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Yang F, Fan J, Yang R, Cun Y. Integrative analysis of blood transcriptome profiles in small-cell lung cancer patients for identification of novel chemotherapy resistance-related biomarkers. Front Immunol 2024; 15:1338162. [PMID: 38957470 PMCID: PMC11217175 DOI: 10.3389/fimmu.2024.1338162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 06/03/2024] [Indexed: 07/04/2024] Open
Abstract
Introduction Chemoresistance constitutes a prevalent factor that significantly impacts thesurvival of patients undergoing treatment for smal-cell lung cancer (SCLC). Chemotherapy resistance in SCLC patients is generally classified as primary or acquired resistance, each governedby distinct mechanisms that remain inadequately researched. Methods In this study, we performed transcriptome screening of peripheral blood plasma obtainedfrom 17 patients before and after receiving combined etoposide and platinum treatment. We firs testimated pseudo-single-cell analysis using xCell and ESTIMATE and identified differentially expressed genes (DEGs), then performed network analysis to discover key hub genes involved in chemotherapy resistance. Results Our analysis showed a significant increase in class-switched memory B cell scores acrossboth chemotherapy resistance patterns, indicating their potential crucial role in mediatingresistance. Moreover, network analysis identifed PRICKLE3, TNFSFI0, ACSLl and EP300 as potential contributors to primary resistance, with SNWl, SENP2 and SMNDCl emerging assignificant factors in acquired resistance, providing valuable insights into chemotherapy resistancein SCLC. Discussion These findings offer valuable insights for understanding chemotherapy resistance and related gene signatures in SCLC, which could help further biological validation studies.
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Affiliation(s)
- Fang Yang
- Department of the Second Medical Oncology, Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Jinhua Fan
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children’s Hospital of Chongqing Medical University, Chongqing, China
- National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Runxiang Yang
- Department of the Second Medical Oncology, Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yupeng Cun
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children’s Hospital of Chongqing Medical University, Chongqing, China
- National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children’s Hospital of Chongqing Medical University, Chongqing, China
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2
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Chen X, Ma C, Li Y, Liang Y, Chen T, Han D, Luo D, Zhang N, Zhao W, Wang L, Yang Q. COL5A1 promotes triple-negative breast cancer progression by activating tumor cell-macrophage crosstalk. Oncogene 2024; 43:1742-1756. [PMID: 38609499 DOI: 10.1038/s41388-024-03030-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
Triple-negative breast cancer (TNBC) is an exceptionally aggressive subtype of breast cancer. Despite the recognized interplay between tumors and tumor-associated macrophages in fostering drug resistance and disease progression, the precise mechanisms leading these interactions remain elusive. Our study revealed that the upregulation of collagen type V alpha 1 (COL5A1) in TNBC tissues, particularly in chemoresistant samples, was closely linked to an unfavorable prognosis. Functional assays unequivocally demonstrated that COL5A1 played a pivotal role in fueling cancer growth, metastasis, and resistance to doxorubicin, both in vitro and in vivo. Furthermore, we found that the cytokine IL-6, produced by COL5A1-overexpressing TNBC cells actively promoted M2 macrophage polarization. In turn, TGFβ from M2 macrophages drived TNBC doxorubicin resistance through the TGFβ/Smad3/COL5A1 signaling pathway, establishing a feedback loop between TNBC cells and macrophages. Mechanistically, COL5A1 interacted with TGM2, inhibiting its K48-linked ubiquitination-mediated degradation, thereby enhancing chemoresistance and increasing IL-6 secretion. In summary, our findings underscored the significant contribution of COL5A1 upregulation to TNBC progression and chemoresistance, highlighting its potential as a diagnostic and therapeutic biomarker for TNBC.
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Affiliation(s)
- Xi Chen
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Chenao Ma
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Yaming Li
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Yiran Liang
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Tong Chen
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Dianwen Han
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Dan Luo
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Ning Zhang
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Wenjing Zhao
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Lijuan Wang
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Qifeng Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China.
- Research Institute of Breast Cancer, Shandong University, Jinan, 250012, Shandong, China.
