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Qin Y, Xu H, Xi Y, Feng L, Chen J, Xu B, Dong X, Li Y, Jiang Z, Lou J. Effects of the SEMA4B gene on hexavalent chromium [Cr(VI)]-induced malignant transformation of human bronchial epithelial cells. Toxicol Res (Camb) 2024; 13:tfae030. [PMID: 38464415 PMCID: PMC10919774 DOI: 10.1093/toxres/tfae030] [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: 10/26/2023] [Revised: 02/02/2024] [Accepted: 02/17/2024] [Indexed: 03/12/2024] Open
Abstract
Our previous study identified the potential of SEMA4B methylation level as a biomarker for hexavalent chromium [Cr(VI)] exposure. This study aimed to investigate the role of the SEMA4B gene in Cr(VI)-mediated malignant transformation of human bronchial epithelial (BEAS-2B) cells. In our population survey of workers, the geometric mean [95% confidence intervals (CIs)] of Cr in blood was 3.80 (0.42, 26.56) μg/L. Following treatment with various doses of Cr(VI), it was found that 0.5 μM had negligible effects on the cell viability of BEAS-2B cells. The expression of SEMA4B was observed to decrease in BEAS-2B cells after 7 days of treatment with 0.5 μM Cr(VI), and this downregulation continued with increasing passages of Cr(VI) treatment. Chronic exposure to 0.5 μM Cr(VI) enhanced the anchorage-independent growth ability of BEAS-2B cells. Furthermore, the use of a methylation inhibitor suppressed the Cr(VI)-mediated anchorage-independent growth in BEAS-2B cells. Considering that Cr levels exceeding 0.5 μM can be found in human blood due to occupational exposure, the results suggested a potential carcinogenic risk associated with occupational Cr(VI) exposure through the promotion of malignant transformation. The in vitro study further demonstrated that Cr(VI) exposure might inhibit the expression of the SEMA4B gene to promote the malignant transformation of BEAS-2B cells.
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Affiliation(s)
- Yao Qin
- School of Public Health, Hangzhou Medical College, No. 182, Tianmushan Road, West Lake District, Hangzhou, Zhejiang 310013, China
| | - Huadong Xu
- School of Public Health, Hangzhou Medical College, No. 182, Tianmushan Road, West Lake District, Hangzhou, Zhejiang 310013, China
| | - Yongyong Xi
- School of Public Health, Hangzhou Medical College, No. 182, Tianmushan Road, West Lake District, Hangzhou, Zhejiang 310013, China
| | - Lingfang Feng
- School of Public Health, Hangzhou Medical College, No. 182, Tianmushan Road, West Lake District, Hangzhou, Zhejiang 310013, China
| | - Junfei Chen
- School of Public Health, Hangzhou Medical College, No. 182, Tianmushan Road, West Lake District, Hangzhou, Zhejiang 310013, China
| | - Biao Xu
- School of Public Health, Hangzhou Medical College, No. 182, Tianmushan Road, West Lake District, Hangzhou, Zhejiang 310013, China
| | - Xiaowen Dong
- School of Public Health, Hangzhou Medical College, No. 182, Tianmushan Road, West Lake District, Hangzhou, Zhejiang 310013, China
| | - Yongxin Li
- School of Public Health, Hangzhou Medical College, No. 182, Tianmushan Road, West Lake District, Hangzhou, Zhejiang 310013, China
| | - Zhaoqiang Jiang
- School of Public Health, Hangzhou Medical College, No. 182, Tianmushan Road, West Lake District, Hangzhou, Zhejiang 310013, China
| | - Jianlin Lou
- School of Public Health, Hangzhou Medical College, No. 182, Tianmushan Road, West Lake District, Hangzhou, Zhejiang 310013, China
- Huzhou Key Laboratory of Precise Prevention and Control of Major Chronic Diseases, School of Medicine, and the First Affiliated Hospital, Huzhou University, No. 158, Square Back Road, Wuxing District, Huzhou, Zhejiang 313000, China
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Wang Z, Shi P, Huang P, Xu C, He Y, Lei W. Identification of secretory pathway-related genes based on Random Forest algorithm to predict the prognosis and immunotherapy response of hepatocellular carcinoma. J Gene Med 2024; 26:e3593. [PMID: 37730948 DOI: 10.1002/jgm.3593] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/31/2023] [Accepted: 08/25/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND The dysfunction of secretory pathways may represent biomarkers or therapeutic targets of cancer. The hepatocellular carcinoma (HCC) phenotype was studied in relation to the genes in the secretory pathway and to screen for a combination of genes that may be a viable therapeutic target for HCC and connected to the pathophysiological features of the tumor. METHODS Using the HCC information from The Cancer Genome Atlas, somatic