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Ma Y, Chen Y, Zhan L, Dong Q, Wang Y, Li X, He L, Zhang J. CEBPB-mediated upregulation of SERPINA1 promotes colorectal cancer progression by enhancing STAT3 signaling. Cell Death Discov 2024; 10:219. [PMID: 38710698 DOI: 10.1038/s41420-024-01990-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
Colorectal cancer (CRC) is a highly malignant carcinoma associated with poor prognosis, and metastasis is one of the most common causes of death in CRC. Serpin Family A Member 1 (SERPINA1) is a serine protease inhibitor from the Serpin family. Till now, the function and mechanism of SERPINA1 in CRC progression have not been fully illustrated. We established highly metastatic colorectal cancer cells named as RKO-H and Caco2-H by mice liver metastasis model. By integrative bioinformatic approaches, we analyzed the prognostic value and clinical significance of SERPINA1 in CRC, and predicted potential transcription factors. Colony formation, EDU, MTS, Transwell and wound healing assay were performed to evaluate the biological functions of SERPINA1 in CRC in vitro. Experiments in vivo were conducted to explore the effects of SERPINA1 on liver metastasis of CRC. ChIP and luciferase reporter gene assays were performed to identify the transcriptional regulatory mechanism of SERPINA1 by CEBPB. Our results show that SERPINA1 is highly expressed in CRC and correlated with poor clinical outcomes. SERPINA1 promotes the proliferation, migration by activating STAT3 pathway. Mechanistically, CEBPB binds SERPINA1 gene promoter sequence and promotes the transcription of SERPINA1. SERPINA1 drives CEBPB-induced tumor cell growth and migration via augmenting STAT3 signaling. Our results suggest that SERPINA1 is a potential prognostic marker and may serve as a novel treatment target for CRC.
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Affiliation(s)
- Yiming Ma
- Department of Medical Oncology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, China
- Liaoning Key Laboratory of Gastrointestinal Cancer Translational Research, Shenyang, Liaoning Province, China
| | - Ying Chen
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Lei Zhan
- Department of Medical Oncology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, China
- Liaoning Key Laboratory of Gastrointestinal Cancer Translational Research, Shenyang, Liaoning Province, China
| | - Qian Dong
- Department of Medical Oncology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, China
- Liaoning Key Laboratory of Gastrointestinal Cancer Translational Research, Shenyang, Liaoning Province, China
| | - Yuanhe Wang
- Department of Medical Oncology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, China
- Liaoning Key Laboratory of Gastrointestinal Cancer Translational Research, Shenyang, Liaoning Province, China
| | - Xiaoyan Li
- Liaoning Key Laboratory of Gastrointestinal Cancer Translational Research, Shenyang, Liaoning Province, China
- Department of Pathology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, China
| | - Lian He
- Department of Pathology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, China
| | - Jingdong Zhang
- Department of Medical Oncology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, China.
- Liaoning Key Laboratory of Gastrointestinal Cancer Translational Research, Shenyang, Liaoning Province, China.
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2
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Mohammadi E, Dashti S, Shafizade N, Jin H, Zhang C, Lam S, Tahmoorespur M, Mardinoglu A, Sekhavati MH. Drug repositioning for immunotherapy in breast cancer using single-cell analysis. NPJ Syst Biol Appl 2024; 10:37. [PMID: 38589404 PMCID: PMC11001976 DOI: 10.1038/s41540-024-00359-z] [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: 01/13/2023] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Immunomodulatory peptides, while exhibiting potential antimicrobial, antifungal, and/or antiviral properties, can play a role in stimulating or suppressing the immune system, especially in pathological conditions like breast cancer (BC). Thus, deregulation of these peptides may serve as an immunotherapeutic strategy to enhance the immune response. In this meta-analysis, we utilized single-cell RNA sequencing data and known therapeutic peptides to investigate the deregulation of these peptides in malignant versus normal human breast epithelial cells. We corroborated our findings at the chromatin level using ATAC-seq. Additionally, we assessed the protein levels in various BC cell lines. Moreover, our in-house drug repositioning approach was employed to identify potential drugs that could positively impact the relapse-free survival of BC patients. Considering significantly deregulated therapeutic peptides and their role in BC pathology, our approach aims to downregulate B2M and SLPI, while upregulating PIGR, DEFB1, LTF, CLU, S100A7, and SCGB2A1 in BC epithelial cells through our drug repositioning pipeline. Leveraging the LINCS L1000 database, we propose BRD-A06641369 for B2M downregulation and ST-4070043 and BRD-K97926541 for SLPI downregulation without negatively affecting the MHC complex as a significantly correlated pathway with these two genes. Furthermore, we have compiled a comprehensive list of drugs for the upregulation of other selected immunomodulatory peptides. Employing an immunotherapeutic approach by integrating our drug repositioning pipeline with single-cell analysis, we proposed potential drugs and drug targets to fortify the immune system against BC.
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Affiliation(s)
- Elyas Mohammadi
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden.