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3
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Kazakova AN, Lukina MM, Anufrieva KS, Bekbaeva IV, Ivanova OM, Shnaider PV, Slonov A, Arapidi GP, Shender VO. Exploring the diversity of cancer-associated fibroblasts: insights into mechanisms of drug resistance. Front Cell Dev Biol 2024; 12:1403122. [PMID: 38818409 PMCID: PMC11137237 DOI: 10.3389/fcell.2024.1403122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/22/2024] [Indexed: 06/01/2024] Open
Abstract
Introduction: Among the various stromal cell types within the tumor microenvironment, cancer-associated fibroblasts (CAFs) emerge as the predominant constituent, exhibiting a diverse array of oncogenic functions not intrinsic to normal fibroblasts. Their involvement spans across all stages of tumorigenesis, encompassing initiation, progression, and metastasis. Current understanding posits the coexistence of distinct subpopulations of CAFs within the tumor microenvironment across a spectrum of solid tumors, showcasing both pro- and antitumor activities. Recent advancements in single-cell transcriptomics have revolutionized our ability to meticulously dissect the heterogeneity inherent to CAF populations. Furthermore, accumulating evidence underscores the pivotal role of CAFs in conferring therapeutic resistance to tumors against various drug modalities. Consequently, efforts are underway to develop pharmacological agents specifically targeting CAFs. Methods: This review embarks on a comprehensive analysis, consolidating data from 36 independent single-cell RNA sequencing investigations spanning 17 distinct human malignant tumor types. Results: Our exploration centers on elucidating CAF population markers, discerning their prognostic relevance, delineating their functional contributions, and elucidating the underlying mechanisms orchestrating chemoresistance. Discussion: Finally, we deliberate on the therapeutic potential of harnessing CAFs as promising targets for intervention strategies in clinical oncology.
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Affiliation(s)
- Anastasia N. Kazakova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Maria M. Lukina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Ksenia S. Anufrieva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Irina V. Bekbaeva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Olga M. Ivanova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia
| | - Polina V. Shnaider
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Andrey Slonov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Georgij P. Arapidi
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Victoria O. Shender
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
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Chen M, Zhang J, Zeng J, Yu Y, Gu C. Circular circRANGAP1 Contributes to Non-small Cell Lung Cancer Progression by Increasing COL11A1 Expression Through Sponging miR-653-5p. Biochem Genet 2023; 61:2580-2598. [PMID: 37193942 DOI: 10.1007/s10528-023-10393-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/01/2023] [Indexed: 05/18/2023]
Abstract
Numerous studies have discovered that hsa_circ_0063526 (also known as circRANGAP1) is an oncogenic circular RNA (circRNA) in some human tumors, including non-small cell lung cancer (NSCLC). However, the concrete molecular mechanism of circRANGAP1 involved in NSCLC is not completely elucidated. CircRANGAP1, microRNA-653-5p (miR-653-5p), and Type XI collagen (COL11A1) contents were determined via real-time quantitative polymerase chain reaction (RT-qPCR). Cell proliferative ability, migration, and invasion were measured using 5-ethynyl-2'-deoxyuridine (EdU), colony formation, wound healing, and transwell assays. E-cadherin, N-cadherin, Vimentin, and COL11A1 protein levels were detected via western blot assay. After Starbase software prediction, the binding between miR-653-5p and circRANGAP1 or COL11A1 was verified using a dual-luciferase reporter assay. Besides, the role of circRANGAP1 on tumor cell growth was analyzed using a xenograft tumor model in vivo. Increased circRANGAP1 and COL11A1, and reduced miR-653-5p were found in NSCLC tissues and cell lines. Furthermore, circRANGAP1 absence might hinder NSCLC cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) in vitro. Mechanically, circRANGAP1 functioned as a sponge of miR-653-5p to increase COL11A1 expression. In vivo experiments illustrated that circRANGAP1 knockdown repressed tumor growth. CircRANGAP1 silencing might suppress NSCLC cell malignant biological behaviors, at least in part, through the miR-653-5p/COL11A1 axis. These results provided a promising strategy for treating NSCLC malignancies.
