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Jin M, Yin C, Yang J, Yang X, Wang J, Zhu J, Yuan J. Identification and validation of calcium extrusion-related genes prognostic signature in colon adenocarcinoma. PeerJ 2024; 12:e17582. [PMID: 39006025 PMCID: PMC11246022 DOI: 10.7717/peerj.17582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 05/25/2024] [Indexed: 07/16/2024] Open
Abstract
Background Disruptions in calcium homeostasis are associated with a wide range of diseases, and play a pivotal role in the development of cancer. However, the construction of prognostic models using calcium extrusion-related genes in colon adenocarcinoma (COAD) has not been well studied. We aimed to identify whether calcium extrusion-related genes serve as a potential prognostic biomarker in the COAD progression. Methods We constructed a prognostic model based on the expression of calcium extrusion-related genes (SLC8A1, SLC8A2, SLC8A3, SLC8B1, SLC24A2, SLC24A3 and SLC24A4) in COAD. Subsequently, we evaluated the associations between the risk score calculated by calcium extrusion-related genes and mutation signature, immune cell infiltration, and immune checkpoint molecules. Then we calculated the immune score, stromal score, tumor purity and estimate score using the Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) algorithm. The response to immunotherapy was assessed using tumor immune dysfunction and exclusion (TIDE). Finally, colorectal cancer cells migration, growth and colony formation assays were performed in RKO cells with the overexpression or knockdown SLC8A3, SLC24A2, SLC24A3, or SLC24A4. Results We found that patients with high risk score of calcium extrusion-related genes tend to have a poorer prognosis than those in the low-risk group. Additionally, patients in high-risk group had higher rates of KRAS mutations and lower MUC16 mutations, implying a strong correlation between KRAS and MUC16 mutations and calcium homeostasis in COAD. Moreover, the high-risk group showed a higher infiltration of regulatory T cells (Tregs) in the tumor microenvironment. Finally, our study identified two previously unreported model genes (SLC8A3 and SLC24A4) that contribute to the growth and migration of colorectal cancer RKO cells. Conclusions Altogether, we developed a prognostic risk model for predicting the prognosis of COAD patients based on the expression profiles of calcium extrusion-related genes, Furthermore, we validated two previously unreported tumor suppressor genes (SLC8A3 and SLC24A4) involved in colorectal cancer progression.
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Affiliation(s)
- Mingpeng Jin
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Chun Yin
- Department of Cardiology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jie Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaoning Yang
- Institute of Materia Medica, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Jing Wang
- Department of Cardiology, the 902nd Hospital of PLA Joint Service Support Force, Bengbu, China
| | - Jianjun Zhu
- Department of Medical Cellular Biology and Genetics, Shanxi Medical University, Taiyuan, China
| | - Jian Yuan
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
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Ogawa M, Moriyama M, Nakamura H, Shibata T, Kuroda K, Sugitani M. Clinical significance of CDT1 mRNA expression in chronic hepatitis C or liver cirrhosis. J Clin Biochem Nutr 2024; 74:169-178. [PMID: 38510682 PMCID: PMC10948353 DOI: 10.3164/jcbn.23-54] [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: 07/09/2023] [Accepted: 08/06/2023] [Indexed: 03/22/2024] Open
Abstract
We have previously reported that chromatin licensing and DNA replication factor 1 (CDT1) is associated with the postoperative recurrence of hepatocellular carcinoma (HCC). Based on this fact, we verified whether CDT1 mRNA expression is also associated with HCC development from chronic hepatitis C (CHC) and liver cirrhosis (LC). There were 142 cases with CHC or LC who underwent liver biopsy. Detection of CDT1 mRNA in liver was performed by RT-qPCR using frozen liver biopsy tissues. We examined the association between the CDT1 mRNA expression and clinical conditions and long-term outcome. We then examined the association between serum cytokine/chemokine levels and CDT1 mRNA expression in 58 cases. The cumulative incidence rates of HCC development in cases with CDT1 mRNA in the low expression group showed significantly lower than those in the high expression group (p = 0.0391). A significant correlation was found between CDT1 mRNA expression and the extent of proliferation of atypical hepatocytes in hematoxylin and eosin-stained sections (p<0.0001). CDT1 mRNA expression has been associated with cytokines involved in tumorigenesis in experimental and human cancers. We found that cases with high CDT1 mRNA expression were at risk for developing HCC, even if they were CHC or LC.
