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Wu X, Tang J, Cheng B. Oral squamous cell carcinoma gene patterns connected with RNA methylation for prognostic prediction. Oral Dis 2024; 30:408-421. [PMID: 35934835 DOI: 10.1111/odi.14341] [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: 05/13/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To determine whether m6A/m1A/m5C/m7G/m6Am/Ψ-related genes influence the prognosis of a patient with oral squamous cell carcinoma. MATERIALS AND METHODS We investigated the changes in regulatory genes using publicly available data from The Cancer Genome Atlas. Consensus clustering by RNA methylation-related regulators was used to describe oral squamous cell carcinomas (OSCCs). Then, we developed the prediction model. The tumor microenvironment was investigated using ESTIMATE. Gene set enrichment analysis was used to determine whether pathways or cell types were enriched in different groups. The association between the model and immune-related risk scores was investigated using correlation analysis. RESULTS We found 22 gene signatures in this analysis and then developed a predictive model that reveals the genes that are highly connected to the overall survival of OSCC patients. The survival and death rates were substantially different in the two groups (high and low risk) classified by the risk scores. The validation cohort verified the phenotypic diversity and prognostic effects of these genes. CONCLUSION Our data reveal that immune cell infiltration, genetic mutation, and survival potential in OSCC patients are linked to m6A/m1A/m5C/m7G/m6Am/Ψ-related genes, and we constructed a dependable prognostic model for OSCC patients.
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Affiliation(s)
- Xuechen Wu
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiezhang Tang
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, China
| | - Bo Cheng
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan, China
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2
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Tang H, Zhao J, Liu J. Comprehensive analysis of the expression of the IGF2BPs gene family in head and neck squamous cell carcinoma: Association with prognostic value and tumor immunity. Heliyon 2023; 9:e20659. [PMID: 37842569 PMCID: PMC10568114 DOI: 10.1016/j.heliyon.2023.e20659] [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: 07/11/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023] Open
Abstract
Background Head and neck squamous cell carcinoma (HNSCC) represents a predominant type of cancer found in the head and neck region, characterized by a high incidence and unfavorable prognosis. The IGF2BPs gene family, which belongs to the RNA-binding protein class, has been critically implicated in several cancers, and its involvement in HNSCC necessitates further exploration. Objective To explore the clinical significance and potential biological functions of the IGF2BPs gene family in HNSCC. Methods A bioinformatic methodology was employed to examine the expression profile, diagnostic and prognostic significance, and biological mechanisms of the IGF2BPs gene family in HNSCC, with a particular emphasis on its involvement in the immune function of HNSCC. This was followed by in vitro investigations to unravel the biological roles of the IGF2BPs gene family in HNSCC. Results This investigation has demonstrated that, in contrast with normal control tissue, HNSCC has a substantial elevation in the expression level of the IGF2BPs gene family. Patients with a high level of IGF2BPs gene family expression demonstrated higher prediction accuracy for HNSCC. Furthermore, patients with HNSCC and elevated IGF2BPs gene family expression levels exhibited poor survival outcomes. The IGF2BPs gene family displayed a significant association with a variety of immune infiltrating cells and immune genes in HNSCC. Studies conducted in vitro have confirmed that IGF2BP2 silencing suppressed the migration, proliferation, and invasion of HNSCC cells. Conclusions It has been determined that the IGF2BPs gene family plays a crucial part in the onset and progression of HNSCC, and its association with tumor immunity has been established. The IGF2BPs gene family holds promising potential as a diagnostic and prognostic biomarker for HNSCC.
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Affiliation(s)
- Hai Tang
- Shenzhen Stomatological Hospital, Southern Medical University, Shenzhen, 518001, China
| | - Jianjiang Zhao
- Shenzhen Stomatological Hospital, Southern Medical University, Shenzhen, 518001, China
| | - Jingpeng Liu
- Stomatological Hospital, Southern Medical University, Guangzhou, 510280, China
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3
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Causer A, Tan X, Lu X, Moseley P, Teoh SM, Molotkov N, McGrath M, Kim T, Simpson PT, Perry C, Frazer IH, Panizza B, Ladwa R, Nguyen Q, Gonzalez-Cruz JL. Deep spatial-omics analysis of Head & Neck carcinomas provides alternative therapeutic targets and rationale for treatment failure. NPJ Precis Oncol 2023; 7:89. [PMID: 37704757 PMCID: PMC10499928 DOI: 10.1038/s41698-023-00444-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
Immune checkpoint inhibitor (ICI) therapy has had limited success (<30%) in treating metastatic recurrent Head and Neck Oropharyngeal Squamous Cell Carcinomas (OPSCCs). We postulate that spatial determinants in the tumor play a critical role in cancer therapy outcomes. Here, we describe the case of a male patient diagnosed with p16+ OPSCC and extensive lung metastatic disease who failed Nivolumab and Pembrolizumab/Lenvatinib therapies. Using advanced integrative spatial proteogenomic analysis on the patient's recurrent OPSCC tumors we demonstrate that: (i) unbiased tissue clustering based on spatial transcriptomics (ST) successfully detected tumor cells and enabled the investigation of phenotypic traits such as proliferation or drug-resistance genes in the tumor's leading-edge and core; (ii) spatial proteomic imagining used in conjunction with ST (SpiCi, Spatial Proteomics inferred Cell identification) can resolve the profiling of tumor infiltrating immune cells, (iii) ST data allows for the discovery and ranking of clinically relevant alternative medicines based on their interaction with their matching ligand-receptor. Importantly, when the spatial profiles of ICI pre- and post-failure OPSCC tumors were compared, they exhibited highly similar PD-1/PD-L1low and VEGFAhigh expression, suggesting that these new tumors were not the product of ICI resistance but rather of Lenvatinib dose reduction due to complications. Our work establishes a path for incorporating spatial-omics in clinical settings to facilitate treatment personalization.
