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Wang S, Zhang B, Lou Z, Hu Y, Wang J, Wang J, Chen Z, Yin S. Single-cell RNA-Seq reveals the heterogeneity of fibroblasts within the tympanojugular paraganglioma microenvironment. Heliyon 2024; 10:e35478. [PMID: 39170307 PMCID: PMC11336777 DOI: 10.1016/j.heliyon.2024.e35478] [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: 07/21/2024] [Accepted: 07/29/2024] [Indexed: 08/23/2024] Open
Abstract
Tympanojugular paragangliomas (TJP) originate from the parasympathetic ganglia in the lateral base of the skull. Although the cellular composition and oncogenic mechanisms of paragangliomas have been evaluated, a comprehensive transcriptomic atlas specific to TJP remains to be established to facilitate further investigations. In this study, single-cell RNA sequencing and whole-exome sequencing were conducted on six surgically excised TJP samples to determine their cellular composition and intratumoral heterogeneity. Fibroblasts were sub-classified into two distinct groups: myofibroblasts and fibroblasts associated with bone remodeling. Additionally, an elaborate regulatory and cell-cell communication network was determined, highlighting the multifaceted role of fibroblasts, which varies depending on expression transitions. The Kit receptor (KIT) signaling pathway mediated interactions between fibroblasts and mast cells, whereas robust connections with endothelial and Schwann cell-like cells were facilitated through the platelet-derived growth factor signaling pathway. These findings establish a foundation for studying the mechanisms underlying protumor angiogenesis and the specific contributions of fibroblasts within the TJP microenvironment. IL6 signaling pathway of fibroblasts interacting with macrophages and endothelial cells may be involved in tumor regrowth. These results enhance our understanding of fibroblast functionality and provide a resource for future therapeutic targeting of TJP.
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Affiliation(s)
- Shengming Wang
- Otolaryngology Institute of Shanghai Jiao Tong University, China
- Department of Otolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Boya Zhang
- Otolaryngology Institute of Shanghai Jiao Tong University, China
- Department of Otolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zihan Lou
- Otolaryngology Institute of Shanghai Jiao Tong University, China
- Department of Otolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yibing Hu
- Otolaryngology Institute of Shanghai Jiao Tong University, China
- Department of Otolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Wang
- School of Communication Sciences and Disorders, Dalhousie University, Halifax, NS, Canada
| | - Jingjing Wang
- Otolaryngology Institute of Shanghai Jiao Tong University, China
- Department of Otolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengnong Chen
- Otolaryngology Institute of Shanghai Jiao Tong University, China
- Department of Otolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shankai Yin
- Otolaryngology Institute of Shanghai Jiao Tong University, China
- Department of Otolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Liu Z, Sun L, Peng X, Zhu J, Wu C, Zhu W, Huang C, Zhu Z. PANoptosis subtypes predict prognosis and immune efficacy in gastric cancer. Apoptosis 2024; 29:799-815. [PMID: 38347337 DOI: 10.1007/s10495-023-01931-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2023] [Indexed: 04/28/2024]
Abstract
PANoptosis is a form of inflammatory programmed cell death that is regulated by the PANoptosome. This PANoptosis possesses key characteristics of pyroptosis, apoptosis, and necroptosis, yet cannot be fully explained by any of these cell death modes. The unique nature of this cell death mechanism has garnered significant interest. However, the specific role of PANoptosis-associated features in gastric cancer (GC) is still uncertain. Patients were categorized into different PAN subtypes based on the expression of genes related to the PANoptosome. We conducted a systematic analysis to investigate the variations in prognosis and tumor microenvironment (TME) among these subtypes. Furthermore, we developed a risk score, called PANoptosis-related risk score (PANS), which is constructed from genes associated with the PANoptosis. We comprehensively analyzed the correlation between PANS and GC prognosis, TME, immunotherapy efficacy and chemotherapeutic drug sensitivity. Additionally, we performed in vitro experiments to validate the impact of Keratin 7 (KRT7) on GC. We identified two PAN subtypes (PANcluster A and B). PANoptosome genes were highly expressed in PANcluster A. PANcluster A has the characteristics of favorable prognosis, abundant infiltration of anti-tumor lymphocytes, and sensitivity to immunotherapy, thus it was categorized as an immune-inflammatory type. Meanwhile, our constructed PANS can effectively predict the prognosis and immune efficacy of GC. Patients with low PANS have a good prognosis, and have the characteristics of high tumor mutation load (TMB), high microsatellite instability (MSI), low tumor purity and sensitivity to immunotherapy. In addition, PANS can also identify suitable populations for different chemotherapy drugs. Finally, we confirmed that KRT7 is highly expressed in GC. Knocking down the expression of KRT7 significantly weakens the proliferation and migration abilities of GC cells. The models based on PANoptosis signature help to identify the TME features of GC and can effectively predict the prognosis and immune efficacy of GC. Furthermore, the experimental verification results of KRT7 provide theoretical support for anti-tumor treatment.