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Affiliation(s)
- Masahiro Ogawa
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Mitsuhiko Moriyama
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
- Sashiogi Recuperation Hospital, 1348-1 Hourai, Nishi-ku, Saitama city, Saitama 331-0074, Japan
| | - Hitomi Nakamura
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Toshikatu Shibata
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Kazumichi Kuroda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Masahiko Sugitani
- Department of Pathology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
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Ogawa M, Moriyama M, Midorikawa Y, Nakamura H, Shibata T, Kuroda K, Nakayama H, Kanemaru K, Miki T, Sugitani M, Takayama T. The significance of CDT1 expression in non-cancerous and cancerous liver in cases with hepatocellular carcinoma. J Clin Biochem Nutr 2023; 73:234-248. [PMID: 37970553 PMCID: PMC10636575 DOI: 10.3164/jcbn.23-43] [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: 05/29/2023] [Accepted: 08/01/2023] [Indexed: 11/17/2023] Open
Abstract
We previously reported that chromatin licensing and DNA replication factor 1 (CDT1) expression was associated with the extent of proliferation of atypical hepatocytes and the time to postoperative recurrence in cases of hepatocellular carcinoma (HCC). This study aimed to clarify the clinical significance or pathogenesis of CDT1 expression in both non-cancerous and cancerous liver in HCC cases, including previously published data. We investigated the association between the expression of CDT1 in non-cancerous or cancerous liver tissues and histologic findings or biochemical examination results in 62 cases. We also examined the dual localization between CDT1 and FbxW7, P57kip2, P53 and c-Myc by confocal laser scanning microscopy. CDT1 mRNA expression was significantly higher in cancerous liver than in non-cancerous liver (p<0.0001). Elevated CDT1 mRNA expression indicates a significantly degree of inflammatory cell infiltration within lobules, along with elevated serum transaminase levels, and hepatic spare decline. CDT1 mRNA was highly expressed in a group of poorly differentiated cancer cells. CDT1 co-localized with P57kip2, Fbwx7, P53 and c-Myc in the nucleus or cytoplasm of hepatocytes and cancer cells. We found that CDT1 mRNA expression could represent the degree of hepatic spare ability and the high carcinogenic state.
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Affiliation(s)
- Masahiro Ogawa
- Division of Gastroenterology and Hepatology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Mitsuhiko Moriyama
- Division of Gastroenterology and Hepatology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
- Sashiogi Recuperation Hospital, 1348-1 Hourai, Nishi-ku, Saitama City, Saitama 331-0074, Japan
| | - Yutaka Midorikawa
- Division of Gastroenterology and Hepatology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Hitomi Nakamura
- Division of Gastroenterology and Hepatology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Toshikatu Shibata
- Division of Gastroenterology and Hepatology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Kazumichi Kuroda
- Division of Gastroenterology and Hepatology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Hisashi Nakayama
- Department of Digestive Surgery, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Kazunori Kanemaru
- Department of Physiology, Division of Biomedical Sciences, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Toshio Miki
- Department of Physiology, Division of Biomedical Sciences, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Masahiko Sugitani
- Department of Pathology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Tadatoshi Takayama
- Department of Digestive Surgery, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
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Ogawa M, Masuzaki R, Kanda T, Matsumura H, Nakamura H, Yamazaki M, Shibata T, Kogure H, Moriyama M. Involvement of proliferation of atypical hepatocytes and CDT 1 in the liver cancer of rats administered the diethylnitrosamine. J Clin Biochem Nutr 2023; 73:138-144. [PMID: 37700853 PMCID: PMC10493214 DOI: 10.3164/jcbn.13-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/21/2023] [Indexed: 09/14/2023] Open
Abstract
We have reported that extent of proliferation of atypical hepatocytes (POAH) in non-cancerous liver in hepatocellular carcinoma and chromatin licensing and DNA replication factor 1 (CDT1) are associated with postoperative recurrence. Here, we investigated whether extent of POAH and expression of CDT1 in liver are also associated with chemically induced liver cancer in rats. Male Fisher strain rats were orally administered diethylnitrosamine (DEN) in their drinking water and sacrificed at 6, 8, 12, or 14 weeks after start of DEN administration. We serially monitored changes in extent of POAH, CDT1 expression by immunohistochemistry (IHC), and CDT1 mRNA expression in liver by real-time quantitative PCR. The extent of POAH in liver progressed in a time-dependent manner after start of DEN administration. CDT1 expression was higher at 8 weeks than at 6 weeks by IHC, suggesting that CDT1 expression may be a marker of POAH severity. CDT1 mRNA expression in liver was significantly higher at 12 weeks than at 6 weeks (p<0.0001). We found that extent of POAH and the expression of CDT1 are also important factors in the development of chemical carcinogen-induced hepatocarcinogenesis. Furthermore, the association with POAH and CDT1 expression in carcinogenic process is important regardless of the cause of hepatocarcinogenesis.