mutation and prognostic association analysis were performed on the secretory pathway genes. Based on prognostic genes in the secretory pathway, the samples were consensus clustered, and a Random Forest model was built. The clinical characteristics, tumor mutation burden, functional status and potential responses to immunotherapy and tumor suppressor medications of various subtypes and risk groups were discussed. RESULTS Of the 84 genes for secretory pathway, 32 were prognostic genes related to HCC, which divided HCC into two categories: C1 and C2. By comparing the two types of HCC samples, it was found that the survival outcome of C1 was inferior, with stronger adaptive and innate immunity, but less sensitive to immunotherapy than C2. The constructed prognostic signature included seven of the 32 prognostic genes in the secretory pathway, which showed significant correlation with the prognosis, somatic mutation, biological pathway status, potential response to immunotherapy and sensitivity of 72 tumor suppressor drugs from different HCC cohorts, and had a feasible prognostic effect for 31 types of cancer and immunotherapy cohorts. CONCLUSIONS In this study, HCC was divided into two molecular subtypes according to prognostic genes in the secretory pathway, and seven of them were combined into one signature, which produced significant results in evaluating the prognosis of different HCC cohorts, pan-cancer cohorts and immunotherapy cohorts, and had potential guiding significance for prophylactic immunotherapy in patients with HCC.
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Affiliation(s)
- Zanzhi Wang
- Department of Emergency Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Pengwei Shi
- Department of Emergency Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Peng Huang
- Department of Emergency Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chun Xu
- Department of Emergency Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yaoquan He
- Department of Emergency Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wenxiong Lei
- Department of Emergency Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Lin Y, Li J, Li S, Chen Y, Luo Y, Wang Y, Yang Z. Long noncoding RNA LINC00482 silencing sensitizes non-small cell lung cancer cells to cisplatin by downregulating CLASRP via E2F1. Funct Integr Genomics 2023; 23:335. [PMID: 37966662 DOI: 10.1007/s10142-023-01260-4] [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: 07/07/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023]
Abstract
Long noncoding RNA LINC00482 (LINC00482) is dysregulated in non-small cell lung cancer cells (NSCLC). Herein, this research examined the actions and specific mechanisms of LINC00482 in cisplatin (DDP) resistance in NSCLC. LINC00482 expression was assessed using RT-qPCR in clinical NSCLC tissues and cell lines. Knockdown and ectopic expression assays were conducted in A549 and HCC44 cells, followed by determination of cell proliferation with CCK-8 and clone formation assays, apoptosis with flow cytometry, and DDP sensitivity. The association between LINC00482, E2F1, and CLASRP was evaluated with dual-luciferase reporter, ChIP, and RIP assays. The role of LINC00482 in NSCLC was confirmed in nude mice. NSCLC tissues and cells had upregulated LINC00482 expression. LINC00482 was mainly localized in the cell nucleus, and LINC00482 recruited E2F1 to enhance CLASRP expression in NSCLC cells. LINC00482 knockdown enhanced the DDP sensitivity and apoptosis of NSCLC cells while reducing cell proliferation, which was negated by overexpressing CLASRP. LINC00482 knockdown restricted tumor growth and enhanced DDP sensitivity in NSCLC in vivo. LINC00482 silencing downregulated CLASRP through E2F1 to facilitate the sensitivity to DDP in NSCLC.
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Affiliation(s)
- Yanming Lin
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, People's Republic of China
| | - Jinmei Li
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, People's Republic of China
| | - Shujun Li
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, People's Republic of China
| | - Yuting Chen
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, People's Republic of China
| | - Yiping Luo
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, People's Republic of China
| | - Yongcun Wang
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, People's Republic of China.
| | - Zhixiong Yang
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, People's Republic of China.