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Affiliation(s)
- Zitao Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Liang Sun
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Xingyu Peng
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Jinfeng Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China
- Hunan Provincial Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
| | - Changlei Wu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Wenjie Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Chao Huang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China.
| | - Zhengming Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China.
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Markowska A, Kojs Z, Twardawa D, Pietras J, Markowska J. Selected markers of ovarian cancer and their relation to targeted therapy (Review). Exp Ther Med 2024; 27:236. [PMID: 38628658 PMCID: PMC11019661 DOI: 10.3892/etm.2024.12523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024] Open
Abstract
Despite advances in surgical treatment techniques and chemotherapy-including anti-angiogenic and immune poly (ADP-ribose) polymerase inhibitors, the 5-year survival rate in ovarian cancer (OC) remains low. The reasons for this are the diagnosis of cancer in advanced clinical stages, chemoresistance and cancer recurrence. New therapeutic approaches are being developed, including the search for new biomarkers that are also targets for targeted therapy. The present review describes new molecular markers with relevance to targeted therapy, which to date have been studied only in experimental research. These include the angiogenic protein angiopoietin-2, the transmembrane glycoprotein ectonucleotide pyrophosphatase/phosphodiesterase 1, the adhesion protein E-cadherin, the TIMP metallopeptidase inhibitor 1 and Kruppel-like factor 7. Drugs affecting cancer stem cells (CSCs) in OC, such as metformin and salinomycin, as well as inhibitors of CSCs markers aldehyde dehydrogenase 1 (with the drug ATRA) and the transcription factor Nanog homeobox (microRNA) are also discussed. A new approach to prevention and possible therapies under investigation such as development of vaccines containing a subpopulation of CD117(+) and CD44(+) stem cells with a promising option for use in women with OC was described.
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Affiliation(s)
- Anna Markowska
- Department of Perinatology and Women's Diseases, Poznan University of Medical Sciences, 60-535 Poznan, Poland
| | - Zbigniew Kojs
- Department of Gynecology and Obstetrics with Gynecologic Oncology, Ludwik Rydygier Memorial Specialized Hospital, 31-826 Kraków, Poland
| | - Damian Twardawa
- Medical Department, Bausch Health Poland, 02-674 Warsaw, Poland
| | - Joanna Pietras
- Department of Perinatology and Women's Diseases, Poznan University of Medical Sciences, 60-535 Poznan, Poland
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Constantinescu DR, Sorop A, Ghionescu AV, Lixandru D, Herlea V, Bacalbasa N, Dima SO. EM-transcriptomic signature predicts drug response in advanced stages of high-grade serous ovarian carcinoma based on ascites-derived primary cultures. Front Pharmacol 2024; 15:1363142. [PMID: 38510654 PMCID: PMC10953505 DOI: 10.3389/fphar.2024.1363142] [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: 12/29/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction: High-grade serous ovarian carcinoma (HGSOC) remains a medical challenge despite considerable improvements in the treatment. Unfortunately, over 75% of patients have already metastasized at the time of diagnosis. Advances in understanding the mechanisms underlying how ascites cause chemoresistance are urgently needed to derive novel therapeutic strategies. This study aimed to identify the molecular markers involved in drug sensitivity and highlight the use of ascites as a potential model to investigate HGSOC treatment options. Methods: After conducting an in silico analysis, eight epithelial-mesenchymal (EM)-associated genes related to chemoresistance were identified. To evaluate differences in EM-associated genes in HGSOC samples, we analyzed ascites-derived HGSOC primary cell culture (AS), tumor (T), and peritoneal nodule (NP) samples. Moreover, in vitro experiments were employed to measure tumor cell proliferation and cell migration in AS, following treatment with doxorubicin (DOX) and cisplatin (CIS) and expression of these markers. Results: Our results showed that AS exhibits a mesenchymal phenotype compared to tumor and peritoneal nodule samples. Moreover, DOX and CIS treatment leads to an invasive-intermediate epithelial-to-mesenchymal transition (EMT) state of the AS by different EM-associated marker expression. For instance, the treatment of AS showed that CDH1 and GATA6 decreased after CIS exposure and increased after DOX treatment. On the contrary, the expression of KRT18 has an opposite pattern. Conclusion: Taken together, our study reports a comprehensive investigation of the EM-associated genes after drug exposure of AS. Exploring ascites and their associated cellular and soluble components is promising for understanding the HGSOC progression and treatment response at a personalized level.