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Samira Dashti
- Department of Internal Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Neda Shafizade
- Department of Internal Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Han Jin
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
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3
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Zhang Z, Zhou Y, Liang S. Correlation Between miR-497-5p Expression With Clinicopathological Characteristics and Prognosis in Patients With Breast Cancer. Appl Immunohistochem Mol Morphol 2024; 32:200-205. [PMID: 38497335 DOI: 10.1097/pai.0000000000001190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 01/26/2024] [Indexed: 03/19/2024]
Abstract
Breast cancer (BC) comprises multiple biological and histologic properties. MicroRNAs show key functions in cancer prognosis. This paper explored the relationship between miR-497-5p with clinicopathological characteristics and prognosis in BC. Cancer tissues and normal adjacent tissues (NATs) were collected from 140 included patients with BC. The clinical baseline data, including age, tumor size, pathologic grade, clinical stage, modified Scraff-Bloom-Richardson grade, and lymph node metastasis, were recorded. miR-497-5p expression in cancer tissues and NAT was determined by reverse transcription-quantitative polymerase chain reaction. Patients with BC were followed up for 5 years to record their survival. Patients were divided into the miR-497-5p low expression and high expression groups to assess the correlation between miR-497-5p expression with clinicopathological characteristics and overall survival of patients. The role of miR-497-5p as an independent risk factor for death was further analyzed by a multivariate Cox regression model. miR-497-5p was downregulated in BC tissues than NAT. Tumor size, clinical stage, and lymph node metastasis showed significant differences among patients with high and low miR-497-5p expression levels. Patients with BC with low miR-497-5p expression presented decreased survival. Lowly-expressed miR-497-5p was an independent risk factor for death in patients. Collectively, cancer tissue miR-497-5p low expression increases the risk of death and serves as an independent risk factor for death in patients with BC.
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Affiliation(s)
- Zhiying Zhang
- Department of Hematology and Blood and Marrow Transplantation
| | - Ying Zhou
- Department of Integrated Chinese and Western Medicine, Tianjin Cancer Hospital Airport Hospital, Tianjin
| | - Shujing Liang
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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4
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Jotanovic J, Tebani A, Hekmati N, Sivertsson Å, Lindskog C, Uhlèn M, Gudjonsson O, Tsatsaris E, Engström BE, Wikström J, Pontén F, Casar-Borota O. Transcriptome Analysis Reveals Distinct Patterns Between the Invasive and Noninvasive Pituitary Neuroendocrine Tumors. J Endocr Soc 2024; 8:bvae040. [PMID: 38505563 PMCID: PMC10949357 DOI: 10.1210/jendso/bvae040] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Indexed: 03/21/2024] Open
Abstract
Although most pituitary neuroendocrine tumors (PitNETs)/pituitary adenomas remain intrasellar, a significant proportion of tumors show parasellar invasive growth and 6% to 8% infiltrate the bone structures, thus affecting the prognosis. There is an unmet need to identify novel markers that can predict the parasellar growth of PitNETs. Furthermore, mechanisms that regulate bone invasiveness of PitNETs and factors related to tumor vascularization are largely unknown. We used genome-wide mRNA analysis in a cohort of 77 patients with PitNETs of different types to explore the differences in gene expression patterns between invasive and noninvasive tumors with respect to the parasellar growth and regarding the rare phenomenon of bone invasiveness. Additionally, we studied the genes correlated to the contrast enhancement quotient, a novel radiological parameter of tumor vascularization. Most of the genes differentially expressed related to the parasellar growth were genes involved in tumor invasiveness. Differentially expressed genes associated with bone invasiveness are involved in NF-κB pathway and antitumoral immune response. Lack of clear clustering regarding the parasellar and bone invasiveness may be explained by the influence of the cell lineage-related genes in this heterogeneous cohort of PitNETs. Our transcriptomics analysis revealed differences in the molecular fingerprints between invasive, including bone invasive, and noninvasive PitNETs, although without clear clustering. The contrast enhancement quotient emerged as a radiological parameter of tumor vascularization, correlating with several angiogenesis-related genes. Several of the top genes related to the PitNET invasiveness and vascularization have potential prognostic and therapeutic application requiring further research.
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Affiliation(s)
- Jelena Jotanovic
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
- Department of Clinical Pathology, Uppsala University Hospital, 75185 Uppsala, Sweden
| | - Abdellah Tebani
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, 17121 Solna, Stockholm, Sweden
- Department of Metabolic Biochemistry, UNIROUEN, INSERM U1245, CHU Rouen, Normandie University, 76000 Rouen, France
| | - Neda Hekmati
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Åsa Sivertsson
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, 17121 Solna, Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Mathias Uhlèn
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, 17121 Solna, Stockholm, Sweden
| | - Olafur Gudjonsson
- Department of Neuroscience, Uppsala University, 75185 Uppsala, Sweden
| | - Erika Tsatsaris
- Endocrinology and Mineral Metabolism, Department of Medical Sciences, Uppsala University, 75185 Uppsala, Sweden
| | - Britt Edén Engström
- Endocrinology and Mineral Metabolism, Department of Medical Sciences, Uppsala University, 75185 Uppsala, Sweden
| | - Johan Wikström
- Neuroradiology, Department of Surgical Sciences, Uppsala University, 75185 Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Olivera Casar-Borota
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
- Department of Clinical Pathology, Uppsala University Hospital, 75185 Uppsala, Sweden
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5
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Yu L, Hong Y, Maishi N, Matsuda AY, Hida Y, Hasebe A, Kitagawa Y, Hida K. Oral bacterium Streptococcus mutans promotes tumor metastasis through thrombosis formation. Cancer Sci 2024; 115:648-659. [PMID: 38096871 PMCID: PMC10859626 DOI: 10.1111/cas.16010] [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: 06/14/2023] [Revised: 10/10/2023] [Accepted: 10/25/2023] [Indexed: 02/13/2024] Open
Abstract
Thrombosis is a well-known cardiovascular disease (CVD) complication that has caused death in many patients with cancer. Oral bacteria have been reported to contribute to systemic diseases, including CVDs, and tumor metastasis. However, whether oral bacteria-induced thrombosis induces tumor metastasis remains poorly understood. In this study, the cariogenic oral bacterium Streptococcus mutans was used to examine thrombosis in vitro and in vivo. Investigation of tumor metastasis to the lungs was undertaken by intravenous S. mutans implantation using a murine breast cancer metastasis model. The results indicated that platelet activation, aggregation, and coagulation were significantly altered in S. mutans-stimulated endothelial cells (ECs), with elevated neutrophil migration, thereby inducing thrombosis formation. Streptococcus mutans stimulation significantly enhances platelet and tumor cell adhesion to the inflamed ECs. Furthermore, S. mutans-induced pulmonary thrombosis promotes breast cancer cell metastasis to the lungs in vivo, which can be reduced by using aspirin, an antiplatelet drug. Our findings indicate that oral bacteria promote tumor metastasis through thrombosis formation. Oral health management is important to prevent CVDs, tumor metastasis, and their associated death.