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Affiliation(s)
- Min Chen
- Department of Respiratory and Critical Care Medicine, Shanghai Tongren Hospital, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, No 1111 XianXia Road, Changning District, Shanghai, 200335, China.
| | - Jing Zhang
- Department of Respiratory and Critical Care Medicine, Shanghai Tongren Hospital, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, No 1111 XianXia Road, Changning District, Shanghai, 200335, China
| | - Jian Zeng
- Department of Respiratory and Critical Care Medicine, Shanghai Tongren Hospital, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, No 1111 XianXia Road, Changning District, Shanghai, 200335, China
| | - Yiming Yu
- Department of Respiratory and Critical Care Medicine, Shanghai Tongren Hospital, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, No 1111 XianXia Road, Changning District, Shanghai, 200335, China
| | - Chenlin Gu
- Department of Respiratory and Critical Care Medicine, Shanghai Tongren Hospital, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, No 1111 XianXia Road, Changning District, Shanghai, 200335, China
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5
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Freire J, García-Berbel P, Caramelo B, García-Berbel L, Ovejero VJ, Cadenas N, Azueta A, Gómez-Román J. Usefulness of COL11A1 as a Prognostic Marker of Tumor Infiltration. Biomedicines 2023; 11:2496. [PMID: 37760937 PMCID: PMC10526338 DOI: 10.3390/biomedicines11092496] [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: 07/21/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Determining the infiltration of carcinomas is essential for the proper follow-up and treatment of cancer patients. However, it continues to be a diagnostic challenge for pathologists in multiple types of tumors. In previous studies (carried out in surgical specimens), the protein COL11A1 has been postulated as an infiltration marker mainly expressed in the extracellular matrix (ECM). We hypothesized that a differential expression of COL11A1 may exist in the peritumoral stroma of tumors that have acquired infiltrating properties and that it may be detected in the small biopsies usually available in normal clinical practice. MATERIAL AND METHODS In our study, we performed immunohistochemical staining in more than 350 invasive and noninvasive small samples obtained via core needle biopsy (CNB), colonoscopy, or transurethral resection of bladder tumor (TURBT) of breast, colorectal, bladder, and ovarian cancer. RESULTS Our results revealed that COL11A1 immunostaining had a sensitivity to classify the samples into infiltrative vs. noninfiltrative tumors of 94% (breast), 97% (colorectal), >90% (bladder), and 74% (ovarian); and a specificity of 97% (breast), 100% (colorectal), and >90% (bladder). In ovarian cancer, the negative predictive value (0.59) did not present improvement over the usual histopathological markers. In all samples tested, the cumulative sensitivity was 86% and the specificity 96% (p < 0.0001). CONCLUSIONS COL11A1-positive immunostaining in small biopsies of breast, colon, bladder and ovarian cancer is an accurate predictive marker of tumor infiltration that can be easily implemented in daily clinical practice.
