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Zhang Y, Huo M, Li W, Zhang H, Liu Q, Jiang J, Fu Y, Huang C. Exosomes in tumor-stroma crosstalk: Shaping the immune microenvironment in colorectal cancer. FASEB J 2024; 38:e23548. [PMID: 38491832 DOI: 10.1096/fj.202302297r] [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: 11/07/2023] [Revised: 01/26/2024] [Accepted: 02/26/2024] [Indexed: 03/18/2024]
Abstract
Colorectal cancer (CRC) is a multifaceted disease characterized by a complex interaction between tumor cells and the surrounding microenvironment. Within this intricate landscape, exosomes have emerged as pivotal players in the tumor-stroma crosstalk, influencing the immune microenvironment of CRC. These nano-sized vesicles, secreted by both tumoral and stromal cells, serve as molecular transporters, delivering a heterogeneous mix of biomolecules such as RNAs, proteins, and lipids. In the CRC context, exosomes exert dual roles: they promote tumor growth, metastasis, and immune escape by altering immune cell functions and activating oncogenic signaling pathways and offer potential as biomarkers for early CRC detection and treatment targets. This review delves into the multifunctional roles of exosomes in the CRC immune microenvironment, highlighting their potential implications for future therapeutic strategies and clinical outcomes.
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Affiliation(s)
- Yawei Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Mingyu Huo
- Department of Gastrointestinal Surgery, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Wenchao Li
- Department of General Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hongyu Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qi Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jianwu Jiang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Fu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Changjun Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Cai M, Zhao J, Ding Q, Wei J. Oncometabolite 2-hydroxyglutarate regulates anti-tumor immunity. Heliyon 2024; 10:e24454. [PMID: 38293535 PMCID: PMC10826830 DOI: 10.1016/j.heliyon.2024.e24454] [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: 09/13/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
"Oncometabolite" 2-hydroxyglutarate (2-HG) is an aberrant metabolite found in tumor cells, exerting a pivotal influence on tumor progression. Recent studies have unveiled its impact on the proliferation, activation, and differentiation of anti-tumor T cells. Moreover, 2-HG regulates the function of innate immune components, including macrophages, dendritic cells, natural killer cells, and the complement system. Elevated levels of 2-HG hinder α-KG-dependent dioxygenases (α-KGDDs), contributing to tumorigenesis by disrupting epigenetic regulation, genome integrity, hypoxia-inducible factors (HIF) signaling, and cellular metabolism. The chiral molecular structure of 2-HG produces two enantiomers: D-2-HG and L-2-HG, each with distinct origins and biological functions. Efforts to inhibit D-2-HG and leverage the potential of L-2-HG have demonstrated efficacy in cancer immunotherapy. This review delves into the metabolism, biological functions, and impacts on the tumor immune microenvironment (TIME) of 2-HG, providing a comprehensive exploration of the intricate relationship between 2-HG and antitumor immunity. Additionally, we examine the potential clinical applications of targeted therapy for 2-HG, highlighting recent breakthroughs as well as the existing challenges.
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Affiliation(s)
- Mengyuan Cai
- Department of Pharmacy, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Jianyi Zhao
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Qiang Ding
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Jifu Wei
- Department of Pharmacy, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
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Hu J, Xu L, Fu W, Sun Y, Wang N, Zhang J, Yang C, Zhang X, Zhou Y, Wang R, Zhang H, Mou R, Du X, Li X, Hu S, Xie R. Development and validation a prognostic model based on natural killer T cells marker genes for predicting prognosis and characterizing immune status in glioblastoma through integrated analysis of single-cell and bulk RNA sequencing. Funct Integr Genomics 2023; 23:286. [PMID: 37650991 DOI: 10.1007/s10142-023-01217-7] [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: 06/20/2023] [Revised: 08/09/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
BACKGROUND Glioblastoma (GBM) is an aggressive and unstoppable malignancy. Natural killer T (NKT) cells, characterized by specific markers, play pivotal roles in many tumor-associated pathophysiological processes. Therefore, investigating the functions and complex interactions of NKT cells is great interest for exploring GBM. METHODS We acquired a single-cell RNA-sequencing (scRNA-seq) dataset of GBM from Gene Expression Omnibus (GEO) database. The weighted correlation network analysis (WGCNA) was employed to further screen genes subpopulations. Subsequently, we integrated the GBM cohorts from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases to describe different subtypes by consensus clustering and developed a prognostic model by least absolute selection and shrinkage operator (LASSO) and multivariate Cox regression analysis. We further investigated differences in survival rates and clinical characteristics among different risk groups. Furthermore, a nomogram was developed by combining riskscore with the clinical characteristics. We investigated the abundance of immune cells in the tumor microenvironment (TME) by CIBERSORT and single sample gene set enrichment analysis (ssGSEA) algorithms. Immunotherapy efficacy assessment was done with the assistance of Tumor Immune Dysfunction and Exclusion (TIDE) and The Cancer Immunome Atlas (TCIA) databases. Real-time quantitative polymerase chain reaction (RT-qPCR) experiments and immunohistochemical profiles of tissues were utilized to validate model genes. RESULTS We identified 945 NKT cells marker genes from scRNA-seq data. Through further screening, 107 genes were accurately identified, of which 15 were significantly correlated with prognosis. We distinguished GBM samples into two distinct subtypes and successfully developed a robust prognostic prediction model. Survival analysis indicated that high expression of NKT cell marker genes was significantly associated with poor prognosis in GBM patients. Riskscore can be used as an independent prognostic factor. The nomogram was demonstrated remarkable utility in aiding clinical decision making. Tumor immune microenvironment analysis revealed significant differences of immune infiltration characteristics between different risk groups. In addition, the expression levels of immune checkpoint-associated genes were consistently elevated in the high-risk group, suggesting more prominent immune escape but also a stronger response to immune checkpoint inhibitors. CONCLUSIONS By integrating scRNA-seq and bulk RNA-seq data analysis, we successfully developed a prognostic prediction model that incorporates two pivotal NKT cells marker genes, namely, CD44 and TNFSF14. This model has exhibited outstanding performance in assessing the prognosis of GBM patients. Furthermore, we conducted a preliminary investigation into the immune microenvironment across various risk groups that contributes to uncover promising immunotherapeutic targets specific to GBM.