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Affiliation(s)
- Andrew Causer
- Institute of Molecular Biology, The University of Queensland, Brisbane, QLD, Australia
| | - Xiao Tan
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Xuehan Lu
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Philip Moseley
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Siok M Teoh
- Institute of Molecular Biology, The University of Queensland, Brisbane, QLD, Australia
| | - Natalie Molotkov
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Margaret McGrath
- Department of Medical Oncology, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Taehyun Kim
- Pathology Queensland, Royal Brisbane & Women's Hospital, Brisbane, QLD, Australia
| | - Peter T Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Christopher Perry
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Department of Otolaryngology-Head & Neck surgery, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Ian H Frazer
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Benedict Panizza
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Department of Otolaryngology-Head & Neck surgery, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Rahul Ladwa
- Department of Medical Oncology, Princess Alexandra Hospital, Brisbane, QLD, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Quan Nguyen
- Institute of Molecular Biology, The University of Queensland, Brisbane, QLD, Australia.
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4
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Gong Y, Bao L, Xu T, Yi X, Chen J, Wang S, Pan Z, Huang P, Ge M. The tumor ecosystem in head and neck squamous cell carcinoma and advances in ecotherapy. Mol Cancer 2023; 22:68. [PMID: 37024932 PMCID: PMC10077663 DOI: 10.1186/s12943-023-01769-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/27/2023] [Indexed: 04/08/2023] Open
Abstract
The development of head and neck squamous cell carcinoma (HNSCC) is a multi-step process, and its survival depends on a complex tumor ecosystem, which not only promotes tumor growth but also helps to protect tumor cells from immune surveillance. With the advances of existing technologies and emerging models for ecosystem research, the evidence for cell-cell interplay is increasing. Herein, we discuss the recent advances in understanding the interaction between tumor cells, the major components of the HNSCC tumor ecosystem, and summarize the mechanisms of how biological and abiotic factors affect the tumor ecosystem. In addition, we review the emerging ecological treatment strategy for HNSCC based on existing studies.
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Affiliation(s)
- Yingying Gong
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Lisha Bao
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Tong Xu
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Xiaofen Yi
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Jinming Chen
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Shanshan Wang
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Zongfu Pan
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China.
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, China.
- Clinical Research Center for Cancer of Zhejiang Province, Hangzhou, People's Republic of China.
| | - Ping Huang
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China.
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, China.
- Clinical Research Center for Cancer of Zhejiang Province, Hangzhou, People's Republic of China.
| | - Minghua Ge
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China.
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, China.
- Clinical Research Center for Cancer of Zhejiang Province, Hangzhou, People's Republic of China.
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5
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Puram SV, Mints M, Pal A, Qi Z, Reeb A, Gelev K, Barrett TF, Gerndt S, Liu P, Parikh AS, Ramadan S, Law T, Mroz EA, Rocco JW, Adkins D, Thorstad WL, Gay HA, Ding L, Paniello RC, Pipkorn P, Jackson RS, Wang X, Mazul A, Chernock R, Zevallos JP, Silva-Fisher J, Tirosh I. Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma. Nat Genet 2023; 55:640-650. [PMID: 37012457 PMCID: PMC10191634 DOI: 10.1038/s41588-023-01357-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/27/2023] [Indexed: 04/05/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) includes a subset of cancers driven by human papillomavirus (HPV). Here we use single-cell RNA-seq to profile both HPV-positive and HPV-negative oropharyngeal tumors, uncovering a high level of cellular diversity within and between tumors. First, we detect diverse chromosomal aberrations within individual tumors, suggesting genomic instability and enabling the identification of malignant cells even at pathologically negative margins. Second, we uncover diversity with respect to HNSCC subtypes and other cellular states such as the cell cycle, senescence and epithelial-mesenchymal transitions. Third, we find heterogeneity in viral gene expression within HPV-positive tumors. HPV expression is lost or repressed in a subset of cells, which are associated with a decrease in HPV-associated cell cycle phenotypes, decreased response to treatment, increased invasion and poor prognosis. These findings suggest that HPV expression diversity must be considered during diagnosis and treatment of HPV-positive tumors, with important prognostic ramifications.
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Affiliation(s)
- Sidharth V Puram
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA.
