNA expression profiling (Affymetrix GeneChip miRNA 2.0 Arrays, n = 12, 9 and 9, respectively), validated by RT-qPCR (n = 35, 19 and 9, respectively), and evaluated for associations with clinical parameters. For HGSC, differentially expressed miRNAs were linked to differentially expressed mRNAs identified previously. RESULTS Differentially expressed miRNAs (n = 78) between HGSC, CCC and OSE were identified (FDR < 0.01%), of which 18 were validated (p < 0.01) using RT-qPCR in an extended cohort. Compared with OSE, miR-205-5p was the most overexpressed miRNA in HGSC. miR-200 family members and miR-182-5p were the most overexpressed in HGSC and CCC compared with OSE, whereas miR-383 was the most underexpressed. miR-205-5p and miR-200 members target epithelial-mesenchymal transition (EMT) regulators, apparently being important in tumor progression. miR-509-3-5p, miR-509-5p, miR-509-3p and miR-510 were among the strongest differentiators between HGSC and CCC, all being significantly overexpressed in CCC compared with HGSC. High miR-200c-3p expression was associated with poor progression-free (p = 0.031) and overall (p = 0.026) survival in HGSC patients. Interacting miRNA and mRNA targets, including those of a TP53-related pathway presented previously, were identified in HGSC. CONCLUSIONS Several miRNAs differentially expressed between HGSC, CCC and OSE have been identified, suggesting a carcinogenetic role for these miRNAs. miR-200 family members, targeting EMT drivers, were mostly overexpressed in both subgroups, among which miR-200c-3p was associated with survival in HGSC patients. A set of miRNAs differentiates CCC from HGSC, of which miR-509-3-5p and miR-509-5p are the strongest classifiers. Several interactions between miRNAs and mRNAs in HGSC were mapped.
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Affiliation(s)
- Bente Vilming Elgaaen
- Department of Gynecological Oncology, Oslo University Hospital (OUH), The Norwegian Radium Hospital, Postbox 4953 Nydalen 0424, Oslo, Norway.
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Mutation spectrum and differential gene expression in cystic and solid vestibular schwannoma. Genet Med 2013; 16:264-70. [DOI: 10.1038/gim.2013.114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 06/24/2013] [Indexed: 01/18/2023] Open
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Morrison BJ, Hastie ML, Grewal YS, Bruce ZC, Schmidt C, Reynolds BA, Gorman JJ, Lopez JA. Proteomic comparison of mcf-7 tumoursphere and monolayer cultures. PLoS One 2012; 7:e52692. [PMID: 23285151 PMCID: PMC3527578 DOI: 10.1371/journal.pone.0052692] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 11/21/2012] [Indexed: 01/09/2023] Open
Abstract
Breast cancer is a heterogenous disease, composed of tumour cells with differing gene expressions and phenotypes. Very few antigens have been identified and a better understanding of tumour initiating-cells as targets for therapy is critically needed. Recently, a rare subpopulation of cells within tumours has been described with the ability to: (i) initiate and sustain tumour growth; (ii) resist traditional therapies and allow for secondary tumour dissemination; and (iii) display some of the characteristics of stem cells such as self-renewal. These cells are termed tumour-initiating cells or cancer stem cells, or alternatively, in the case of breast cancer, breast cancer stem cells. Previous studies have demonstrated that breast cancer stem cells can be enriched for in “tumoursphere” culture. Proteomics represents a novel way to investigate protein expression between cells. We hypothesise that characterisation of the proteome of the breast cancer line MCF-7 tumourspheres compared to adherent/differentiated cells identifies proteins of novel interest for further isolating or targeting breast cancer stem cells. We present evidence that: (i) the proteome of adherent cells is different to the proteome of cells grown in sphere medium from either early passage (passage 2) or late passage (passage 5) spheres; (ii) that spheres are enriched in expression of a variety of tumour-relevant proteins (including MUC1 and Galectin-3); and (iii) that targeting of one of these identified proteins (galectin-3) using an inhibitor (N-acetyllactosamine) decreases sphere formation/self-renewal of MCF-7 cancer stem cells in vitro and tumourigenicity in vivo. Hence, proteomic analysis of tumourspheres may find use in identifying novel targets for future therapy. The therapeutic targeting of breast cancer stem cells, a highly clinically relevant sub-population of tumour cells, has the potential to eliminate residual disease and may become an important component of a multi-modality treatment of cancer.