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Affiliation(s)
- Jiahe Hu
- Department of Digestive Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lei Xu
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Zhejiang, Hangzhou, China
| | - Wenchao Fu
- The Heilongjiang Key Laboratory of Anesthesia and Intensive Care Research, Harbin Medical University, Harbin, China
| | - Yanan Sun
- Department of Digestive Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Nan Wang
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Zhejiang, Hangzhou, China
| | - Jiheng Zhang
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Zhejiang, Hangzhou, China
| | - Chengyun Yang
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Zhejiang, Hangzhou, China
- Materials Science and Engineering, Zhejiang University of Technology, Zhejiang, Hangzhou, China
| | - Xiaoling Zhang
- Department of Digestive Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yuxin Zhou
- Department of Digestive Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Rongfang Wang
- Department of Digestive Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Haoxin Zhang
- Department of Digestive Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ruishu Mou
- Department of Digestive Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xinlian Du
- Department of Digestive Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xuedong Li
- Department of Digestive Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shaoshan Hu
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Zhejiang, Hangzhou, China.
| | - Rui Xie
- Department of Digestive Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, China.
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Fan Z, Xu H, Ge Q, Li W, Zhang J, Pu Y, Chen Z, Zhang S, Xue J, Shen B, Ding L, Wei Z. Identification of an immune subtype-related prognostic signature of clear cell renal cell carcinoma based on single-cell sequencing analysis. Front Oncol 2023; 13:1067987. [PMID: 37035172 PMCID: PMC10073649 DOI: 10.3389/fonc.2023.1067987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/10/2023] [Indexed: 04/11/2023] Open
Abstract
Background There is growing evidence that immune cells are strongly associated with the prognosis and treatment of clear cell renal cell carcinoma (ccRCC). Our aim is to construct an immune subtype-related model to predict the prognosis of ccRCC patients and to provide guidance for finding appropriate treatment strategies. Methods Based on single-cell analysis of the GSE152938 dataset from the GEO database, we defined the immune subtype-related genes in ccRCC. Immediately afterwards, we used Cox regression and Lasso regression to build a prognostic model based on TCGA database. Then, we carried out a series of evaluation analyses around the model. Finally, we proved the role of VMP1 in ccRCC by cellular assays. Result Initially, based on TCGA ccRCC patient data and GEO ccRCC single-cell data, we successfully constructed a prognostic model consisting of five genes. Survival analysis showed that the higher the risk score, the worse the prognosis. We also found that the model had high predictive accuracy for patient prognosis through ROC analysis. In addition, we found that patients in the high-risk group had stronger immune cell infiltration and higher levels of immune checkpoint gene expression. Finally, cellular experiments demonstrated that when the VMP1 gene was knocked down, 786-O cells showed reduced proliferation, migration, and invasion ability and increased levels of apoptosis. Conclusion Our study can provide a reference for the diagnosis and treatment of patients with ccRCC.
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Affiliation(s)
- Zongyao Fan
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, The Second Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Hewei Xu
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, The Second Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Qingyu Ge
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, The Second Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Weilong Li
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, The Second Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Junjie Zhang
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, The Second Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Yannan Pu
- Department of Rehabilitation Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhengsen Chen
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, The Second Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Sicong Zhang
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, The Second Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Jun Xue
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, The Second Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Baixin Shen
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, The Second Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Liucheng Ding
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, The Second Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Zhongqing Wei
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, The Second Clinical Medical College of Nanjing Medical University, Nanjing, China
- *Correspondence: Zhongqing Wei,
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Ghosal S, Hadrava Vanova K, Uher O, Das S, Patel M, Meuter L, Huynh TT, Jha A, Talvacchio S, Knue M, Prodanov T, Zeiger MA, Nilubol N, Taieb D, Crona J, Shankavaram UT, Pacak K. Immune signature of pheochromocytoma and paraganglioma in context of neuroendocrine neoplasms associated with prognosis. Endocrine 2023; 79:171-179. [PMID: 36370152 PMCID: PMC10683554 DOI: 10.1007/s12020-022-03218-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022]
Abstract
PURPOSE To understand prognostic immune cell infiltration signatures in neuroendocrine neoplasms (NENs), particularly pheochromocytoma and paraganglioma (PCPG), we analyzed tumor transcriptomic data from The Cancer Genome Atlas (TCGA) and other published tumor transcriptomic data of NENs. METHODS We used CIBERSORT to infer immune cell infiltrations from bulk tumor transcriptomic data from PCPGs, in comparison to gastroenteropancreatic neuroendocrine tumors (GEPNETs) and small cell lung carcinomas (SCLCs). PCPG immune signature was validated with NanoString immune panel in an independent cohort. Unsupervised clustering of the immune infiltration scores from CIBERSORT was used to find immune clusters. A prognostic immune score model for PCPGs and the other NENs were calculated as a linear combination of the estimated infiltration of activated CD8+/CD4+ T cells, activated NK cells, and M0 and M2 macrophages. RESULTS In PCPGs, we found five dominant immune clusters, associated with M2 macrophages, monocytes, activated NK cells, M0 macrophages and regulatory T cells, and CD8+/CD4+ T cells respectively. Non-metastatic tumors were associated with activated NK cells and metastatic tumors were associated with M0 macrophages and regulatory T cells. In GEPNETs and SCLCs, M0 macrophages and regulatory T cells were associated with unfavorable outcomes and features, such as metastasis and high-grade tumors. The prognostic immune score model for PCPGs and the NENs could predict non-aggressive and non-metastatic diseases. In PCPGs, the immune score was also an independent predictor of metastasis-free survival in a multivariate Cox regression analysis. CONCLUSION The transcriptomic immune signature in PCPG correlates with clinical features like metastasis and prognosis.