| | - Michael Mints
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Ananya Pal
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Zongtai Qi
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Ashley Reeb
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Kyla Gelev
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Thomas F Barrett
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Sophie Gerndt
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Ping Liu
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Anuraag S Parikh
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Salma Ramadan
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Travis Law
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Edmund A Mroz
- Department of Otolaryngology-Head and Neck Surgery, Ohio State University, Columbus, OH, USA
| | - James W Rocco
- Department of Otolaryngology-Head and Neck Surgery, Ohio State University, Columbus, OH, USA
| | - Doug Adkins
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Wade L Thorstad
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Hiram A Gay
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Li Ding
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Randal C Paniello
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Patrik Pipkorn
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryan S Jackson
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Xiaowei Wang
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Angela Mazul
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Rebecca Chernock
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jose P Zevallos
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Jessica Silva-Fisher
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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6
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Zhang S, Bacon W, Peppelenbosch MP, van Kemenade F, Stubbs AP. Deciphering Tumour Microenvironment of Liver Cancer through Deconvolution of Bulk RNA-Seq Data with Single-Cell Atlas. Cancers (Basel) 2022; 15:153. [PMID: 36612149 PMCID: PMC9818189 DOI: 10.3390/cancers15010153] [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: 11/11/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022] Open
Abstract
Liver cancers give rise to a heavy burden on healthcare worldwide. Understanding the tumour microenvironment (TME) underpins the development of precision therapy. Single-cell RNA sequencing (scRNA-seq) technology has generated high-quality cell atlases of the TME, but its wider application faces enormous costs for various clinical circumstances. Fortunately, a variety of deconvolution algorithms can instead repurpose bulk RNA-seq data, alleviating the need for generating scRNA-seq datasets. In this study, we reviewed major public omics databases for relevance in this study and utilised eight RNA-seqs and one microarray dataset from clinical studies. To decipher the TME of liver cancer, we estimated the fractions of liver cell components by deconvoluting the samples with Cibersortx using three reference scRNA-seq atlases. We also confirmed that Cibersortx can accurately deconvolute cell types/subtypes of interest. Compared with non-tumorous liver, liver cancers showed multiple decreased cell types forming normal liver microarchitecture, as well as elevated cell types involved in fibrogenesis, abnormal angiogenesis, and disturbed immune responses. Survival analysis shows that the fractions of five cell types/subtypes significantly correlated with patient outcomes, indicating potential therapeutic targets. Therefore, deconvolution of bulk RNA-seq data with scRNA-seq atlas references can be a useful tool to help understand the TME.
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Affiliation(s)
- Shaoshi Zhang
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Erasmus University Medical Centre, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Wendi Bacon
- School of Life, Health & Chemical Sciences, Faculty of Science, Technology, Engineering & Mathematics, The Open University, Milton Keynes MK7 6AA, UK
| | - Maikel P. Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus University Medical Centre, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Folkert van Kemenade
- School of Life, Health & Chemical Sciences, Faculty of Science, Technology, Engineering & Mathematics, The Open University, Milton Keynes MK7 6AA, UK
| | - Andrew Peter Stubbs
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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7
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Hua Y, Sun X, Luan K, Wang C. Prognostic signature related to the immune environment of oral squamous cell carcinoma. Open Life Sci 2022; 17:1135-1147. [PMID: 36185403 PMCID: PMC9482419 DOI: 10.1515/biol-2022-0467] [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: 11/30/2021] [Revised: 05/17/2022] [Accepted: 06/20/2022] [Indexed: 11/24/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) prognosis remains poor. Here we aimed to identify an effective prognostic signature for predicting the survival of patients with OSCC. Gene-expression and clinical data were obtained from the Cancer Genome Atlas database. Immune microenvironment-associated genes were identified using bioinformatics. Subtype and risk-score analyses were performed for these genes. Kaplan–Meier analysis and immune cell infiltration level were explored in different subtypes and risk-score groups. The prognostic ability, independent prognosis, and clinical features of the risk score were assessed. Furthermore, immunotherapy response based on the risk score was explored. Finally, a conjoint analysis of the subtype and risk-score groups was performed to determine the best prognostic combination. We found 11 potential prognostic genes and constructed a risk-score model. The subtype cluster 2 and a high-risk group showed the worst overall survival; differences in survival status might be due to the different immune cell infiltration levels. The risk score showed good performance, independent prognostic value, and valuable clinical application. Higher risk scores showed higher Tumor Immune Dysfunction and Exclusion scores, indicating that patients with a high-risk score were less likely to benefit from immunotherapy. Finally, conjoint analysis for the subgroups and risk groups showed the best predictive ability.
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Affiliation(s)
- Yingjie Hua
- Department of Stomatology, Affiliated Hospital of Weifang Medical University, 2428 Yuhe Road, Kuiwen District, Weifang City, Shandong Province, 261041, China
| | - Xuehui Sun
- Department of Stomatology, Affiliated Hospital of Weifang Medical University, 2428 Yuhe Road, Kuiwen District, Weifang City, Shandong Province, 261041, China
| | - Kefeng Luan
- Department of Stomatology, Affiliated Hospital of Weifang Medical University, 2428 Yuhe Road, Kuiwen District, Weifang City, Shandong Province, 261041, China
| | - Changlei Wang
- Department of Stomatology, Affiliated Hospital of Weifang Medical University, 2428 Yuhe Road, Kuiwen District, Weifang City, Shandong Province, 261041, China
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8
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Li D, Dong K, Su J, Xue H, Tian J, Wu Y, Wang J. The analysis of tumor-infiltrating immune cell and ceRNA networks in laryngeal squamous cell carcinoma. Medicine (Baltimore) 2022; 101:e29555. [PMID: 35945754 PMCID: PMC9351901 DOI: 10.1097/md.0000000000029555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Laryngeal squamous cell carcinoma (LSCC) is one of the most common forms of head and neck cancers. However, few studies have focused on the correlation between competing endogenous RNA (ceRNAs) and immune cells in LSCC. METHODS RNAseq expression of LSCC and adjacent tissues were downloaded from The Cancer Genome Atlas to establish a ceRNA network. The key gene in ceRNA was screened by the cox regression analysis to establish a prognostic risk assessment model. The CIBERSORT algorithm was then used to screen important tumor-infiltrating cells related to LSCC. Finally, co-expression analysis was applied to explore the relationship between key genes in the ceRNA network and tumor-infiltrating cells. The external datasets were used to validate critical biomarkers. RESULTS We constructed a prognostic risk assessment model of key genes in the ceRNA network. As it turned out, Kaplan-Meier survival analysis showed significant differences in overall survival rates between high-risk and low-risk groups (P < .001). The survival rate of the high-risk group was drastically lower than that of the low-risk group, and the AUC of 1 year, 3 years, and 5 years were all above 0.7. In addition, some immune infiltrating cells were also found to be related to LSCC. In the co-expression analysis, there is a negative correlation between plasma cells and TUBB3 (r = -0.33, P = .0013). External dataset validation also supports this result. CONCLUSION In this study, we found that some key genes (SLC35C1, CLDN23, HOXB7, STC2, TMEM158, TNFRSF4, TUBB3) and immune cells (plasma cells) may correspond to the prognosis of LSCC.