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Affiliation(s)
| | - Andrei Sorop
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | | | - Daniela Lixandru
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
| | - Vlad Herlea
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
- Department of Pathology-Fundeni Clinical Institute, Bucharest, Romania
| | - Nicolae Bacalbasa
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Simona Olimpia Dima
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
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5
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Yadav S, Zhou S, He B, Du Y, Garmire LX. Deep learning and transfer learning identify breast cancer survival subtypes from single-cell imaging data. COMMUNICATIONS MEDICINE 2023; 3:187. [PMID: 38114659 PMCID: PMC10730890 DOI: 10.1038/s43856-023-00414-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/23/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Single-cell multiplex imaging data have provided new insights into disease subtypes and prognoses recently. However, quantitative models that explicitly capture single-cell resolution cell-cell interaction features to predict patient survival at a population scale are currently missing. METHODS We quantified hundreds of single-cell resolution cell-cell interaction features through neighborhood calculation, in addition to cellular phenotypes. We applied these features to a neural-network-based Cox-nnet survival model to identify survival-associated features. We used non-negative matrix factorization (NMF) to identify patient survival subtypes. We identified atypical subpopulations of triple-negative breast cancer (TNBC) patients with moderate prognosis and Luminal A patients with poor prognosis and validated these subpopulations by label transferring using the UNION-COM method. RESULTS The neural-network-based Cox-nnet survival model using all cellular phenotype and cell-cell interaction features is highly predictive of patient survival in the test data (Concordance Index > 0.8). We identify seven survival subtypes using the top survival features, presenting distinct profiles of epithelial, immune, and fibroblast cells and their interactions. We reveal atypical subpopulations of TNBC patients with moderate prognosis (marked by GATA3 over-expression) and Luminal A patients with poor prognosis (marked by KRT6 and ACTA2 over-expression and CDH1 under-expression). These atypical subpopulations are validated in TCGA-BRCA and METABRIC datasets. CONCLUSIONS This work provides an approach to bridge single-cell level information toward population-level survival prediction.
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Affiliation(s)
- Shashank Yadav
- Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, MI, 48105, USA
| | - Shu Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, MI, 48105, USA
| | - Bing He
- Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, MI, 48105, USA
| | - Yuheng Du
- Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, MI, 48105, USA
| | - Lana X Garmire
- Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, MI, 48105, USA.
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Zhang B, Chen X, Wang Z, Guo F, Zhang X, Huang B, Ma S, Xia S, Shang D. Identifying endoplasmic reticulum stress-related molecular subtypes and prognostic model for predicting the immune landscape and therapy response in pancreatic cancer. Aging (Albany NY) 2023; 15:10549-10579. [PMID: 37815881 PMCID: PMC10599750 DOI: 10.18632/aging.205094] [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: 05/26/2023] [Accepted: 09/09/2023] [Indexed: 10/12/2023]
Abstract
Endoplasmic reticulum stress (ERS) is caused by the accumulation of intracellular misfolded or unfolded proteins and is associated with cancer development. In this study, pan-cancer analysis revealed complex genetic variations, including copy number variation, methylation, and somatic mutations for ERS-related genes (ERGs) in 33 kinds of cancer. Consensus clustering divided pancreatic cancer (PC) patients from TCGA and GEO databases into two ERS-related subtypes: ERGcluster A and B. Compared with ERGcluster A, ERGcluster B had a more active ERS state and worse prognosis. Subsequently, the ERS-related prognostic model was established to quantify the ERS score for a single sample. The patient with a low ERS score had remarkably longer survival times. ssGSEA and CIBERSORT algorithms revealed that activated B cells and CD8+ T cells had higher infiltration in the low ERS score group, but higher infiltration of activated CD4+ T cells, activated dendritic cells, macrophages, and neutrophils in the high ERS score group. Drug sensitivity analysis indicated the low ERS score group had a better response to gemcitabine, paclitaxel, 5-fluorouracil, oxaliplatin, and irinotecan. RT-qPCR validated that MET, MUC16, and KRT7 in the model had higher expression levels in pancreatic tumour tissues. Single-cell analysis further revealed that MET, MUC16, and KRT7 were mainly expressed in cancer cells in PC tumour microenvironment. In all, we first constructed the ERS-related molecular subtypes and prognostic model in PC. Our research highlighted the vital role of ERS in PC and contributed to further research on molecular mechanisms and novel therapeutic strategies for PC in the future.