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Affiliation(s)
- Suman Ghosal
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Katerina Hadrava Vanova
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ondrej Uher
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Medical Biology, Faculty of Science, University of South Bohemia, Ceske Budejovice, 37005, Czech Republic
| | - Shaoli Das
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mayank Patel
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Leah Meuter
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Thanh-Truc Huynh
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Abhishek Jha
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sara Talvacchio
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marianne Knue
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tamara Prodanov
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Martha A Zeiger
- Office of Surgeon Scientists Programs, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Naris Nilubol
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David Taieb
- Department of Nuclear Medicine, La Timone University Hospital, Aix-Marseille University, Marseille, France
- European Center for Research in Medical Imaging, Aix-Marseille University, Marseille, France
| | - Joakim Crona
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Medical Sciences, Uppsala University, Akademiska Sjukhuset ing 78, 75185, Uppsala, Sweden
| | - Uma T Shankavaram
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Karel Pacak
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
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Li G, Xu S, Yang S, Wu C, Zhang L, Wang H. An immune infiltration-related long non-coding RNAs signature predicts prognosis for hepatocellular carcinoma. Front Genet 2022; 13:1029576. [PMID: 36568382 PMCID: PMC9773198 DOI: 10.3389/fgene.2022.1029576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
Background: With a high incidence and dismal survival rate, hepatocellular carcinoma (HCC) tops the list of the world's most frequent malignant tumors. Immunotherapy is a new approach to cancer treatment, and its effect on prolonging overall survival (OS) varies from patient to patient. For a more effective prognosis and treatment of HCC, we are committed to identifying immune infiltration-related long non-coding RNAs (IIRLs) with prognostic value in hepatocellular carcinoma. Methods: In our study, we calculated immune scores of 369 hepatocellular carcinoma samples from the Cancer Genome Atlas (TCGA) database by using an estimation algorithm, and obtained long non-coding RNAs (lncRNAs) associated with immune infiltration by using Weighted Gene Co-expression Network analysis (WGCNA). For training cohort, univariate Cox, least absolute shrinkage and selection operator (Lasso) and multivariate Cox regression analysis were used to determine prognostic IIRLs, we established a prognostic IIRLs signature. By testing cohort and entire cohort, we confirmed that the signature is practical. The prognosis of people with different clinicopathological stages and risk scores were predicted by the nomogram we constructed. In addition, Immune cell infiltration analysis and prediction of therapeutic drugs were performed. Results: 93 IIRLs were obtained by WGCNA. Furthermore, the prognostic value of these IIRLs were evaluated by using univariate Cox, Lasso and multivariate Cox analysis. Four IIRLs were used to create a signature with a prognosis. Time-related receiver operating characteristic (ROC) curve revealed that this model had an acceptable prognostic value for HCC patients. By using univariate and multivariate Cox regression analysis, this risk score has been shown to be an independent prognostic factor for HCC. The nomogram we made showed good predictions. Except for that, the treatment with immune checkpoint inhibitors (ICI) was likely to be more effective for low-risk patients. Conclusion: Based on four IIRLs, a prognostic signature was created in this research showed good accuracy in predicting OS. This study also provided valuable references for Immunotherapy of hepatocellular carcinoma.
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Affiliation(s)
- Gen Li
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Shaodian Xu
- Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Shuai Yang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Cong Wu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Liangliang Zhang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Hongbing Wang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China,*Correspondence: Hongbing Wang,
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Pacak K. New Biology of Pheochromocytoma and Paraganglioma. Endocr Pract 2022; 28:1253-1269. [PMID: 36150627 PMCID: PMC9982632 DOI: 10.1016/j.eprac.2022.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 12/13/2022]
Abstract
Pheochromocytomas and paragangliomas continue to be defined by significant morbidity and mortality despite their several recent advances in diagnosis, localization, and management. These adverse outcomes are largely related to mass effect as well as catecholamine-induced hypertension, tachyarrhythmias and consequent target organ damage, acute coronary syndromes, and strokes (ischemic and hemorrhagic stroke). Thus, a proper understanding of the physiology and pathophysiology of these tumors and recent advances are essential to affording optimal care. These major developments largely include a redefinition of metastatic behavior, a novel clinical categorization of these tumors into 3 genetic clusters, and an enhanced understanding of catecholamine metabolism and consequent specific biochemical phenotypes. Current advances in imaging of these tumors are shifting the paradigm from poorly specific anatomical modalities to more precise characterization of these tumors using the advent and development of functional imaging modalities. Furthermore, recent advances have revealed new molecular events in these tumors that are linked to their genetic landscape and, therefore, provide new therapeutic platforms. A few of these prospective therapies translated into new clinical trials, especially for patients with metastatic or inoperable tumors. Finally, outcomes are ever-improving as patients are cared for at centers with cumulative experience and well-established multidisciplinary tumor boards. In parallel, these centers have supported national and international collaborative efforts and worldwide clinical trials. These concerted efforts have led to improved guidelines collaboratively developed by healthcare professionals with a growing expertise in these tumors and consequently improving detection, prevention, and identification of genetic susceptibility genes in these patients.