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Affiliation(s)
- Brian J. Morrison
- School of Biomolecular and Physical Sciences, Griffith University, Brisbane, Queensland, Australia
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Marcus L. Hastie
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Yadveer S. Grewal
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Zara C. Bruce
- School of Biomolecular and Physical Sciences, Griffith University, Brisbane, Queensland, Australia
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Chris Schmidt
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Brent A. Reynolds
- McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Jeffrey J. Gorman
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - J. Alejandro Lopez
- School of Biomolecular and Physical Sciences, Griffith University, Brisbane, Queensland, Australia
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia
- * E-mail:
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Kita Y, Hashimoto S, Nakajima T, Nakatani H, Nishimatsu S, Nishida Y, Kanamaru N, Kaneda Y, Takamori Y, McMurray D, Tan EV, Cang ML, Saunderson P, Dela Cruz EC, Okada M. Novel therapeutic vaccines [(HSP65 + IL-12)DNA-, granulysin- and Ksp37-vaccine] against tuberculosis and synergistic effects in the combination with chemotherapy. Hum Vaccin Immunother 2012; 9:526-33. [PMID: 23249609 DOI: 10.4161/hv.23230] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Multi-drug resistant tuberculosis (MDR-TB) and extremely drug resistant (XDR) TB are big problems in the world. We have developed novel TB therapeutic vaccines, HVJ-Envelope/HSP65 + IL-12 DNA vaccine (HSP65-vaccine), granulysin vaccine and killer specific secretory protein of 37kDa (Ksp37) vaccine. METHODS AND RESULTS HSP65 vaccine showed strong therapeutic effect against both MDR-TB and XDR-TB in mice. Intradermal immunization of HSP65-vaccine showed stronger therapeutic effect against TB than intramuscular or subcutaneous immunization. Furthermore, the synergistic therapeutic effect was observed when the vaccine was administrated in combination with Isoniazid (INH), which is a first line drug for chemotherapy. The combination of types of vaccines (HSP65- and granulysin- vaccines) also showed synergistic therapeutic effect. In the monkey model, granulysin-vaccine prolonged the survival period after the infection of TB and long-term survival was observed in vaccine-treated group. We examined the potential of two kinds of novel DNA vaccines (Ksp37-vaccine and granulysin-vaccine). Both vaccines augmented in vivo differentiation of CTL against TB. We measured the amount of Ksp37 protein in human serum and revealed that the level of Ksp37 protein of patients with tuberculosis was lower than that of healthy volunteers. Therefore, we established Ksp37 transgenic mice as well as granulysin transgenic mice to elucidate the function of those proteins. Both transgenic mice were resistant to TB infection. CONCLUSION These data indicate the potential of combinational therapy; the combination of two DNA vaccines or combination of DNA vaccine with antibiotic drug. Thus, it will provide a novel strategy for the treatment of MDR-TB.