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Affiliation(s)
- Dan Li
- Department of Otolaryngology, The First Hospital of Hebei Medical University, Hebei ProvinceChina
| | - Kaifeng Dong
- Department of Otolaryngology, The First Hospital of Hebei Medical University, Hebei ProvinceChina
| | - Jing Su
- Department of Otolaryngology, The First Hospital of Hebei Medical University, Hebei ProvinceChina
| | - Haitao Xue
- Department of Otolaryngology, The First Hospital of Hebei Medical University, Hebei ProvinceChina
| | - Junhai Tian
- Department of Otolaryngology, The First Hospital of Hebei Medical University, Hebei ProvinceChina
| | - Yongfeng Wu
- Department of Otolaryngology, The First Hospital of Hebei Medical University, Hebei ProvinceChina
| | - Jingtian Wang
- Otorhinolaryngology Surgery, The Fourth Hospital of Hebei Medical University, Hebei ProvinceChina
- * Correspondence: Jingtian Wang, MD, Otorhinolaryngology Surgery, The Fourth Hospital of Hebei Medical University, 12 Jiankang Road, Chang’an District, Shijiazhuang, Hebei Province 050011, China (e-mail: )
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9
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Abstract
The human liver is a complex organ made up of multiple specialized cell types that carry out key physiological functions. An incomplete understanding of liver biology limits our ability to develop therapeutics to prevent chronic liver diseases, liver cancers, and death as a result of organ failure. Recently, single-cell modalities have expanded our understanding of the cellular phenotypic heterogeneity and intercellular cross-talk in liver health and disease. This review summarizes these findings and looks forward to highlighting new avenues for the application of single-cell genomics to unravel unknown pathogenic pathways and disease mechanisms for the development of new therapeutics targeting liver pathology. As these technologies mature, their integration into clinical data analysis will aid in patient stratification and in developing treatment plans for patients suffering from liver disease.
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Affiliation(s)
- Jawairia Atif
- Ajmera Transplant Centre, Schwartz Reisman Liver Research Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Medical Sciences Building, Toronto, Ontario, Canada
| | - Cornelia Thoeni
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Gary D. Bader
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Ian D. McGilvray
- Ajmera Transplant Centre, Schwartz Reisman Liver Research Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Sonya A. MacParland
- Ajmera Transplant Centre, Schwartz Reisman Liver Research Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Medical Sciences Building, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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10
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Chen Y, Feng Y, Yan F, Zhao Y, Zhao H, Guo Y. A Novel Immune-Related Gene Signature to Identify the Tumor Microenvironment and Prognose Disease Among Patients With Oral Squamous Cell Carcinoma Patients Using ssGSEA: A Bioinformatics and Biological Validation Study. Front Immunol 2022; 13:922195. [PMID: 35935989 PMCID: PMC9351622 DOI: 10.3389/fimmu.2022.922195] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/01/2022] [Indexed: 11/14/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most invasive oral malignancy in adults and is associated with a poor prognosis. Accurate prognostic models are urgently needed, however, knowledge of the probable mechanisms behind OSCC tumorigenesis and prognosis remain limited. The clinical importance of the interplay between the immune system and tumor microenvironment has become increasingly evident. This study explored immune-related alterations at the multi-omics level to extract accurate prognostic markers linked to the immune response and presents a more accurate landscape of the immune genomic map during OSCC. The Cancer Genome Atlas (TCGA) OSCC cohort (n = 329) was used to detect the immune infiltration pattern of OSCC and categorize patients into two immunity groups using single-sample gene set enrichment analysis (ssGSEA) and hierarchical clustering analysis. Multiple strategies, including lasso regression (LASSO), Cox proportional hazards regression, and principal component analysis (PCA) were used to screen clinically significant signatures and identify an incorporated prognosis model with robust discriminative power on the survival status of both the training and testing set. We identified two OSCC subtypes based on immunological characteristics: Immunity-high and immunity low, and verified that the categorization was accurate and repeatable. Immunity_ high cluster with a higher immunological and stromal score. 1047 differential genes (DEGs) integrate with immune genes to obtain 319 immue-related DEGs. A robust model with five signatures for OSCC patient prognosis was established. The GEO cohort (n = 97) were used to validate the risk model’s predictive value. The low-risk group had a better overall survival (OS) than the high-risk group. Significant prognostic potential for OSCC patients was found using ROC analysis and immune checkpoint gene expression was lower in the low-risk group. We also investigated at the therapeutic sensitivity of a number of frequently used chemotherapeutic drugs in patients with various risk factors. The underlying biological behavior of the OSCC cell line was preliminarily validated. This study characterizes a reliable marker of OSCC disease progression and provides a new potential target for immunotherapy against this disease.