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Affiliation(s)
- Masahiro Ogawa
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Ryota Masuzaki
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Tatsuo Kanda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Hiroshi Matsumura
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Hitomi Nakamura
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Motomi Yamazaki
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Toshikatu Shibata
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Hirofumi Kogure
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Mitsuhiko Moriyama
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-Kamimachi, Itabashi-ku, Tokyo 173-8610, Japan
- Sashiogi Recuperation Hospital, 1348-1 Hourai, Nishi-ku, Saitama, 331-0074, Japan
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5
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Jing Q, Yuan C, Zhou C, Jin W, Wang A, Wu Y, Shang W, Zhang G, Ke X, Du J, Li Y, Shao F. Comprehensive analysis identifies CLEC1B as a potential prognostic biomarker in hepatocellular carcinoma. Cancer Cell Int 2023; 23:113. [PMID: 37308868 DOI: 10.1186/s12935-023-02939-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/06/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND C-type lectin domain family 1 member B (CLEC1B, encoding the CLEC-2 protein), a member of the C-type lectin superfamily, is a type II transmembrane receptor involved in platelet activation, angiogenesis, and immune and inflammatory responses. However, data regarding its function and clinical prognostic value in hepatocellular carcinoma (HCC) remain scarce. METHODS The expression of CLEC1B was explored using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. RT-qPCR, western blot, and immunohistochemistry assays were employed to validate the downregulation of CLEC1B. Univariate Cox regression and survival analyses were used to evaluate the prognostic value of CLEC1B. Gene Set Enrichment Analysis (GSEA) was conducted to investigate the potential association between cancer hallmarks and CLEC1B expression. The TISIDB database was applied to search for the correlation between immune cell infiltration levels and CLEC1B expression. The association between CLEC1B and immunomodulators was conducted by Spearman correlation analysis based on the Sangerbox platform. Annexin V-FITC/PI apoptosis kit was used for the detection of cell apoptosis. RESULTS The expression of CLEC1B was low in various tumors and exhibited a promising clinical prognostic value for HCC patients. The expression level of CLEC1B was tightly associated with the infiltration of various immune cells in the HCC tumor microenvironment (TME) and positively correlated with a bulk of immunomodulators. In addition, CLEC1B and its related genes or interacting proteins are implicated in multiple immune-related processes and signaling pathways. Moreover, overexpression of CLEC1B significantly influenced the treatment effects of sorafenib on HCC cells. CONCLUSIONS Our results reveal that CLEC1B could serve as a potential prognostic biomarker and may be a novel immunoregulator for HCC. However, its function in immune regulation should be further explored.
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Grants
- 2021KY077, 2022KY503, 2022KY046, 2022KY074, 2022KY290 Medical and Health Science and Technology Project of Zhejiang Province
- 2021KY077, 2022KY503, 2022KY046, 2022KY074, 2022KY290 Medical and Health Science and Technology Project of Zhejiang Province
- 2021KY077, 2022KY503, 2022KY046, 2022KY074, 2022KY290 Medical and Health Science and Technology Project of Zhejiang Province
- 2020ZA098, 2021ZB245 Traditional Chinese Medicine Science and Technology Project of Zhejiang Province
- 2020ZA098, 2021ZB245 Traditional Chinese Medicine Science and Technology Project of Zhejiang Province
- LGF21H010008, LGF20H080005, LBY23H080004, LGF22H080008 Zhejiang Provincial Natural Science Foundation of China
- LGF21H010008, LGF20H080005, LBY23H080004, LGF22H080008 Zhejiang Provincial Natural Science Foundation of China
- LGF21H010008, LGF20H080005, LBY23H080004, LGF22H080008 Zhejiang Provincial Natural Science Foundation of China
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Affiliation(s)
- Qiangan Jing
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Department of Central Laboratory, Affiliated Hangzhou first people's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Chen Yuan
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Chaoting Zhou
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Weidong Jin
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Aiwei Wang
- Department of Hematology, The first people's Hospital of Fuyang Hangzhou, Hangzhou, Zhejiang, China
| | - Yanfang Wu
- Department of Hematology, The first people's Hospital of Fuyang Hangzhou, Hangzhou, Zhejiang, China
| | - Wenzhong Shang
- Department of Hematology, The first people's Hospital of Fuyang Hangzhou, Hangzhou, Zhejiang, China
| | - Guibing Zhang
- Department of Hematology, The first people's Hospital of Fuyang Hangzhou, Hangzhou, Zhejiang, China
| | - Xia Ke
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Jing Du
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China.
