1
|
Zhang K, Zhu Z, Zhou J, Shi M, Wang N, Yu F, Xu L. Disulfidptosis-related gene expression reflects the prognosis of drug-resistant cancer patients and inhibition of MYH9 reverses sorafenib resistance. Transl Oncol 2024; 49:102091. [PMID: 39146597 PMCID: PMC11375144 DOI: 10.1016/j.tranon.2024.102091] [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: 10/18/2023] [Revised: 05/03/2024] [Accepted: 08/11/2024] [Indexed: 08/17/2024] Open
Abstract
The onset of drug resistance in advanced cancer patients markedly diminishes their prognosis. Recently, disulfidptosis, a novel form of cell death, has been identified, triggered by excessive disulfide formation leading to cell shrinkage and F-actin contraction. Previous studies have identified 15 essential genes (FLNA, FLNB, MYH9, TLN1, ACTB, MYL6, MYH10, CAPZB, DSTN, IQGAP1, ACTN4, PDLIM1, CD2AP, INF2, SLC7A11) associated with disulfidptosis. This study sourced pan-cancer mRNA expression data from Xena to thoroughly evaluate the molecular and clinical characteristics of disulfidptosis-related genes. Through unsupervised clustering, mRNA expression data identified the expression levels of disulfidptosis-related genes and potential clusters related to this form of cell death. Kaplan-Meier survival curves illustrated the correlation between different clusters and overall survival. The findings reveal that high expression of disulfidptosis-related genes is linked to poor survival in liver cancer. The GDSC database was utilized to analyze the relationship between disulfidptosis-related genes and the AUC of 198 drugs. The results demonstrate that 12 disulfidptosis-related genes influence sorafenib resistance, as revealed by the intersection of differential genes related to sorafenib resistance from the GSE109211 dataset. Among them, the MYH9 gene was found to play a crucial role in both. Finally, experimental evidence confirmed that MYH9 mitigates sorafenib resistance in hepatocellular carcinoma through disulfidptosis-like changes. This study identifies disulfidptosis as a promising avenue for enhancing the sensitivity of tumor cells to drugs, offering new therapeutic perspectives for future research on disulfidptosis and drug resistance in cancer patients.
Collapse
Affiliation(s)
- Kangnan Zhang
- Department of Gastroenterology, Shanghai Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200336, China
| | - Zhenhua Zhu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200001, China
| | - Jingyi Zhou
- Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Min Shi
- Department of Gastroenterology, Shanghai Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200336, China
| | - Na Wang
- Department of Gastroenterology, Shanghai Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200336, China.
| | - Fudong Yu
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Public Health School, Fudan University, Shanghai, 200030, China.
| | - Ling Xu
- Department of Gastroenterology, Shanghai Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200336, China.
| |
Collapse
|
2
|
Yule MS, Brown LR, Skipworth RJE, Laird BJA. Central neural mechanisms of cancer cachexia. Curr Opin Support Palliat Care 2024; 18:138-144. [PMID: 38752576 DOI: 10.1097/spc.0000000000000707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
PURPOSE OF REVIEW Cachexia is a devasting syndrome which impacts a large number of patients with cancer. This review aims to provide a comprehensive overview of the central mechanisms of cancer cachexia. In particular, it focuses on the role of the central nervous system (CNS), the melanocortin system, circulating hormones and molecules which are produced by and act on the CNS and the psychological symptoms of cancer cachexia. RECENT FINDINGS A growing body of evidence suggests that a central mechanism of action underpins this multi-system disorder. Recent research has focused on the role of neuroinflammation that drives the sickness behaviour seen in cancer cachexia, with emphasis on the role of the hypothalamus. Melanocortin receptor antagonists are showing promise in preclinical studies. There are also new pharmacological developments to overcome the short half-life of ghrelin. GDF-15 has been identified as a core target and trials of compounds that interfere with its signalling or its central receptor are underway. SUMMARY Understanding the central mechanisms of cancer cachexia is pivotal for enhancing treatment outcomes in patients. While emerging pharmacological interventions targeting these pathways have shown promise, further research is essential.
Collapse
Affiliation(s)
- Michael S Yule
- St Columba's Hospice
- Edinburgh Cancer Research Centre, University of Edinburgh
| | - Leo R Brown
- Clinical Surgery, University of Edinburgh, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Richard J E Skipworth
- Clinical Surgery, University of Edinburgh, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Barry J A Laird
- St Columba's Hospice
- Edinburgh Cancer Research Centre, University of Edinburgh
| |
Collapse
|
3
|
Moragas N, Fernandez-Nogueira P, Recalde-Percaz L, Inman JL, López-Plana A, Bergholtz H, Noguera-Castells A, Del Burgo PJ, Chen X, Sorlie T, Gascón P, Bragado P, Bissell M, Carbó N, Fuster G. The SEMA3F-NRP1/NRP2 axis is a key factor in the acquisition of invasive traits in in situ breast ductal carcinoma. Breast Cancer Res 2024; 26:122. [PMID: 39138514 PMCID: PMC11320849 DOI: 10.1186/s13058-024-01871-0] [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: 02/15/2024] [Accepted: 07/12/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND A better understanding of ductal carcinoma in situ (DCIS) is urgently needed to identify these preinvasive lesions as distinct clinical entities. Semaphorin 3F (SEMA3F) is a soluble axonal guidance molecule, and its coreceptors Neuropilin 1 (NRP1) and NRP2 are strongly expressed in invasive epithelial BC cells. METHODS We utilized two cell line models to represent the progression from a healthy state to the mild-aggressive or ductal carcinoma in situ (DCIS) stage and, ultimately, to invasive cell lines. Additionally, we employed in vivo models and conducted analyses on patient databases to ensure the translational relevance of our results. RESULTS We revealed SEMA3F as a promoter of invasion during the DCIS-to-invasive ductal carcinoma transition in breast cancer (BC) through the action of NRP1 and NRP2. In epithelial cells, SEMA3F activates epithelialmesenchymal transition, whereas it promotes extracellular matrix degradation and basal membrane and myoepithelial cell layer breakdown. CONCLUSIONS Together with our patient database data, these proof-of-concept results reveal new SEMA3F-mediated mechanisms occurring in the most common preinvasive BC lesion, DCIS, and represent potent and direct activation of its transition to invasion. Moreover, and of clinical and therapeutic relevance, the effects of SEMA3F can be blocked directly through its coreceptors, thus preventing invasion and keeping DCIS lesions in the preinvasive state.
Collapse
MESH Headings
- Humans
- Neuropilin-1/metabolism
- Neuropilin-1/genetics
- Female
- Breast Neoplasms/pathology
- Breast Neoplasms/metabolism
- Breast Neoplasms/genetics
- Neuropilin-2/metabolism
- Neuropilin-2/genetics
- Neoplasm Invasiveness
- Carcinoma, Intraductal, Noninfiltrating/metabolism
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Cell Line, Tumor
- Nerve Tissue Proteins/metabolism
- Nerve Tissue Proteins/genetics
- Epithelial-Mesenchymal Transition/genetics
- Animals
- Membrane Proteins/metabolism
- Membrane Proteins/genetics
- Mice
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/genetics
- Gene Expression Regulation, Neoplastic
- Signal Transduction
Collapse
Affiliation(s)
- Núria Moragas
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona (UB), 08028, Barcelona, Spain
- Institute of Biomedicine of the Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Patricia Fernandez-Nogueira
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona (UB), 08028, Barcelona, Spain
- Institute of Biomedicine of the Universitat de Barcelona (IBUB), Barcelona, Spain
- Department of Biomedicine, School of Medicine, Universitat de Barcelona (UB), 08036, Barcelona, Spain
| | - Leire Recalde-Percaz
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona (UB), 08028, Barcelona, Spain
- Institute of Biomedicine of the Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Jamie L Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA, 94720, USA
| | - Anna López-Plana
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona (UB), 08028, Barcelona, Spain
- Institute of Biomedicine of the Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Helga Bergholtz
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, 0450, Oslo, Norway
| | - Aleix Noguera-Castells
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona (UB), 08028, Barcelona, Spain
- Institute of Biomedicine of the Universitat de Barcelona (IBUB), Barcelona, Spain
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Department of Biosciences, Faculty of Science, Technology and Engineering, University of Vic - Central University of Catalonia (UVic-UCC), Vic, Barcelona, Catalonia, Spain
| | - Pedro J Del Burgo
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona (UB), 08028, Barcelona, Spain
| | - Xieng Chen
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona (UB), 08028, Barcelona, Spain
| | - Therese Sorlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, 0450, Oslo, Norway
| | - Pere Gascón
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona (UB), 08028, Barcelona, Spain
| | - Paloma Bragado
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Universidad Complutense de Madrid, Health Research Institute of the Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Mina Bissell
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA, 94720, USA
| | - Neus Carbó
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona (UB), 08028, Barcelona, Spain
- Institute of Biomedicine of the Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Gemma Fuster
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona (UB), 08028, Barcelona, Spain.
- Institute of Biomedicine of the Universitat de Barcelona (IBUB), Barcelona, Spain.
- Tissue Repair and Regeneration Laboratory (TR2Lab), Institute of Research and Innovation of Life Sciences and Health, Catalunya Central (IRIS-CC), UVIC-UCC, Vic, Spain.
| |
Collapse
|
4
|
Chen X, Li R, Yin YH, Liu X, Zhou XJ, Qu YQ. Pan-cancer prognosis, immune infiltration, and drug resistance characterization of lung squamous cell carcinoma tumor microenvironment-related genes. Biochem Biophys Rep 2024; 38:101722. [PMID: 38711549 PMCID: PMC11070325 DOI: 10.1016/j.bbrep.2024.101722] [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: 11/16/2023] [Revised: 04/21/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024] Open
Abstract
Background The tumor microenvironment (TME) plays an important role in cancer development; however, its implications in lung squamous cell carcinoma (LUSC) and pan-cancer have been poorly understood. Methods In this study, The Cancer Genome Atlas (TCGA) and Estimation of Stromal and Immune cells in Malignant Tumor tissue using Expression Data (ESTIMATE) datasets were applied to identify differentially expressed genes. Additionally, online public databases were utilized for in-depth bioinformatics analysis of pan-cancer datasets to investigate the prognostic implications of TME-related genes further. Results Our study demonstrated a significant association between stromal scores, immune scores, and specific clinical characteristics in LUSC patients. C3AR1, CSF1R, CCL2, CCR1, and CD14 were identified as prognostic genes related to the TME. All TME-related prognostic genes demonstrated varying degrees of correlation with immune infiltration subtypes and tumor cell stemness. Moreover, our study revealed that TME-related prognostic genes, particularly C3AR1 and CCR1, might contribute to drug resistance in cancer cells. Conclusions The identified TME-related prognostic genes, particularly C3AR1 and CCR1, have potential implications for understanding and targeting drug resistance mechanisms in cancer cells.