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Qian Y, Li YJ, Fu YW, Liu CX, Wang J, Yang B. tRNA-Uridine Aminocarboxypropyltransferase DTW Domain Containing 2 Suppresses Colon Adenocarcinoma Progression. Int J Genomics 2023; 2023:4354536. [PMID: 37745798 PMCID: PMC10517874 DOI: 10.1155/2023/4354536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/07/2023] [Accepted: 08/20/2023] [Indexed: 09/26/2023] Open
Abstract
Background DTW Domain Containing 2 (DTWD2) is a newly identified transfer RNA-uridine aminocarboxypropyltransferase. Dysregulated expression of DTWD1 has been reported in several malignancies, nevertheless, the role of DTWD2 in cancers remains completely unknown. Here, we aimed to initially investigate the expression and role of DTWD2 in colon adenocarcinoma. Methods We first evaluated the transcription and mRNA levels of DTWD2 using data from The Cancer Genome Atlas. Besides, we tested its mRNA and protein expression in our enrolled retrospective cohort. Univariate and multivariate analyses were conducted to assess its prognostic value. Cellular experiments and xenografts were also performed to validate the role of DTWD2 in colon cancer progression. Results DTWD2 was downregulated in colon adenocarcinoma and associated with poor prognosis. Lymph node metastasis, distant metastasis, and advanced tumor stage are all characterized by lower DTWD2 levels. Furthermore, Cox regression analysis demonstrated that DTWD2 is a novel independent prognostic factor for colon cancer patients. Finally, cellular and xenograft data demonstrated that silencing DTWD2 significantly enhanced colon cancer growth. Conclusion Low expression of DTWD2 may be a potential molecular marker for poor prognosis in colon cancer.
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Affiliation(s)
- Yun Qian
- Department of Digestive, Taizhou People's Hospital Affiliated to Nanjing Medical University, Taizhou 225300, China
| | - Yu-Jiang Li
- Department of Digestive, Taizhou People's Hospital Affiliated to Nanjing Medical University, Taizhou 225300, China
| | - Yi-Wei Fu
- Department of Digestive, Taizhou People's Hospital Affiliated to Nanjing Medical University, Taizhou 225300, China
| | - Cui-Xia Liu
- Department of Digestive, Taizhou People's Hospital Affiliated to Nanjing Medical University, Taizhou 225300, China
| | - Juan Wang
- Department of Digestive, Taizhou People's Hospital Affiliated to Nanjing Medical University, Taizhou 225300, China
| | - Bin Yang
- Department of Digestive, Taizhou People's Hospital Affiliated to Nanjing Medical University, Taizhou 225300, China
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Gu Q, Wu J, Xu H, Cao H, Zhang J, Jing C, Wang Z, Du M, Ma R, Feng J. CLASRP oncogene as a novel target for colorectal cancer. Funct Integr Genomics 2023; 23:290. [PMID: 37658940 PMCID: PMC10474993 DOI: 10.1007/s10142-023-01208-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 09/05/2023]
Abstract
Clk4-associated serine/arginine-rich protein (CLASRP), an alternative splicing regulator, may be involved in the development and progression of cancer by regulating the activity of the CDC-like kinase (Clk) family. This study explored the biological function of CLASRP in colorectal cancer (CRC). The expression of CLASRP, which is associated with clinicopathological features, was analysed in CRC tissues and paired noncancer tissues by RT-PCR. The roles of CLASRP were investigated in CRC cells transfected with plasmids or shRNA through proliferation, migration and invasion assays in vitro and a xenograft model in vivo. Apoptosis was analysed using CLASRP-overexpressing CRC cells by western blotting. Clk inhibitors were used to perform functional research on CLASRP in CLASRP-overexpressing CRC cells. CLASRP was significantly upregulated in CRC cell lines, while high CLASRP expression was correlated with metastasis in CRC patients. Functionally, overexpression of CLASRP significantly promoted the proliferation, migration and invasion of CRC cells in vitro and tumour growth in vivo. Mechanistically, the proliferation, migration and invasion of CLASRP-overexpressing CRC cells were inhibited by Clk inhibitors, accompanied by low expression of CLASRP at the gene and protein levels. Clk inhibitors induced apoptosis of CLASRP-overexpressing CRC cells, resulting in direct blockade of cell growth. The expression levels of cleaved caspase 3 and cleaved caspase 8 were increased in CLASRP-overexpressing CRC cells treated with Clk inhibitors. CLASRP might serve as a promotional oncogene in CRC cells and be suppressed by Clk inhibitors through activation of caspase pathways.