| | - Yanchun Li
- Department of Central Laboratory, Affiliated Hangzhou first people's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Fangchun Shao
- Cancer Center, Department of Pulmonary and Critical Care Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China.
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He Y, Wu Y, Song M, Yang Y, Yu Y, Xu S. Establishment and validation of a ferroptosis-related prognostic signature for hepatocellular carcinoma. Front Oncol 2023; 13:1149370. [PMID: 37143953 PMCID: PMC10151679 DOI: 10.3389/fonc.2023.1149370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/31/2023] [Indexed: 05/06/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer with high heterogeneity. The prognosis of HCC is quite poor and the prognostic prediction also has challenges. Ferroptosis is recently recognized as a kind of iron-dependent cell death, which is involved in tumor progression. However, further study is needed to validate the influence of drivers of ferroptosis (DOFs) on the prognosis of HCC. Methods The FerrDb database and the Cancer Genome Atlas (TCGA) database were applied to retrieve DOFs and information of HCC patients respectively. HCC patients were randomly divided into training and testing cohorts with a 7:3 ratio. Univariate Cox regression, LASSO and multivariate Cox regression analyses were carried out to identify the optimal prognosis model and calculate the risk score. Then, univariate and multivariate Cox regression analyses were performed to assess the independence of the signature. At last, gene functional, tumor mutation and immune-related analyses were conducted to explore the underlying mechanism. Internal and external databases were used to confirm the results. Finally, the tumor tissue and normal tissue from HCC patients were applied to validate the gene expression in the model. Results Five genes were identified to develop as a prognostic signature in the training cohort relying on the comprehensive analysis. Univariate and multivariate Cox regression analyses confirmed that the risk score was able to be an independent factor for the prognosis of HCC patients. Low-risk patients showed better overall survival than high-risk patients. Receiver operating characteristic (ROC) curve analysis confirmed the signature's predictive capacity. Furthermore, internal and external cohorts were consistent with our results. There was a higher proportion of nTreg cell, Th1 cell, macrophage, exhausted cell and CD8+T cell in the high-risk group. The Tumor Immune Dysfunction and Exclusion (TIDE) score suggested that high-risk patients could respond better to immunotherapy. Besides, the experimental results showed that some genes were differentially expressed between tumor and normal tissues. Conclusion In summary, the five ferroptosis gene signature showed potential in prognosis of patients with HCC and could also be regarded as a value biomarker for immunotherapy response in these patients.
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Affiliation(s)
- Yixian He
- National Key Laboratory of Medical Immunology and Institute of Immunology, Naval Medical University, Shanghai, China
| | - Yunyang Wu
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, China
- Department of Traditional Chinese Medicine, Naval Medical University, Shanghai, China
| | - Mengqi Song
- National Key Laboratory of Medical Immunology and Institute of Immunology, Naval Medical University, Shanghai, China
| | - Yanlong Yang
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, China
- Department of Traditional Chinese Medicine, Naval Medical University, Shanghai, China
| | - Yizhi Yu
- National Key Laboratory of Medical Immunology and Institute of Immunology, Naval Medical University, Shanghai, China
- *Correspondence: Yizhi Yu, ; Sheng Xu,
| | - Sheng Xu
- National Key Laboratory of Medical Immunology and Institute of Immunology, Naval Medical University, Shanghai, China
- *Correspondence: Yizhi Yu, ; Sheng Xu,
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7
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Kasavi C. Gene co-expression network analysis revealed novel biomarkers for ovarian cancer. Front Genet 2022; 13:971845. [PMID: 36338962 PMCID: PMC9627302 DOI: 10.3389/fgene.2022.971845] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 10/10/2022] [Indexed: 09/18/2023] Open
Abstract
Ovarian cancer is the second most common gynecologic cancer and remains the leading cause of death of all gynecologic oncologic disease. Therefore, understanding the molecular mechanisms underlying the disease, and the identification of effective and predictive biomarkers are invaluable for the development of diagnostic and treatment strategies. In the present study, a differential co-expression network analysis was performed via meta-analysis of three transcriptome datasets of serous ovarian adenocarcinoma to identify novel candidate biomarker signatures, i.e. genes and miRNAs. We identified 439 common differentially expressed genes (DEGs), and reconstructed differential co-expression networks using common DEGs and considering two conditions, i.e. healthy ovarian surface epithelia samples and serous ovarian adenocarcinoma epithelia samples. The modular analyses of the constructed networks indicated a co-expressed gene module consisting of 17 genes. A total of 11 biomarker candidates were determined through receiver operating characteristic (ROC) curves of gene expression of module genes, and miRNAs targeting these genes were identified. As a result, six genes (CDT1, CNIH4, CRLS1, LIMCH1, POC1A, and SNX13), and two miRNAs (mir-147a, and mir-103a-3p) were suggested as novel candidate prognostic biomarkers for ovarian cancer. Further experimental and clinical validation of the proposed biomarkers could help future development of potential diagnostic and therapeutic innovations in ovarian cancer.