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Affiliation(s)
- Biao Zhang
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xu Chen
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Zhizhou Wang
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Fangyue Guo
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Xiaonan Zhang
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Bingqian Huang
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Shurong Ma
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Shilin Xia
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Dong Shang
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
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7
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Machino H, Dozen A, Konaka M, Komatsu M, Nakamura K, Ikawa N, Shozu K, Asada K, Kaneko S, Yoshida H, Kato T, Nakayama K, Saloura V, Kyo S, Hamamoto R. Integrative analysis reveals early epigenetic alterations in high-grade serous ovarian carcinomas. Exp Mol Med 2023; 55:2205-2219. [PMID: 37779141 PMCID: PMC10618212 DOI: 10.1038/s12276-023-01090-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/02/2023] [Accepted: 07/06/2023] [Indexed: 10/03/2023] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) is the most lethal gynecological malignancy. To date, the profiles of gene mutations and copy number alterations in HGSOC have been well characterized. However, the patterns of epigenetic alterations and transcription factor dysregulation in HGSOC have not yet been fully elucidated. In this study, we performed integrative omics analyses of a series of stepwise HGSOC model cells originating from human fallopian tube secretory epithelial cells (HFTSECs) to investigate early epigenetic alterations in HGSOC tumorigenesis. Assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and RNA sequencing (RNA-seq) methods were used to analyze HGSOC samples. Additionally, protein expression changes in target genes were confirmed using normal HFTSECs, serous tubal intraepithelial carcinomas (STICs), and HGSOC tissues. Transcription factor motif analysis revealed that the DNA-binding activity of the AP-1 complex and GATA family proteins was dysregulated during early tumorigenesis. The protein expression levels of JUN and FOSL2 were increased, and those of GATA6 and DAB2 were decreased in STIC lesions, which were associated with epithelial-mesenchymal transition (EMT) and proteasome downregulation. The genomic region around the FRA16D site, containing a cadherin cluster region, was epigenetically suppressed by oncogenic signaling. Proteasome inhibition caused the upregulation of chemokine genes, which may facilitate immune evasion during HGSOC tumorigenesis. Importantly, MEK inhibitor treatment reversed these oncogenic alterations, indicating its clinical effectiveness in a subgroup of patients with HGSOC. This result suggests that MEK inhibitor therapy may be an effective treatment option for chemotherapy-resistant HGSOC.
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Affiliation(s)
- Hidenori Machino
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan.
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Ai Dozen
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Obstetrics and Gynecology, Keio University School of Medicine, 35 Shinanomachi, Shinjyuku-ku, Tokyo, 160-8582, Japan
| | - Mariko Konaka
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Masaaki Komatsu
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Kohei Nakamura
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjyuku-ku, Tokyo, 160-8582, Japan
| | - Noriko Ikawa
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Kanto Shozu
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Obstetrics and Gynecology, University of Toyama, 2630 Sugitani, Toyama-shi, Toyama, 930-0152, Japan
| | - Ken Asada
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Syuzo Kaneko
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hiroshi Yoshida
- Division of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Tomoyasu Kato
- Department of Gynecology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Kentaro Nakayama
- Department of Obstetrics and Gynecology, Shimane University Faculty of Medicine, 89-1 Enyacho, Izumo-shi, Shimane, 693-8501, Japan
| | - Vassiliki Saloura
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Satoru Kyo
- Department of Obstetrics and Gynecology, Shimane University Faculty of Medicine, 89-1 Enyacho, Izumo-shi, Shimane, 693-8501, Japan
| | - Ryuji Hamamoto
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan.
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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8
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Yadav S, Zhou S, He B, Du Y, Garmire LX. Deep-learning and transfer learning identify new breast cancer survival subtypes from single-cell imaging data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.14.23295578. [PMID: 37745392 PMCID: PMC10516066 DOI: 10.1101/2023.09.14.23295578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Quantitative models that explicitly capture single-cell resolution cell-cell interaction features to predict patient survival at population scale are currently missing. Here, we computationally extracted hundreds of features describing single-cell based cell-cell interactions and cellular phenotypes from a large, published cohort of cyto-images of breast cancer patients. We applied these features to a neural-network based Cox-nnet survival model and obtained high accuracy in predicting patient survival in test data (Concordance Index > 0.8). We identified seven survival subtypes using the top survival features, which present distinct profiles of epithelial, immune, fibroblast cells, and their interactions. We identified atypical subpopulations of TNBC patients with moderate prognosis (marked by GATA3 over-expression) and Luminal A patients with poor prognosis (marked by KRT6 and ACTA2 over-expression and CDH1 under-expression). These atypical subpopulations are validated in TCGA-BRCA and METABRIC datasets. This work provides important guidelines on bridging single-cell level information towards population-level survival prediction. STATEMENT OF TRANSLATIONAL RELEVANCE Our findings from a breast cancer population cohort demonstrate the clinical utility of using the single-cell level imaging mass cytometry (IMC) data as a new type of patient prognosis prediction marker. Not only did the prognosis prediction achieve high accuracy with a Concordance index score greater than 0.8, it also enabled the discovery of seven survival subtypes that are more distinguishable than the molecular subtypes. These new subtypes present distinct profiles of epithelial, immune, fibroblast cells, and their interactions. Most importantly, this study identified and validated atypical subpopulations of TNBC patients with moderate prognosis (GATA3 over-expression) and Luminal A patients with poor prognosis (KRT6 and ACTA2 over-expression and CDH1 under-expression), using multiple large breast cancer cohorts.