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Affiliation(s)
- Karel Pacak
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
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Cao H, Gao S, Jogani R, Sugimura R. The Tumor Microenvironment Reprograms Immune Cells. Cell Reprogram 2022; 24:343-352. [PMID: 36301256 DOI: 10.1089/cell.2022.0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Tumor tissue comprises a highly complex network of diverse cell types. The tumor microenvironment (TME) can be mainly subdivided into cancer cells and stromal cell compartments, the latter include different types of immune cells, fibroblasts, endothelial cells, and pericytes. Tumor cells reprogram immune cells and other stromal cells in the TME to constrain their antitumor capacity by creating an immunosuppressive milieu and metabolism competition. Moreover, the reprogramming effect on immune cells is localized not only in the tumor but also at the systemic level. With wide application of single-cell sequencing technology, tumor-specific characteristics of immune cells and other stromal cells in the TME have been dissected. In this review, we mainly focus on how tumor cells reprogram immune cells both within the TME and peripheral blood. This information can further help us to improve the efficiency of current immunotherapy as well as bring up new ideas to combat cancer.
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Affiliation(s)
- Handi Cao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong.,Centre for Translational Stem Cell Biology, Science Park, Hong Kong
| | - Sanxing Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
| | - Ritika Jogani
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
| | - Ryohichi Sugimura
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong.,Centre for Translational Stem Cell Biology, Science Park, Hong Kong
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Jubelin C, Muñoz-Garcia J, Griscom L, Cochonneau D, Ollivier E, Heymann MF, Vallette FM, Oliver L, Heymann D. Three-dimensional in vitro culture models in oncology research. Cell Biosci 2022; 12:155. [PMID: 36089610 PMCID: PMC9465969 DOI: 10.1186/s13578-022-00887-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/18/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractCancer is a multifactorial disease that is responsible for 10 million deaths per year. The intra- and inter-heterogeneity of malignant tumors make it difficult to develop single targeted approaches. Similarly, their diversity requires various models to investigate the mechanisms involved in cancer initiation, progression, drug resistance and recurrence. Of the in vitro cell-based models, monolayer adherent (also known as 2D culture) cell cultures have been used for the longest time. However, it appears that they are often less appropriate than the three-dimensional (3D) cell culture approach for mimicking the biological behavior of tumor cells, in particular the mechanisms leading to therapeutic escape and drug resistance. Multicellular tumor spheroids are widely used to study cancers in 3D, and can be generated by a multiplicity of techniques, such as liquid-based and scaffold-based 3D cultures, microfluidics and bioprinting. Organoids are more complex 3D models than multicellular tumor spheroids because they are generated from stem cells isolated from patients and are considered as powerful tools to reproduce the disease development in vitro. The present review provides an overview of the various 3D culture models that have been set up to study cancer development and drug response. The advantages of 3D models compared to 2D cell cultures, the limitations, and the fields of application of these models and their techniques of production are also discussed.
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Zhou S, Han Y, Yang R, Pi X, Li J. TIMM13 as a prognostic biomarker and associated with immune infiltration in skin cutaneous melanoma (SKCM). Front Surg 2022; 9:990749. [PMID: 36061054 PMCID: PMC9428353 DOI: 10.3389/fsurg.2022.990749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/01/2022] [Indexed: 11/21/2022] Open
Abstract
Objective Providing protection against aggregation and guiding hydrophobic precursors through the mitochondria’s intermembrane space, this protein functions as a chaperone-like protein. SLC25A12 is imported by TIMM8 as a result of its interaction with TIMM13. In spite of this, it is still unknown how TIMM13 interacts with skin cutaneous melanoma (SKCM) and tumor-infiltrating lymphocytes (TILs). Methods Aberrant expression of TIMM13 in SKCM and its clinical outcome was evaluated with the help of multiple databases, including the Xiantao tool (https://www.xiantao.love/), HPA, and UALCAN. TISIDB and Tumor Immune Estimation Resources (TIMER) databases were applied to explore the association between TIMM13 and tumor infiltration immune cells. OS nomogram was constructed, and model performance was examined. Finally, TIMM13 protein expression was validated by immunohistochemistry (IHC). Results TIMM13 expression was higher in SKCM samples than in peritumor samples. TIMM13 was strongly associated with sample type, subgroup, cancer stage, lymph node stage, and worse survival. Further, upregulation of TIMM13 was significantly associated with immunoregulators, and chemokines, as well as T cells, B cells, monocytes, neutrophils, macrophages, and T-cell regulators. An analysis of bioinformatic data uncovered that TIMM13 expression was strongly associated with PD1 (T-cell exhaustion marker). The nomogram showed good predictive performance based on calibration plot. TIMM13 was highly expressed in melanoma tissue samples than in normal samples. Conclusion In brief, TIMM13 may be a prognostic biomarker for SKCM. It might modulate the tumor immune microenvironment and lead to a poorer prognosis. In addition, it is necessary to study the targeted therapy of TIMM13.