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Affiliation(s)
- Javier Freire
- Pathology Department, University Hospital Marques de Valdecilla, Avda. Marqués de Valdecilla s/n, 39008 Santander, Spain
| | - Pilar García-Berbel
- Pathology and Molecular Pathology Unit, IDIVAL, Avenida Cardenal Herrera Oria s/n, 39011 Santander, Spain
| | - Belén Caramelo
- Pathology and Molecular Pathology Unit, IDIVAL, Avenida Cardenal Herrera Oria s/n, 39011 Santander, Spain
| | - Lucía García-Berbel
- Breast Unit, Gynecology Department, University Hospital Puerta del Mar. Av. Ana de Viya, 21, 11009 Cádiz, Spain
| | - Victor J. Ovejero
- Surgery Department, University Hospital Marques de Valdecilla, Avda. Marqués de Valdecilla s/n, 39008 Santander, Spain
| | - Nuria Cadenas
- El Alisal Health Center, Cantabrian Health Service, C. los Ciruelos, 48, 39011 Santander, Spain
| | - Ainara Azueta
- Pathology Department, University Hospital Marques de Valdecilla, Avda. Marqués de Valdecilla s/n, 39008 Santander, Spain
| | - Javier Gómez-Román
- Pathology Department, University Hospital Marques de Valdecilla, Avda. Marqués de Valdecilla s/n, 39008 Santander, Spain
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6
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Dong L, Fu L, Zhu T, Wu Y, Li Z, Ding J, Zhang J, Wang X, Zhao J, Yu G. A five-collagen-based risk model in lung adenocarcinoma: prognostic significance and immune landscape. Front Oncol 2023; 13:1180723. [PMID: 37476379 PMCID: PMC10354438 DOI: 10.3389/fonc.2023.1180723] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/22/2023] [Indexed: 07/22/2023] Open
Abstract
As part of the tumor microenvironment (TME), collagen plays a significant role in cancer fibrosis formation. However, the collagen family expression profile and clinical features in lung adenocarcinoma (LUAD) are poorly understood. The objective of the present work was to investigate the expression pattern of genes from the collagen family in LUAD and to develop a predictive signature based on collagen family. The Cancer Genome Atlas (TCGA) samples were used as the training set, and five additional cohort samples obtained from the Gene Expression Omnibus (GEO) database were used as the validation set. A predictive model based on five collagen genes, including COL1A1, COL4A3, COL5A1, COL11A1, and COL22A1, was created by analyzing samples from the TCGA cohort using LASSO Cox analysis and univariate/multivariable Cox regression. Using Collagen-Risk scores, LUAD patients were then divided into high- and low-risk groups. KM survival analysis showed that collagen signature presented a robust prognostic power. GO and KEGG analyses confirmed that collagen signature was associated with extracellular matrix organization, ECM-receptor interaction, PI3K-Akts and AGE-RAGE signaling activation. High-risk patients exhibited a considerable activation of the p53 pathway and cell cycle, according to GSEA analysis. The Collage-Risk model showed unique features in immune cell infiltration and tumor-associated macrophage (TAM) polarization of the TME. Additionally, we deeply revealed the association of collagen signature with immune checkpoints (ICPs), tumor mutation burden (TMB), and tumor purity. We first constructed a reliable prognostic model based on TME principal component-collagen, which would enable clinicians to treat patients with LUAD more individually.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Guangmao Yu
- Department of Thoracic Surgery, Shaoxing People’s Hospital, Shaoxing, Zhejiang, China
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7
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Bhardwaj A, Liyanage SI, Weaver DF. Cancer and Alzheimer's Inverse Correlation: an Immunogenetic Analysis. Mol Neurobiol 2023; 60:3086-3099. [PMID: 36797545 DOI: 10.1007/s12035-023-03260-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/05/2023] [Indexed: 02/18/2023]
Abstract
Numerous studies have demonstrated an inverse link between cancer and Alzheimer's disease (AD), with data suggesting that people with Alzheimer's have a decreased risk of cancer and vice versa. Although other studies have investigated mechanisms to explain this relationship, the connection between these two diseases remains largely unexplained. Processes seen in cancer, such as decreased apoptosis and increased cell proliferation, seem to be reversed in AD. Given the need for effective therapeutic strategies for AD, comparisons with cancer could yield valuable insights into the disease process and perhaps result in new treatments. Here, through a review of existing literature, we compared the expressions of genes involved in cell proliferation and apoptosis to establish a genetic basis for the reciprocal association between AD and cancer. We discuss an array of genes involved in the aforementioned processes, their relevance to both diseases, and how changes in those genes produce varying effects in either disease.
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Affiliation(s)
- Aditya Bhardwaj
- Krembil Discovery Tower, Krembil Brain Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
| | - S Imindu Liyanage
- Krembil Discovery Tower, Krembil Brain Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
| | - Donald F Weaver
- Krembil Discovery Tower, Krembil Brain Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada.
- Departments of Medicine and Chemistry, University of Toronto, Toronto, Canada.