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9
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Tenhami M, Polari L, Kujari H, Löyttyniemi E, Toivola DM, Voutilainen M. Keratin 7 expression in different anatomical parts of colonic epithelium in inflammatory bowel diseases and its prognostic value: a 3-year follow-up study. Sci Rep 2023; 13:11979. [PMID: 37488244 PMCID: PMC10366087 DOI: 10.1038/s41598-023-39066-w] [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: 05/04/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023] Open
Abstract
The diagnosis of inflammatory bowel diseases (IBD) may be challenging and their clinical course, characterized by relapses and spontaneous or drug-induced remissions, is difficult to predict. Novel prognostic biomarkers are needed. Keratin 7 (K7) is a cytoskeletal intermediate filament protein which is not normally expressed in the colonic epithelium. It was recently shown that K7 expression in the colonic epithelium is associated with ulcerative colitis and Crohn's disease, the two main subtypes of IBD. Here we investigated IBD associated K7 neo-expression in different regions of colon and terminal ileum. The correlation of the K7 expression with the inflammatory activity of the epithelium was analyzed in each region. The prognostic value of K7 was estimated by comparing the clinical disease activity after 3 years with the K7 expression at the time of enrollment. Our data shows that the level of K7 expression in inflamed epithelium varies depending on the anatomical region and it is the most pronounced in ascending and descending colon, but it did not predict the severity of IBD for the following 3 years. These results warrant future studies focusing on the biological role of K7 in colon and its utilization as potential IBD biomarker.
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Affiliation(s)
- Mervi Tenhami
- Division of Digestive Surgery, Turku University Hospital and University of Turku, P.O. Box 52, 20521, Turku, Finland.
| | - Lauri Polari
- Cell Biology, Biosciences, Åbo Akademi University, Turku, Finland
- InFlames Research Flagship Center, Åbo Akademi University, Turku, Finland
| | - Harry Kujari
- Department of Pathology, University of Turku and Turku University Hospital, Turku, Finland
| | - Eliisa Löyttyniemi
- Department of Biostatistics, University of Turku and Turku University Hospital, Turku, Finland
| | - Diana M Toivola
- Cell Biology, Biosciences, Åbo Akademi University, Turku, Finland
- InFlames Research Flagship Center, Åbo Akademi University, Turku, Finland
| | - Markku Voutilainen
- Department of Medicine, University of Turku and Turku University Hospital, Turku, Finland
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10
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Lei J, Xu JY, Hu M, Wu SG, Zhou J. MOB kinase activator 1A acts as an oncogene by targeting PI3K/AKT/mTOR in ovarian cancer. Discov Oncol 2023; 14:100. [PMID: 37314589 DOI: 10.1007/s12672-023-00705-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/29/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND To illuminate the precise roles of MOB Kinase Activator 1 A (MOB1A) in the development of ovarian cancer (OC). METHODS MOB1A expression and clinical data of OC were obtained from the public database on gene expression and proteomics. Meanwhile, verification of expression was carried out in Gene Expression Omnibus, the Human Protein Atlas, and OC cell lines. The prognosis of MOB1A was explored in the Kaplan-Meier plotter. RNA interference and lentivirus vectors were applied to construct knockdown and overexpressed cell models. Changes in the malignant behaviors of OC cells were detected by cholecystokinin octopeptide cell counting kit, wound healing, colony formation assay, transwell, flow cytometry assays, and in vivo experiments. Changes in proteins in the PI3K and autophagy-related makers were detected by western blot analysis. RESULTS The expression of MOB1A was significantly upregulated and accompanied by an inferior survival rate in OC. Knockdown of MOB1A inhibited the proliferation, invasion, migration, and cell cycle of OC cells, whereas induced cell autophagy. MOB1A upregulation had the opposite effects. In addition, bioinformatics analysis and western blot experiments showed that MOB1A plays an important role in the PI3K/AKT/mTOR pathway. CONCLUSIONS Our findings indicated that MOB1A is highly expressed and related to poor prognosis in OC. MOB1A plays a role in promoting the malignant biological behavior of tumor cells through PI3K/AKT/mTOR signaling pathway.