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Affiliation(s)
- Sitong Zhou
- Department of Dermatology, The First People’s Hospital of Foshan, Foshan, China
| | - Yuanyuan Han
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China
| | - Ronghua Yang
- Department of Burn and Plastic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
- Correspondence: Jiehua Li Xiaobing Pi Ronghua Yang
| | - Xiaobing Pi
- Department of Dermatology, The First People’s Hospital of Foshan, Foshan, China
- Correspondence: Jiehua Li Xiaobing Pi Ronghua Yang
| | - Jiehua Li
- Department of Dermatology, The First People’s Hospital of Foshan, Foshan, China
- Correspondence: Jiehua Li Xiaobing Pi Ronghua Yang
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11
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Yu D, Liu S, Chen Y, Yang L. Integrative Bioinformatics Analysis Reveals CHEK1 and UBE2C as Luminal A Breast Cancer Subtype Biomarkers. Front Genet 2022; 13:944259. [PMID: 35903365 PMCID: PMC9322798 DOI: 10.3389/fgene.2022.944259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/23/2022] [Indexed: 12/09/2022] Open
Abstract
In light of the limited number of targetable oncogenic drivers in breast cancer (BRCA), it is important to identify effective and druggable gene targets for the treatment of this devastating disease. Herein, the GSE102484 dataset containing expression profiling data from 683 BRCA patients was re-analyzed using weighted gene co-expression network analysis (WGCNA). The yellow module with the highest correlation to BRCA progression was screened out, followed by functional enrichment analysis and establishment of a protein–protein interaction (PPI) network. After further validation through survival analysis and expression evaluation, CHEK1 and UBE2C were finally identified as hub genes related to the progression of BRCA, especially the luminal A breast cancer subtype. Notably, both hub genes were found to be dysregulated in multiple types of immune cells and closely correlated with tumor infiltration, as revealed by Tumor Immune Estimation Resource (TIMER) along with other bioinformatic tools. Construction of transcription factors (TF)-hub gene network further confirmed the existence of 11 TFs which could regulate both hub genes simultaneously. Our present study may facilitate the invention of targeted therapeutic drugs and provide novel insights into the understanding of the mechanism beneath the progression of BRCA.
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12
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Corti C, Antonarelli G, Valenza C, Nicolò E, Rugo H, Cortés J, Harbeck N, Carey LA, Criscitiello C, Curigliano G. Histology-agnostic approvals for antibody-drug conjugates in solid tumours: is the time ripe? Eur J Cancer 2022; 171:25-42. [PMID: 35696887 DOI: 10.1016/j.ejca.2022.04.039] [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: 03/19/2022] [Revised: 04/11/2022] [Accepted: 04/29/2022] [Indexed: 11/15/2022]
Abstract
Several antibody-drug conjugates (ADCs) have been recently approved to treat solid tumours. Since ADCs seem to have activity in multiple malignancies sharing the expression of a specific antigen, they may be mirroring the experience of histology-agnostic-targeted treatments. So, the possibility to interpret the activity of some ADCs across different cancer types in a biomarker-driven perspective arises. However, relevant biological, methodological, and regulatory challenges should be highlighted and addressed, in order to grant ADCs biomarker-driven regulatory approvals in the next future. In this review, we discuss challenges and opportunities posed by the pan-histological expansion of ADCs in solid tumours. In particular, we provide an overview about technological and manufacturing advancements; we offer up-to-date highlights of the current evidence from clinical trials investigating ADCs in solid tumours; we discuss the need for the identification of optimal predictive biomarkers, as well as major methodological, statistical, and regulatory considerations for a biomarker-driven histology-agnostic approach.
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Affiliation(s)
- Chiara Corti
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - Gabriele Antonarelli
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - Carmine Valenza
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - Eleonora Nicolò
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - Hope Rugo
- San Francisco, UCSF Helen Diller Family Comprehensive Cancer Center Precision Medicine Cancer Building, San Francisco, CA, USA
| | - Javier Cortés
- International Breast Cancer Center (IBCC), Quironsalud Group, Barcelona, Spain; Faculty of Biomedical and Health Sciences, Department of Medicine, Universidad Europea de Madrid, Spain
| | - Nadia Harbeck
- Breast Center, Dept OB&GYN and CCCMunich, LMU University Hospital, Munich, Germany
| | - Lisa A Carey
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
| | - Carmen Criscitiello
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - Giuseppe Curigliano
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy.