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Affiliation(s)
- Yun Chen
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yunzhi Feng
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Fei Yan
- Hunan Key Laboratory of Oral Health Research, Hunan 3D Printing Engineering Research Center of Oral Care, Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, China
| | - Yaqiong Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Han Zhao
- Department of Ophthalmology, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai, China
- Laboratory of Myopia, National Health Commission (NHC) Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China
- *Correspondence: Han Zhao, ; Yue Guo,
| | - Yue Guo
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Han Zhao, ; Yue Guo,
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11
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Mullins R, Pal A, Barrett TF, Neal MEH, Puram SV. Epithelial-Mesenchymal Plasticity in Tumor Immune Evasion. Cancer Res 2022; 82:2329-2343. [PMID: 35363853 PMCID: PMC9256788 DOI: 10.1158/0008-5472.can-21-4370] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/05/2022] [Accepted: 03/29/2022] [Indexed: 01/07/2023]
Abstract
Epithelial-mesenchymal transition (EMT) is a fundamental process that occurs during embryogenesis and tissue repair. However, EMT can be hijacked by malignant cells, where it may promote immune evasion and metastasis. Classically considered a dichotomous transition, EMT in cancer has recently been considered a plastic process whereby malignant cells display and interconvert among hybrid epithelial/mesenchymal (E/M) states. Epithelial-mesenchymal plasticity (EMP) and associated hybrid E/M states are divergent from classical EMT, with unique immunomodulatory effects. Here, we review recent insights into the EMP-immune cross-talk, highlighting possible mechanisms of immune evasion conferred by hybrid E/M states and roles of immune cells in EMP.
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Affiliation(s)
- Riley Mullins
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, U.S.A.,Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri, U.S.A
| | - Ananya Pal
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, U.S.A.,Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri, U.S.A
| | - Thomas F Barrett
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, U.S.A.,Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri, U.S.A
| | - Molly E Heft Neal
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri, U.S.A
| | - Sidharth V Puram
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, U.S.A.,Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri, U.S.A.,Corresponding author: Sidharth V. Puram, MD PhD, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8115, St. Louis, MO 63110, (314) 362-7509,
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12
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Dai Y, Wang Z, Yan E, Li J, Ge H, Xiao N, Cheng J, Diao P. Development of a novel signature derived from single cell RNA-sequencing for preoperative prediction of lymph node metastasis in head and neck squamous cell carcinoma. Head Neck 2022; 44:2171-2180. [PMID: 35726502 DOI: 10.1002/hed.27126] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/11/2022] [Accepted: 06/07/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Lymph node metastasis (LNM) is considered as an adverse prognostic indicator for cancer patients. Preoperative knowledge of LNM is valuable for pretreatment decision making. Here, we sought to develop and validate an LNM signature for preoperative prediction of LNM in patients with head and neck squamous cell carcinoma (HNSCC). METHODS By studying single cell RNA-sequencing data (scRNA-seq), differentially expressed mRNA were selected and analyzed through univariate logistic regression and least absolute shrinkage and selection operator (LASSO) to identify an LNM signature. Multivariate logistic regression was utilized to establish an LNM nomogram incorporating LNM signature and T-classification. RESULTS The LNM signature was significantly associated with lymph node status and prognosis. The LNM signature and LNM nomogram displayed a robust predictive effect. CONCLUSION Our study reveals that LNM signature is a powerful biomarker for preoperative prediction of LNM in patients with HNSCC, which may be effective to realize individualized outcome prediction.
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Affiliation(s)
- Yibin Dai
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Ziyu Wang
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Jiangsu, China
| | - Enshi Yan
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Jiangsu, China
| | - Jin Li
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Jiangsu, China
| | - Han Ge
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Jiangsu, China
| | - Na Xiao
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Jiangsu, China
| | - Jie Cheng
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Jiangsu, China
| | - Pengfei Diao
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Jiangsu, China
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13
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Rozowsky JS, Meesters-Ensing JI, Lammers JAS, Belle ML, Nierkens S, Kranendonk MEG, Kester LA, Calkoen FG, van der Lugt J. A Toolkit for Profiling the Immune Landscape of Pediatric Central Nervous System Malignancies. Front Immunol 2022; 13:864423. [PMID: 35464481 PMCID: PMC9022116 DOI: 10.3389/fimmu.2022.864423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
The prognosis of pediatric central nervous system (CNS) malignancies remains dismal due to limited treatment options, resulting in high mortality rates and long-term morbidities. Immunotherapies, including checkpoint inhibition, cancer vaccines, engineered T cell therapies, and oncolytic viruses, have promising results in some hematological and solid malignancies, and are being investigated in clinical trials for various high-grade CNS malignancies. However, the role of the tumor immune microenvironment (TIME) in CNS malignancies is mostly unknown for pediatric cases. In order to successfully implement immunotherapies and to eventually predict which patients would benefit from such treatments, in-depth characterization of the TIME at diagnosis and throughout treatment is essential. In this review, we provide an overview of techniques for immune profiling of CNS malignancies, and detail how they can be utilized for different tissue types and studies. These techniques include immunohistochemistry and flow cytometry for quantifying and phenotyping the infiltrating immune cells, bulk and single-cell transcriptomics for describing the implicated immunological pathways, as well as functional assays. Finally, we aim to describe the potential benefits of evaluating other compartments of the immune system implicated by cancer therapies, such as cerebrospinal fluid and blood, and how such liquid biopsies are informative when designing immune monitoring studies. Understanding and uniformly evaluating the TIME and immune landscape of pediatric CNS malignancies will be essential to eventually integrate immunotherapy into clinical practice.