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Affiliation(s)
- Li Yu
- Vascular Biology and Molecular Pathology, Faculty of Dental Medicine and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Yuying Hong
- Vascular Biology and Molecular Pathology, Faculty of Dental Medicine and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
- Oral Diagnosis and Medicine, Faculty of Dental Medicine and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Nako Maishi
- Vascular Biology and Molecular Pathology, Faculty of Dental Medicine and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Aya Yanagawa Matsuda
- Vascular Biology and Molecular Pathology, Faculty of Dental Medicine and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Yasuhiro Hida
- Advanced Robotic and Endoscopic Surgery, School of MedicineFujita Health UniversityToyoakeJapan
| | - Akira Hasebe
- Oral Molecular Microbiology, Faculty of Dental Medicine and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Yoshimasa Kitagawa
- Oral Diagnosis and Medicine, Faculty of Dental Medicine and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
| | - Kyoko Hida
- Vascular Biology and Molecular Pathology, Faculty of Dental Medicine and Graduate School of Dental MedicineHokkaido UniversitySapporoJapan
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6
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Liu J, Lu J, Wang G, Gu L, Li W. Prognostic characteristics of a six-gene signature based on ssGSEA in sarcoma. Aging (Albany NY) 2024; 16:1536-1554. [PMID: 38240704 PMCID: PMC10866427 DOI: 10.18632/aging.205443] [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: 10/05/2023] [Accepted: 12/07/2023] [Indexed: 02/06/2024]
Abstract
BACKGROUND Sarcoma is a rare malignant tumor originating of the interstitial or connective tissue with a poor prognosis. Next-generation sequencing technology offers new opportunities for accurate diagnosis and treatment of sarcomas. There is an urgent need for new gene signature to predict prognosis and evaluate treatment outcomes. METHODS We used transcriptome data from the Cancer Genome Atlas (TCGA) database and single sample gene set enrichment analysis (ssGSEA) to explore the cancer hallmarks most associated with prognosis in sarcoma patients. Then, weighted gene coexpression network analysis, univariate COX regression analysis and random forest algorithm were used to construct prognostic gene characteristics. Finally, the prognostic value of gene markers was validated in the TCGA and Integrated Gene Expression (GEO) (GSE17118) datasets, respectively. RESULTS MYC targets V1 and V2 are the main cancer hallmarks affecting the overall survival (OS) of sarcoma patients. A six-gene signature including VEGFA, HMGB3, FASN, RCC1, NETO2 and BIRC5 were constructed. Kaplan-Meier analysis suggested that higher risk scores based on the six-gene signature associated with poorer OS (P < 0.001). The receiver Operating characteristic curve showed that the risk score based on the six-gene signature was a good predictor of sarcoma, with an area under the curve (AUC) greater than 0.73. In addition, the prognostic value of the six-gene signature was validated in GSE17118 with an AUC greater than 0.72. CONCLUSION This six-gene signature is an independent prognostic factor in patients with sarcoma and is expected to be a potential therapeutic target for sarcoma.