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13
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Zuccato JA, Patil V, Mansouri S, Liu JC, Nassiri F, Mamatjan Y, Chakravarthy A, Karimi S, Almeida JP, Bernat AL, Hasen M, Singh O, Khan S, Kislinger T, Sinha N, Froelich S, Adle-Biassette H, Aldape KD, De Carvalho DD, Zadeh G. DNA Methylation based prognostic subtypes of chordoma tumors in tissue and plasma. Neuro Oncol 2021; 24:442-454. [PMID: 34614192 DOI: 10.1093/neuonc/noab235] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Chordomas are rare malignant bone cancers of the skull-base and spine. Patient survival is variable and not reliably predicted using clinical factors or molecular features. This study identifies prognostic epigenetic chordoma subtypes that are detected non-invasively using plasma methylomes. METHODS Methylation profiles of 68 chordoma surgical samples were obtained between 1996-2018 across three international centres along with matched plasma methylomes where available. RESULTS Consensus clustering identified two stable tissue clusters with a disease-specific survival difference that was independent of clinical factors in a multivariate Cox analysis (HR=14.2, 95%CI: 2.1-94.8, p=0.0063). Immune-related pathways with genes hypomethylated at promoters and increased immune cell abundance were observed in the poor-performing "Immune-infiltrated" subtype. Cell-to-cell interaction plus extracellular matrix pathway hypomethylation and higher tumor purity was observed in the better-performing "Cellular" subtype. The findings were validated in additional DNA methylation and RNA sequencing datasets as well as with immunohistochemical staining. Plasma methylomes distinguished chordomas from other clinical differential diagnoses by applying fifty chordoma-versus-other binomial generalized linear models in random 20% testing sets (mean AUROC=0.84, 95%CI: 0.52-1.00). Tissue-based and plasma-based methylation signals were highly correlated in both prognostic clusters. Additionally, leave-one-out models accurately classified all tumors into their correct cluster based on plasma methylation data. CONCLUSIONS Here, we show the first identification of prognostic epigenetic chordoma subtypes and first use of plasma methylome-based biomarkers to non-invasively diagnose and subtype chordomas. These results may transform patient management by allowing treatment aggressiveness to be balanced with patient risk according to prognosis.
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Affiliation(s)
- Jeffrey A Zuccato
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada.,Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Vikas Patil
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Sheila Mansouri
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey C Liu
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Farshad Nassiri
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada.,Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Yasin Mamatjan
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Ankur Chakravarthy
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shirin Karimi
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Joao Paulo Almeida
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Laure Bernat
- Neurosurgery Department, Hôpital Lariboisiere, APHP, Université Paris Diderot, Paris, France
| | - Mohammed Hasen
- Section of Neurosurgery, Division of Surgery, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Canada.,Department of Neurosurgery, King Fahad University Hospital, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Olivia Singh
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Namita Sinha
- Department of Pathology, Shared Health, HSC, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sébastien Froelich
- Neurosurgery Department, Hôpital Lariboisiere, APHP, Université Paris Diderot, Paris, France
| | - Homa Adle-Biassette
- Department of Pathology, Lariboisière Hospital, Assistance Publique - Hôpitaux de Paris, Université de Paris, Paris, France
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Gelareh Zadeh
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada.,Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
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14
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Identification of a Tumor Microenvironment-Related Gene Signature Indicative of Disease Prognosis and Treatment Response in Colon Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6290261. [PMID: 34497681 PMCID: PMC8420973 DOI: 10.1155/2021/6290261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/24/2021] [Indexed: 01/05/2023]
Abstract
Background The tumor microenvironment (TME) is associated with disease outcomes and treatment response in colon cancer. Here, we constructed a TME-related gene signature that is prognosis of disease survival and may predict response to immunotherapy in colon cancer. Methods We calculated immune and stromal scores for 385 colon cancer samples from The Cancer Genome Atlas (TCGA) database using the ESTIMATE algorithm. We identified nine TME-related prognostic genes using Cox regression analysis. We evaluated associations between protein expression, extent of immune cell infiltrate, and patient survival. We calculated risk scores and built a clinical predictive model for the TME-related gene signature. Receiver operating characteristic (ROC) curves were generated to assess the predictive power of the signature. We estimated the half-maximal inhibitory concentration (IC50) of chemotherapeutic drugs in patients using the pRRophetic algorithm. The expression of immune checkpoint genes was evaluated. Results High immune and stromal scores are significantly associated with poor overall survival (p < 0.05). We identified 773 differential TME-related prognostic genes associated with survival; these genes were enriched in immune-related pathways. Nine key prognostic genes were identified and were used to construct a TME-related prognostic signature: CADM3, LEP, CD1B, PDE1B, CCL22, ABI3BP, IGLON5, SELE, and TGFB1. This signature identified a high-risk group with worse survival outcomes, based on Kaplan-Meier analysis. A nomogram composed of clinicopathological factors and risk score exhibited good accuracy. Drug sensitivity analysis identified no difference in sensitivity between the high-risk and low-risk groups. High-risk patients had higher expression of PD-1, PDL-1, and CTLA-4 and lower expression of LAG-3 and VSIR. Infiltration of dendritic cells was higher in the high-risk group. Conclusions We identified a novel prognostic TME-related gene expression signature in colon cancer. Stratification of patients based on this gene signature could be used to improve outcomes and guide better therapy for colon cancer patients.