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Affiliation(s)
| | | | | | - Muriël L. Belle
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Stefan Nierkens
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | | | - Friso G. Calkoen
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
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14
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Jovic D, Liang X, Zeng H, Lin L, Xu F, Luo Y. Single-cell RNA sequencing technologies and applications: A brief overview. Clin Transl Med 2022; 12:e694. [PMID: 35352511 PMCID: PMC8964935 DOI: 10.1002/ctm2.694] [Citation(s) in RCA: 257] [Impact Index Per Article: 128.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/09/2021] [Accepted: 12/20/2021] [Indexed: 12/19/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technology has become the state-of-the-art approach for unravelling the heterogeneity and complexity of RNA transcripts within individual cells, as well as revealing the composition of different cell types and functions within highly organized tissues/organs/organisms. Since its first discovery in 2009, studies based on scRNA-seq provide massive information across different fields making exciting new discoveries in better understanding the composition and interaction of cells within humans, model animals and plants. In this review, we provide a concise overview about the scRNA-seq technology, experimental and computational procedures for transforming the biological and molecular processes into computational and statistical data. We also provide an explanation of the key technological steps in implementing the technology. We highlight a few examples on how scRNA-seq can provide unique information for better understanding health and diseases. One important application of the scRNA-seq technology is to build a better and high-resolution catalogue of cells in all living organism, commonly known as atlas, which is key resource to better understand and provide a solution in treating diseases. While great promises have been demonstrated with the technology in all areas, we further highlight a few remaining challenges to be overcome and its great potentials in transforming current protocols in disease diagnosis and treatment.
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Affiliation(s)
- Dragomirka Jovic
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesQingdaoChina
- BGI‐ShenzhenShenzhenChina
| | - Xue Liang
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesQingdaoChina
- BGI‐ShenzhenShenzhenChina
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Hua Zeng
- Nanjing University of Chinese MedicineNanjingChina
| | - Lin Lin
- Department of BiomedicineAarhus UniversityAarhusDenmark
- Steno Diabetes Center AarhusAarhus University HospitalAarhusDenmark
| | - Fengping Xu
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesQingdaoChina
- BGI‐ShenzhenShenzhenChina
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesQingdaoChina
- BGI‐ShenzhenShenzhenChina
- Department of BiomedicineAarhus UniversityAarhusDenmark
- Steno Diabetes Center AarhusAarhus University HospitalAarhusDenmark
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15
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Hu H, Liu R, Zhao C, Lu Y, Xiong Y, Chen L, Jin J, Ma Y, Su J, Yu Z, Cheng F, Ye F, Liu L, Zhao Q, Shuai J. CITEMOXMBD: A flexible single-cell multimodal omics analysis framework to reveal the heterogeneity of immune cells. RNA Biol 2022; 19:290-304. [PMID: 35130112 PMCID: PMC8824218 DOI: 10.1080/15476286.2022.2027151] [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] [Indexed: 11/27/2022] Open
Abstract
Simultaneous measurement of multiple modalities in single-cell analysis, represented by CITE-seq, is a promising approach to link transcriptional changes to cellular phenotype and function, requiring new computational methods to define cellular subtypes and states based on multiple data types. Here, we design a flexible single-cell multimodal analysis framework, called CITEMO, to integrate the transcriptome and antibody-derived tags (ADT) data to capture cell heterogeneity from the multi omics perspective. CITEMO uses Principal Component Analysis (PCA) to obtain a low-dimensional representation of the transcriptome and ADT, respectively, and then employs PCA again to integrate these low-dimensional multimodal data for downstream analysis. To investigate the effectiveness of the CITEMO framework, we apply CITEMO to analyse the cell subtypes of Cord Blood Mononuclear Cells (CBMC) samples. Results show that the CITEMO framework can comprehensively analyse single-cell multimodal samples and accurately identify cell subtypes. Besides, we find some specific immune cells that co-express multiple ADT markers. To better describe the co-expression phenomenon, we introduce the co-expression entropy to measure the heterogeneous distribution of the ADT combinations. To further validate the robustness of the CITEMO framework, we analyse Human Bone Marrow Cell (HBMC) samples and identify different states of the same cell type. CITEMO has an excellent performance in identifying cell subtypes and states for multimodal omics data. We suggest that the flexible design idea of CITEMO can be an inspiration for other single-cell multimodal tasks. The complete source code and dataset of the CITEMO framework can be obtained from https://github.com/studentiz/CITEMO.
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Affiliation(s)
- Huan Hu
- Department of Physics, And Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, and State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
- Wenzhou Institute, University of Chinese Academy of Sciences, and Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, China
| | - Ruiqi Liu
- State Key Laboratories for Agrobiotechnology, Department of Nutrition and Health, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chunlin Zhao
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuer Lu
- Department of Physics, And Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Yichun Xiong
- Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Lingling Chen
- Department of Physics, And Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Jun Jin
- Department of Physics, And Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, and State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
| | - Yunlong Ma
- Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Jianzhong Su
- Wenzhou Institute, University of Chinese Academy of Sciences, and Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, China
| | - Zhengquan Yu
- State Key Laboratories for Agrobiotechnology, Department of Nutrition and Health, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Feng Cheng
- Department of Physics, And Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Fangfu Ye
- Wenzhou Institute, University of Chinese Academy of Sciences, and Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, China
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter and Biological Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liyu Liu
- Wenzhou Institute, University of Chinese Academy of Sciences, and Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, China
- Chongqing Key Laboratory of Soft Condensed Matter Physics and Smart Materials, College of Physics, Chongqing University, Chongqing, China
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, China
| | - Jianwei Shuai
- Department of Physics, And Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, and State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
- Wenzhou Institute, University of Chinese Academy of Sciences, and Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, China
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16