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8
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Feng J, Ouyang H, Wang J, Pan D, Sheng L, Xu C, Lin W, Hu D, Chang C, Jia D. MPZL1 upregulation promotes tumor metastasis and correlates with unfavorable prognosis in non-small cell lung cancer. Carcinogenesis 2022; 43:919-929. [PMID: 35727197 DOI: 10.1093/carcin/bgac055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/18/2022] [Accepted: 06/16/2022] [Indexed: 01/13/2023] Open
Abstract
Non-small cell lung cancer (NSCLC), accounting for 85% of all lung cancer, is one of the leading causes of cancer-related death worldwide. Previously, we demonstrated that MPZL1 gene amplification promotes liver cancer metastasis through activating Src/Cortactin pathway. However, the clinical relevance and biological roles of the MPZL1 gene in lung cancer are still unknown. Here, we found that MPZL1 expression upregulates in human NSCLC, which is partly due to the copy number amplification of this gene. Next, we observed that high MPZL1 expression correlates with unfavorable prognosis of NSCLC patients. We further demonstrated that ectopic MPZL1 overexpression promotes in vitro migratory but not proliferation and colony formation abilities of both H1299 and H460 cells. Consistently, we found that MPZL1 knockdown impairs the migratory abilities of A549 and H1775 cells. Moreover, we found that MPZL1 knockdown inhibits in vivo metastatic but not tumor growth abilities of the A549 cells. Additionally, a total of 297 differentially expressed genes (DEGs) were identified by RNA sequencing in A549 cells upon MPZL1 knockdown. By integrative analysis of DEGs regulated by MPZL1 in A549 cells and human NSCLC tissues, we revealed that COL11A1 is the potential effector gene that positively regulated by MPZL1 and correlates with poor prognosis of NSCLC patients. In conclusion, our work indicates that one of the mechanisms by which MPZL1 promotes NSCLC metastasis is through upregulating the COL11A1, and MPZL1 can be used as a biomarker to predict the prognosis of NSCLC patients.
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Affiliation(s)
- Jian Feng
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Huiling Ouyang
- Laboratory of Cancer Genomics and Biology, Department of Urology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Thoracic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Wang
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China
| | - Deshen Pan
- Laboratory of Cancer Genomics and Biology, Department of Urology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Thoracic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Luoyan Sheng
- Laboratory of Cancer Genomics and Biology, Department of Urology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Thoracic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaoliang Xu
- Laboratory of Cancer Genomics and Biology, Department of Urology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Thoracic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weihong Lin
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China
| | - Dingzhong Hu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Cheng Chang
- Department of Nuclear Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Deshui Jia
- Laboratory of Cancer Genomics and Biology, Department of Urology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Thoracic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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9
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Parker AL, Bowman E, Zingone A, Ryan BM, Cooper WA, Kohonen-Corish M, Harris CC, Cox TR. Extracellular matrix profiles determine risk and prognosis of the squamous cell carcinoma subtype of non-small cell lung carcinoma. Genome Med 2022; 14:126. [PMID: 36404344 PMCID: PMC9677915 DOI: 10.1186/s13073-022-01127-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/14/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Squamous cell carcinoma (SqCC) is a subtype of non-small cell lung cancer for which patient prognosis remains poor. The extracellular matrix (ECM) is critical in regulating cell behavior; however, its importance in tumor aggressiveness remains to be comprehensively characterized. METHODS Multi-omics data of SqCC human tumor specimens was combined to characterize ECM features associated with initiation and recurrence. Penalized logistic regression was used to define a matrix risk signature for SqCC tumors and its performance across a panel of tumor types and in SqCC premalignant lesions was evaluated. Consensus clustering was used to define prognostic matreotypes for SqCC tumors. Matreotype-specific tumor biology was defined by integration of bulk RNAseq with scRNAseq data, cell type deconvolution, analysis of ligand-receptor interactions and enriched biological pathways, and through cross comparison of matreotype expression profiles with aging and idiopathic pulmonary fibrosis lung profiles. RESULTS This analysis revealed subtype-specific ECM signatures associated with tumor initiation that were predictive of premalignant progression. We identified an ECM-enriched tumor subtype associated with the poorest prognosis. In silico analysis indicates that matrix remodeling programs differentially activate intracellular signaling in tumor and stromal cells to reinforce matrix remodeling associated with resistance and progression. The matrix subtype with the poorest prognosis resembles ECM remodeling in idiopathic pulmonary fibrosis and may represent a field of cancerization associated with elevated cancer risk. CONCLUSIONS Collectively, this analysis defines matrix-driven features of poor prognosis to inform precision medicine prevention and treatment strategies towards improving SqCC patient outcome.