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15
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Identification and Validation of a Tumor Microenvironment-Related Gene Signature for Prognostic Prediction in Advanced-Stage Non-Small-Cell Lung Cancer. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8864436. [PMID: 33860055 PMCID: PMC8028741 DOI: 10.1155/2021/8864436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/29/2020] [Accepted: 01/13/2021] [Indexed: 01/06/2023]
Abstract
The development of immunotherapy has greatly changed the advanced-stage non-small-cell lung cancer (NSCLC) treatment landscape. The complexity and heterogeneity of tumor microenvironment (TME) lead to discrepant immunotherapy effects among patients at the same pathologic stages. This study is aimed at exploring potential biomarkers of immunotherapy and accurately predicting the prognosis for advanced NSCLC patients. RNA-seq data and clinical information on stage III/IV NSCLC were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). In TCGA-NSCLC with stage III/IV (n = 192), immune scores and stromal scores were calculated by using the ESTIMATE algorithms. Univariate, LASSO, and multivariate Cox regression analyses were performed to screen prognostic TME-related genes (TMERGs) and constructed a gene signature risk score model. It was validated in external dataset including GSE41271 (n = 91) and GSE81089 (n = 36). Additionally, a nomogram incorporating TMERG signature risk score and clinical characteristics was established. Further, we accessed the proportion of 22 types of tumor-infiltrating immune cells (TIIC) from the CIBERSORT website and analyzed the difference between two risk groups. OS of patients with high immune/stromal scores were higher (log-rank P = 0.044/log-rank P = 0.048). Multivariate Cox regression identified six prognostic TMERGs, including CD200, CHI3L2, CNTN1, CTSL, FYB1, and SLC52A1. We developed a six-gene risk score model, which was validated as an independent prognostic factor for OS (HR: 3.32, 95% CI: 2.16-5.09). Time-ROC curves showed useful discrimination for TCGA-NSCLC cohort (1-, 2-, and 3-year AUCs were 0.718, 0.761, and 0.750). The predictive robustness was validated in the external dataset. The C-index and 1-, 2-, and 3-year AUCs of nomogram were the largest, which demonstrated the nomogram had the greatest predictive accuracy and effectiveness and could be used for clinical guidance. Besides, the increased infiltration of T cells regulatory (Tregs) and macrophages M2 in the high-risk group suggested that chronic inflammation may reduce survival probability in patients with advanced NSCLC. We conducted a comprehensive analysis of the tumor microenvironment and identified the TMERG signature, which could predict prognosis accurately and provide a reference for the personalized immunotherapy for advanced NSCLC patients.
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16
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Kim A, Lim SM, Kim JH, Seo JS. Integrative Genomic and Transcriptomic Analyses of Tumor Suppressor Genes and Their Role on Tumor Microenvironment and Immunity in Lung Squamous Cell Carcinoma. Front Immunol 2021; 12:598671. [PMID: 33717076 PMCID: PMC7948518 DOI: 10.3389/fimmu.2021.598671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/18/2021] [Indexed: 12/22/2022] Open
Abstract
Non-small-cell lung cancers (NSCLCs) are largely classified into lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), which have different therapeutic options according to its molecular profiles and immune checkpoint expression, especially PD-L1, which is a suppressive factor in the tumor microenvironment. The tumor microenvironment can be altered by the genomic mutations on specific innate immune genes as well as tumor suppressor genes, so it is essential to comprehend the association between tumor microenvironment and tumor suppressor genes to discover the promising immunotherapeutic strategy to overcome the resistance of immune check point blockade. In this study, we aimed to analyze how the somatic mutations in tumor suppressor genes affect the tumor immune microenvironment through a comprehensive analysis of mutational profiling on the representative tumor suppressor genes (TP53, CDKN2A, PTEN, RB1, BRCA1, BRCA2) and immune gene expression in The Cancer Genome Atlas (TCGA) 155 lung squamous cell carcinoma (LUSC) and 196 lung adenocarcinoma (LUAD) samples. Several microenvironmental factors, such as the infiltrating immune and stromal cells, were suppressed by the mutated tumor suppressor genes in LUSC, unlike in the LUAD samples. In particular, infiltrating immune cells such as macrophage, neutrophil, and dendritic cells were significantly reduced in tumors with mutated tumor suppressor genes' group. In addition, the gene expressions for interleukin production and lymphocyte differentiation and PGC, C7, HGF, PLA2G2A, IL1RL1, CCR2, ALOX15B, CXCL11, FCN3 were significantly down-regulated, which were key immune genes for the cross-talk between LUSC microenvironment and tumor suppressors. Therefore, we generated evidence that TSG mutations in LUSC have an impact on tumor immune microenvironment, which suggests that TSG non-mutated patients will have the more inflamed tumors and are more likely to respond to immune checkpoint blockade therapy.
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Affiliation(s)
- Ahreum Kim
- Department of Medicine, CHA University School of Medicine, Seongnam, South Korea.,Precision Medicine Center, Seoul National University Bundang Hospital, Seongnamsi, South Korea
| | - Sun Min Lim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
| | - Joo-Hang Kim
- Department of Medicine, CHA University School of Medicine, Seongnam, South Korea.,Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam-si, South Korea
| | - Jeong-Sun Seo
- Precision Medicine Center, Seoul National University Bundang Hospital, Seongnamsi, South Korea.,Precision Medicine Institute, Macrogen Inc., Seoul, South Korea
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17
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Källberg D, Vidman L, Rydén P. Comparison of Methods for Feature Selection in Clustering of High-Dimensional RNA-Sequencing Data to Identify Cancer Subtypes. Front Genet 2021; 12:632620. [PMID: 33719342 PMCID: PMC7943624 DOI: 10.3389/fgene.2021.632620] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/03/2021] [Indexed: 11/13/2022] Open
Abstract
Cancer subtype identification is important to facilitate cancer diagnosis and select effective treatments. Clustering of cancer patients based on high-dimensional RNA-sequencing data can be used to detect novel subtypes, but only a subset of the features (e.g., genes) contains information related to the cancer subtype. Therefore, it is reasonable to assume that the clustering should be based on a set of carefully selected features rather than all features. Several feature selection methods have been proposed, but how and when to use these methods are still poorly understood. Thirteen feature selection methods were evaluated on four human cancer data sets, all with known subtypes (gold standards), which were only used for evaluation. The methods were characterized by considering mean expression and standard deviation (SD) of the selected genes, the overlap with other methods and their clustering performance, obtained comparing the clustering result with the gold standard using the adjusted Rand index (ARI). The results were compared to a supervised approach as a positive control and two negative controls in which either a random selection of genes or all genes were included. For all data sets, the best feature selection approach outperformed the negative control and for two data sets the gain was substantial with ARI increasing from (-0.01, 0.39) to (0.66, 0.72), respectively. No feature selection method completely outperformed the others but using the dip-rest statistic to select 1000 genes was overall a good choice. The commonly used approach, where genes with the highest SDs are selected, did not perform well in our study.