Collapse
Affiliation(s)
- Xiao Chen
- Department of Respiratory Medicine, Tai'an City Central Hospital, Tai'an, China
| | - Rui Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Yun-Hong Yin
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xiao Liu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xi-Jia Zhou
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Yi-Qing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| |
Collapse
|
5
|
Chong ZX, Ho WY, Yeap SK. Decoding the tumour-modulatory roles of LIMK2. Life Sci 2024; 347:122609. [PMID: 38580197 DOI: 10.1016/j.lfs.2024.122609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/19/2024] [Accepted: 04/01/2024] [Indexed: 04/07/2024]
Abstract
LIM domains kinase 2 (LIMK2) is a 72 kDa protein that regulates actin and cytoskeleton reorganization. Once phosphorylated by its upstream activator (ROCK1), LIMK2 can phosphorylate cofilin to inactivate it. This relieves the levering stress on actin and allows polymerization to occur. Actin rearrangement is essential in regulating cell cycle progression, apoptosis, and migration. Dysregulation of the ROCK1/LIMK2/cofilin pathway has been reported to link to the development of various solid cancers such as breast, lung, and prostate cancer and liquid cancer like leukemia. This review aims to assess the findings from multiple reported in vitro, in vivo, and clinical studies on the potential tumour-regulatory role of LIMK2 in different human cancers. The findings of the selected literature unraveled that activated AKT, EGF, and TGF-β pathways can upregulate the activities of the ROCK1/LIMK2/cofilin pathway. Besides cofilin, LIMK2 can modulate the cellular levels of other proteins, such as TPPP1, to promote microtubule polymerization. The tumour suppressor protein p53 can transactivate LIMK2b, a splice variant of LIMK2, to induce cell cycle arrest and allow DNA repair to occur before the cell enters the next phase of the cell cycle. Additionally, several non-coding RNAs, such as miR-135a and miR-939-5p, could also epigenetically regulate the expression of LIMK2. Since the expression of LIMK2 is dysregulated in several human cancers, measuring the tissue expression of LIMK2 could potentially help diagnose cancer and predict patient prognosis. As LIMK2 could play tumour-promoting and tumour-inhibiting roles in cancer development, more investigation should be conducted to carefully evaluate whether introducing a LIMK2 inhibitor in cancer patients could slow cancer progression without posing clinical harms.
Collapse
Affiliation(s)
- Zhi Xiong Chong
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
| | - Wan Yong Ho
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia.
| |
Collapse
|
6
|
Dai YW, Pan YT, Lin DF, Chen XH, Zhou X, Wang WM. Bulk anda single-cell transcriptome profiling reveals the molecular characteristics of T cell-mediated tumor killing in pancreatic cancer. Heliyon 2024; 10:e27216. [PMID: 38449660 PMCID: PMC10915414 DOI: 10.1016/j.heliyon.2024.e27216] [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: 08/25/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
Background Despite the potential of immune checkpoint blockade (ICB) as a promising treatment for Pancreatic adenocarcinoma (PAAD), there is still a need to identify specific subgroups of PAAD patients who may benefit more from ICB. T cell-mediated tumor killing (TTK) is the primary concept behind ICB. We explored subtypes according to genes correlated with the sensitivity to TKK and unraveled their underlying associations for PAAD immunotherapies. Methods Genes that control the responsiveness of T cell-induced tumor destruction (GSTTK) were examined in PAAD, focusing on their varying expression levels and association with survival results. Moreover, samples with PAAD were separated into two subsets using unsupervised clustering based on GSTTK. Variability was evident in the tumor immune microenvironment, genetic mutation, and response to immunotherapy among different groups. In the end, we developed TRGscore, an innovative scoring system, and investigated its clinical and predictive significance in determining sensitivity to immunotherapy. Results Patients with PAAD were categorized into 2 clusters based on the expression of 52 GSTTKs, which showed varying levels and prognostic relevance, revealing unique TTK patterns. Survival outcome, immune cell infiltration, immunotherapy responses, and functional enrichment are also distinguished among the two clusters. Moreover, we found the CATSPER1 gene promotes the progression of PAAD through experiments. In addition, the TRGscore effectively predicted the responses to chemotherapeutics or immunotherapy in patients with PAAD and overall survival. Conclusions TTK exerted a vital influence on the tumor immune environment in PAAD. A greater understanding of TIME characteristics was gained through the evaluation of the variations in TTK modes across different tumor types. It highlights variations in the performance of T cells in PAAD and provides direction for improved treatment approaches.
Collapse
Affiliation(s)
- Yin-wei Dai
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ya-ting Pan
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dan-feng Lin
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiao-hu Chen
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiang Zhou
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wei-ming Wang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
7
|
Gali A, Bijnsdorp IV, Piersma SR, Pham TV, Gutiérrez-Galindo E, Kühnel F, Tsolakos N, Jimenez CR, Hausser A, Alexopoulos LG. Protein kinase D drives the secretion of invasion mediators in triple-negative breast cancer cell lines. iScience 2024; 27:108958. [PMID: 38323010 PMCID: PMC10844833 DOI: 10.1016/j.isci.2024.108958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/28/2023] [Accepted: 01/15/2024] [Indexed: 02/08/2024] Open
Abstract
The protein kinase D (PKD) family members regulate the fission of cargo vesicles at the Golgi complex and play a pro-oncogenic role in triple-negative breast cancer (TNBC). Whether PKD facilitates the secretion of tumor-promoting factors in TNBC, however, is still unknown. Using the pharmacological inhibition of PKD activity and siRNA-mediated depletion of PKD2 and PKD3, we identified the PKD-dependent secretome of the TNBC cell lines MDA-MB-231 and MDA-MB-468. Mass spectrometry-based proteomics and antibody-based assays revealed a significant downregulation of extracellular matrix related proteins and pro-invasive factors such as LIF, MMP-1, MMP-13, IL-11, M-CSF and GM-CSF in PKD-perturbed cells. Notably, secretion of these proteins in MDA-MB-231 cells was predominantly controlled by PKD2 and enhanced spheroid invasion. Consistently, PKD-dependent secretion of pro-invasive factors was more pronounced in metastatic TNBC cell lines. Our study thus uncovers a novel role of PKD2 in releasing a pro-invasive secretome.
Collapse
Affiliation(s)
- Alexia Gali
- Biomedical Systems Laboratory, National Technical University of Athens, 15780 Athens, Greece
- Protavio Ltd, Demokritos Science Park, 15341 Athens, Greece
| | - Irene V. Bijnsdorp
- Department of Urology, Cancer Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, de Boelelaan 1117, Amsterdam 1081 HV, the Netherlands
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, OncoProteomics Laboratory, de Boelelaan 1117, , Amsterdam 1081 HV, the Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, OncoProteomics Laboratory, de Boelelaan 1117, , Amsterdam 1081 HV, the Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, OncoProteomics Laboratory, de Boelelaan 1117, , Amsterdam 1081 HV, the Netherlands
| | | | - Fiona Kühnel
- Institute of Cell Biology and Immunology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Nikos Tsolakos
- Protavio Ltd, Demokritos Science Park, 15341 Athens, Greece
| | - Connie R. Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, OncoProteomics Laboratory, de Boelelaan 1117, , Amsterdam 1081 HV, the Netherlands
| | - Angelika Hausser
- Institute of Cell Biology and Immunology, University of Stuttgart, 70569 Stuttgart, Germany
- Stuttgart Research Center for Systems Biology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Leonidas G. Alexopoulos
- Biomedical Systems Laboratory, National Technical University of Athens, 15780 Athens, Greece
- Protavio Ltd, Demokritos Science Park, 15341 Athens, Greece
| |
Collapse
|
8
|
Lin R, Gu JG, Wang ZF, Zeng XX, Xiao HW, Chen JC, He J. Mechanism of action of Shaoyao-Gancao decoction in relieving chronic inflammatory pain via Sema3G protein regulation in the dorsal root ganglion. Heliyon 2024; 10:e23617. [PMID: 38192809 PMCID: PMC10772129 DOI: 10.1016/j.heliyon.2023.e23617] [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: 01/06/2023] [Revised: 11/22/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Objective The purpose of this study was to analyze the impact of Shaoyao-Gancao decoction (SGD) on proteins with significant changes in the dorsal root ganglion (DRG) in rats and to explore the role of the Semaphorin 3G (Sema3G) protein in the DRG and its downstream factors, interleukin-6 (IL-6) and CC-motif chemokine ligand 2(CCL2), in the treatment of chronic inflammatory pain (CIP). Methods We created a CIP rat model using 100 μL of complete Freund's adjuvant (CFA) that was injected into the left posterior plantar of rats. Then, we administered SGD intragastrically. We tested the animals for behavioral changes and protein expression levels in DRG pre- and post-drug intervention. Results Rats in the SGD group showed significantly increased paw withdrawal threshold (PWT), paw withdrawal latency (PWL), and relative expression levels of the Sema3G protein in the DRG (all P < 0.05), while the relative mRNA expression levels of IL-6 and CCL2 in the DRG of the rats were significantly decreased (P < 0.05) when compared with the model group. Conclusion In this study, we found that Shaoyao-Gancao decoction was effective in improving the PWT and PWL of rats with CIP. It reduced CIP by upregulating the expression of Sema3G in the DRG and inhibiting the relative mRNA expression levels of IL-6 and CCL2.
Collapse
Affiliation(s)
- Rong Lin
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China
| | - Jun-Gang Gu
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China
| | - Zhi-Fu Wang
- Affiliated Rehabilitation Hospital, Fujian University of Traditional Chinese Medicine, Fuzhou, 350003, China
| | - Xiao-Xia Zeng
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China
| | - Hong-Wei Xiao
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China
| | - Jin-Cheng Chen
- Affiliated Rehabilitation Hospital, Fujian University of Traditional Chinese Medicine, Fuzhou, 350003, China
| | - Jian He
- Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China
- Zhangzhou Health Vocational College, Zhangzhou, 363000, China
| |
Collapse
|
9
|
Song B, Peng Y, Zheng Y, Zhu Y, Liu W, Wang K, Cui Z, Song B. Role of single-cell ferroptosis regulation in intercellular communication and skin cutaneous melanoma progression and immunotherapy. Cancer Immunol Immunother 2023; 72:3523-3541. [PMID: 37638981 PMCID: PMC10991472 DOI: 10.1007/s00262-023-03504-5] [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: 06/21/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND The involvement of ferroptosis in the pathogenesis and progression of various cancers has been well established. However, limited studies have investigated the role of ferroptosis-mediated tumor microenvironment (TME) in skin cutaneous melanoma (SKCM). METHODS By leveraging single-cell RNA sequencing data, the nonnegative matrix factorization (NMF) approach was employed to comprehensively characterize and identify distinct gene signatures within ferroptosis-associated TME cell clusters. Prognostic and treatment response analyses were conducted using both bulk datasets and external cancer cohort to evaluate the clinical implications of TME clusters. RESULTS This NMF-based analysis successfully delineated fibroblasts, macrophages, T cells, and B cells into multiple clusters, enabling the identification of unique gene expression patterns and the annotation of distinct TME clusters. Furthermore, pseudotime trajectories, enrichment analysis, cellular communication analysis, and gene regulatory network analysis collectively demonstrated significant intercellular communication between key TME cell clusters, thereby influencing tumor cell development through diverse mechanisms. Importantly, our bulk RNA-seq analysis revealed the prognostic significance of ferroptosis-mediated TME cell clusters in SKCM patients. Moreover, our analysis of immune checkpoint blockade highlighted the crucial role of TME cell clusters in tumor immunotherapy, facilitating the discovery of potential immunotherapeutic targets. CONCLUSIONS In conclusion, this pioneering study employing NMF-based analysis unravels the intricate cellular communication mediated by ferroptosis within the TME and its profound implications for the pathogenesis and progression of SKCM. We provide compelling evidence for the prognostic value of ferroptosis-regulated TME cell clusters in SKCM, as well as their potential as targets for immunotherapy.