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Affiliation(s)
- Jian Lei
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361003, China
- Department of Obstetrics and Gynecology, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Jing-Ying Xu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Min Hu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - San-Gang Wu
- Department of Radiation Oncology, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361003, China.
| | - Juan Zhou
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361003, China.
- Department of Radiation Oncology, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361003, China.
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11
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Fan S, Xing J, Jiang Z, Zhang Z, Zhang H, Wang D, Tang D. Effects of Long Non-Coding RNAs Induced by the Gut Microbiome on Regulating the Development of Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14235813. [PMID: 36497293 PMCID: PMC9735521 DOI: 10.3390/cancers14235813] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 11/29/2022] Open
Abstract
Although an imbalanced gut microbiome is closely associated with colorectal cancer (CRC), how the gut microbiome affects CRC is not known. Long non-coding RNAs (lncRNAs) can affect important cellular functions such as cell division, proliferation, and apoptosis. The abnormal expression of lncRNAs can promote CRC cell growth, proliferation, and metastasis, mediating the effects of the gut microbiome on CRC. Generally, the gut microbiome regulates the lncRNAs expression, which subsequently impacts the host transcriptome to change the expression of downstream target molecules, ultimately resulting in the development and progression of CRC. We focused on the important role of the microbiome in CRC and their effects on CRC-related lncRNAs. We also reviewed the impact of the two main pathogenic bacteria, Fusobacterium nucleatum and enterotoxigenic Bacteroides fragilis, and metabolites of the gut microbiome, butyrate, and lipopolysaccharide, on lncRNAs. Finally, available therapies that target the gut microbiome and lncRNAs to prevent and treat CRC were proposed.
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Affiliation(s)
- Shiying Fan
- Clinical Medical College, Yangzhou University, Yangzhou 225000, China
| | - Juan Xing
- Clinical Medical College, Yangzhou University, Yangzhou 225000, China
| | - Zhengting Jiang
- Clinical Medical College, Yangzhou University, Yangzhou 225000, China
| | - Zhilin Zhang
- Clinical Medical College, Yangzhou University, Yangzhou 225000, China
| | - Huan Zhang
- Clinical Medical College, Yangzhou University, Yangzhou 225000, China
| | - Daorong Wang
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Northern Jiangsu People’s Hospital, Yangzhou University, Yangzhou 225000, China
| | - Dong Tang
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Northern Jiangsu People’s Hospital, Yangzhou University, Yangzhou 225000, China
- Correspondence: ; Tel.: +86-18952783556
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12
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Kielbik M, Szulc-Kielbik I, Klink M. E-Cadherin Expression in Relation to Clinicopathological Parameters and Survival of Patients with Epithelial Ovarian Cancer. Int J Mol Sci 2022; 23:ijms232214383. [PMID: 36430858 PMCID: PMC9695266 DOI: 10.3390/ijms232214383] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
It is generally accepted that loss/reduction of E-cadherin expression on tumor cells promotes their migration, invasiveness, and metastasis. It is also an indicator of cancer cells' aggressiveness. The aim of this study was to assess how the expression of E-cadherin varies in primary ovarian cancer tissue in regard to overall survival of patients; FIGO stage; grade; histopathological type of tumor; and potential factors discriminating malignant and nonmalignant ovarian tumors. Our analysis was based on literature research (1 January 2000-8 November 2021) conducted according to the PRISMA guidelines. Most studies support the assumption that loss/reduced expression of E-cadherin results in shorter overall survival of EOC patients. Moreover, most research has shown that there is a correlation between the low level of E-cadherin and the advancement stage of disease, especially in high-grade serous ovarian carcinoma type. However, E-cadherin expression seems to not be helpful to distinguish malignant and nonmalignant tumors. In conclusion, reduced E-cadherin expression in primary ovarian cancer tissue may indicate a less favorable disease outcome and is associated with high advancement of the disease.