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Affiliation(s)
- Ceyda Kasavi
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
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PRR7-AS1 Correlates with Immune Cell Infiltration and Is a Diagnostic and Prognostic Marker for Hepatocellular Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:1939368. [PMID: 36059812 PMCID: PMC9439911 DOI: 10.1155/2022/1939368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/04/2022] [Accepted: 08/11/2022] [Indexed: 01/27/2023]
Abstract
Hepatocellular carcinoma (HCC) is a highly aggressive malignant disease, and numerous studies have shown that certain functional long noncoding RNAs (lncRNAs) are implicated in the progression of several cancers. The purpose of the research was to determine, using a database, bioinformatics, and statistical analysis, whether or not lncRNA PRR7-AS1 (PRR7-AS1) was related to HCC. TCGA datasets were used to conduct research on the PRR7-AS1 expression pattern in HCC. In order to evaluate the efficacy of GIHCG as a prognostic tool, both survival and Cox regression analyses were carried out. Furthermore, an investigation of the connection between the expression of PRR7-AS1 and immune infiltration in HCC was carried out. In this study, we identified 125 lncRNAs that were significantly dysregulated in HCC and were associated with long-term survival. Among the above 125 lncRNAs, our attention focused on PRR7-AS1. We found that PRR7-AS1 expressions were distinctly overexpressed in HCC samples compared with nontumor samples. ROC assays revealed that PRR7-AS1 effectively differentiated HCC specimens from normal tissues with an AUC of 0.875 (95% CI: 0.840 to 0.911). Moreover, the high PRR7-AS1 expression was associated with advanced clinical stage and poor prognosis of HCC patients. Importantly, the multivariate Cox proportional hazards model suggested that up-expression of PRR7-AS1 was an independent prognostic marker indicating shorter overall survival and disease-specific survival for HCC patients. Finally, we found that PRR7-AS1 expression was associated with the expression of NK CD56bright cells, Th2 cells, TFH, macrophages, Th1 cells, aDC, T helper cells, cytotoxic cells, DC, Tgd, neutrophils, and Th17 cells. Overall, the results of our study show that PRR7-AS1 was a biomarker that could be utilized to predict the prognosis of HCC patients and was linked to the infiltration of immune cells in HCC.