Collapse
Affiliation(s)
- Binyu Song
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Chanle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Yixuan Peng
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Chanle West Road, Xi'an, 710032, Shaanxi Province, China
- School of Basic Medicine, The Fourth Military Medical University, 169 Changle West Road, Xi'an, 710032, China
| | - Yu Zheng
- Hospital for Skin Disease (Institute of Dermatology), Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
| | - Yuhan Zhu
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Chanle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Wei Liu
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Chanle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Kai Wang
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Chanle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Zhiwei Cui
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Chanle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Baoqiang Song
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Chanle West Road, Xi'an, 710032, Shaanxi Province, China.
| |
Collapse
|
10
|
Bhasin S, Dusek C, Peacock JW, Cherkasov A, Wang Y, Gleave M, Ong CJ. Dependency of Tamoxifen Sensitive and Resistant ER + Breast Cancer Cells on Semaphorin 3C (SEMA3C) for Growth. Cells 2023; 12:1715. [PMID: 37443749 PMCID: PMC10341167 DOI: 10.3390/cells12131715] [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: 05/05/2023] [Revised: 06/17/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Estrogen receptor positive (ER+) breast cancer (BCa) accounts for the highest proportion of breast cancer-related deaths. While endocrine therapy is highly effective for this subpopulation, endocrine resistance remains a major challenge and the identification of novel targets is urgently needed. Previously, we have shown that Semaphorin 3C (SEMA3C) is an autocrine growth factor that drives the growth and treatment resistance of various cancers, but its role in breast cancer progression and endocrine resistance is poorly understood. Here, we report that SEMA3C plays a role in maintaining the growth of ER+ BCa cells and is a novel, tractable therapeutic target for the treatment of ER+ BCa patients. Analyses of publicly available clinical datasets indicate that ER+ BCa patients express significantly higher levels of SEMA3C mRNA than other subtypes. Furthermore, SEMA3C mRNA expression was positively correlated with ESR1 mRNA expression. ER+ BCa cell lines (MCF7 and T47D) expressed higher levels of SEMA3C mRNA and protein than a normal mammary epithelial MCF10A cell line. ER siRNA knockdown was suppressed, while dose-dependent beta-estradiol treatment induced SEMA3C expression in both MCF7 and T47D cells, suggesting that SEMA3C is an ER-regulated gene. The stimulation of ER+ BCa cells with recombinant SEMA3C activated MAPK and AKT signaling in a dose-dependent manner. Conversely, SEMA3C silencing inhibited Estrogen Receptor (ER) expression, MAPK and AKT signaling pathways while simultaneously inducing apoptosis, as monitored by flow cytometry and Western blot analyses. SEMA3C silencing significantly inhibited the growth of ER+ BCa cells, implicating a growth dependency of ER+ BCa cells on SEMA3C. Moreover, the analysis of tamoxifen resistant (TamR) cell models (TamC3 and TamR3) showed that SEMA3C levels remain high despite treatment with tamoxifen. Tamoxifen-resistant cells remained dependent on SEMA3C for growth and survival. Treatment with B1SP Fc fusion protein, a SEMA3C pathway inhibitor, attenuated SEMA3C-induced signaling and growth across a panel of tamoxifen sensitive and resistant ER+ breast cancer cells. Furthermore, SEMA3C silencing and B1SP treatment were associated with decreased EGFR signaling in TamR cells. Here, our study implicates SEMA3C in a functional role in ER+ breast cancer signaling and growth that suggests ER+ BCa patients may benefit from SEMA3C-targeted therapy.
Collapse
Affiliation(s)
- Satyam Bhasin
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (S.B.); (C.D.); (J.W.P.); (A.C.); (Y.W.); (M.G.)
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Christopher Dusek
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (S.B.); (C.D.); (J.W.P.); (A.C.); (Y.W.); (M.G.)
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - James W. Peacock
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (S.B.); (C.D.); (J.W.P.); (A.C.); (Y.W.); (M.G.)
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (S.B.); (C.D.); (J.W.P.); (A.C.); (Y.W.); (M.G.)
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (S.B.); (C.D.); (J.W.P.); (A.C.); (Y.W.); (M.G.)
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (S.B.); (C.D.); (J.W.P.); (A.C.); (Y.W.); (M.G.)
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Christopher J. Ong
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (S.B.); (C.D.); (J.W.P.); (A.C.); (Y.W.); (M.G.)
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| |
Collapse
|
11
|
Yao J, Liang Z, Duan L, G Y, Liu J, An G. Construction of a novel immune response prediction signature to predict the efficacy of immune checkpoint inhibitors in clear cell renal cell carcinoma patients. Heliyon 2023; 9:e15925. [PMID: 37484396 PMCID: PMC10360603 DOI: 10.1016/j.heliyon.2023.e15925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 04/12/2023] [Accepted: 04/26/2023] [Indexed: 07/25/2023] Open
Abstract
Background Immune checkpoint inhibitor (ICI) treatment has enhanced survival outcomes in clear cell renal cell carcinoma (ccRCC) patients. Nevertheless, the effectiveness of immunotherapy in ccRCC patients is restricted and we intended to develop and characterize an immune response prediction signature (IRPS) to forecast the efficacy of immunotherapy. Methods RNA-seq expression profile and clinicopathologic characteristics of 539 kidney cancer and 72 patients with normal specimens, were downloaded from the Cancer Genome Atlas (TCGA) database, while the Gene Expression Omnibus (GEO) database was used as the validation set, which included 24 ccRCC samples. Utilization of the TCGA data and immune genes databases (ImmPort and the InnateDB), we explored through Weighted Gene Co-expression Network Analysis (WGCNA), along with Least Absolute Shrinkage and Selection Operator method (LASSO), and constructed an IRPS for kidney cancer patients. GSEA and CIBERSORT were performed to declare the molecular and immunologic mechanism underlying the predictive value of IRPS. The Human Protein Atlas (HPA) was deployed to verify the protein expressions of IRPS genes. Tumor immune dysfunction and exclusion (TIDE) score and immunophenoscore (IPS) were computed to determine the risk of immune escape and value the discrimination of IRPS. A ccRCC cohort with anti-PD-1 therapy was obtained as an external validation data set to verify the predictive value of IRPS. Results We constructed a 10 gene signature related to the prognosis and immune response of ccRCC patients. Considering the IRPS risk score, patients were split into high and low risk groups. Patients with high risk in the TCGA cohort tended towards advanced tumor stage and grade with poor prognosis (p < 0.001), which was validated in GEO database (p = 0.004). High-risk group tumors were related with lower PD-L1 expression, higher TMB, higher MSIsensor score, lower IPS, higher TIDE score, and enriched Treg cells, which might be the potential mechanism of immune dysfunction and exclusion. Patients in the IRPS low risk group had better PFS (HR:0.73; 95% CI: 0.54-1.0; P = 0.047). Conclusion A novel biomarker of IRPS was constructed to predict the benefit of immunotherapy, which might lead to more individualized prognoses and tailored therapy for kidney cancer patients.
Collapse
Affiliation(s)
- Jiannan Yao
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Ziwei Liang
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Ling Duan
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Yang G
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Jian Liu
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Guangyu An
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| |
Collapse
|
12
|
Dhamdhere MR, Gowda CP, Singh V, Liu Z, Carruthers N, Grant CN, Sharma A, Dovat S, Sundstrom JM, Wang HG, Spiegelman VS. IGF2BP1 regulates the cargo of extracellular vesicles and promotes neuroblastoma metastasis. Oncogene 2023; 42:1558-1571. [PMID: 36973517 PMCID: PMC10547097 DOI: 10.1038/s41388-023-02671-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/09/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
Neuroblastoma is a highly metastatic cancer, and thus is one of the leading causes of cancer-related mortalities in pediatric patients. More than 50% of NB cases exhibit 17q21-ter partial chromosomal gain, which is independently associated with poor survival, suggesting the clinical importance of genes at this locus in NB. IGF2BP1 is one such proto-oncogene located at 17q locus, and was found to be upregulated in patients with metastatic NBs. Here, utilizing multiple immunocompetent mouse models, along with our newly developed highly metastatic NB cell line, we demonstrate the role of IGF2BP1 in promoting NB metastasis. Importantly, we show the significance of small extracellular vesicles (EVs) in NB progression, and determine the pro-metastatic function of IGF2BP1 by regulating the NB-EV-protein cargo. Through unbiased proteomic analysis of EVs, we discovered two novel targets (SEMA3A and SHMT2) of IGF2BP1, and reveal the mechanism of IGF2BP1 in NB metastasis. We demonstrate that IGF2BP1 directly binds and governs the expression of SEMA3A/SHMT2 in NB cells, thereby modulating their protein levels in NB-EVs. IGF2BP1-affected levels of SEMA3A and SHMT2 in the EVs, regulate the formation of pro-metastatic microenvironment at potential metastatic organs. Finally, higher levels of SEMA3A/SHMT2 proteins in the EVs derived from NB-PDX models indicate the clinical significance of the two proteins and IGF2BP1-SEMA3A/SHMT2 axis in NB metastasis.
Collapse
Affiliation(s)
- Mayura R Dhamdhere
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Chethana P Gowda
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Vikash Singh
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Zhenqiu Liu
- Department of Public Health Sciences, The Pennsylvania State University College of Medicine, Penn State Cancer Institute, Hershey, PA, USA
| | - Nicholas Carruthers
- Bioinformatics Core, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christa N Grant
- Division of Pediatric Surgery, Department of Surgery, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Arati Sharma
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Sinisa Dovat
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jeffrey M Sundstrom
- Department of Ophthalmology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Hong-Gang Wang
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Vladimir S Spiegelman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
| |
Collapse
|
13
|
Xiao Z, Liu X, Mo Y, Chen W, Zhang S, Yu Y, Weng H. Prognosis and clinical features analysis of EMT-related signature and tumor Immune microenvironment in glioma. J Med Biochem 2023; 42:122-137. [PMID: 36819132 PMCID: PMC9920870 DOI: 10.5937/jomb0-39234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/30/2022] [Indexed: 11/02/2022] Open
Abstract
Background As the most common primary malignant intracranial tumor, glioblastoma has a poor prognosis with limited treatment options. It has a high propensity for recurrence, invasion, and poor immune prognosis due to the complex tumor microenvironment. Methods Six groups of samples from four datasets were included in this study. We used consensus ClusterPlus to establish two subgroups by the EMT-related gene. The difference in clinicopathological features, genomic characteristics, immune infiltration, treatment response and prognoses were evaluated by multiple algorithms. By using LASSO regression, multi-factor Cox analysis, stepAIC method, a prognostic risk model was constructed based on the final screened genes. Results The consensusClusterPlus analyses revealed two subtypes of glioblastoma (C1 and C2), which were characterized by different EMT-related gene expression patterns. C2 subtype with the worse prognosis had the more malignant clinical and pathology manifestations, higher Immune infiltration and tumor-associated molecular pathways scores, and poorer response to treatment. Additionally, our EMT-related genes risk prediction model can provide valuable support for clinical evaluations of glioma. Conclusions The assessment system and prediction model displayed good performance in independent prognostic risk assessment and individual patient treatment response prediction. This can help with clinical treatment decisions and the development of effective treatments.
Collapse
Affiliation(s)
- Zheng Xiao
- Southern Medical University, Zhujiang Hospital, Department of Neurosurgery, Guangzhou, China
| | - Xiaoyan Liu
- Jinan University, The First Affiliated Hospital of Jinan University, Department of Neurology, Guangzhou, China
| | - Yixiang Mo
- Southern Medical University, Zhujiang Hospital, Department of Neurosurgery, Guangzhou, China
| | - Weibo Chen
- Southern Medical University, Zhujiang Hospital, Department of Neurosurgery, Guangzhou, China
| | - Shizhong Zhang
- Southern Medical University, Zhujiang Hospital, Department of Neurosurgery, Guangzhou, China
| | - Yingwei Yu
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Huiwen Weng
- The First Affiliated Hospital of Sun Yat-sen University, Department of Oncology, Guangzhou, China
| |
Collapse
|
14
|
Shao W, Zhao H, Zhang S, Ding Q, Guo Y, Hou K, Kan Y, Deng F, Xu Q. A pan-cancer landscape of IGF2BPs and their association with prognosis, stemness and tumor immune microenvironment. Front Oncol 2023; 12:1049183. [PMID: 36686749 PMCID: PMC9846525 DOI: 10.3389/fonc.2022.1049183] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Background The human insulin-like growth factor 2 mRNA binding proteins 1-3 (IGF2BP1-3, also called IMP1-3) play essential roles in mRNA regulation, including its splicing, translocation, stability, and translation. However, knowledge regarding the involvement of IGF2BPs in tumor immunity and stemness across cancer types is still lacking. Methods In this study, we comprehensively analyzed pan-cancer multi-omic data to determine the correlation of IGF2BPs mRNA and protein expression with various cancer parameters such as mutation frequency, prognostic value, the tumor microenvironment (TME), checkpoint blockade, tumor immune infiltration, stemness and drug sensitivity. Validation of the expression of IGF2BPs in cancer samples and glioma cells were performed by quantitative real-time (qRT)-PCR, and immunofluorescence staining. Investigation of the functional role of IGF2BP3 in glioma stem cells(GSCs) were performed by sphere formation, cytotoxicity, transwell, and wound healing assays. Results We found that IGF2BP1 and 3 are either absent or expressed at very low levels in most normal tissues. However, IGF2BP1-3 can be re-expressed in a broad range of cancer types and diverse cancer cell lines, where their expression often correlates with poor prognosis. Immunofluorescence staining and qRT-PCR analyses also showed that the expression of IGF2BP2 and IGF2BP3 were higher in cancer tissues than that in adjacent normal tissues. Moreover, IGF2BPs are associated with TME and stemness in human pan-cancer. Remarkably, IGF2BP3 participated in the maintenance and self-renewal of glioma stem cell (GSCs). Knockdown of IGF2BP3 attenuated GSC and glioma cell proliferation, invasion, and migration. Conclusions Our systematic pan-cancer study confirmed the identification of IGF2BPs as therapeutic targets and highlighted the need to study their association with stemness, and the TME, which contribute to the cancer drug-discovery research. Especially, preliminary studies demonstrate the IGF2BP3 as a potential negative regulator of glioma tumorigenesis by modulating stemness.