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Affiliation(s)
- Amelia L. Parker
- grid.415306.50000 0000 9983 6924Matrix and Metastasis Lab, Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, 384 Victoria St, Darlinghurst, NSW 2052 Australia ,grid.1005.40000 0004 4902 0432School of Clinical Medicine, UNSW Sydney, Sydney, 2052 Australia
| | - Elise Bowman
- grid.48336.3a0000 0004 1936 8075Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA
| | - Adriana Zingone
- grid.48336.3a0000 0004 1936 8075Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA
| | - Brid M. Ryan
- grid.48336.3a0000 0004 1936 8075Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA ,Present address: MiNA Therapeutics, London, UK
| | - Wendy A. Cooper
- grid.413249.90000 0004 0385 0051Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050 Australia ,grid.1013.30000 0004 1936 834XSydney Medical School, University of Sydney, Sydney, NSW 2050 Australia ,grid.1029.a0000 0000 9939 5719Discipline of Pathology, School of Medicine, Western Sydney University, Liverpool, NSW 2170 Australia
| | - Maija Kohonen-Corish
- grid.417229.b0000 0000 8945 8472Woolcock Institute of Medical Research, Sydney, NSW 2037 Australia ,grid.1005.40000 0004 4902 0432Microbiome Research Centre, School of Clinical Medicine, UNSW Sydney, Sydney, 2052 Australia ,grid.415306.50000 0000 9983 6924Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
| | - Curtis C. Harris
- grid.48336.3a0000 0004 1936 8075Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA
| | - Thomas R. Cox
- grid.415306.50000 0000 9983 6924Matrix and Metastasis Lab, Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, 384 Victoria St, Darlinghurst, NSW 2052 Australia ,grid.1005.40000 0004 4902 0432School of Clinical Medicine, UNSW Sydney, Sydney, 2052 Australia
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10
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Yi X, Luo L, Zhu Y, Deng H, Liao H, Shen Y, Zheng Y. SPP1 facilitates cell migration and invasion by targeting COL11A1 in lung adenocarcinoma. Cancer Cell Int 2022; 22:324. [PMID: 36266702 PMCID: PMC9583566 DOI: 10.1186/s12935-022-02749-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/05/2022] [Indexed: 12/03/2022] Open
Abstract
Background Secreted phosphoprotein 1 (SPP1), an extracellular secreted glycol phosphoprotein, is closely related to tumor biologies, such as proliferation, migration, and invasion. However, the role and biological function of SPP1 in lung adenocarcinoma (LUAD) was still ambiguous. Methods SPP1 expression in LUAD tissues and its associations with clinical features and prognosis was investigated using meta-analysis, immunohistochemistry (IHC) staining methods, and quantitative real-time polymerase chain reaction (qRT-PCR). Moreover, the potential mechanism related to SPP1 was identified by using the Gene Set Enrichment Analysis (GSEA) method. A series of function assays were conducted to determine the biological role of SPP1 in LUAD cell migration and invasion in vitro and vivo. The co-expressed genes of SPP1 were obtained and verified by western blot assays. The influence of SPP1 on Collagen type XI alpha 1 (COL11A1) expression and epithelial-mesenchymal transition (EMT) markers was analyzed using western blot assays. Results The expression of SPP1 in LUAD tissues and cells was significantly higher than that in normal tissues and cells. And positively associations of SPP1 expression with TNM stage, lymph node metastasis, and invasion depth were observed. Patients with high SPP1 expression had unfavorable survival. The multivariable Cox regression analysis revealed that SPP1 expression was an independent prognostic factor of LUAD patients. Furthermore, downregulation of SPP1 could inhibit cell migration and invasion both in vitro and vivo, reduce the expression of epithelial marker (E-cadherin), and increase the expression of mesenchymal markers (N-cadherin and vimentin). Using bioinformatics and western blot assays, we confirmed that COL11A1 acted as the downstream of SPP1, and SPP1 knockdown could significantly downregulate the COL11A1 expression. Importantly, suppression of cell migration and invasion and the expression changes of EMT markers induced by SPP1 downregulation could be reversed by COL11A1 overexpression. Conclusions SPP1 facilitates cell migration and invasion by upregulating COL11A1 expression and that acts as a potential biomarker of metastasis and prognosis for LUAD. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02749-x.