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Sarafidis M, Lambrou GI, Zoumpourlis V, Koutsouris D. An Integrated Bioinformatics Analysis towards the Identification of Diagnostic, Prognostic, and Predictive Key Biomarkers for Urinary Bladder Cancer. Cancers (Basel) 2022; 14:cancers14143358. [PMID: 35884419 PMCID: PMC9319344 DOI: 10.3390/cancers14143358] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/03/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Bladder cancer is evidently a challenge as far as its prognosis and treatment are concerned. The investigation of potential biomarkers and therapeutic targets is indispensable and still in progress. Most studies attempt to identify differential signatures between distinct molecular tumor subtypes. Therefore, keeping in mind the heterogeneity of urinary bladder tumors, we attempted to identify a consensus gene-related signature between the common expression profile of bladder cancer and control samples. In the quest for substantive features, we were able to identify key hub genes, whose signatures could hold diagnostic, prognostic, or therapeutic significance, but, primarily, could contribute to a better understanding of urinary bladder cancer biology. Abstract Bladder cancer (BCa) is one of the most prevalent cancers worldwide and accounts for high morbidity and mortality. This study intended to elucidate potential key biomarkers related to the occurrence, development, and prognosis of BCa through an integrated bioinformatics analysis. In this context, a systematic meta-analysis, integrating 18 microarray gene expression datasets from the GEO repository into a merged meta-dataset, identified 815 robust differentially expressed genes (DEGs). The key hub genes resulted from DEG-based protein–protein interaction and weighted gene co-expression network analyses were screened for their differential expression in urine and blood plasma samples of BCa patients. Subsequently, they were tested for their prognostic value, and a three-gene signature model, including COL3A1, FOXM1, and PLK4, was built. In addition, they were tested for their predictive value regarding muscle-invasive BCa patients’ response to neoadjuvant chemotherapy. A six-gene signature model, including ANXA5, CD44, NCAM1, SPP1, CDCA8, and KIF14, was developed. In conclusion, this study identified nine key biomarker genes, namely ANXA5, CDT1, COL3A1, SPP1, VEGFA, CDCA8, HJURP, TOP2A, and COL6A1, which were differentially expressed in urine or blood of BCa patients, held a prognostic or predictive value, and were immunohistochemically validated. These biomarkers may be of significance as prognostic and therapeutic targets for BCa.
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Affiliation(s)
- Michail Sarafidis
- Biomedical Engineering Laboratory, School of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., 15780 Athens, Greece;
- Correspondence: ; Tel.: +30-210-772-2430
| | - George I. Lambrou
- Choremeio Research Laboratory, First Department of Pediatrics, National and Kapodistrian University of Athens, 8 Thivon & Levadeias Str., 11527 Athens, Greece;
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, 8 Thivon & Levadeias Str., 11527 Athens, Greece
| | - Vassilis Zoumpourlis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vas. Konstantinou Ave., 11635 Athens, Greece;
| | - Dimitrios Koutsouris
- Biomedical Engineering Laboratory, School of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., 15780 Athens, Greece;
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Chen L, Lin YH, Liu GQ, Huang JE, Wei W, Yang ZH, Hu YM, Xie JH, Yu HZ. Clinical Significance and Potential Role of LSM4 Overexpression in Hepatocellular Carcinoma: An Integrated Analysis Based on Multiple Databases. Front Genet 2022; 12:804916. [PMID: 35096017 PMCID: PMC8793693 DOI: 10.3389/fgene.2021.804916] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/27/2021] [Indexed: 01/30/2023] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a solid tumor with high recurrence rate and high mortality. It is crucial to discover available biomarkers to achieve early diagnosis and improve the prognosis. The effect of LSM4 in HCC still remains unrevealed. Our study is dedicated to exploring the expression of LSM4 in HCC, demonstrating its clinical significance and potential molecular mechanisms. Methods: Clinical information and LSM4 expression values of HCC were obtained from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Survival analysis and receiver operating characteristic (ROC) curve analysis were applied to evaluate the prognostic and diagnostic significance of LSM4. Calculating pooled standardized mean difference (SMD) and performing summary receiver operating characteristic (sROC) curve analysis to further determine its expression status and diagnostic significance. LSM4-related co-expressed genes (CEGs) were obtained and explored their clinical significance in HCC. LSM4-associated pathways were identified through Gene set enrichment analysis (GSEA). Results: Up-regulated LSM4 was detected in HCC tissues (SMD = 1.56, 95% CI: 1.29–1.84) and overexpressed LSM4 had excellent distinguishing ability (AUC = 0.91, 95% CI: 0.88–0.93). LSM4 was associated with clinical stage, tumor grade, and lymph node metastasis status (p < 0.05). Survival analysis showed that high LSM4 expression was related to poor overall survival (OS) of HCC patients. Cox regression analysis suggested that high LSM4 expression may be an independent risk factor for HCC. We obtained nine up-regulated CEGs of LSM4 in HCC tissues, and six CEGs had good prognostic and diagnostic significance. GSEA analysis showed that up-regulated LSM4 was closely related to the cell cycle, cell replication, focal adhesion, and several metabolism-associated pathways, including fatty acid metabolism. Conclusion: Overexpressed LSM4 may serve as a promising diagnostic and prognostic biomarker of HCC. Besides, LSM4 may play a synergistic effect with CEGs in promoting the growth and metastasis of HCC cells via regulating crucial pathways such as cell cycle, focal adhesion, and metabolism-associated pathways.