Collapse
Affiliation(s)
- Wei Shao
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Hui Zhao
- The Department of Science and Technology, Zhengzhou Revogene Ltd, Zhengzhou, Henan, China
| | - Shoudu Zhang
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Qian Ding
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Yugang Guo
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Kaiqi Hou
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Fan Deng
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China,*Correspondence: Qian Xu, ; Fan Deng,
| | - Qian Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China,*Correspondence: Qian Xu, ; Fan Deng,
| |
Collapse
|
15
|
Wang C, Song D, Huang Q, Liu Q. Advances in SEMA3F regulation of clinically high-incidence cancers. Cancer Biomark 2023; 38:131-142. [PMID: 37599522 DOI: 10.3233/cbm-230085] [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] [Indexed: 08/22/2023]
Abstract
Cancer has become a leading cause of morbidity and mortality in recent years. Its high prevalence has had a severe impact on society. Researchers have achieved fruitful results in the causative factors, pathogenesis, treatment strategies, and cancer prevention. Semaphorin 3F (SEMA3F), a member of the signaling family, was initially reported in the literature to inhibit the growth, invasion, and metastasis of cancer cells in lung cancer. Later studies showed it has cancer-inhibiting effects in malignant tumors such as breast, colorectal, ovarian, oral squamous cell carcinoma, melanoma, and head and neck squamous carcinoma. In contrast, recent studies have reported that SEMA3F is expressed more in hepatocellular carcinoma than in normal tissue and promotes metastasis of hepatocellular carcinoma. We chose lung, breast, colorectal, and hepatocellular carcinomas with high clinical prevalence to review the roles and molecular mechanisms of SEMA3F in these four carcinomas. We concluded with an outlook on clinical interventions for patients targeting SEMA3F.
Collapse
Affiliation(s)
- Chaofeng Wang
- Guangxi Key Laboratory of Regenerative Medicine, Orthopaedic Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Dezhi Song
- Guangxi Key Laboratory of Regenerative Medicine, Orthopaedic Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Qian Huang
- Guangxi Key Laboratory of Regenerative Medicine, Orthopaedic Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Qian Liu
- Guangxi Key Laboratory of Regenerative Medicine, Orthopaedic Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| |
Collapse
|
16
|
Standing S, Tran S, Murguia-Favela L, Kovalchuk O, Bose P, Narendran A. Identification of Altered Primary Immunodeficiency-Associated Genes and Their Implications in Pediatric Cancers. Cancers (Basel) 2022; 14:5942. [PMID: 36497424 PMCID: PMC9741011 DOI: 10.3390/cancers14235942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Cancer is the leading cause of disease-related mortality in children and malignancies are more frequently observed in individuals with primary immunodeficiencies (PIDs). This study aimed to identify and highlight the molecular mechanisms, such as oncogenesis and immune evasion, by which PID-related genes may lead to the development of pediatric cancers. METHOD We implemented a novel bioinformatics framework using patient data from the TARGET database and performed a comparative transcriptome analysis of PID-related genes in pediatric cancers between normal and cancer tissues, gene ontology enrichment, and protein-protein interaction analyses, and determined the prognostic impacts of commonly mutated and differentially expressed PID-related genes. RESULTS From the Fulgent Genetics Comprehensive Primary Immunodeficiency panel of 472 PID-related genes, 89 genes were significantly differentially expressed between normal and cancer tissues, and 20 genes were mutated in two or more patients. Enrichment analysis highlighted many immune system processes as well as additional pathways in the mutated PID-related genes related to oncogenesis. Survival outcomes for patients with altered PID-related genes were significantly different for 75 of the 89 DEGs, often resulting in a poorer prognosis. CONCLUSIONS Overall, multiple PID-related genes demonstrated the connection between PIDs and cancer development and should be studied further, with hopes of identifying new therapeutic targets.
Collapse
Affiliation(s)
- Shaelene Standing
- Section of Pediatric Oncology and Blood and Marrow Transplantation, Division of Pediatrics, Alberta Children’s Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Son Tran
- Section of Pediatric Oncology and Blood and Marrow Transplantation, Division of Pediatrics, Alberta Children’s Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Luis Murguia-Favela
- Section of Pediatric Hematology and Immunology, Division of Pediatrics, Alberta Children’s Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Pinaki Bose
- Departments of Oncology, Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Aru Narendran
- Section of Pediatric Oncology and Blood and Marrow Transplantation, Division of Pediatrics, Alberta Children’s Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| |
Collapse
|
17
|
Ou Z, Lin S, Qiu J, Ding W, Ren P, Chen D, Wang J, Tong Y, Wu D, Chen A, Deng Y, Cheng M, Peng T, Lu H, Yang H, Wang J, Jin X, Ma D, Xu X, Wang Y, Li J, Wu P. Single-Nucleus RNA Sequencing and Spatial Transcriptomics Reveal the Immunological Microenvironment of Cervical Squamous Cell Carcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203040. [PMID: 35986392 PMCID: PMC9561780 DOI: 10.1002/advs.202203040] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/10/2022] [Indexed: 05/07/2023]
Abstract
The effective treatment of advanced cervical cancer remains challenging. Herein, single-nucleus RNA sequencing (snRNA-seq) and SpaTial enhanced resolution omics-sequencing (Stereo-seq) are used to investigate the immunological microenvironment of cervical squamous cell carcinoma (CSCC). The expression levels of most immune suppressive genes in the tumor and inflammation areas of CSCC are not significantly higher than those in the non-cancer samples, except for LGALS9 and IDO1. Stronger signals of CD56+ NK cells and immature dendritic cells are found in the hypermetabolic tumor areas, whereas more eosinophils, immature B cells, and Treg cells are found in the hypometabolic tumor areas. Moreover, a cluster of pro-tumorigenic cancer-associated myofibroblasts (myCAFs) are identified. The myCAFs may support the growth and metastasis of tumors by inhibiting lymphocyte infiltration and remodeling of the tumor extracellular matrix. Furthermore, these myCAFs are associated with poorer survival probability in patients with CSCC, predict resistance to immunotherapy, and might be present in a small fraction (< 30%) of patients with advanced cancer. Immunohistochemistry and multiplex immunofluorescence staining are conducted to validate the spatial distribution and potential function of myCAFs. Collectively, these findings enhance the understanding of the immunological microenvironment of CSCC and shed light on the treatment of advanced CSCC.
Collapse
|
18
|
Huang A, Lv B, Zhang Y, Yang J, Li J, Li C, Yu Z, Xia J. Construction of a tumor immune infiltration macrophage signature for predicting prognosis and immunotherapy response in liver cancer. Front Mol Biosci 2022; 9:983840. [PMID: 36120553 PMCID: PMC9479109 DOI: 10.3389/fmolb.2022.983840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Liver cancer is an extraordinarily heterogeneous malignant disease. The tumor microenvironment (TME) and tumor-associated macrophages (TAMs) are the major drivers of liver cancer initiation and progression. It is critical to have a better understanding of the complicated interactions between liver cancer and the immune system for the development of cancer immunotherapy. Based on the gene expression profiles of tumor immune infiltration cells (TIICs), upregulated genes in TAMs and downregulated genes in other types of immune cells were identified as macrophage-specific genes (MSG). In this study, we combined MSG, immune subtypes, and clinical information on liver cancer to develop a tumor immune infiltration macrophage signature (TIMSig). A four-gene signature (S100A9, SLC22A15, TRIM54, and PPARGC1A) was identified as the TAM-related prognostic genes for liver cancer, independent of multiple clinicopathological parameters. Survival analyses showed that patients with low TIMSig had a superior survival rate than those with high TIMSig. Additionally, clinical immunotherapy response and TIMSig was observed as highly relevant. In addition, TIMSig could predict the response to chemotherapy. Collectively, the TIMSig could be a potential tool for risk-stratification, clinical decision making, treatment planning, and oncology immunotherapeutic drug development.
Collapse
Affiliation(s)
- Anmin Huang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Translational Medicine Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- The First Clinical Medical College, Wenzhou Medical University, Wenzhou, China
| | - Bei Lv
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yunjie Zhang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Translational Medicine Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- The First Clinical Medical College, Wenzhou Medical University, Wenzhou, China
| | - Junhui Yang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Translational Medicine Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- The First Clinical Medical College, Wenzhou Medical University, Wenzhou, China
| | - Jie Li
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Translational Medicine Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- The First Clinical Medical College, Wenzhou Medical University, Wenzhou, China
| | - Chengjun Li
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Translational Medicine Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- The First Clinical Medical College, Wenzhou Medical University, Wenzhou, China
| | - Zhijie Yu
- Wenzhou Key Laboratory of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Zhijie Yu, ; Jinglin Xia,
| | - Jinglin Xia
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Intervention, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Zhijie Yu, ; Jinglin Xia,
| |
Collapse
|
19
|
Xie L, Wu S, He R, Li S, Lai X, Wang Z. Identification of epigenetic dysregulation gene markers and immune landscape in kidney renal clear cell carcinoma by comprehensive genomic analysis. Front Immunol 2022; 13:901662. [PMID: 36059531 PMCID: PMC9433776 DOI: 10.3389/fimmu.2022.901662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/28/2022] [Indexed: 12/24/2022] Open
Abstract
Kidney cancer is one the most lethal cancers of the urinary system, but current treatments are limited and its prognosis is poor. This study focused on kidney renal clear cell carcinoma (KIRC) and analyzed the relationship between epigenetic alterations and KIRC prognosis, and explored the prognostic significance of these findings in KIRC patients. Based on multi-omics data, differentially expressed histone-modified genes were identified using the R package limma package. Gene enhancers were detected from data in the FANTOM5 database. Gene promoters were screened using the R package ChIPseeker, and the Bumphunter in the R package CHAMP was applied to screen differentially methylated regions (DMR). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Ontology (GO) functional enrichment analysis of genes was performed using the R package clusterProfiler. We identified 51 dysregulated epigenetic protein coding genes (epi-PCGs) from 872 epi-PCGs, and categorized three molecular subtypes (C1, C2, and C3) of KIRC samples with significantly different prognosis. Notably, among the three molecular subtypes, we found a markedly differential immune features in immune checkpoints, cytokines, immune signatures, and immune cell distribution. C2 subtype had significantly lower enrichment score of IFNγ, cytotoxic score (CYT), and angiogenesis. In addition, an 8-gene signature containing 8 epi-PCGs (ETV4, SH2B3, FATE1, GRK5, MALL, HRH2, SEMA3G, and SLC10A6) was developed for predicting KIRC prognosis. Prognosis of patients with a high 8-gene signature score was significantly worse than those with a low 8-gene signature score, which was also validated by the independent validation data. The 8-gene signature had a better performance compared with previous signatures of KIRC. Overall, this study highlighted the important role of epigenetic regulation in KIRC development, and explored prognostic epi-PCGs, which may provide a guidance for exploiting further pathological mechanisms of KIRC and for developing novel drug targets.