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Affiliation(s)
- Quan Gu
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China
| | - Jianzhong Wu
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China
| | - Heng Xu
- Jiangsu Provincial Institute of Materia Medica, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Haixia Cao
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China
| | - Junying Zhang
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China
| | - Changwen Jing
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China
| | - Zhuo Wang
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China
| | - Mengjie Du
- Jiangsu Provincial Institute of Materia Medica, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Rong Ma
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China.
| | - Jifeng Feng
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China.
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Zhang D, Ni Y, Wang Y, Feng J, Zhuang N, Li J, Liu L, Shen W, Zheng J, Zheng W, Qian C, Shan J, Zhou Z. Spatial heterogeneity of tumor microenvironment influences the prognosis of clear cell renal cell carcinoma. J Transl Med 2023; 21:489. [PMID: 37474942 PMCID: PMC10360235 DOI: 10.1186/s12967-023-04336-8] [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: 03/18/2023] [Accepted: 07/09/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is an immunologically and histologically diverse tumor. However, how the structural heterogeneity of tumor microenvironment (TME) affects cancer progression and treatment response remains unclear. Hence, we characterized the TME architectures of ccRCC tissues using imaging mass cytometry (IMC) and explored their associations with clinical outcome and therapeutic response. METHODS Using IMC, we profiled the TME landscape of ccRCC and paracancerous tissue by measuring 17 markers involved in tissue architecture, immune cell and immune activation. In the ccRCC tissue, we identified distinct immune architectures of ccRCC tissue based on the mix score and performed cellular neighborhood (CN) analysis to subdivide TME phenotypes. Moreover, we assessed the relationship between the different TME phenotypes and ccRCC patient survival, clinical features and treatment response. RESULTS We found that ccRCC tissues had higher levels of CD8+ T cells, CD163- macrophages, Treg cells, endothelial cells, and fibroblasts than paracancerous tissues. Immune infiltrates in ccRCC tissues distinctly showed clustered and scattered patterns. Within the clustered pattern, we identified two subtypes with different clinical outcomes based on CN analysis. The TLS-like phenotype had cell communities resembling tertiary lymphoid structures, characterized by cell-cell interactions of CD8+ T cells-B cells and GZMB+CD8+ T cells-B cells, which exhibited anti-tumor features and favorable outcomes, while the Macrophage/T-clustered phenotype with macrophage- or T cell-dominated cell communities had a poor prognosis. Patients with scattered immune architecture could be further divided into scattered-CN-hot and scattered-CN-cold phenotypes based on the presence or absence of immune CNs, but both had a better prognosis than the macrophage/T-clustered phenotype. We further analyzed the relationship between the TME phenotypes and treatment response in five metastatic ccRCC patients treated with sunitinib, and found that all three responders were scattered-CN-hot phenotype while both non-responders were macrophage/T-clustered phenotype. CONCLUSION Our study revealed the structural heterogeneity of TME in ccRCC and its impact on clinical outcome and personalized treatment. These findings highlight the potential of IMC and CN analysis for characterizing TME structural units in cancer research.
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Affiliation(s)
- Dawei Zhang
- Department of Urology, The Southwest Hospital, Army Medical University, No. 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Yuanli Ni
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, No. 181 Hanyu Road, Shapingba District, Chongqing, 400030, China
| | - Yongquan Wang
- Department of Urology, The Southwest Hospital, Army Medical University, No. 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Juan Feng
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, No. 181 Hanyu Road, Shapingba District, Chongqing, 400030, China
| | - Na Zhuang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, No. 181 Hanyu Road, Shapingba District, Chongqing, 400030, China
| | - Jiatao Li
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, No. 181 Hanyu Road, Shapingba District, Chongqing, 400030, China
| | - Limei Liu
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, No. 181 Hanyu Road, Shapingba District, Chongqing, 400030, China
| | - Wenhao Shen
- Department of Urology, The Southwest Hospital, Army Medical University, No. 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Ji Zheng
- Department of Urology, The Southwest Hospital, Army Medical University, No. 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Wei Zheng
- Anesthesiology Department, The 80th Army Hospital of Chinese PLA, Weifang, 261021, Shandong, China
| | - Cheng Qian
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, No. 181 Hanyu Road, Shapingba District, Chongqing, 400030, China.
| | - Juanjuan Shan
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, No. 181 Hanyu Road, Shapingba District, Chongqing, 400030, China.
| | - Zhansong Zhou
- Department of Urology, The Southwest Hospital, Army Medical University, No. 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China.