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13
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Song J, Ruze R, Chen Y, Xu R, Yin X, Wang C, Xu Q, Zhao Y. Construction of a novel model based on cell-in-cell-related genes and validation of KRT7 as a biomarker for predicting survival and immune microenvironment in pancreatic cancer. BMC Cancer 2022; 22:894. [PMID: 35974300 PMCID: PMC9380297 DOI: 10.1186/s12885-022-09983-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/08/2022] [Indexed: 12/16/2022] Open
Abstract
Background Pancreatic cancer (PC) is a highly malignant tumor featured with high intra-tumoral heterogeneity and poor prognosis. Cell-in-cell (CIC) structures have been reported in multiple cancers, and their presence is associated with disease progression. Nonetheless, the prognostic values and biological functions of CIC-related genes in PC remain poorly understood. Methods The sequencing data, as well as corresponding clinicopathological information of PC were collected from public databases. Random forest screening, least absolute shrinkage, and selection operator (LASSO) regression and multivariate Cox regression analysis were performed to construct a prognostic model. The effectiveness and robustness of the model were evaluated using receiver operating characteristic (ROC) curves, survival analysis and establishing the nomogram model. Functional enrichment analyses were conducted to annotate the biological functions. The immune infiltration levels were evaluated by ESTIMATE and CIBERSORT algorithms. The expression of KRT7 (Keratin 7) was validated by quantitative real-time PCR (qRT-PCR), western blotting and immunohistochemistry (IHC) staining. The CIC formation, cell clusters, cell proliferation, migration and invasion assays were applied to investigate the effects of silencing the expression of KRT7. Results A prognostic model based on four CIC-related genes was constructed to stratify the patients into the low- and high-risk subgroups. The high-risk group had a poorer prognosis, higher tumor mutation burden and lower immune cell infiltration than the low-risk group. Functional enrichment analyses showed that numerous terms and pathways associated with invasion and metastasis were enriched in the high-risk group. KRT7, as the most paramount risk gene in the prognostic model, was significantly associated with a worse prognosis of PC in TCGA dataset and our own cohort. High expression of KRT7 might be responsible for the immunosuppression in the PC microenvironment. KRT7 knockdown was significantly suppressed the abilities of CIC formation, cell cluster, cell proliferation, migration, and invasion in PC cell lines. Conclusions Our prognostic model based on four CIC-related genes has a significant potential in predicting the prognosis and immune microenvironment of PC, which indicates that targeting CIC processes could be a therapeutic option with great interests. Further studies are needed to reveal the underlying molecular mechanisms and biological implications of CIC phenomenon and related genes in PC progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09983-6.
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Affiliation(s)
- Jianlu Song
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Rexiati Ruze
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yuan Chen
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Ruiyuan Xu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xinpeng Yin
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Chengcheng Wang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Qiang Xu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Yupei Zhao
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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Minaei E, Mueller SA, Ashford B, Thind AS, Mitchell J, Perry JR, Genenger B, Clark JR, Gupta R, Ranson M. Cancer Progression Gene Expression Profiling Identifies the Urokinase Plasminogen Activator Receptor as a Biomarker of Metastasis in Cutaneous Squamous Cell Carcinoma. Front Oncol 2022; 12:835929. [PMID: 35480116 PMCID: PMC9035872 DOI: 10.3389/fonc.2022.835929] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/03/2022] [Indexed: 12/16/2022] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) of the head and neck region is the second most prevalent skin cancer, with metastases to regional lymph nodes occurring in 2%–5% of cases. To further our understanding of the molecular events characterizing cSCC invasion and metastasis, we conducted targeted cancer progression gene expression and pathway analysis in non-metastasizing (PRI-) and metastasizing primary (PRI+) cSCC tumors of the head and neck region, cognate lymph node metastases (MET), and matched sun-exposed skin (SES). The highest differentially expressed genes in metastatic (MET and PRI+) versus non-metastatic tumors (PRI-) and SES included PLAU, PLAUR, MMP1, MMP10, MMP13, ITGA5, VEGFA, and various inflammatory cytokine genes. Pathway enrichment analyses implicated these genes in cellular pathways and functions promoting matrix remodeling, cell survival and migration, and epithelial to mesenchymal transition, which were all significantly activated in metastatic compared to non-metastatic tumors (PRI-) and SES. We validated the overexpression of urokinase plasminogen activator receptor (uPAR, encoded by PLAUR) in an extended patient cohort by demonstrating higher uPAR staining intensity in metastasizing tumors. As pathway analyses identified epidermal growth factor (EGF) as a potential upstream regulator of PLAUR, the effect of EGF on uPAR expression levels and cell motility was functionally validated in human metastatic cSCC cells. In conclusion, we propose that uPAR is an important driver of metastasis in cSCC and represents a potential therapeutic target in this disease.