Collapse
Affiliation(s)
- Linli Xie
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Shuang Wu
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Rong He
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Sisi Li
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xiaodan Lai
- Department of Pharmacy, No. 958 Hospital of Chinese People's Liberation Army (PLA), Chongqing, China
- *Correspondence: Xiaodan Lai, ; Zhe Wang,
| | - Zhe Wang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- *Correspondence: Xiaodan Lai, ; Zhe Wang,
| |
Collapse
|
20
|
Dai Z, Peng X, Guo Y, Shen X, Ding W, Fu J, Liang Z, Song J. Metabolic pathway-based molecular subtyping of colon cancer reveals clinical immunotherapy potential and prognosis. J Cancer Res Clin Oncol 2022; 149:2393-2416. [PMID: 35731273 DOI: 10.1007/s00432-022-04070-6] [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: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 11/28/2022]
Abstract
PURPOSE Colon cancer presents challenges to clinical diagnosis and management due to its high heterogeneity. For more efficient and convenient diagnosis and treatment of colon cancer, we are committed to characterizing the molecular features of colon cancer by pioneering a classification system based on metabolic pathways. METHODS Based on the 113 metabolic pathways and genes collected in the previous stage, we scored and filtered the metabolic pathways of each sample in the training set by ssGSEA, and obtained 16 metabolic pathways related to colon cancer recurrence. In consistent clustering of training set samples with recurrence-related metabolic pathway scores, we identified two robust molecular subtypes of colon cancer (MC1 and MC2). Furthermore, we performed multi-angle analysis on the survival differences of subtypes, metabolic characteristics, clinical characteristics, functional enrichment, immune infiltration, differences with other subtypes, stemness indices, TIDE prediction, and drug sensitivity, and finally constructed colon cancer prognostic model. RESULTS The results showed that the MC1 subtype had a poor prognosis based on higher immune activity and immune checkpoint gene expression. The MC2 subtype is associated with high metabolic activity and low expression of immune checkpoint genes and a better prognosis. The MC2 subtype was more responsive to PD-L1 immunotherapy than the MC1 subclass. However, we did not observe significant differences in tumor mutational burden between the two. CONCLUSION Two molecular subtypes of colon cancer based on metabolic pathways have distinct immune signatures. Constructing prognostic models based on subtype differential genes provides valuable reference for personalized therapy targeting unique tumor metabolic signatures.
Collapse
Affiliation(s)
- Zhujiang Dai
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Xiang Peng
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Yuegui Guo
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Xia Shen
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Wenjun Ding
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Jihong Fu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Zhonglin Liang
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China. .,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China.
| | - Jinglue Song
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China. .,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China.
| |
Collapse
|
21
|
Wu X, Song P, Wang S, Qian Z, Ying J, Gao S, Li W. A Pan-Cancer Analysis of the Oncogenic Role of WD Repeat Domain 74 in Multiple Tumors. Front Genet 2022; 13:860940. [PMID: 35559034 PMCID: PMC9086290 DOI: 10.3389/fgene.2022.860940] [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: 01/27/2022] [Accepted: 03/21/2022] [Indexed: 11/17/2022] Open
Abstract
Although emerging patient-derived samples and cellular-based evidence support the relationship between WDR74 (WD Repeat Domain 74) and carcinogenesis in multiple cancers, no systematic pan-cancer analysis is available. Our preliminary research demonstrated that WDR74 is over-expressed in lung squamous cell carcinoma (LUSC) and related with worse survival. We thus investigated the potential oncogenic roles of WDR74 across 33 tumors based on the database of TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus). WDR74 is highly expressed in most cancers and correlated with poor prognosis in several cancers (all p < 0.05). Mutation analysis demonstrated that WDR74 is frequently mutated in promoter regions of lung cancer. Moreover, we found that CD8+ T-cells and the fibroblast infiltration level increased in WDR74 over-expressed cancer cells. The GO (Gene Ontology) enrichment analysis of the WDR74 pathway revealed its participation in cellular biogenesis of the RNA metabolism and its critical role in cancer initiation and progression through the tumor cell energy metabolism. Our first pan-cancer study inferred a relatively comprehensive understanding of the oncogenic roles of WDR74 across various cancers.
Collapse
Affiliation(s)
- Xiaoxuan Wu
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peng Song
- Department of Thoracic Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shun Wang
- Beidou Academic and Research Center, Beidou Life Science, Guangzhou, China
| | - Zhirong Qian
- Beidou Academic and Research Center, Beidou Life Science, Guangzhou, China.,Guangdong Provincial Key Laboratory of Digestive Cancer Research, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.,Department of Radiation Oncology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenbin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
22
|
Semaphorin-3F/Neuropilin-2 Transcriptional Expression as a Predictive Biomarker of Occult Lymph Node Metastases in HNSCC. Cancers (Basel) 2022; 14:cancers14092259. [PMID: 35565388 PMCID: PMC9100497 DOI: 10.3390/cancers14092259] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/23/2022] [Accepted: 04/28/2022] [Indexed: 12/24/2022] Open
Abstract
The expression of the semaphorin-3F (SEMA3F) and neuropilin-2 (NRP2) is involved in the regulation of lymphangiogenesis. The present study analyzes the relationship between the transcriptional expression of the SEMA3F-NRP2 genes and the presence of occult lymph node metastases in patients with cN0 head and neck squamous cell carcinomas. We analyzed the transcriptional expression of SEMA3F and NRP2 in a cohort of 53 patients with cN0 squamous cell carcinoma treated with an elective neck dissection. Occult lymph node metastases were found in 37.7% of the patients. Patients with occult lymph node metastases (cN0/pN+) had significantly lower SEMA3F expression values than patients without lymph node involvement (cN0/pN0). Considering the expression of the SEMA3F-NRP2 genes, patients were classified into two groups according to the risk of occult nodal metastasis: Group 1 (n = 34), high SEMA3F/low NRP2 expression, with a low risk of occult nodal involvement (14.7% cN0/pN+); Group 2 (n = 19), low SEMA3F or high SEMA3F/high NRP2 expression, with a high risk of occult nodal involvement (78.9% cN0/pN+). Multivariate analysis showed that patients in Group 2 had a 26.2 higher risk of lymph node involvement than patients in Group 1. There was a significant relationship between the transcriptional expression values of the SEMA3F-NRP2 genes and the risk of occult nodal metastases.
Collapse
|
23
|
Jiang A, Wang J, Liu N, Zheng X, Li Y, Ma Y, Zheng H, Chen X, Fan C, Zhang R, Fu X, Yao Y. Integration of Single-Cell RNA Sequencing and Bulk RNA Sequencing Data to Establish and Validate a Prognostic Model for Patients With Lung Adenocarcinoma. Front Genet 2022; 13:833797. [PMID: 35154287 PMCID: PMC8829512 DOI: 10.3389/fgene.2022.833797] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/14/2022] [Indexed: 12/27/2022] Open
Abstract
Background: Lung adenocarcinoma (LUAD) remains a lethal disease worldwide, with numerous studies exploring its potential prognostic markers using traditional RNA sequencing (RNA-seq) data. However, it cannot detect the exact cellular and molecular changes in tumor cells. This study aimed to construct a prognostic model for LUAD using single-cell RNA-seq (scRNA-seq) and traditional RNA-seq data. Methods: Bulk RNA-seq data were downloaded from The Cancer Genome Atlas (TCGA) database. LUAD scRNA-seq data were acquired from Gene Expression Omnibus (GEO) database. The uniform manifold approximation and projection (UMAP) was used for dimensionality reduction and cluster identification. Weighted Gene Correlation Network Analysis (WGCNA) was utilized to identify key modules and differentially expressed genes (DEGs). The non-negative Matrix Factorization (NMF) algorithm was used to identify different subtypes based on DEGs. The Cox regression analysis was used to develop the prognostic model. The characteristics of mutation landscape, immune status, and immune checkpoint inhibitors (ICIs) related genes between different risk groups were also investigated. Results: scRNA-seq data of four samples were integrated to identify 13 clusters and 9cell types. After applying differential analysis, NK cells, bladder epithelial cells, and bronchial epithelial cells were identified as significant cell types. Overall, 329 DEGs were selected for prognostic model construction through differential analysis and WGCNA. Besides, NMF identified two clusters based on DEGs in the TCGA cohort, with distinct prognosis and immune characteristics being observed. We developed a prognostic model based on the expression levels of six DEGs. A higher risk score was significantly correlated with poor survival outcomes but was associated with a more frequent TP53 mutation rate, higher tumor mutation burden (TMB), and up-regulation of PD-L1. Two independent external validation cohorts were also adopted to verify our results, with consistent results observed in them. Conclusion: This study constructed and validated a prognostic model for LUAD by integrating 10× scRNA-seq and bulk RNA-seq data. Besides, we observed two distinct subtypes in this population, with different prognosis and immune characteristics.
Collapse
Affiliation(s)
- Aimin Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jingjing Wang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Na Liu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoqiang Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yimeng Li
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yuyan Ma
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Haoran Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xue Chen
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Chaoxin Fan
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Rui Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiao Fu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yu Yao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
24
|
Wang Z, Wei Y, An L, Wang K, Hong D, Shi Y, Zang A, Su S, Li W. SEMA3D Plays a Critical Role in Peptic Ulcer Disease-Related Carcinogenesis Induced by H. pylori Infection. Int J Gen Med 2022; 15:1239-1260. [PMID: 35173464 PMCID: PMC8841493 DOI: 10.2147/ijgm.s343635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Affiliation(s)
- Zhiyu Wang
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Baoding, Hebei Province, People’s Republic of China
| | - Yaning Wei
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Baoding, Hebei Province, People’s Republic of China
| | - lin An
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Baoding, Hebei Province, People’s Republic of China
| | - Kunjie Wang
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Baoding, Hebei Province, People’s Republic of China
| | - Dan Hong
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Baoding, Hebei Province, People’s Republic of China
| | - Yan Shi
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Baoding, Hebei Province, People’s Republic of China
| | - Aimin Zang
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Baoding, Hebei Province, People’s Republic of China
| | - Shenyong Su
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Baoding, Hebei Province, People’s Republic of China
| | - Wenwen Li
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Baoding, Hebei Province, People’s Republic of China
- Correspondence: Wenwen Li, Department of Medical Oncology, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei Province, People’s Republic of China, Email
| |
Collapse
|
25
|
A Pan-Cancer Study of KMT2 Family as Therapeutic Targets in Cancer. JOURNAL OF ONCOLOGY 2022; 2022:3982226. [PMID: 35058979 PMCID: PMC8766195 DOI: 10.1155/2022/3982226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022]
Abstract
Objective Exome sequencing studies have shown that the histone-lysine N-methyltransferase 2 (KMT2) gene is one of the most commonly mutated genes in a range of human malignancies and is linked to some of the most common and deadly solid tumors. However, the connection between this gene family's function and tumor type, immunological subtype, and molecular subtype dependency is still unknown. Methods We examine the expression patterns of the histone-lysine N-methyltransferase 2 (KMT2) gene, as well as their relationship to patient survival. We also used a pan-cancer analysis to link their function to immunological subtypes, the tumor microenvironment, and treatment sensitivity. Results Using the TCGA pan-cancer data, researchers looked at and examined KMT2 expression patterns and their links to patient survival and the tumor microenvironment in 33 cancer types. The expression of the KMT2 family changes significantly across and within cancer types, indicating significant inter- and intracancer heterogeneity. Patients' overall survival was often linked to the expression of KMT2 family members. However, the direction of the link differed depending on the KMT2 isoform and cancer type studied. Notably, in all cancer types examined, nearly all KMT2 family members were substantially linked with overall survival in patients with renal clear cell carcinoma (KIRC). Furthermore, all KMT2 genes have a strong relationship with immune infiltrate subtypes, as well as varying degrees of stromal cell infiltration and tumor cell stemness. Finally, we discovered that higher expression of KMT2s, particularly KMT2F and KMT2G, was linked to greater chemotherapeutic sensitivity in several cell lines. Conclusions The necessity to investigate each KMT2 member as a distinct entity inside each particular cancer type is highlighted by our comprehensive investigation of KMT2 gene expression and its relationship with immune infiltrates, tumor microenvironment, and cancer patient outcomes. Our research also confirmed the identification of KMT2 as a potential therapeutic target in cancer, but further laboratory testing is required.