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Affiliation(s)
- Liang Chen
- Department of General Surgery, Fuyang Hospital Affiliated to Anhui Medical Universitsy, Fuyang, China
| | - Yun-Hua Lin
- The First Clinical Medical College, Guangxi Medical University, Nanning, China
| | - Guo-Qing Liu
- The First Clinical Medical College, Guangxi Medical University, Nanning, China
| | - Jing-En Huang
- Department of General Surgery, Hospital of Traditional Chinese Medicine, Baise, China
| | - Wei Wei
- Department of General Surgery, Fuyang Hospital Affiliated to Anhui Medical Universitsy, Fuyang, China
| | - Zhong-Hua Yang
- Department of General Surgery, Fuyang Hospital Affiliated to Anhui Medical Universitsy, Fuyang, China
| | - Yi-Ming Hu
- College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Jia-Heng Xie
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hong-Zhu Yu
- Department of General Surgery, Fuyang Hospital Affiliated to Anhui Medical Universitsy, Fuyang, China
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Cheng X, Li D, Qi T, Sun J, Zhou T, Zheng WV. Objective to identify and verify the regulatory mechanism of DTNBP1 as a prognostic marker for hepatocellular carcinoma. Sci Rep 2022; 12:211. [PMID: 34997064 PMCID: PMC8742032 DOI: 10.1038/s41598-021-04055-4] [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: 07/09/2021] [Accepted: 12/09/2021] [Indexed: 11/09/2022] Open
Abstract
Although the overall survival of hepatocellular carcinoma (HCC) patients has been significantly improved, prognostic clinical evaluation remains a substantial problem owing to the heterogeneity and complexity of tumor. A reliable and accurate predictive biomarker may assist physicians in better monitoring of patient treatment outcomes and follow the overall survival of patients. Accumulating evidence has revealed that DTNBP1 plays functional roles in cancer prognosis. Therefore, the expression and function of DTNBP1in HCC was systematically investigated in our study. The expression and prognostic value of DTNBP1 were investigated using the data from Cancer Genome Atlas (TCGA) database, Gene Expression Omnibus (GEO) cohorts and clinical samples. A series of cellular function assays were performed to elucidate the effect of DTNBP1 on cellular proliferation, apoptosis and metastasis. Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment and Protein–protein interaction (PPI) network construction were performed to screen the genes with highest interaction scores with DTNBP1. Finally, the underlying mechanism was also analyzed using Gene Set Enrichment Analysis (GSEA) and confirmed using RT-qPCR and western blotting. DTNBP1 was upregulated in many types of cancers, especially in HCC. The DTNBP1 expression levels is associated with clinicopathologic variables and patient survival status. The differential expression of DTNBP1 could be used to determine the risk stratification of patients with HCC. DTNBP1 deficiency inhibited cell proliferation and metastasis, but promoted cell apoptosis. Mechanistically, DTNBP1 regulated the cell cycle progression through affecting the expression of cell cycle-related genes such as CDC25A, CCNE1, CDK2, CDC20, CDC25B, CCNB1, and CDK1. DTNBP1, which regulates the cell cycle progression, may be used as a prognostic marker for HCC.
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Affiliation(s)
- Xianyi Cheng
- Intervention and Cell Therapy Center, Peking University Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China
| | - Dezhi Li
- Intervention and Cell Therapy Center, Peking University Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China
| | - Tiangyang Qi
- Ascentawits Pharmaceuticals, Ltd., Biomedical Innovation Industrial Park, No. 14 Jinhui Road, Jinsha Community, Kengzi Street, Pingshan District, Shenzhen, Guangdong, People's Republic of China
| | - Jia Sun
- Intervention and Cell Therapy Center, Peking University Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China.,ShenZhen Beike Biotechnology Research Institute, Shenzhen, 518057, People's Republic of China
| | - Tao Zhou
- Intervention and Cell Therapy Center, Peking University Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China
| | - Wei V Zheng
- Intervention and Cell Therapy Center, Peking University Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China.
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12
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Mi Y, Wang X. Comprehensive Investigation of Genes Associated Cell Cycle Pathways for Prognosis and Immunotherapy in Bladder Urothelial Carcinoma. J Environ Pathol Toxicol Oncol 2022; 41:1-12. [DOI: 10.1615/jenvironpatholtoxicoloncol.2022041342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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