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Affiliation(s)
- Elahe Minaei
- Illawarra Health and Medical Research Institute (IHMRI), Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Simon A. Mueller
- Department of Head and Neck Surgery, Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Department for Otorhinolaryngology, Head and Neck Surgery, Zurich University Hospital University of Zurich, Zurich, Switzerland
| | - Bruce Ashford
- Illawarra Health and Medical Research Institute (IHMRI), Wollongong, NSW, Australia
- Department of Head and Neck Surgery, Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Illawarra and Shoalhaven Local Health District (ISLHD), Wollongong, NSW, Australia
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
| | - Amarinder Singh Thind
- Illawarra Health and Medical Research Institute (IHMRI), Wollongong, NSW, Australia
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
| | - Jenny Mitchell
- Illawarra and Shoalhaven Local Health District (ISLHD), Wollongong, NSW, Australia
| | - Jay R. Perry
- Illawarra Health and Medical Research Institute (IHMRI), Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Benjamin Genenger
- Illawarra Health and Medical Research Institute (IHMRI), Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Jonathan R. Clark
- Department of Head and Neck Surgery, Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Royal Prince Alfred Institute of Academic Surgery, Sydney Local Health District, Sydney, NSW, Australia
- Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Ruta Gupta
- Department of Head and Neck Surgery, Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- NSW Health Pathology, Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Marie Ranson
- Illawarra Health and Medical Research Institute (IHMRI), Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- *Correspondence: Marie Ranson,
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15
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High Keratin-7 Expression in Benign Peri-Tumoral Prostatic Glands Is Predictive of Bone Metastasis Onset and Prostate Cancer-Specific Mortality. Cancers (Basel) 2022; 14:cancers14071623. [PMID: 35406395 PMCID: PMC8997075 DOI: 10.3390/cancers14071623] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 03/21/2022] [Indexed: 12/10/2022] Open
Abstract
BACKGROUND New predictive biomarkers are needed to accurately predict metastasis-free survival (MFS) and cancer-specific survival (CSS) in localized prostate cancer (PC). Keratin-7 (KRT7) overexpression has been associated with poor prognosis in several cancers and is described as a novel prostate progenitor marker in the mouse prostate. METHODS KRT7 expression was evaluated in prostatic cell lines and in human tissue by immunohistochemistry (IHC, on advanced PC, n = 91) and immunofluorescence (IF, on localized PC, n = 285). The KRT7 mean fluorescence intensity (MFI) was quantified in different compartments by digital analysis and correlated to clinical endpoints in the localized PC cohort. RESULTS KRT7 is expressed in prostatic cell lines and found in the basal and supra-basal compartment from healthy prostatic glands and benign peri-tumoral glands from localized PC. The KRT7 staining is lost in luminal cells from localized tumors and found as an aberrant sporadic staining (2.2%) in advanced PC. In the localized PC cohort, high KRT7 MFI above the 80th percentile in the basal compartment was significantly and independently correlated with MFS and CSS, and with hypertrophic basal cell phenotype. CONCLUSION High KRT7 expression in benign glands is an independent biomarker of MFS and CSS, and its expression is lost in tumoral cells. These results require further validation on larger cohorts.
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16
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Wan Z, Xiong H, Tan X, Su T, Xia K, Wang D. Integrative Multi-Omics Analysis Reveals Candidate Biomarkers for Oral Squamous Cell Carcinoma. Front Oncol 2022; 11:794146. [PMID: 35096593 PMCID: PMC8795899 DOI: 10.3389/fonc.2021.794146] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/17/2021] [Indexed: 01/10/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is one of the most common types of cancer worldwide. Due to the lack of early detection and treatment, the survival rate of OSCC remains poor and the incidence of OSCC has not decreased during the past decades. To explore potential biomarkers and therapeutic targets for OSCC, we analyzed differentially expressed genes (DEGs) associated with OSCC using RNA sequencing technology. Methylation-regulated and differentially expressed genes (MeDEGs) of OSCC were further identified via an integrative approach by examining publicly available methylomic datasets together with our transcriptomic data. Protein-protein interaction (PPI) networks of MeDEGs were constructed and highly connected hub MeDEGs were identified from these PPI networks. Subsequently, expression and survival analyses of hub genes were performed using The Cancer Genome Atlas (TCGA) database and the Gene Expression Profiling Interactive Analysis (GEPIA) online tool. A total of 56 upregulated MeDEGs and 170 downregulated MeDEGs were identified in OSCC. Eleven hub genes with high degree of connectivity were picked out from the PPI networks constructed by those MeDEGs. Among them, the expression level of four hub genes (CTLA4, CDSN, ACTN2, and MYH11) were found to be significantly changed in the head and neck squamous carcinoma (HNSC) patients. Three hypomethylated hub genes (CTLA4, GPR29, and TNFSF11) and one hypermethylated hub gene (ISL1) were found to be significantly associated with overall survival (OS) of HNSC patients. Therefore, these hub genes may serve as potential DNA methylation biomarkers and therapeutic targets of OSCC.
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Affiliation(s)
- Zhengqing Wan
- Hengyang Medical School, University of South China, Hengyang, China.,The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China.,Postdoctoral Station for Basic Medicine, Hengyang Medical School, University of South China, Hengyang, China
| | - Haofeng Xiong
- Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Xian Tan
- Hengyang Medical School, University of South China, Hengyang, China
| | - Tong Su
- Xiangya Hospital, Central South University, Changsha, China
| | - Kun Xia
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Danling Wang
- Hengyang Medical School, University of South China, Hengyang, China.,The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
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