Collapse
|
26
|
Jiang A, Chen X, Zheng H, Liu N, Ding Q, Li Y, Fan C, Fu X, Liang X, Tian T, Ruan Z, Yao Y. Lipid metabolism-related gene prognostic index (LMRGPI) reveals distinct prognosis and treatment patterns for patients with early-stage pulmonary adenocarcinoma. Int J Med Sci 2022; 19:711-728. [PMID: 35582412 PMCID: PMC9108406 DOI: 10.7150/ijms.71267] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/14/2022] [Indexed: 11/05/2022] Open
Abstract
Background: Lipid metabolism plays a pivotal role in cancer progression and metastasis. This study aimed to investigate the prognostic value of lipid metabolism-related genes (LMRGs) in early-stage lung adenocarcinoma (LUAD) and develop a lipid metabolism-related gene prognostic index (LMRGPI) to predict their overall survival (OS) and treatment response. Methods: A total of 774 early-stage LUAD patients were identified from The Cancer Genome Atlas (TCGA, 403 patients) database and Gene Expression Omnibus (GEO, 371 patients) database. The non-negative Matrix Factorization (NMF) algorithm was used to identify different population subtypes based on LMRGs. The Least Absolute Shrinkage and Selection Operator (LASSO) and multivariate Cox regression analyses were used to develop the LMRGPI, with receiver operating characteristic (ROC) curves and concordance index being used to evaluate its performance. The characteristics of mutation landscape, enriched pathways, tumor microenvironment (TME), and treatment response between different LMRGPI groups were also investigated. Results: We identified two population subtypes based on LMRGs in the TCGA-LUAD cohort, with distinct prognosis, TME, and immune status being observed. LMRGPI was developed based on the expression levels of six LMRGs, including ANGPTL4, NPAS2, SLCO1B3, ACOXL, ALOX15, and B3GALNT1. Higher LMRGPI was correlated with poor OS both in TCGA and GSE68465 cohorts. Two nomograms were established to predict the survival probability of early-stage LUAD, with higher consistencies being observed between the predicted and actual OS. Higher LMRGPI was significantly correlated with more frequent TP53 mutation, higher tumor mutation burden (TMB), and up-regulation of CD274. Besides, patients with higher LMRGPI presented unremarkable responses for gefitinib, erlotinib, cisplatin, and vinorelbine, while they tend to have a favorable response for immune checkpoint inhibitors (ICIs). The opposite results were observed in the low-LMRGPI group. Conclusions: We comprehensively investigated the prognostic value of LMRGs in early-stage LUAD. Given its good prognostic ability, LMRGPI could serve as a promising biomarker to predict the OS and treatment response of these patients.
Collapse
Affiliation(s)
- Aimin Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Xue Chen
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Haoran Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Na Liu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Qianqian Ding
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Yimeng Li
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Chaoxin Fan
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Xiao Fu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Xuan Liang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Tao Tian
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Zhiping Ruan
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Yu Yao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| |
Collapse
|
27
|
Zhang Y, Chen X, Fu Q, Wang F, Zhou X, Xiang J, He N, Hu Z, Jin X. Comprehensive analysis of pyroptosis regulators and tumor immune microenvironment in clear cell renal cell carcinoma. Cancer Cell Int 2021; 21:667. [PMID: 34906145 PMCID: PMC8670029 DOI: 10.1186/s12935-021-02384-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/30/2021] [Indexed: 01/05/2023] Open
Abstract
Background Increasing evidence has indicated that pyroptosis could regulate the tumor immune microenvironment (TIME) to affect the tumor development. As a highly immunogenic tumor, clear cell renal cell carcinoma (ccRCC) can benefit from immunotherapy, but related research on pyroptosis in the TIME of ccRCC is still deficient. Methods Available data derived from TCGA and GEO databases were analyzed to identify the different expression profiles of pyroptosis in ccRCC and normal tissues, and the correlation of pyroptosis regulators with TIME was evaluated in ccRCC. Results According to consensus clustering analysis, two differential expression levels of subtypes were identified to affect patient prognosis, and were related to histological tumor stage and grade. Immune cells were calculated by the CIBERSORT algorithm. Higher infiltrated levels of B cells naive, T cells CD4 memory resting, NK cells resting, monocytes, macrophages were observed in Cluster 1, while higher infiltrated levels of CD8+ T cells, T follicular helper cells, and Tregs were observed in Cluster 2. Gene set enrichment analysis indicated that Cluster 2 was enriched in multiple immune-related pathways, including the JAK-STAT signaling pathway. Moreover, overexpression of eight immune checkpoints was related to ccRCC development, especially in Cluster 2. As four potentially key pyroptosis regulators, AIM2, CASP5, NOD2, and GZMB were confirmed to be upregulated in ccRCC by RT-qPCR analysis and further verified by the HPA database. Further pan-cancer analysis suggested that these four pyroptosis regulators were differentially expressed and related to the TIME in multiple cancers. Conclusion The present study provided a comprehensive view of pyroptosis regulators in the TIME of ccRCC, which may provide potential value for immunotherapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02384-y.
Collapse
Affiliation(s)
- Yan Zhang
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, People's Republic of China
| | - Xianwu Chen
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, People's Republic of China
| | - Qinghe Fu
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, People's Republic of China
| | - Feifan Wang
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, People's Republic of China
| | - Xuejian Zhou
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, People's Republic of China
| | - Jiayong Xiang
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, People's Republic of China
| | - Ning He
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, People's Republic of China
| | - Zhenghui Hu
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, People's Republic of China.
| | - Xiaodong Jin
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, People's Republic of China.
| |
Collapse
|
28
|
Ren Z, Hu M, Wang Z, Ge J, Zhou X, Zhang G, Zheng H. Ferroptosis-Related Genes in Lung Adenocarcinoma: Prognostic Signature and Immune, Drug Resistance, Mutation Analysis. Front Genet 2021; 12:672904. [PMID: 34434214 PMCID: PMC8381737 DOI: 10.3389/fgene.2021.672904] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/20/2021] [Indexed: 12/25/2022] Open
Abstract
It is reported that ferroptosis has close relation with tumorigenesis and drug resistance. However, the clinical significance of ferroptosis in lung adenocarcinoma (LUAD) remains elusive, and the potential targets for ferroptosis-based treatment are limited. In this study, we constructed a 15-gene prognostic signature predicting overall survival based on ferroptosis-related genes (ferroptosis driver genes VDAC2, GLS2, FLT3, TLR4, PHKG2, phosphogluconate dehydrogenase (PGD), PANX1, KRAS, PEBP1, ALOX15, and ALOX12B, and suppressor genes ACSL3, CISD1, FANCD2, and SLC3A2) in The Cancer Genome Atlas (TCGA)-LUAD cohort. The signature’s predictive ability was validated in the GSE68465 and GSE72094 cohorts by survival analysis and independent prognostic analysis with clinical features. Nomograms were provided for clinical reference. Functional analysis revealed that ferroptosis was closely related to cell cycle, cell metabolism, and immune pathways. Pan-cancer analysis comprehensively analyzed these 15 genes in 33 cancer types, indicating that the heterogeneity of 15 genes was evident across different cancer types. Besides, these genes were critical regulators modulating drug resistance, tumor microenvironment infiltration, and cancer stemness. Then, we screened 10 genes (TLR4, PHKG2, PEBP1, GLS2, FLT3, ALOX15, ACSL3, CISD1, FANCD2, and SLC3A2) as potential targets for further research because their biological functions in ferroptosis were consistent with their prognostic significance. Somatic mutation and copy number variation analysis revealed that the alteration rates of KRAS, PGD, and ALOX15 were more than 1% and significantly associated with overall survival in LUAD. Moreover, the expression of KRAS and PGD was positively related to tumor mutation burden, indicating that KRAS and PGD could serve as novel biomarkers for predicting immunotherapy response rate. Our study identified and validated a ferroptosis-related gene signature for LUAD, provided a 10-gene set for future research, and screened KRAS and PGD as potential novel immunotherapy biomarkers.
Collapse
Affiliation(s)
- Ziyuan Ren
- Basic Medical School, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Minghui Hu
- Clinical Lab, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhonglin Wang
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States
| | - Junpeng Ge
- Department of Biology Engineering, Shandong Jianzhu University, Jinan, China
| | - Xiaoyan Zhou
- Clinical Lab, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Guoming Zhang
- Basic Medical School, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hongying Zheng
- Clinical Lab, The Affiliated Hospital of Qingdao University, Qingdao, China
| |
Collapse
|
29
|
Chen H, Yang J, Wu W. Seven key hub genes identified by gene co-expression network in cutaneous squamous cell carcinoma. BMC Cancer 2021; 21:852. [PMID: 34301206 PMCID: PMC8306372 DOI: 10.1186/s12885-021-08604-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 07/16/2021] [Indexed: 11/10/2022] Open
Abstract
Background Cutaneous squamous cell carcinoma (cSCC) often follows actinic keratosis (AK) and is the second most common skin cancer worldwide. To reduce metastasis risk, it is important to diagnose and treat cSCC early. This study aimed to identify hub genes associated with cSCC and AK. Methods This study used three datasets GSE45216, GSE98774, and GSE108008. We combined samples from the GSE45216 and GSE98774 datasets into the new dataset GSE45216–98774. We applied a weighted gene co-expression network analysis (WGCNA) to investigate key modules and hub genes associated with cSCC and AK. We considered the hub genes found in both the GSE45216–98774 and GSE108008 datasets as validated hub genes. We tested whether the expression of hub genes could predict patient survival outcomes in other cancers using TCGA pan-cancer data. Results We identified modules most relevant to cSCC and AK. Additionally, we identified and validated seven hub genes of cSCC: GATM, ARHGEF26, PTHLH, MMP1, POU2F3, MMP10 and GATA3. We did not find validated hub genes for AK. Each hub gene was significantly associated with the survival of various cancer types. Only GATA3 was significantly associated with melanoma survival. Conclusions We applied WGCNA to find seven hub genes that play important roles in cSCC tumorigenesis. These results provide new insights that help explain the pathogenesis of cSCC. These hub genes may become biomarkers or therapeutic targets for accurate diagnosis and treatment of cSCC in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08604-y.