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Roos K, Rooda I, Keif RS, Liivrand M, Smolander OP, Salumets A, Velthut-Meikas A. Single-cell RNA-seq analysis and cell-cluster deconvolution of the human preovulatory follicular fluid cells provide insights into the pathophysiology of ovarian hyporesponse. Front Endocrinol (Lausanne) 2022; 13:945347. [PMID: 36339426 PMCID: PMC9635625 DOI: 10.3389/fendo.2022.945347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
Reduction in responsiveness to gonadotropins or hyporesponsiveness may lead to the failure of in vitro fertilization (IVF), due to a low number of retrieved oocytes. The ovarian sensitivity index (OSI) is used to reflect the ovarian responsiveness to gonadotropin stimulation before IVF. Although introduced to clinical practice already years ago, its usefulness to predict clinical outcomes requires further research. Nevertheless, pathophysiological mechanisms of ovarian hyporesponse, along with advanced maternal age and in younger women, have not been fully elucidated. Follicles consist of multiple cell types responsible for a repertoire of biological processes including responding to pituitary gonadotropins necessary for follicle growth and oocyte maturation as well as ovulation. Encouraging evidence suggests that hyporesponse could be influenced by many contributing factors, therefore, investigating the variability of ovarian follicular cell types and their gene expression in hyporesponders is highly informative for increasing their prognosis for IVF live birth. Due to advancements in single-cell analysis technologies, the role of somatic cell populations in the development of infertility of ovarian etiology can be clarified. Here, somatic cells were collected from the fluid of preovulatory ovarian follicles of patients undergoing IVF, and RNA-seq was performed to study the associations between OSI and gene expression. We identified 12 molecular pathways differentially regulated between hypo- and normoresponder patient groups (FDR<0.05) from which extracellular matrix organization, post-translational protein phosphorylation, and regulation of Insulin-like Growth Factor (IGF) transport and uptake by IGF Binding Proteins were regulated age-independently. We then generated single-cell RNA-seq data from matching follicles revealing 14 distinct cell clusters. Using cell cluster-specific deconvolution from the bulk RNA-seq data of 18 IVF patients we integrated the datasets as a novel approach and discovered that the abundance of three cell clusters significantly varied between hypo- and normoresponder groups suggesting their role in contributing to the deviations from normal ovarian response to gonadotropin stimulation. Our work uncovers new information regarding the differences in the follicular gene expression between hypo- and normoresponders. In addition, the current study fills the gap in understanding the inter-patient variability of cell types in human preovulatory follicles, as revealed by single-cell analysis of follicular fluid cells.
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Affiliation(s)
- Kristine Roos
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- Nova Vita Clinic AS, Tallinn, Estonia
| | - Ilmatar Rooda
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Robyn-Stefany Keif
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Maria Liivrand
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Olli-Pekka Smolander
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Andres Salumets
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Agne Velthut-Meikas
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- *Correspondence: Agne Velthut-Meikas,
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17
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den bossche VV, Zaryouh H, Vara-Messler M, Vignau J, Machiels JP, Wouters A, Schmitz S, Corbet C. Microenvironment-driven intratumoral heterogeneity in head and neck cancers: clinical challenges and opportunities for precision medicine. Drug Resist Updat 2022; 60:100806. [DOI: 10.1016/j.drup.2022.100806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 02/06/2023]
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18
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Kałafut J, Czerwonka A, Anameriç A, Przybyszewska-Podstawka A, Misiorek JO, Rivero-Müller A, Nees M. Shooting at Moving and Hidden Targets-Tumour Cell Plasticity and the Notch Signalling Pathway in Head and Neck Squamous Cell Carcinomas. Cancers (Basel) 2021; 13:6219. [PMID: 34944837 PMCID: PMC8699303 DOI: 10.3390/cancers13246219] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/15/2022] Open
Abstract
Head and Neck Squamous Cell Carcinoma (HNSCC) is often aggressive, with poor response to current therapies in approximately 40-50% of the patients. Current therapies are restricted to operation and irradiation, often combined with a small number of standard-of-care chemotherapeutic drugs, preferentially for advanced tumour patients. Only very recently, newer targeted therapies have entered the clinics, including Cetuximab, which targets the EGF receptor (EGFR), and several immune checkpoint inhibitors targeting the immune receptor PD-1 and its ligand PD-L1. HNSCC tumour tissues are characterized by a high degree of intra-tumour heterogeneity (ITH), and non-genetic alterations that may affect both non-transformed cells, such as cancer-associated fibroblasts (CAFs), and transformed carcinoma cells. This very high degree of heterogeneity likely contributes to acquired drug resistance, tumour dormancy, relapse, and distant or lymph node metastasis. ITH, in turn, is likely promoted by pronounced tumour cell plasticity, which manifests in highly dynamic and reversible phenomena such as of partial or hybrid forms of epithelial-to-mesenchymal transition (EMT), and enhanced tumour stemness. Stemness and tumour cell plasticity are strongly promoted by Notch signalling, which remains poorly understood especially in HNSCC. Here, we aim to elucidate how Notch signal may act both as a tumour suppressor and proto-oncogenic, probably during different stages of tumour cell initiation and progression. Notch signalling also interacts with numerous other signalling pathways, that may also have a decisive impact on tumour cell plasticity, acquired radio/chemoresistance, and metastatic progression of HNSCC. We outline the current stage of research related to Notch signalling, and how this pathway may be intricately interconnected with other, druggable targets and signalling mechanisms in HNSCC.
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Affiliation(s)
- Joanna Kałafut
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, ul. Chodzki 1, 20-093 Lublin, Poland; (J.K.); (A.C.); (A.A.); (A.P.-P.); (A.R.-M.)
| | - Arkadiusz Czerwonka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, ul. Chodzki 1, 20-093 Lublin, Poland; (J.K.); (A.C.); (A.A.); (A.P.-P.); (A.R.-M.)
| | - Alinda Anameriç
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, ul. Chodzki 1, 20-093 Lublin, Poland; (J.K.); (A.C.); (A.A.); (A.P.-P.); (A.R.-M.)
| | - Alicja Przybyszewska-Podstawka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, ul. Chodzki 1, 20-093 Lublin, Poland; (J.K.); (A.C.); (A.A.); (A.P.-P.); (A.R.-M.)
| | - Julia O. Misiorek
- Department of Molecular Neurooncology, Institute of Bioorganic Chemistry Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznan, Poland;
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, ul. Chodzki 1, 20-093 Lublin, Poland; (J.K.); (A.C.); (A.A.); (A.P.-P.); (A.R.-M.)
| | - Matthias Nees
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, ul. Chodzki 1, 20-093 Lublin, Poland; (J.K.); (A.C.); (A.A.); (A.P.-P.); (A.R.-M.)