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Kotov A, Zinovyev A, Monsoro-Burq AH. scEvoNet: a gradient boosting-based method for prediction of cell state evolution. BMC Bioinformatics 2023; 24:83. [PMID: 36879200 PMCID: PMC9990205 DOI: 10.1186/s12859-023-05213-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
BACKGROUND Exploring the function or the developmental history of cells in various organisms provides insights into a given cell type's core molecular characteristics and putative evolutionary mechanisms. Numerous computational methods now exist for analyzing single-cell data and identifying cell states. These methods mostly rely on the expression of genes considered as markers for a given cell state. Yet, there is a lack of scRNA-seq computational tools to study the evolution of cell states, particularly how cell states change their molecular profiles. This can include novel gene activation or the novel deployment of programs already existing in other cell types, known as co-option. RESULTS Here we present scEvoNet, a Python tool for predicting cell type evolution in cross-species or cancer-related scRNA-seq datasets. ScEvoNet builds the confusion matrix of cell states and a bipartite network connecting genes and cell states. It allows a user to obtain a set of genes shared by the characteristic signature of two cell states even between distantly-related datasets. These genes can be used as indicators of either evolutionary divergence or co-option occurring during organism or tumor evolution. Our results on cancer and developmental datasets indicate that scEvoNet is a helpful tool for the initial screening of such genes as well as for measuring cell state similarities. CONCLUSION The scEvoNet package is implemented in Python and is freely available from https://github.com/monsoro/scEvoNet . Utilizing this framework and exploring the continuum of transcriptome states between developmental stages and species will help explain cell state dynamics.
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Affiliation(s)
- Aleksandr Kotov
- Faculté Des Sciences d'Orsay, Université Paris Saclay, Orsay, France.,Institut Curie, PSL Research University, Paris, France
| | - Andrei Zinovyev
- Institut Curie, PSL Research University, Paris, France.,INSERM, Paris, France.,CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France
| | - Anne-Helene Monsoro-Burq
- Faculté Des Sciences d'Orsay, Université Paris Saclay, Orsay, France. .,Institut Curie, PSL Research University, Paris, France. .,Institut Universitaire de France, Paris, France.
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Sun X, Liu P. Prognostic biomarker NEIL3 and its association with immune infiltration in renal clear cell carcinoma. Front Oncol 2023; 13:1073941. [PMID: 36816967 PMCID: PMC9932331 DOI: 10.3389/fonc.2023.1073941] [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: 10/19/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Background Kidney renal clear cell carcinoma (KIRC) is a malignant tumor with a high degree of immune infiltration. Identifying immune biomarkers is essential for the treatment of KIRC. Studies have identified the potential of NEIL3 to modulate the immune microenvironment and promote tumor progression. However, the role of NEIL3 in KIRC remains uncertain. This study was to investigate the effect of NEIL3 on the prognosis and immune infiltration of patients with KIRC. Methods TCGA and GEO databases were used to study the expression of NEIL3 in KIRC. Cox regression analysis was used to examine the relationship between the expression of NEIL3 and clinicopathological variables and survival. Furthermore, Gene Set Cancer Analysis (GSCA) was applied to study the impact of NEIL3 methylation on outcomes of KIRC. Through gene ontology (GO) and Gene set enrichment (GSEA) analysis, the biological processes and signal pathways related to NEIL3 expression were identified. In addition, immune infiltration analysis was conducted via CIBERSORT analysis, ssGSEA analysis and TISIDB database. Results NEIL3 was overexpressed in KIRC, and it was significantly related with histologic grade, pathologic stage, T stage, M stage, and vital status of KIRC patients (P < 0.001). The expression of NEIL3 was associated with worse outcomes. Univariate and multivariate Cox analysis showed that NEIL3 may be an indicator of adverse outcomes in KIRC. GSEA analysis revealed that NEIL3 may be involved in signal pathways including cell cycle, DNA replication, mismatch repair, P53 signal pathway, and antigen processing and presentation. In addition, immune infiltration analysis showed a positive correlation between NEIL3 expression and multiple immune cells (activated CD8 T cells, activated dendritic cells, myeloid-derived suppressor cells, follicular helper T cells, and regulatory T cells) and immunoinhibitors (PD1, CTLA4, LAG3, TIGHT, IL10, and CD96). Conclusion NEIL3 is a potential independent biomarker of KIRC, which is relevant to immune infiltration.