Collapse
Affiliation(s)
- Huizhen Chen
- School of Basic Medical Sciences, Dali University, Dali, Yunnan, 671000, People's Republic of China.,Institute of Translational Medicine for Metabolic Diseases, Dali University, Dali, Yunnan, 671000, People's Republic of China
| | - Jiankang Yang
- School of Basic Medical Sciences, Dali University, Dali, Yunnan, 671000, People's Republic of China. .,Institute of Translational Medicine for Metabolic Diseases, Dali University, Dali, Yunnan, 671000, People's Republic of China.
| | - Wenjuan Wu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650000, People's Republic of China.
| |
Collapse
|
30
|
Wang Z, Ren Z, Li R, Ge J, Zhang G, Xin Y, Qu Y. Multi-Omics Integrative Bioinformatics Analyses Reveal Long Non-coding RNA Modulates Genomic Integrity via Competing Endogenous RNA Mechanism and Serves as Novel Biomarkers for Overall Survival in Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:691540. [PMID: 34368141 PMCID: PMC8339593 DOI: 10.3389/fcell.2021.691540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/28/2021] [Indexed: 11/23/2022] Open
Abstract
Long non-coding RNA (lncRNA) plays a crucial role in modulating genome instability, immune characteristics, and cancer progression, within which genome instability was identified as a critical regulator in tumorigenesis and tumor progression. However, the existing accounts fail to detail the regulatory role of genome instability in lung adenocarcinoma (LUAD). We explored the clinical value of genome instability-related lncRNA in LUAD with multi-omics bioinformatics analysis. We extracted the key genome instability-related and LUAD-related gene modules using weighted gene co-expression network analysis (WGCNA) and established a competing endogenous RNA (ceRNA) network using four lncRNAs (LINC01224, LINC00346, TRPM2-AS, and CASC9) and seven target mRNAs (CCNF, PKMYT1, GCH1, TK1, PSAT1, ADAM33, and DDX11). We found that LINC01224 is primarily located in the cytoplasm and that LINC00346 and TRPM2-AS are primarily located in the nucleus (CASC9 unknown). We found that all 11 genes were positively related to tumor mutational burden and involve drug resistance, cancer stemness, and tumor microenvironment infiltration. Additionally, an eight-lncRNA genome instability-related lncRNA signature was established and validated, predicting the overall survival and immunotherapy outcomes in LUAD. To conclude, we discovered that sponging microRNA, genome instability-related lncRNA functions as ceRNA, modulating genomic integrity. This research provides clinical references for LUAD immunotherapy and prognosis and interprets a potential genome instability-related ceRNA regulatory network in which LINC01224-miR-485-5p/miR-29c-3p-CCNF-RRM2 and LINC01224-miR485-5p-PKMYT1-CDK1 axes were the most promising pathways. However, the potential mechanisms underlying our findings still need biological validation through in vitro and in vivo experiments.
Collapse
Affiliation(s)
- Zhonglin Wang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,School of Physical Science, University of California, Irvine, Irvine, CA, United States
| | - Ziyuan Ren
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Rui Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Junpeng Ge
- Department of Biology Engineering, Shandong Jianzhu University, Jinan, China
| | - Guoming Zhang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yaodong Xin
- School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai, China
| | - Yiqing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| |
Collapse
|
31
|
Guo X, Liang X, Wang Y, Cheng A, Zhang H, Qin C, Wang Z. Significance of Tumor Mutation Burden Combined With Immune Infiltrates in the Progression and Prognosis of Advanced Gastric Cancer. Front Genet 2021; 12:642608. [PMID: 34306002 PMCID: PMC8299211 DOI: 10.3389/fgene.2021.642608] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/17/2021] [Indexed: 12/11/2022] Open
Abstract
Gastric cancer (GC) is a serious malignant tumor with high mortality and poor prognosis. The prognosis and survival are much worse for advanced gastric cancer (AGC). Recently, immunotherapy has been widely promoted for AGC patients, and studies have shown that tumor mutation burden (TMB) is closely related to immunotherapy response. Here, RNA-seq data, matched clinical information, and MAF files were downloaded from the cancer genome atlas (TCGA)-STAD project in the TCGA database. The collation and visual analysis of mutation data were implemented by the “maftools” package in R. We calculated the TMB values for AGC patients and divided the patients into high- and low-TMB groups according to the median value of TMB. Then, the correlation between high or low TMB and clinicopathological parameters was calculated. Next, we examined the differences in gene expression patterns between the two groups by using the “limma” R package and identified the immune-related genes among the DEGs. Through univariate Cox regression analysis, 15 genes related to prognosis were obtained. Furthermore, the two hub genes (APOD and SLC22A17) were used to construct a risk model to evaluate the prognosis of AGC patients. ROC and survival curves and GEO data were used as a validation set to verify the reliability of this risk model. In addition, the correlation between TMB and tumor-infiltrating immune cells was examined. In conclusion, our results suggest that AGC patients with high TMB have a better prognosis. By testing the patient’s TMB, we could better guide immunotherapy and understand patient response to immunotherapy.
Collapse
Affiliation(s)
- Xiong Guo
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaolong Liang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yujun Wang
- Department of Pathology, Daping Hospital, Army Military Medical University, Chongqing, China
| | - Anqi Cheng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Han Zhang
- Department of Digestive Oncology, Three Gorges Hospital, Chongqing University, Chongqing, China
| | - Chuan Qin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Gastrointestinal Surgery, Three Gorges Hospital, Chongqing University, Chongqing, China
| | - Ziwei Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| |
Collapse
|
32
|
Guo X, Liang X, Wang Y, Cheng A, Zhang H, Qin C, Wang Z. Significance of Tumor Mutation Burden Combined With Immune Infiltrates in the Progression and Prognosis of Advanced Gastric Cancer. Front Genet 2021. [DOI: 10.3389/fgene.2021.642608
expr 881161437 + 993839471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Gastric cancer (GC) is a serious malignant tumor with high mortality and poor prognosis. The prognosis and survival are much worse for advanced gastric cancer (AGC). Recently, immunotherapy has been widely promoted for AGC patients, and studies have shown that tumor mutation burden (TMB) is closely related to immunotherapy response. Here, RNA-seq data, matched clinical information, and MAF files were downloaded from the cancer genome atlas (TCGA)-STAD project in the TCGA database. The collation and visual analysis of mutation data were implemented by the “maftools” package in R. We calculated the TMB values for AGC patients and divided the patients into high- and low-TMB groups according to the median value of TMB. Then, the correlation between high or low TMB and clinicopathological parameters was calculated. Next, we examined the differences in gene expression patterns between the two groups by using the “limma” R package and identified the immune-related genes among the DEGs. Through univariate Cox regression analysis, 15 genes related to prognosis were obtained. Furthermore, the two hub genes (APOD and SLC22A17) were used to construct a risk model to evaluate the prognosis of AGC patients. ROC and survival curves and GEO data were used as a validation set to verify the reliability of this risk model. In addition, the correlation between TMB and tumor-infiltrating immune cells was examined. In conclusion, our results suggest that AGC patients with high TMB have a better prognosis. By testing the patient’s TMB, we could better guide immunotherapy and understand patient response to immunotherapy.
Collapse
|
33
|
Li R, Yin YH, Ji XL, Liu X, Li JP, Qu YQ. Pan-Cancer Prognostic, Immunity, Stemness, and Anticancer Drug Sensitivity Characterization of N6-Methyladenosine RNA Modification Regulators in Human Cancers. Front Mol Biosci 2021; 8:644620. [PMID: 34150845 PMCID: PMC8211991 DOI: 10.3389/fmolb.2021.644620] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/10/2021] [Indexed: 12/12/2022] Open
Abstract
N6-methyladenosine RNA modification plays a significant role in the progression of multiple tumorigenesis. Our study identified the imperative role of m6A regulators in the tumor immune microenvironment, survival, stemness score, and anticancer drug sensitivity of pan-cancer. The Wilcox test was to identify the differential expression between 17 m6A regulators across 33 TCGA cancer types and their normal tissues from UCSC Xena GDC pan-cancer. Survival analysis of m6A-related regulators in 33 TCGA cancer types was identified using the "survival" and "survminer" package. The Spearman correlation test and Pearson correlation test were used to identify the correlation relationship between m6A regulators expression and tumor microenvironment, tumor stem cell score, and drug sensitivity of anticancer drugs. ConsensusPathDB was used for exploring m6A regulators functional enrichment. The 17 (METTL3, WTAP, METTL14, RBM15, RBM15B, VIRMA, HNRNPC, HNRNPA2B1, YTHDC1, ZC3H13, YTHDF1, YTHDC2, YTHDF2, IGF2BP3, IGF2BP1, FTO, and ALKBH5) m6A regulators were differentially expressed in 18 TCGA cancer types and adjacent normal tissues. Correlation analysis indicated that the relationship between the expression of 17 m6A regulators and tumor microenvironment indicated that the higher expression of m6A regulators, the higher the degree of tumor stem cells. The anticancer drug sensitivity analysis indicated that ZC3H13 expression had a positive relationship with anticancer drugs such as selumetinib, dabrafenib, cobimetinib, trametinib, and hypothemycin (p < 0.001). YTHDF2 expression was significantly negatively correlated with the anticancer drug dasatinib (p < 0.001). The pan-cancer immune subtype analysis showed that the 17 m6A regulators were significantly different in immune subtype C1 (wound healing), C3 (inflammatory), C2 (IFN-gamma dominant), C5 (immunological quiet), C4 (lymphocyte depleted), and C6 (TGF-beta dominant) (p < 0.001). Our study provides a comprehensive insight for revealing the significant role of m6A regulators in the tumor immune microenvironment, stemness score, and anticancer drug sensitivity of human cancers.
Collapse
Affiliation(s)
- Rui Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yun-Hong Yin
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xiu-Li Ji
- Department of Pulmonary Disease, Traditional Chinese Medicine Hospital of Jinan, Jinan, China
| | - Xiao Liu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jian-Ping Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yi-Qing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| |
Collapse
|
34
|
Valentini E, Di Martile M, Del Bufalo D, D'Aguanno S. SEMAPHORINS and their receptors: focus on the crosstalk between melanoma and hypoxia. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:131. [PMID: 33858502 PMCID: PMC8050914 DOI: 10.1186/s13046-021-01929-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/25/2021] [Indexed: 12/11/2022]
Abstract
Hypoxia, a condition of oxygen deprivation, is considered a hallmark of tumor microenvironment regulating several pathways and promoting cancer progression and resistance to therapy. Semaphorins, a family of about 20 secreted, transmembrane and GPI-linked glycoproteins, and their cognate receptors (plexins and neuropilins) play a pivotal role in the crosstalk between cancer and stromal cells present in the tumor microenvironment. Many studies reported that some semaphorins are involved in the development of a permissive tumor niche, guiding cell-cell communication and, consequently, the development and progression, as well as the response to therapy, of different cancer histotypes, including melanoma. In this review we will summarize the state of art of semaphorins regulation by hypoxic condition in cancer with different origin. We will also describe evidence about the ability of semaphorins to affect the expression and activity of transcription factors activated by hypoxia, such as hypoxia-inducible factor-1. Finally, we will focus our attention on findings reporting the role of semaphorins in melanocytes transformation, melanoma progression and response to therapy. Further studies are necessary to understand the mechanisms through which semaphorins induce their effect and to shed light on the possibility to use semaphorins or their cognate receptors as prognostic markers and/or therapeutic targets in melanoma or other malignancies.