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Affiliation(s)
- David Källberg
- Department of Statistics, USBE, Umeå University, Umeå, Sweden
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
| | - Linda Vidman
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Patrik Rydén
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
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18
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Kuchar M, Strizova Z, Capkova L, Komarc M, Skrivan J, Bartunkova J, Smrz D, Plzak J. The Periphery of Salivary Gland Carcinoma Tumors Reveals a PD-L1/PD-1 Biomarker Niche for the Evaluation of Disease Severity and Tumor-Immune System Interplay. Biomedicines 2021; 9:97. [PMID: 33498270 PMCID: PMC7909271 DOI: 10.3390/biomedicines9020097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/27/2022] Open
Abstract
The treatment options for patients with advanced salivary gland cancers (SGCs) are limited. Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment. However, the response to ICI immunotherapy is largely driven by the immune cell signatures within the tumor tissue and the para-tumoral tissue compartments. To date, there are no data on the expression of programed cell death protein-1/programed cell death protein-ligand 1 (PD-1/PD-L1) in SGC, which may enable the implementation of ICI immunotherapy for this disease. Thus, we performed an immunohistochemical analysis of PD-1 and PD-L1 expression in tumor cells and tumor-infiltrating immune cells (TIICs) in the tumor center and periphery of 62 SGC patients. The tumor periphery showed significantly higher expression of PD-L1 in tumor cells than in TIICs. Moreover, peripheral TIICs had significantly higher PD-1 expression than peripheral tumor cells. PD-1-positive tumor cells were detected exclusively in the tumor center of high-grade tumors, and most importantly, the presence of lymph node (LN) metastases and primary tumor stage significantly correlated with the presence of PD-L1-positive tumor cells in the tumor periphery. The PD-1/PD-L1 molecular signatures in SGC are clustered predominantly in the tumor periphery, reflect disease severity, and may predict the response to ICI immunotherapy in SGC patients.
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Affiliation(s)
- Martin Kuchar
- Department of Otorhinolaryngology and Head and Neck Surgery, First Faculty of Medicine, Charles University and University Hospital Motol, 15006 Prague, Czech Republic; (M.K.); (J.P.)
| | - Zuzana Strizova
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, 15006 Prague, Czech Republic; (J.B.); (D.S.)
| | - Linda Capkova
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University and University Hospital Motol, 15006 Prague, Czech Republic;
| | - Martin Komarc
- Department of Methodology, Faculty of Physical Education and Sport, Charles University, 16252 Prague, Czech Republic;
| | - Jiri Skrivan
- Department of Otorhinolaryngology, Second Faculty of Medicine, Charles University and University Hospital Motol, 15006 Prague, Czech Republic;
| | - Jirina Bartunkova
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, 15006 Prague, Czech Republic; (J.B.); (D.S.)
| | - Daniel Smrz
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, 15006 Prague, Czech Republic; (J.B.); (D.S.)
| | - Jan Plzak
- Department of Otorhinolaryngology and Head and Neck Surgery, First Faculty of Medicine, Charles University and University Hospital Motol, 15006 Prague, Czech Republic; (M.K.); (J.P.)
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19
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Zhang X, Zhao H, Shi X, Jia X, Yang Y. Identification and validation of an immune-related gene signature predictive of overall survival in colon cancer. Aging (Albany NY) 2020; 12:26095-26120. [PMID: 33401247 PMCID: PMC7803520 DOI: 10.18632/aging.202317] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
The heterogeneity and complexity of tumor-immune microenvironments lead to diverse immunotherapy effects among colon cancer patients. It is crucial to identify immune microenvironment-related biomarkers and construct prognostic risk models. In this study, the immune and stromal scores of 415 cases from TCGA were calculated using the ESTIMATE algorithm. AXIN2, CCL22, CLEC10A, CRIP2, RUNX3, and TRPM5 were screened and established a prognostic immune-related gene (IRG) signature using by univariate, LASSO, and multivariate Cox regression models. The predicted performance of IRG signature was external validated by GSE39582 (n=519). Stratified survival analysis showed IRG signature was an effective predictor of survival in patients with different clinical characteristics. The protein expression level of six genes was validated by immunohistochemistry analysis. Difference analysis indicated the mutation rate, immune cell of resting NK cells and regulatory T cells infiltration and four immune checkpoints of PD-1, PD-L1, LAG3 and VSIR expression levels in the high-risk group were significantly higher than those in the low-risk group. A nomogram incorporating the gene signatures and clinical factors was demonstrated had a good accuracy (1-, 3-, and 5-year AUC= 0.799, 0.791, 0.738). Our study identified a novel IRG signature, which may provide some references for the clinical precision immunotherapy of patients.
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Affiliation(s)
- Xuening Zhang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Hao Zhao
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Xuezhong Shi
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Xiaocan Jia
- Zhengzhou University Library, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yongli Yang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China
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