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Affiliation(s)
- Jun Liu
- Department of Clinical Laboratory, Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan 523005, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515000, China
| | - Jianjun Lu
- Department of Quality Control and Evaluation, First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Gefei Wang
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515000, China
| | - Liming Gu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515000, China
| | - Wenli Li
- Department of Clinical Laboratory, Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan 523005, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515000, China
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7
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Yang S, Chen S, Zhao Y, Wu T, Wang Y, Li T, Fu L, Ye T, Hu Y, Chen H. Identification of a coagulation-related signature correlated with immune infiltration and their prognostic implications in lung adenocarcinoma. Thorac Cancer 2023; 14:3295-3308. [PMID: 37795779 PMCID: PMC10665780 DOI: 10.1111/1759-7714.15121] [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: 06/19/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is a fatal form of lung cancer with a poor prognosis. Coagulation system had been confirmed closely related to tumor progression and the hypercoagulable state encouraged the immune infiltration and development of tumor cells, leading to a poor prognosis in cancer patients. However, the use of the coagulation-related genes (CRGs) for prognosis in LUAD has yet to be determined. In this study, we constructed an immune-related signature (CRRS) and identified a potential coagulation-related biomarker (P2RX1). METHODS We obtained a total of 209 CRGs based on two coagulation-related KEGG pathways, then developed the CRRS signature by using the TCGA-LUAD RNA-seq data via the procedure of LASSO-Cox regression, stepwise-Cox regression, univariate and multivariate Cox regression. Grouped by the CRRS, Kaplan-Meier survival curves and receiver operating characteristic curves were drawn for the training and validation sets, respectively. In addition, single-sample gene set enrichment analysis was exploited to explore immune infiltration level. Moreover, immunophenotypes and immunotherapy grouped by CRRS were further analyzed. RESULTS We developed an immune-related signature (CRRS) composed of COL1A2, F2, PLAUR, C4BPA, and P2RX1 in LUAD. CRRS was an independent risk factor for overall survival and displayed stable and powerful performance. Additionally, CRRS possessed distinctly superior accuracy than traditional clinical variables and molecular features. Functional analysis indicated that the differentially high expressed genes in the low-risk group significantly enriched in T cell and B cell receptor signaling pathways. The low-risk group was sensitive to anti-PD-1/PD-L1 immunotherapy and displayed abundant immune infiltration and immune checkpoint gene expression. Finally, we identified an independent prognostic gene P2RX1. Low expression of P2RX1 associated with poor overall survival and decreased immune infiltration. CONCLUSIONS Our study revealed a significant correlation between CRRS and immune infiltration. CRRS could serve as a promising tool to improve the clinical outcomes for individual LUAD patients.
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Affiliation(s)
- Siqian Yang
- Department of Thoracic Surgery and State Key Laboratory of Genetic EngineeringFudan University Shanghai Cancer CenterShanghaiChina
- Institute of Biostatistics, School of Life Sciences, Human Phenome InstituteFudan UniversityShanghaiChina
| | - Shiqi Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic EngineeringFudan University Shanghai Cancer CenterShanghaiChina
- Institute of Thoracic OncologyFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Yue Zhao
- Department of Thoracic Surgery and State Key Laboratory of Genetic EngineeringFudan University Shanghai Cancer CenterShanghaiChina
- Institute of Thoracic OncologyFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Tao Wu
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yuquan Wang
- Department of Thoracic Surgery and State Key Laboratory of Genetic EngineeringFudan University Shanghai Cancer CenterShanghaiChina
- Institute of Biostatistics, School of Life Sciences, Human Phenome InstituteFudan UniversityShanghaiChina
| | - Tingting Li
- Department of Thoracic Surgery and State Key Laboratory of Genetic EngineeringFudan University Shanghai Cancer CenterShanghaiChina
- Institute of Biostatistics, School of Life Sciences, Human Phenome InstituteFudan UniversityShanghaiChina
| | - Liwan Fu
- Center for Non‐communicable Disease ManagementBeijing Children's HospitalBeijingChina
| | - Ting Ye
- Department of Thoracic Surgery and State Key Laboratory of Genetic EngineeringFudan University Shanghai Cancer CenterShanghaiChina
- Institute of Thoracic OncologyFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Yue‐Qing Hu
- Department of Thoracic Surgery and State Key Laboratory of Genetic EngineeringFudan University Shanghai Cancer CenterShanghaiChina
- Institute of Biostatistics, School of Life Sciences, Human Phenome InstituteFudan UniversityShanghaiChina
- Shanghai Center for Mathematical SciencesFudan UniversityShanghaiChina
| | - Haiquan Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic EngineeringFudan University Shanghai Cancer CenterShanghaiChina
- Institute of Biostatistics, School of Life Sciences, Human Phenome InstituteFudan UniversityShanghaiChina
- Institute of Thoracic OncologyFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
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8
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Zhang F, Zhang R, Zong J, Hou Y, Zhou M, Yan Z, Li T, Gan W, Lv S, Yang L, Zeng Z, Zhao W, Yang M. Computational identification and clinical validation of a novel risk signature based on coagulation-related lncRNAs for predicting prognosis, immunotherapy response, and chemosensitivity in colorectal cancer patients. Front Immunol 2023; 14:1279789. [PMID: 37928532 PMCID: PMC10620970 DOI: 10.3389/fimmu.2023.1279789] [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: 08/18/2023] [Accepted: 09/27/2023] [Indexed: 11/07/2023] Open
Abstract
Background Coagulation is critically involved in the tumor microenvironment, cancer progression, and prognosis assessment. Nevertheless, the roles of coagulation-related long noncoding RNAs (CRLs) in colorectal cancer (CRC) remain unclear. In this study, an integrated computational framework was constructed to develop a novel coagulation-related lncRNA signature (CRLncSig) to stratify the prognosis of CRC patients, predict response to immunotherapy and chemotherapy in CRC, and explore the potential molecular mechanism. Methods CRC samples from The Cancer Genome Atlas (TCGA) were used as the training set, while the substantial bulk or single-cell RNA transcriptomics from Gene Expression Omnibus (GEO) datasets and real-time quantitative PCR (RT-qPCR) data from CRC cell lines and paired frozen tissues were used for validation. We performed unsupervised consensus clustering of CRLs to classify patients into distinct molecular subtypes. We then used stepwise regression to establish the CRLncSig risk model, which stratified patients into high- and low-risk groups. Subsequently, diversified bioinformatics algorithms were used to explore prognosis, biological pathway alteration, immune microenvironment, immunotherapy response, and drug sensitivity across patient subgroups. In addition, weighted gene coexpression network analysis was used to construct an lncRNA-miRNA-mRNA competitive endogenous network. Expression levels of CRLncSig, immune checkpoints, and immunosuppressors were determined using RT-qPCR. Results We identified two coagulation subclusters and constructed a risk score model using CRLncSig in CRC, where the patients in cluster 2 and the low-risk group had a better prognosis. The cluster and CRLncSig were confirmed as the independent risk factors, and a CRLncSig-based nomogram exhibited a robust prognostic performance. Notably, the cluster and CRLncSig were identified as the indicators of immune cell infiltration, immunoreactivity phenotype, and immunotherapy efficiency. In addition, we identified a new endogenous network of competing CRLs with microRNA/mRNA, which will provide a foundation for future mechanistic studies of CRLs in the malignant progression of CRC. Moreover, CRLncSig strongly correlated with drug susceptibility. Conclusion We developed a reliable CRLncSig to predict the prognosis, immune landscape, immunotherapy response, and drug sensitivity in patients with CRC, which might facilitate optimizing risk stratification, guiding the applications of immunotherapy, and individualized treatments for CRC.