Collapse
Affiliation(s)
- Elisabetta Valentini
- Preclinical Models and New Therapeutic Agents Unit, IRCCS Regina Elena National Cancer Institute, Rome, Via Chianesi 53 (00144), Rome, Italy
| | - Marta Di Martile
- Preclinical Models and New Therapeutic Agents Unit, IRCCS Regina Elena National Cancer Institute, Rome, Via Chianesi 53 (00144), Rome, Italy
| | - Donatella Del Bufalo
- Preclinical Models and New Therapeutic Agents Unit, IRCCS Regina Elena National Cancer Institute, Rome, Via Chianesi 53 (00144), Rome, Italy.
| | - Simona D'Aguanno
- Preclinical Models and New Therapeutic Agents Unit, IRCCS Regina Elena National Cancer Institute, Rome, Via Chianesi 53 (00144), Rome, Italy
| |
Collapse
|
35
|
Pancancer Analysis of Neurovascular-Related NRP Family Genes as Potential Prognostic Biomarkers of Bladder Urothelial Carcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5546612. [PMID: 33937395 PMCID: PMC8062179 DOI: 10.1155/2021/5546612] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/08/2021] [Accepted: 03/20/2021] [Indexed: 12/14/2022]
Abstract
Background Neurovascular-related genes have been implicated in the development of cancer. Studies have shown that a high expression of neuropilins (NRPs) promotes tumourigenesis and tumour malignancy. Method A multidimensional bioinformatics analysis was performed to examine the relationship between NRP genes and prognostic and pathological features, tumour mutational burden (TMB), microsatellite instability (MSI), and immunological features based on public databases and find the potential prognostic value of NRPs in pancancer. Results Survival analysis revealed that a low NRP1 expression in adrenocortical carcinoma (ACC), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), low-grade glioma (LGG), and stomach adenocarcinoma (STAD) was associated with poor prognosis. A high NRP2 expression in bladder urothelial carcinoma (BLCA), kidney renal papillary cell carcinoma (KIRP), and mesothelioma (MESO) was associated with poor prognosis. Moreover, NRP1 and NRP2 were associated with TMB and MSI. Subsequent analyses showed that NRP1 and NRP2 were correlated with immune infiltration and immune checkpoints. Genome-wide association analysis revealed that the NRP1 expression was strongly associated with kidney renal clear cell carcinoma (KIRC), whereas the NRP2 expression was closely associated with BLCA. Ultimately, NRP2 was found to be involved in the development of BLCA. Conclusions Neurovascular-related NRP family genes are significantly correlated with cancer prognosis, TME, and immune infiltration, particularly in BLCA.
Collapse
|
36
|
Mastrantonio R, You H, Tamagnone L. Semaphorins as emerging clinical biomarkers and therapeutic targets in cancer. Theranostics 2021; 11:3262-3277. [PMID: 33537086 PMCID: PMC7847692 DOI: 10.7150/thno.54023] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/06/2020] [Indexed: 12/15/2022] Open
Abstract
Semaphorins are a large family of developmental regulatory signals, characterized by aberrant expression in human cancers. These molecules crucially control cell-cell communication, cell migration, invasion and metastasis, tumor angiogenesis, inflammatory and anti-cancer immune responses. Semaphorins comprise secreted and cell surface-exposed molecules and their receptors are mainly found in the Plexin and Neuropilin families, which are further implicated in a signaling network controlling the tumor microenvironment. Accumulating evidence indicates that semaphorins may be considered as novel clinical biomarkers for cancer, especially for the prediction of patient survival and responsiveness to therapy. Moreover, preclinical experimental studies have demonstrated that targeting semaphorin signaling can interfere with tumor growth and/or metastatic dissemination, suggesting their relevance as novel therapeutic targets in cancer; this has also prompted the development of semaphorin-interfering molecules for application in the clinic. Here we will survey, in diverse human cancers, the current knowledge about the relevance of semaphorin family members, and conceptualize potential lines of future research development in this field.
Collapse
|
37
|
A Methylation-Based Reclassification of Bladder Cancer Based on Immune Cell Genes. Cancers (Basel) 2020; 12:cancers12103054. [PMID: 33092083 PMCID: PMC7593922 DOI: 10.3390/cancers12103054] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Bladder cancer (BC) development is highly related to immune cell infiltration. In this study, we aimed to construct a new classification of bladder cancer molecular subtypes based on immune-cell-associated CpG(Methylation) sites. The classification was accurate and stable. BC patients were successfully divided into three subtypes based on the immune-cell-associated CpG sites. The clinicopathologic features, distribution of immune cells, level of expression of checkpoints, stromal score, immune score, ESTIMATEScore, tumor purity, APC co_inhibition, APC co_stimulation, HLA, MHC class_I, Type I IFN_respons, Type II IFN response, and DNA stemness score (DNAss) presented significant differences among the three subgroups. The specific genomic alteration was also different across subgroups. High-level immune infiltration showed a correlation with high-level methylation. A lower RNA stemness score (RNAss) was associated with higher immune infiltration. Cluster 2 demonstrated a better response to chemotherapy. The anti-cancer targeted drug therapy results are different among the three subgroups. Abstract Background: Bladder cancer is highly related to immune cell infiltration. This study aimed to develop a new classification of BC molecular subtypes based on immune-cell-associated CpG sites. Methods: The genes of 28 types of immune cells were obtained from previous studies. Then, methylation sites corresponding to immune-cell-associated genes were acquired. Differentially methylated sites (DMSs) were identified between normal samples and bladder cancer samples. Unsupervised clustering analysis of differentially methylated sites was performed to divide the sites into several subtypes. Then, the potential mechanism of different subtypes was explored. Results: Bladder cancer patients were divided into three groups. The cluster 3 subtype had the best prognosis. Cluster 1 had the poorest prognosis. The distribution of immune cells, level of expression of checkpoints, stromal score, immune score, ESTIMATEScore, tumor purity, APC co_inhibition, APC co_stimulation, HLA, MHC class_I, Type I IFN Response, Type II IFN Response, and DNAss presented significant differences among the three subgroups. The distribution of genomic alterations was also different. Conclusions: The proposed classification was accurate and stable. BC patients could be divided into three subtypes based on the immune-cell-associated CpG sites. Specific biological signaling pathways, immune mechanisms, and genomic alterations were varied among the three subgroups. High-level immune infiltration was correlated with high-level methylation. The lower RNAss was associated with higher immune infiltration. The study of the intratumoral immune microenvironment may provide a new perspective for BC therapy.
Collapse
|
38
|
Lins MP, Medeiros NC, Carmo J, Porto FL, dos Santos Reis MD, Smaniotto S. The Responsiveness of Thymic Stromal Cells to semaphorin-3A. Immunol Invest 2020; 51:395-410. [DOI: 10.1080/08820139.2020.1834578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Marvin Paulo Lins
- Laboratory of Cell Biology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, Brazil
- Brazilian National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Návylla Candeia Medeiros
- Laboratory of Cell Biology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, Brazil
| | - Julianderson Carmo
- Laboratory of Cell Biology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, Brazil
- Brazilian National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Felipe Lima Porto
- Laboratory of Cell Biology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, Brazil
| | - Maria Danielma dos Santos Reis
- Laboratory of Cell Biology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, Brazil
- Brazilian National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Salete Smaniotto
- Laboratory of Cell Biology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, Brazil
- Brazilian National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| |
Collapse
|
39
|
Markers of Angiogenesis, Lymphangiogenesis, and Epithelial-Mesenchymal Transition (Plasticity) in CIN and Early Invasive Carcinoma of the Cervix: Exploring Putative Molecular Mechanisms Involved in Early Tumor Invasion. Int J Mol Sci 2020; 21:ijms21186515. [PMID: 32899940 PMCID: PMC7554870 DOI: 10.3390/ijms21186515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 02/01/2023] Open
Abstract
The establishment of a proangiogenic phenotype and epithelial-to-mesenchymal transition (EMT) are considered as critical events that promote the induction of invasive growth in epithelial tumors, and stimulation of lymphangiogenesis is believed to confer the capacity for early dissemination to cancer cells. Recent research has revealed substantial interdependence between these processes at the molecular level as they rely on common signaling networks. Of great interest are the molecular mechanisms of (lymph-)angiogenesis and EMT associated with the earliest stages of transition from intraepithelial development to invasive growth, as they could provide the source of potentially valuable tools for targeting tumor metastasis. However, in the case of early-stage cervical cancer, the players of (lymph-)angiogenesis and EMT processes still remain substantially uncharacterized. In this study, we used RNA sequencing to compare transcriptomes of HPV(+) preinvasive neoplastic lesions and early-stage invasive carcinoma of the cervix and to identify (lymph-)angiogenesis- and EMT-related genes and pathways that may underlie early acquisition of invasive phenotype and metastatic properties by cervical cancer cells. Second, we applied flow cytometric analysis to evaluate the expression of three key lymphangiogenesis/EMT markers (VEGFR3, MET, and SLUG) in epithelial cells derived from enzymatically treated tissue specimens. Overall, among 201 differentially expressed genes, a considerable number of (lymph-)angiogenesis and EMT regulatory factors were identified, including genes encoding cytokines, growth factor receptors, transcription factors, and adhesion molecules. Pathway analysis confirmed enrichment for angiogenesis, epithelial differentiation, and cell guidance pathways at transition from intraepithelial neoplasia to invasive carcinoma and suggested immune-regulatory/inflammatory pathways to be implicated in initiation of invasive growth of cervical cancer. Flow cytometry showed cell phenotype-specific expression pattern for VEGFR3, MET, and SLUG and revealed correlation with the amount of tumor-infiltrating lymphocytes at the early stages of cervical cancer progression. Taken together, these results extend our understanding of driving forces of angiogenesis and metastasis in HPV-associated cervical cancer and may be useful for developing new treatments.
Collapse
|
40
|
Zhang X, Shao S, Li L. Characterization of Class-3 Semaphorin Receptors, Neuropilins and Plexins, as Therapeutic Targets in a Pan-Cancer Study. Cancers (Basel) 2020; 12:cancers12071816. [PMID: 32640719 PMCID: PMC7409005 DOI: 10.3390/cancers12071816] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/03/2020] [Indexed: 12/19/2022] Open
Abstract
Class-3 semaphorins (SEMA3s), initially characterized as axon guidance cues, have been recognized as key regulators for immune responses, angiogenesis, tumorigenesis and drug responses. The functions of SEMA3s are attributed to the activation of downstream signaling cascades mainly mediated by cell surface receptors neuropilins (NRPs) and plexins (PLXNs), yet their roles in human cancers are not completely understood. Here, we provided a detailed pan-cancer analysis of NRPs and PLXNs in their expression, and association with key signal transducers, patient survival, tumor microenvironment (TME), and drug responses. The expression of NRPs and PLXNs were dysregulated in many cancer types, and the majority of them were further dysregulated in metastatic tumors, indicating a role in metastatic progression. Importantly, the expression of these genes was frequently associated with key transducers, patient survival, TME, and drug responses; however, the direction of the association varied for the particular gene queried and the specific cancer type/subtype tested. Specifically, NRP1, NRP2, PLXNA1, PLXNA3, PLXNB3, PLXNC1, and PLXND1 were primarily associated with aggressive phenotypes, whereas the rest were more associated with favorable prognosis. These data highlighted the need to study each as a separate entity in a cancer type- and subtype-dependent manner.
Collapse
Affiliation(s)
- Xiaoli Zhang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 320B Lincoln Tower, 1800 Cannon Dr., Columbus, OH 43210, USA;
- Correspondence:
| | - Shuai Shao
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43201, USA;
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 320B Lincoln Tower, 1800 Cannon Dr., Columbus, OH 43210, USA;
| |
Collapse
|
41
|
Zhang C, Mathé E, Ning X, Zhao Z, Wang K, Li L, Guo Y. The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): computational methods and applications in medical genomics. BMC Med Genomics 2020; 13:47. [PMID: 32241271 PMCID: PMC7119270 DOI: 10.1186/s12920-020-0678-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In this editorial, we briefly summarized the International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019) that was held on June 9-11, 2019 at Columbus, Ohio, USA. We further introduced the 19 research articles included in this supplement issue, covering four major areas, namely computational method development, genomics analysis, network-based analysis and biomarker prediction. The selected papers perform cutting edge computational research applied to a broad range of human diseases such as cancer, neural degenerative and chronic inflammatory disease. They also proposed solutions for fundamental medical genomics problems range from basic data processing and quality control to functional interpretation, biomarker and drug prediction, and database releasing.
Collapse
Affiliation(s)
- Chi Zhang
- Department of Medical & Molecular Genetics, School of Medicine, Indiana University, Indianapolis, IN 46202 USA
| | - Ewy Mathé
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210 USA
| | - Xia Ning
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210 USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Lang Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210 USA
| | - Yan Guo
- Department of internal medicine, comprehensive cancer center, University of New Mexico, Albuquerque, NM 87131 USA
| |
Collapse
|