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Affiliation(s)
- Xuan Yi
- Jiangxi Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, China.,Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, China
| | - Linlin Luo
- Second Department of Respiratory Disease, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330000, China
| | - Yanzhen Zhu
- Department of Anesthesia and Perioperative Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, China
| | - Hong Deng
- Pharmacy Department, Jiujiang Hospital of Traditional Chinese Medicine, Jiujiang, 332000, China
| | - Huitian Liao
- Financial Department, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, China
| | - Yang Shen
- Jiangxi Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, China.,Department of Medical Genetics, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, China
| | - Yan Zheng
- Jiangxi Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, China. .,Department of Medical Genetics, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, China.
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11
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Necula L, Matei L, Dragu D, Pitica I, Neagu A, Bleotu C, Diaconu CC, Chivu-Economescu M. Collagen Family as Promising Biomarkers and Therapeutic Targets in Cancer. Int J Mol Sci 2022; 23:ijms232012415. [PMID: 36293285 PMCID: PMC9604126 DOI: 10.3390/ijms232012415] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
Despite advances in cancer detection and therapy, it has been estimated that the incidence of cancers will increase, while the mortality rate will continue to remain high, a fact explained by the large number of patients diagnosed in advanced stages when therapy is often useless. Therefore, it is necessary to invest knowledge and resources in the development of new non-invasive biomarkers for the early detection of cancer and new therapeutic targets for better health management. In this review, we provided an overview on the collagen family as promising biomarkers and on how they may be exploited as therapeutic targets in cancer. The collagen family tridimensional structure, organization, and functions are very complex, being in a tight relationship with the extracellular matrix, tumor, and immune microenvironment. Moreover, accumulating evidence underlines the role of collagens in promoting tumor growth and creating a permissive tumor microenvironment for metastatic dissemination. Knowledge of the molecular basis of these interactions may help in cancer diagnosis and prognosis, in overcoming chemoresistance, and in providing new targets for cancer therapies.
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Affiliation(s)
- Laura Necula
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania
- Faculty of Medicine, Titu Maiorescu University, 040441 Bucharest, Romania
- Correspondence: ; Tel.: +40-21-324-2592
| | - Lilia Matei
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania
| | - Denisa Dragu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania
| | - Ioana Pitica
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania
| | - Ana Neagu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania
| | - Coralia Bleotu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania
| | - Carmen C. Diaconu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania
| | - Mihaela Chivu-Economescu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania
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12
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Di YB, Bao Y, Guo J, Liu W, Zhang SX, Zhang GH, Li TK. COL11A1 as a potential prognostic target for oral squamous cell carcinoma. Medicine (Baltimore) 2022; 101:e30989. [PMID: 36221427 PMCID: PMC9542892 DOI: 10.1097/md.0000000000030989] [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
Oral squamous cell carcinoma (OSCC) is a malignant tumor occurring in the oral cavity. However, the molecular mechanism of OSCC is not clear. Bioinformatics was used to screen and identify role of collagen type X1 alpha 1 (COL11A1) on OSCC. 200 patients with OSCC were recruited. Clinical and follow-up data were recorded and COL11A1 expression levels were tested. Pearson chi-square test and Spearman correlation coefficient were used to analyze relationship between prognosis and related parameters in patients with OSCC. Univariate and multivariate Logistic regression, univariate and multivariate Cox proportional risk regression were used for further analysis, survival curve was drawn. Through bioinformatics analysis, OSCC patients with higher expression of COL11A1 have poor overall survival compare with OSCC patients with lower expression of COL11A1 (hazard ratios [HR] = 1.32, P = .047). Pearson chi-square test showed that age (P = .011), tumor grade (P = .023), COL11A1 (P < .001) was significantly correlated with prognosis of OSCC. Univariate