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Affiliation(s)
- Xiaomei Sun
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Pengfei Liu
- Department of Medical Oncology, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, China,*Correspondence: Pengfei Liu,
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Meng L, Lu H, Li Y, Zhao J, He S, Wang Z, Shen J, Huang H, Xiao J, Sooranna SR, Song J. Human papillomavirus infection can alter the level of tumour stemness and T cell infiltration in patients with head and neck squamous cell carcinoma. Front Immunol 2022; 13:1013542. [PMID: 36420261 PMCID: PMC9676257 DOI: 10.3389/fimmu.2022.1013542] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/17/2022] [Indexed: 07/20/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) usually has a poor prognosis and is associated with a high mortality rate. Its etiology is mainly the result from long-term exposure to either alcohol, tobacco or human papillomavirus (HPV) infection or a combination of these insults. However, HNSCC patients with HPV have been found to show a survival advantage over those without the virus, but the mechanism that confers this advantage is unclear. Due to the large number of HPV-independent HNSCC cases, there is a possibility that the difference in prognosis between HPV-positive (HPV+) and negative (HPV-) patients is due to different carcinogens. To clarify this, we used scRNA data and viral tracking methods in order to identify HPV+ and HPV- cells in the tumour tissues of patients infected with HPV. By comparing HPV+ and HPV- malignant cells, we found a higher level of tumour stemness in HPV- tumour cells. Using tumour stemness-related genes, we established a six-gene prognostic signature that was used to divide the patients into low- and high-risk groups. It was found that HPV patients who were at low-risk of contracting HNSCC had a higher number of CD8+ T-cells as well as a higher expression of immune checkpoint molecules. Correspondingly, we found that HPV+ tumour cells expressed higher levels of CCL4, and these were highly correlated with CD8+ T cells infiltration and immune checkpoint molecules. These data suggest that the stemness features of tumour cells are not only associated with the prognostic risk, but that it could also affect the immune cell interactions and associated signalling pathways.
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Affiliation(s)
- Lingzhang Meng
- Institute of Cardiovascular Sciences, Guangxi Academy of Medical Sciences, Nanning, China
- Center for Systemic Inflammation Research (CSIR), School of Preclinical Medicine, Youjiang Medical University for Nationalities, Baise, China
| | - Heming Lu
- Second Division of Department of Radiation Oncology, Guangxi Academy of Medical Sciences, Nanning, China
- Second Division of Department of Radiation Oncology, the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yueyong Li
- Department of Interventive Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jingjie Zhao
- Life Science and Clinical Research Center, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Siyuan He
- Center for Systemic Inflammation Research (CSIR), School of Preclinical Medicine, Youjiang Medical University for Nationalities, Baise, China
| | - Zechen Wang
- Center for Systemic Inflammation Research (CSIR), School of Preclinical Medicine, Youjiang Medical University for Nationalities, Baise, China
| | - Jiajia Shen
- Center for Systemic Inflammation Research (CSIR), School of Preclinical Medicine, Youjiang Medical University for Nationalities, Baise, China
| | - Huixian Huang
- Second Division of Department of Radiation Oncology, Guangxi Academy of Medical Sciences, Nanning, China
- Second Division of Department of Radiation Oncology, the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jinru Xiao
- Graduate School, Guangxi University of Chinese Medicine, Nanning, China
| | - Suren Rao Sooranna
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Chelsea & Westminster Hospital, London, United Kingdom
| | - Jian Song
- Institute of Cardiovascular Sciences, Guangxi Academy of Medical Sciences, Nanning, China
- Center for Systemic Inflammation Research (CSIR), School of Preclinical Medicine, Youjiang Medical University for Nationalities, Baise, China
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10