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Affiliation(s)
- Yoko Kita
- Clinical Research Center; National Hospital Organization Kinki-chuo Chest Medical Center; Kitaku, Sakai Japan
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Okada M, Kita Y, Nakajima T, Hashimoto S, Nakatani H, Nishimatsu S, Nishida Y, Kanamaru N, Kaneda Y, Takamori Y, McMurray D, Tan EV, Cang ML, Saunderson P, Dela Cruz EC. The study of novel DNA vaccines against tuberculosis: induction of pathogen-specific CTL in the mouse and monkey models of tuberculosis. Hum Vaccin Immunother 2012; 9:515-25. [PMID: 23249543 DOI: 10.4161/hv.23229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
RESULTS HSP65 + IL-12 DNA vaccine showed higher protective efficacy compared with BCG in both mouse and monkey models of TB. It induced the TB-specific CTL in the mouse model of TB, while little level of activity was observed after the injection of BCG. It also showed strong therapeutic efficacy against MDR-TB. In the monkey model, the vaccine augmented the production of IFN-γ and IL-2 from PBL and the therapeutic effect was correlated with the level of IL-2. We next evaluated the potential of DNA vaccine encoding a granulysin, which is an important defensive molecule expressed by human T cells. We found that granulysin-encoding vaccine induced the differentiation of the CTL in vitro and in vivo. It also showed therapeutic efficacy against TB in the monkey as well as the mouse model. The DNA vaccine encoding a Ksp37 also induced the TB-specific CTL in vitro and in vivo in the mouse model. It augmented the production of IL-2, IFN-γ and IL-6 from T cells and spleen cells. A synergistic effect on the activation of the TB-specific CTL was observed by the combination of Ksp37 DNA vaccine with granulysin DNA vaccine. PURPOSE AND METHODS Emergence of the multi-drug resistant (MDR) Mycobacterium tuberculosis (TB) is a big problem in the world. We have developed novel TB vaccines [DNA vaccines encoding HSP65 + IL-12, granulysin or killer-specific secretory protein of 37kDa (Ksp37)] using Hemagglutinating virus of Japan -envelope (HVJ-E). It is suggested that the activity of the TB-specific CTL is one of the most important factor for the resistance to TB and immunity for TB in chronic human TB disease. Therefore, we examined the level of activation of the TB-specific CTL after the administration of these vaccines. CONCLUSION These data indicate that our novel vaccines (HSP65 + IL-12 DNA, granulysin and Ksp37) have a capability to activate the TB-specific CTL and will be very strong protective and therapeutic vaccines against TB.
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Affiliation(s)
- Masaji Okada
- Clinical Research Center; National Hospital Organization Kinki-chuo Chest Medical Center; Kitaku, Sakai Japan
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Elgaaen BV, Olstad OK, Sandvik L, Odegaard E, Sauer T, Staff AC, Gautvik KM. ZNF385B and VEGFA are strongly differentially expressed in serous ovarian carcinomas and correlate with survival. PLoS One 2012; 7:e46317. [PMID: 23029477 PMCID: PMC3460818 DOI: 10.1371/journal.pone.0046317] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 08/29/2012] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The oncogenesis of ovarian cancer is poorly understood. The aim of this study was to identify mRNAs differentially expressed between moderately and poorly differentiated (MD/PD) serous ovarian carcinomas (SC), serous ovarian borderline tumours (SBOT) and superficial scrapings from normal ovaries (SNO), and to correlate these mRNAs with clinical parameters including survival. METHODS Differences in mRNA expression between MD/PD SC, SBOT and SNO were analyzed by global gene expression profiling (n = 23), validated by RT-qPCR (n = 41) and correlated with clinical parameters. RESULTS Thirty mRNAs differentially expressed between MD/PD SC, SBOT and SNO were selected from the global gene expression analyses, and 21 were verified (p<0.01) by RT-qPCR. Of these, 13 mRNAs were differentially expressed in MD/PD SC compared with SNO (p<0.01) and were correlated with clinical parameters. ZNF385B was downregulated (FC = -130.5, p = 1.2×10(-7)) and correlated with overall survival (p = 0.03). VEGFA was upregulated (FC = 6.1, p = 6.0×10(-6)) and correlated with progression-free survival (p = 0.037). Increased levels of TPX2 and FOXM1 mRNAs (FC = 28.5, p = 2.7×10(-10) and FC = 46.2, p = 5.6×10(-4), respectively) correlated with normalization of CA125 (p = 0.03 and p = 0.044, respectively). Furthermore, we present a molecular pathway for MD/PD SC, including VEGFA, FOXM1, TPX2, BIRC5 and TOP2A, all significantly upregulated and directly interacting with TP53. CONCLUSIONS We have identified 21 mRNAs differentially expressed (p<0.01) between MD/PD SC, SBOT and SNO. Thirteen were differentially expressed in MD/PD SC, including ZNF385B and VEGFA correlating with survival, and FOXM1 and TPX2 with normalization of CA125. We also present a molecular pathway for MD/PD SC.
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