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Affiliation(s)
- Fang Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rixin Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinbao Zong
- Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
- Qingdao Hospital of Traditional Chinese Medicine, The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Yufang Hou
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingxuan Zhou
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Yan
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tiegang Li
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenqiang Gan
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Silin Lv
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liu Yang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zifan Zeng
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenyi Zhao
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Min Yang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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9
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Ward J, Martin P. Live-imaging studies reveal how microclots and the associated inflammatory response enhance cancer cell extravasation. J Cell Sci 2023; 136:jcs261225. [PMID: 37671502 PMCID: PMC10561694 DOI: 10.1242/jcs.261225] [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: 04/11/2023] [Accepted: 08/31/2023] [Indexed: 09/07/2023] Open
Abstract
Previous clinical studies and work in mouse models have indicated that platelets and microclots might enable the recruitment of immune cells to the pre-metastatic cancer niche, leading to efficacious extravasation of cancer cells through the vessel wall. Here, we investigated the interaction between platelets, endothelial cells, inflammatory cells, and engrafted human and zebrafish cancer cells by live-imaging studies in translucent zebrafish larvae, and show how clotting (and clot resolution) act as foci and as triggers for extravasation. Fluorescent tagging in each lineage revealed their dynamic behaviour and potential roles in these events, and we tested function by genetic and drug knockdown of the contributing players. Morpholino knockdown of fibrinogen subunit α (fga) and warfarin treatment to inhibit clotting both abrogated extravasation of cancer cells. The inflammatory phenotype appeared fundamental, and we show that forcing a pro-inflammatory, tnfa-positive phenotype is inhibitory to extravasation of cancer cells.
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Affiliation(s)
- Juma Ward
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Paul Martin
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, UK
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Li L, Yang W, Jia D, Zheng S, Gao Y, Wang G. Establishment of a N1-methyladenosine-related risk signature for breast carcinoma by bioinformatics analysis and experimental validation. Breast Cancer 2023:10.1007/s12282-023-01458-1. [PMID: 37178414 DOI: 10.1007/s12282-023-01458-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/09/2023] [Indexed: 05/15/2023]
Abstract
OBJECTIVES Breast carcinoma (BRCA) has resulted in a huge health burden globally. N1-methyladenosine (m1A) RNA methylation has been proven to play key roles in tumorigenesis. Nevertheless, the function of m1A RNA methylation-related genes in BRCA is indistinct. METHODS The RNA sequencing (RNA-seq), copy-number variation (CNV), single-nucleotide variant (SNV), and clinical data of BRCA were acquired via The Cancer Genome Atlas (TCGA) database. In addition, the GSE20685 dataset, the external validation set, was acquired from the Gene Expression Omnibus (GEO) database. 10 m1A RNA methylation regulators were obtained from the previous literature, and further analyzed through differential expression analysis by rank-sum test, mutation by SNV data, and mutual correlation by Pearson Correlation Analysis. Furthermore, the differentially expressed m1A-related genes were selected through overlapping m1A-related module genes obtained by weighted gene co-expression network analysis (WGCNA), differentially expressed genes (DEGs) in BRCA and DEGs between high- and low- m1A score subgroups. The m1A-related model genes in the risk signature were derived by univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analyses. In addition, a nomogram was built through univariate and multivariate Cox analyses. After that, the immune infiltration between the high- and low-risk groups was investigated through ESTIMATE and CIBERSORT. Finally, the expression trends of model genes in clinical BRCA samples were further confirmed by quantitative real-time PCR (RT‒qPCR). RESULTS Eighty-five differentially expressed m1A-related genes were obtained. Among them, six genes were selected as prognostic biomarkers to build the risk model. The validation results of the risk model showed that its prediction was reliable. In addition, Cox independent prognosis analysis revealed that age, risk score, and stage were independent prognostic factors for BRCA. Moreover, 13 types of immune cells were different between the high- and low-risk groups and the immune checkpoint molecules TIGIT, IDO1, LAG3, ICOS, PDCD1LG2, PDCD1, CD27, and CD274 were significantly different between the two risk groups. Ultimately, RT-qPCR results confirmed that the model genes MEOX1, COL17A1, FREM1, TNN, and SLIT3 were significantly up-regulated in BRCA tissues versus normal tissues. CONCLUSIONS An m1A RNA methylation regulator-related prognostic model was constructed, and a nomogram based on the prognostic model was constructed to provide a theoretical reference for individual counseling and clinical preventive intervention in BRCA.