- Western Finland Cancer Centre (FICAN West), Institute of Biomedicine, University of Turku, 20101 Turku, Finland
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19
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Identification of Immune-Related Risk Signatures for the Prognostic Prediction in Oral Squamous Cell Carcinoma. J Immunol Res 2021; 2021:6203759. [PMID: 34497859 PMCID: PMC8420972 DOI: 10.1155/2021/6203759] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 08/02/2021] [Indexed: 11/18/2022] Open
Abstract
Background Oral squamous cell carcinoma (OSCC) is the most common type of oral cancer, which remains a major cause of morbidity and mortality in patients with head and neck cancers. However, the critical immune-related signatures and their prognostic values have rarely been investigated. Materials and Methods Gene differential analysis was used to measure the differences of gene expression between the groups. Correlation analysis was used to assess the association between the gene expression levels and immune-related risk score/DNA methylation levels. The gene set enrichment analysis (GSEA) was used to identify the pathways or cell types enriched by those identified differentially expressed genes (DEGs). Results In this study, we identified four immune-related gene signatures, including CTSG, TNFRSF4, LCORL, and PLAU, that were significantly associated with the overall survival in OSCC patients from the Cancer Genome Atlas (TCGA) OSCC cohort. Moreover, these four immune-related signatures were differentially expressed between the OSCC and nontumor tissues. The two groups (high and low risk) stratified by the immune-related risk scores had significantly different OS and mortality rates. The gene expression patterns and prognostic values of these immune-related signatures were also verified in two independent validation cohorts. Furthermore, the downregulated genes in the high-risk group (which were also upregulated in the low-risk group) were significantly enriched in the cell type-specific signatures of type 2 T helper cell (Th2), plasmacytoid dendritic cell (pDC), and memory B cell. In contrast, the upregulated genes in the high-score group were enriched in growth factor receptor-related signaling pathways, such as the VEGFA-VEGFR2 signaling pathway, PI3K-Akt signaling pathway, focal adhesion-PI3K-Akt-mTOR signaling pathway, and PDGF pathway, suggesting that those pathways were inversely correlated with immune cell infiltration. Conclusion In summary, the immune-related signatures had the potential for predicting the risk of OSCC patients. Moreover, the present study also improved our understanding of the association between the growth factor receptor pathways and immune cell infiltration in OSCC.
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Kim N, Eum HH, Lee HO. Clinical Perspectives of Single-Cell RNA Sequencing. Biomolecules 2021; 11:biom11081161. [PMID: 34439827 PMCID: PMC8394304 DOI: 10.3390/biom11081161] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/16/2022] Open
Abstract
The ability of single-cell genomics to resolve cellular heterogeneity is highly appreciated in cancer and is being exploited for precision medicine. In the recent decade, we have witnessed the incorporation of cancer genomics into the clinical decision-making process for molecular-targeted therapies. Compared with conventional genomics, which primarily focuses on the specific and sensitive detection of the molecular targets, single-cell genomics addresses intratumoral heterogeneity and the microenvironmental components impacting the treatment response and resistance. As an exploratory tool, single-cell genomics provides an unprecedented opportunity to improve the diagnosis, monitoring, and treatment of cancer. The results obtained upon employing bulk cancer genomics indicate that single-cell genomics is at an early stage with respect to exploration of clinical relevance and requires further innovations to become a widely utilized technology in the clinic.
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Affiliation(s)
- Nayoung Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (N.K.); (H.H.E.)
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
| | - Hye Hyeon Eum
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (N.K.); (H.H.E.)
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
| | - Hae-Ock Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (N.K.); (H.H.E.)
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
- Correspondence: ; Tel.: +82-2-2258-8155
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Partial EMT in head and neck cancer biology: a spectrum instead of a switch. Oncogene 2021; 40:5049-5065. [PMID: 34239045 PMCID: PMC8934590 DOI: 10.1038/s41388-021-01868-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/03/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022]
Abstract
Our understanding of epithelial-to-mesenchymal transition (EMT) has slowly evolved from a simple two state, binary model to a multi-step, dynamic continuum of epithelial-to-mesenchymal plasticity, with metastable intermediate transition states that may drive cancer metastasis. Head and neck cancer is no exception, and in this review, we use head and neck as a case study for how partial-EMT (p-EMT) cell states may play an important role in cancer progression. In particular, we summarize recent in vitro and in vivo studies that uncover these intermediate transition states, which exhibit both epithelial and mesenchymal properties and appear to have distinct advantages in migration, survival in the bloodstream, and seeding and propagation within secondary metastatic sites. We then summarize the common and distinct regulators of p-EMT as well as methodologies for identifying this unique cellular subpopulation, with a specific emphasis on the role of cutting-edge technologies, such as single cell approaches. Finally, we propose strategies to target p-EMT cells, highlighting potential opportunities for therapeutic intervention to specifically target the process of metastasis. Thus, although significant challenges remain, including numerous gaps in current knowledge, a deeper understanding of EMT plasticity and a genuine identification of EMT as spectrum rather than a switch will be critical for improving patient diagnosis and treatment across oncology.
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