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Liu J, Li M, Wu J, Qi Q, Li Y, Wang S, Liang S, Zhang Y, Zhu Z, Huang R, Yan J, Zhu R. Identification of ST3GAL5 as a prognostic biomarker correlating with CD8+ T cell exhaustion in clear cell renal cell carcinoma. Front Immunol 2022; 13:979605. [PMID: 36172374 PMCID: PMC9510991 DOI: 10.3389/fimmu.2022.979605] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/25/2022] [Indexed: 11/23/2022] Open
Abstract
Aberrant sialylation is frequently observed in tumor development, but which sialyltransferases are involved in this event are not well known. Herein, we performed comprehensive analyses on six ST3GAL family members, the α-2,3 sialyltransferases, in clear cell renal cell carcinoma (ccRCC) from public datasets. Only ST3GAL5 was consistently and significantly overexpressed in ccRCC (n = 791 in total), compared with normal kidney tissues. Its overexpression was positively correlated with tumor stage, grade, and the poor prognosis in ccRCC patients. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses indicated the involvement of ST3GAL5 in tumor immunoregulation. Then we revealed that ST3GAL5 expression showed a positive correlation with CD8+ T cell infiltration, using multiple tools on TIMER2.0 web server. Notably, ST3GAL5 overexpression was further identified to be associated with expression signature of CD8+ T cell exhaustion in ccRCC samples from three datasets (n = 867 in total; r > 0.3, p < 0.001). In our own ccRCC cohort (n = 45), immunohistochemistry and immunofluorescence staining confirmed that ST3GAL5 overexpression was accompanied by high CD8+ T cell infiltration with the increased exhaustion markers. Altogether, ST3GAL5 as a promising prognostic biomarker with CD8+ T cell exhaustion in ccRCC is indicated.
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Affiliation(s)
- Jiakuan Liu
- Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
- Department of Laboratory Animal Science, Fudan University, Shanghai, China
| | - Meiqian Li
- Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
- Model Animal Research Center of Nanjing University, Nanjing University, Jiangsu, China
| | - Jiajun Wu
- Department of Laboratory Animal Science, Fudan University, Shanghai, China
| | - Qi Qi
- Department of Laboratory Animal Science, Fudan University, Shanghai, China
| | - Yang Li
- Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Simei Wang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shengjie Liang
- Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Yuqing Zhang
- Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Zhitao Zhu
- Department of Laboratory Animal Science, Fudan University, Shanghai, China
| | - Ruimin Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Ruimin Huang, ; Jun Yan, ; Rujian Zhu,
| | - Jun Yan
- Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
- Department of Laboratory Animal Science, Fudan University, Shanghai, China
- *Correspondence: Ruimin Huang, ; Jun Yan, ; Rujian Zhu,
| | - Rujian Zhu
- Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
- *Correspondence: Ruimin Huang, ; Jun Yan, ; Rujian Zhu,
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11
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Heterogeneity in NK Cell Subpopulations May Be Involved in Kidney Cancer Metastasis. J Immunol Res 2022; 2022:6378567. [PMID: 36046723 PMCID: PMC9424044 DOI: 10.1155/2022/6378567] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022] Open
Abstract
Although substantial progress has been made in the immunotherapy of kidney cancer, its efficacy varies from patient to patient, with many responding suboptimally or even developing metastases. Thus, research on the tumour immune microenvironment and immune cell heterogeneity is essential for kidney cancer treatment. In this study, natural killer (NK) cell populations were isolated using signature genes from the single-cell sequencing data of clear cell renal cell carcinoma (ccRCC) and normal kidney tissues and divided into three subpopulations according to the differences in gene expression profiles: NK(GZMH), NK(EGR1), and NK(CAPG). Gene set enrichment analysis revealed that NK(EGR1) and NK(CAPG) were closely related to tumour metastasis, as shown by kidney cancer metastasis to Hodgkin lymphoma, T-cell leukaemia, and Ki-1+ anaplastic large cell lymphoma. Thus, these two NK cell subpopulations are promising targets for inhibiting metastasis in ccRCC. Our findings revealed heterogeneity in the infiltrating NK cells of kidney cancer, which can serve as a reference for the mechanisms underlying metastasis in kidney cancer.