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Affiliation(s)
- Leilei Li
- Department of Pathology, Kunming Medical University, Kunming, Yunnan, 650500, People's Republic of China
| | - Wenhui Yang
- Department of Digestive Oncology, Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030032, People's Republic of China
| | - Daqi Jia
- Department of Pathology, Kunming Medical University, Kunming, Yunnan, 650500, People's Republic of China
| | - Shiqi Zheng
- Department of Pathology, Kunming Medical University, Kunming, Yunnan, 650500, People's Republic of China
| | - Yuzhe Gao
- Department of Breast Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, 550002, People's Republic of China.
| | - Guanghui Wang
- Department of Breast Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, 550002, People's Republic of China.
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11
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Xu C, Wang Y, Hong Y, Yao R, Wu L, Shen X, Qu Y, Zhang Z, Zhu W, Yang Y, Chen W, Zhou Y, Liang Z. Identification of genetic and immune signatures for the recurrence of HER2-positive breast cancer after trastuzumab-based treatment. Breast Cancer Res Treat 2023; 199:603-615. [PMID: 37084155 DOI: 10.1007/s10549-023-06931-1] [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: 03/17/2023] [Accepted: 03/30/2023] [Indexed: 04/22/2023]
Abstract
PURPOSE To determine the genetic and immune features associated with the recurrence of human epidermal growth factor receptor2-positive (HER2 +) breast cancer (BC) after trastuzumab-based treatment. METHODS A retrospective cohort study of 48 patients who received trastuzumab-based treatment was divided into recurrent and non-recurrent groups according to clinical follow-up. Baseline samples from all 48 patients were analyzed for genetic variation, HLA allele type, gene expression, and immune features, which were linked to HER2 + BC recurrence. Statistics included logistic regression models, Kaplan-Meier plots, and Univariate Cox proportional hazards models. RESULTS Compared with the non-recurrent group, the extracellular matrix-related pathway and 3 Hallmark gene sets were enriched in the recurrent group. The infiltration levels of immature B cells and activated B cells were significantly increased in the non-recurrent group, which correlated remarkably with improved overall survival (OS) in two other published gene expression datasets, including TCGA and METABRIC. In the TCGA cohort (n = 275), activated B cells (HR 0.23, 95%CI 0.13-0.43, p < 0.0001), and immature B cells (HR 0.26, 95%CI 0.12-0.59, p < 0.0001). In the METABRIC cohort (n = 236), activated B cells (HR 0.60, 95%CI 0.43-0.83, p = 0.002), and immature B cells (HR 0.65, 95%CI 0.47-0.91, p = 0.011). Cox regression suggested that immature B cells and activated B cells were protective factors for outcome OS. CONCLUSIONS Aberrant activation of multiple pathways and low baseline tumor-infiltrating B cells are related to HER2 + BC trastuzumab-based recurrence, which primarily affects the antitumor activity of trastuzumab.
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Affiliation(s)
- Chi Xu
- Department of Breast Surgery, Peking Union Medical College Hospital, Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yahui Wang
- Genecast Biotechnology Co., Ltd, Wuxi, Jiangsu, China
| | - Yuanyuan Hong
- Genecast Biotechnology Co., Ltd, Wuxi, Jiangsu, China
| | - Ru Yao
- Department of Breast Surgery, Peking Union Medical College Hospital, Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lijia Wu
- Genecast Biotechnology Co., Ltd, Wuxi, Jiangsu, China
| | - Xi Shen
- Department of Breast Surgery, Peking Union Medical College Hospital, Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Qu
- Department of Breast Surgery, Peking Union Medical College Hospital, Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhuo Zhang
- Genecast Biotechnology Co., Ltd, Wuxi, Jiangsu, China
| | - Wei Zhu
- Genecast Biotechnology Co., Ltd, Wuxi, Jiangsu, China
| | - Ying Yang
- Genecast Biotechnology Co., Ltd, Wuxi, Jiangsu, China
| | - Weizhi Chen
- Genecast Biotechnology Co., Ltd, Wuxi, Jiangsu, China
| | - Yidong Zhou
- Department of Breast Surgery, Peking Union Medical College Hospital, Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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12
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Neagu AN, Whitham D, Seymour L, Haaker N, Pelkey I, Darie CC. Proteomics-Based Identification of Dysregulated Proteins and Biomarker Discovery in Invasive Ductal Carcinoma, the Most Common Breast Cancer Subtype. Proteomes 2023; 11:proteomes11020013. [PMID: 37092454 PMCID: PMC10123686 DOI: 10.3390/proteomes11020013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Invasive ductal carcinoma (IDC) is the most common histological subtype of malignant breast cancer (BC), and accounts for 70–80% of all invasive BCs. IDC demonstrates great heterogeneity in clinical and histopathological characteristics, prognoses, treatment strategies, gene expressions, and proteomic profiles. Significant proteomic determinants of the progression from intraductal pre-invasive malignant lesions of the breast, which characterize a ductal carcinoma in situ (DCIS), to IDC, are still poorly identified, validated, and clinically applied. In the era of “6P” medicine, it remains a great challenge to determine which patients should be over-treated versus which need to be actively monitored without aggressive treatment. The major difficulties for designating DCIS to IDC progression may be solved by understanding the integrated genomic, transcriptomic, and proteomic bases of invasion. In this review, we showed that multiple proteomics-based techniques, such as LC–MS/MS, MALDI-ToF MS, SELDI-ToF-MS, MALDI-ToF/ToF MS, MALDI-MSI or MasSpec Pen, applied to in-tissue, off-tissue, BC cell lines and liquid biopsies, improve the diagnosis of IDC, as well as its prognosis and treatment monitoring. Classic proteomics strategies that allow the identification of dysregulated protein expressions, biological processes, and interrelated pathway analyses based on aberrant protein–protein interaction (PPI) networks have been improved to perform non-invasive/minimally invasive biomarker detection of early-stage IDC. Thus, in modern surgical oncology, highly sensitive, rapid, and accurate MS-based detection has been coupled with “proteome point sampling” methods that allow for proteomic profiling by in vivo “proteome point characterization”, or by minimal tissue removal, for ex vivo accurate differentiation and delimitation of IDC. For the detection of low-molecular-weight proteins and protein fragments in bodily fluids, LC–MS/MS and MALDI-MS techniques may be coupled to enrich and capture methods which allow for the identification of early-stage IDC protein biomarkers that were previously invisible for MS-based techniques. Moreover, the detection and characterization of protein isoforms, including posttranslational modifications of proteins (PTMs), is also essential to emphasize specific molecular mechanisms, and to assure the early-stage detection of IDC of the breast.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd. No. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Logan Seymour
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Norman Haaker
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Isabella Pelkey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
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Tao L, Zhu Y, Liu J. Identification of new co-diagnostic genes for sepsis and metabolic syndrome using single-cell data analysis and machine learning algorithms. Front Genet 2023; 14:1129476. [PMID: 37007944 PMCID: PMC10060809 DOI: 10.3389/fgene.2023.1129476] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Sepsis, a serious inflammatory response that can be fatal, has a poorly understood pathophysiology. The Metabolic syndrome (MetS), however, is associated with many cardiometabolic risk factors, many of which are highly prevalent in adults. It has been suggested that Sepsis may be associated with MetS in several studies. Therefore, this study investigated diagnostic genes and metabolic pathways associated with both diseases. In addition to microarray data for Sepsis, PBMC single cell RNA sequencing data for Sepsis and microarray data for MetS were downloaded from the GEO database. Limma differential analysis identified 122 upregulated genes and 90 downregulated genes in Sepsis and MetS. WGCNA identified brown co-expression modules as Sepsis and MetS core modules. Two machine learning algorithms, RF and LASSO, were used to screen seven candidate genes, namely, STOM, BATF, CASP4, MAP3K14, MT1F, CFLAR and UROD, all with an AUC greater than 0.9. XGBoost assessed the co-diagnostic efficacy of Hub genes in Sepsis and MetS. The immune infiltration results show that Hub genes were expressed at high levels in all immune cells. After performing Seurat analysis on PBMC from normal and Sepsis patients, six immune subpopulations were identified. The metabolic pathways of each cell were scored and visualized using ssGSEA, and the results show that CFLAR plays an important role in the glycolytic pathway. Our study identified seven Hub genes that serve as co-diagnostic markers for Sepsis and MetS and revealed that diagnostic genes play an important role in immune cell metabolic pathway.
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Affiliation(s)
- Linfeng Tao
- Department of Critical Care Medicine, Suzhou Municipal Hospital, Suzhou Clinical Medical Center of Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School of Nanjing Medical University, Suzhou, China
| | - Yue Zhu
- Department of Breast and Thyroid Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China
| | - Jun Liu
- Department of Critical Care Medicine, Suzhou Municipal Hospital, Suzhou Clinical Medical Center of Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School of Nanjing Medical University, Suzhou, China
- *Correspondence: Jun Liu,
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14
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Zhang J, Xiao J, Wang Y, Zheng X, Cui J, Wang C. A universal co-expression gene network and prognostic model for hepatic-biliary-pancreatic cancers identified by integrative analyses. FEBS Open Bio 2022; 12:2006-2024. [PMID: 36054420 PMCID: PMC9623511 DOI: 10.1002/2211-5463.13478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/12/2022] [Accepted: 08/25/2022] [Indexed: 01/25/2023] Open
Abstract
Hepatic, biliary and pancreatic cancers are a diverse set of malignancies with poor prognoses. It is possible that common molecular mechanisms are involved in the carcinogenesis of these cancers. Here, we identified LINC01537 and seven protein-coding genes by integrative analysis of transcriptomes of mRNAs, microRNAs and long non-coding RNAs from cholangiocarcinoma, hepatocellular carcinoma and pancreatic adenocarcinoma cohorts in TCGA. A predictive model constructed from seven biomarkers was established to successfully predict the survival rate of patients, which was then further verified in external cohorts. Additionally, patients with high-risk scores in our model were prone to epithelial-mesenchymal transition. Finally, activation of the biomarker PDE2A significantly attenuated migration and epithelial-mesenchymal transition in the HepG2 liver cancer cell line.