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12
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Jiang J, Lu Y, Zhang F, Pan T, Zhang Z, Wan Y, Ren X, Zhang R. Semaphorin 4B promotes tumor progression and associates with immune infiltrates in lung adenocarcinoma. BMC Cancer 2022; 22:632. [PMID: 35676688 PMCID: PMC9178879 DOI: 10.1186/s12885-022-09696-w] [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: 03/10/2022] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Semaphorins have been found to play important roles in multiple malignancy-related processes. However, the role of Semaphorin 4B (SEMA4B) in lung cancer remains unclear. Here, we aimed to explore the biological functions of SEMA4B in through bioinformatic analysis, in vitro and in vivo assays. In the present study, the possible mechanism by which SEMA4B affected the tumor growth and microenvironment of lung adenocarcinoma (LUAD) were investigated. METHODS The expression of SEMA4B in LUAD was analyzed by bioinformatic analysis and verified by the immunohistochemistry staining. The prognostic value of SEMA4B in LUAD was investigated using the Kaplan-Meier survival and Cox's regression model. After silencing SEMA4B expression, the functions of SEMA4B in LUAD cells were investigated by in vitro experiments, including CCK-8 and plate clone formation. And the effect of SEMA4B on tumor growth and immune infiltration was explored in C57BL/6 mice tumor-bearing models. RESULTS SEMA4B expression was upregulated in LUAD tissues and correlated with later pathological stages and poor prognosis of LUAD patients. Further study found that SEMA4B silencing suppressed the proliferation of lung cancer cells both in vitro and in vivo. Bioinformatic analysis showed that SEMA4B expression was correlated with the increased infiltration of myeloid-derived suppressor cells (MDSCs), T-regs and the decreased infiltration of CD8+ T cell in LUAD. Importantly, in vivo study verified that the infiltration of T-regs and MDSCs in tumor microenvironment (TME) of Xenograft tissues was decreased after SEMA4B silencing. CONCLUSIONS These findings demonstrated SEMA4B might play an oncogenic role in LUAD progression, and be a promising therapeutic target for lung cancer.
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Affiliation(s)
- Jun Jiang
- Department of Health Service, Base of Health Service, Fourth Military Medical University, Xi'an, China
| | - Yuan Lu
- Department of Respiratory and Critical Care Medicine, Zhongda Hospital, Southeast University, Nanjing, China
| | - Fang Zhang
- Department of Respiratory and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Tao Pan
- Department of Respiratory and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhipei Zhang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Yi Wan
- Department of Health Service, Base of Health Service, Fourth Military Medical University, Xi'an, China
| | - Xinling Ren
- Department of Respiratory and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China. .,Department of Pulmonary Medicine, Shenzhen General Hospital, Shenzhen University, Shenzhen, 518055, Guangdong, China.
| | - Rui Zhang
- State Key Laboratory of Cancer Biology, Department of Immunology, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China.
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13
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Endothelial Cells Potentially Participate in the Metastasis of Triple-Negative Breast Cancer. J Immunol Res 2022; 2022:5412007. [PMID: 35265720 PMCID: PMC8898858 DOI: 10.1155/2022/5412007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 12/13/2022] Open
Abstract
Inhibition of triple-negative breast cancer metastasis has long been a challenge, mainly due to the difficulty in identifying factors that contribute to this process. In this study, freshly isolated triple-negative breast cancer biopsied cells obtained from consenting patients were subjected to flow cytometry and bioinformatic analysis to identify three endothelial cell subclusters: EC (ATP1B3), EC (HSPA1B), and EC (KRT7) in the tumor microenvironment. These endothelial cell subclusters exhibited distinguishing biological features. Based on differentially expressed genes derived from the subclusters, gene set enrichment analysis showed that EC (ATP1B3) and EC (HSPA1B) contribute to the process of metastasis, for example, in fibrosarcoma and anaplastic carcinoma. In this study, we identified the heterogeneity of endothelial cells in the human breast cancer and have provided insights into its role in metastasis.
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