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Affiliation(s)
- Jing Zhang
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Juan Xiao
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and RepairAffiliated Hospital of Guilin Medical UniversityChina
| | - Yixuan Wang
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Xiao Zheng
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Jiajun Cui
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Chaochen Wang
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
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15
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Qian H, Cui N, Zhou Q, Zhang S. Identification of miRNA biomarkers for stomach adenocarcinoma. BMC Bioinformatics 2022; 23:181. [PMID: 35578189 PMCID: PMC9112558 DOI: 10.1186/s12859-022-04719-6] [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: 01/14/2022] [Accepted: 05/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stomach adenocarcinoma (STAD) is a common malignant tumor in the world and its prognosis is poor, miRNA plays a role mainly by influencing the expression of mRNAs, and participates in the occurrence and development of tumors. However, reliable miRNA prognostic models for stomach adenocarcinoma remain to be identified. RESULTS Using the data from the Cancer Genome Atlas (TCGA), a prognostic model of stomach adenocarcinoma was established including tumor stage and expression levels of 4 miRNAs (hsa-miR-379-3p, hsa-miR-2681-3p, hsa-miR-6499-5p and hsa-miR-6807-3p). A total of 50 ultimate target genes of these miRNAs were obtained through prediction. Enrichment analysis revealed that target genes were mainly concentrated in neural function and TGF-β and FoxO signaling pathways. Survival analysis showed that three model miRNAs (hsa-miR-379-3p, hsa-miR-2681-3p and hsa-miR-6807-3p) and five final target genes (DLC1, LRFN5, NOVA1, POU3F2 and PRICKLE2) were associated with the patient's overall survival outcome. CONCLUSIONS We used bioinformatics methods to screen new prognostic miRNA markers from TCGA and established a prognostic model of STAD, so as to provide a basis for the diagnosis, prognosis, and treatment of STAD in the future.
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Affiliation(s)
- Hao Qian
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei Province, China
| | - Nanxue Cui
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei Province, China
| | - Qiao Zhou
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei Province, China
| | - Shihai Zhang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei Province, China.
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Liu J, Lu J, Li W. Transcriptome analysis reveals the prognostic and immune infiltration characteristics of glycolysis and hypoxia in head and neck squamous cell carcinoma. BMC Cancer 2022; 22:352. [PMID: 35361159 PMCID: PMC8969218 DOI: 10.1186/s12885-022-09449-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/22/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND This study aims to construct a new prognostic gene signature in survival prediction and risk stratification for patients with Head and neck squamous cell carcinoma (HNSCC). METHOD The transcriptome profiling data and hallmark gene sets in the Molecular Signatures Database was used to explore the cancer hallmarks most relevant to the prognosis of HNSCC patients. Differential gene expression analysis, weighted gene co-expression network analysis, univariate COX regression analysis, random forest algorithm and multiple combinatorial screening were used to construct the prognostic gene signature. The predictive ability of gene signature was verified in the TCGA HNSCC cohort as the training set and the GEO HNSCC cohorts (GSE41613 and GSE42743) as the validation sets, respectively. Moreover, the correlations between risk scores and immune infiltration patterns, as well as risk scores and genomic changes were explored. RESULTS A total of 3391 differentially expressed genes in HNSCC were screened. Glycolysis and hypoxia were screened as the main risk factors for OS in HNSCC. Using univariate Cox analysis, 97 prognostic candidates were identified (P < 0.05). Top 10 important genes were then screened out by random forest. Using multiple combinatorial screening, a combination with less genes and more significant P value was used to construct the prognostic gene signature (RNF144A, STC1, P4HA1, FMNL3, ANO1, BASP1, MME, PLEKHG2 and DKK1). Kaplan-Meier analysis showed that patients with higher risk scores had worse overall survival (p < 0.001). The ROC curve showed that the risk score had a good predictive efficiency (AUC > 0.66). Subsequently, the predictive ability of the risk score was verified in the validation sets. Moreover, the two-factor survival analysis combining the cancer hallmarks and risk scores suggested that HNSCC patients with the high hypoxia or glycolysis & high risk-score showed the worst prognosis. Besides, a nomogram based on the nine-gene signature was established for clinical practice. Furthermore, the risk score was significantly related to tumor immune infiltration profiles and genome changes. CONCLUSION This nine-gene signature associated with glycolysis and hypoxia can not only be used for prognosis prediction and risk stratification, but also may be a potential therapeutic target for patients with HNSCC.
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Affiliation(s)
- Jun Liu
- Reproductive Medicine Center, Yue Bei People's Hospital, Shantou University Medical College, 133 Huimin South Road, Shaoguan, 512025, China
- Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
| | - Jianjun Lu
- Department of Medical Affairs, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510080, China
| | - Wenli Li
- Reproductive Medicine Center, Yue Bei People's Hospital, Shantou University Medical College, 133 Huimin South Road, Shaoguan, 512025, China
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