Logistic regression analysis showed age (odds ratio [OR] = 2.102, 95% confidence intervals [95%CI]: 1.180-3.746, P = .012), tumor grade (OR = 1.919, 95%CI: 1.093-3.372, P = .023) and COL11A1 (OR = 12.775, 95%CI: 6.509-25.071, P < .001). Multivariate Logistic regression analysis showed that COL11A1 (OR = 12.066, 95%CI: 6.042-24.096, P < .001) was significantly associated with prognosis of patients with OSCC. Univariate Cox regression analysis showed that age (HR = 1.592, 95%CI: 1.150-2.205, P = .005), tumor grade (HR = 1.460, 95%CI: 1.067-1.999, P = .018) and COL11A1 (HR = 1.848, 95%CI: 1.340-2.548, P < .001) were significantly correlated with survival time of OSCC patients. Multivariate Cox regression analysis showed that tumor grade (HR = 1.466, 95%CI: 1.064-2.020, P = .019) and COL11A1 (HR = 1.645, 95%CI: 1.164-2.325, P = .005) were significantly correlated with survival time of OSCC patients. COL11A1 is significantly correlated with occurrence of OSCC. When COL11A1 is highly expressed, prognosis of patients with OSCC is worse and the survival time is shorter.
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Affiliation(s)
- Yong-Bin Di
- Department of Stomatology, The First Hospital of Hebei Medical University, Shijiazhuang, P.R. China
| | - Yang Bao
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, P.R. China
| | - Jie Guo
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, P.R. China
| | - Wei Liu
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, P.R. China
| | - Su-Xin Zhang
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, P.R. China
| | - Guan-Hua Zhang
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, P.R. China
| | - Tian-Ke Li
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, P.R. China
- *Correspondence: Tian-Ke Li, Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050000, P.R. China (e-mail: )
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13
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Luo Q, Li J, Su X, Tan Q, Zhou F, Xie S. COL11A1 serves as a biomarker for poor prognosis and correlates with immune infiltration in breast cancer. Front Genet 2022; 13:935860. [PMID: 36160004 PMCID: PMC9500398 DOI: 10.3389/fgene.2022.935860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/26/2022] [Indexed: 12/25/2022] Open
Abstract
Breast cancer is the malignant tumor with the highest incidence rate at present, and its incidence rate ranks first in the female population. COL11A1 is an important component of collagen XI and is considered to play an important role in a variety of connective tissue diseases. Recent studies have shown that COL11A1 is associated with the occurrence and development of many kinds of malignant tumors. However, its prognostic value in breast cancer and its correlation with immune cell infiltration in tumor tissue are not clear. In this paper, we reveal the prognostic value of COL11A1 in breast cancer and its tumor immune-related function through in-depth bioinformatics analysis. The expression of COL11A1 is abnormally upregulated in breast cancer and is significantly related to the poor prognosis of breast cancer. In the analysis of the clinical characteristics of the patients, we found that the expression level of COLL11A1 was closely related to lymph node metastasis, PAM50 (Prediction Analysis of Microarray 50) expression, clinical stage and so on. Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) all suggest that COL11A1 is related to tumor immunity. Further study found that the COL11A1 expression was significantly correlated with the degree of immune infiltration and the expression of a variety of immune cell markers in tumor tissue. More importantly, COL11A1 can affect the prognosis of breast cancer patients by participating in the regulation of tumor immune infiltration. Therefore, we believe that COL11A1 is a very potential target for diagnosis and treatment of breast cancer.
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Affiliation(s)
- Qi Luo
- Department of Academician (expert) Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Biological Targeting Laboratory of Breast Cancer, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Outpatient, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Jinsui Li
- Department of Academician (expert) Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Biological Targeting Laboratory of Breast Cancer, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Thyroid and Breast Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xiaohan Su
- Department of Academician (expert) Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Biological Targeting Laboratory of Breast Cancer, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Thyroid and Breast Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Qiao Tan
- Department of Academician (expert) Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Biological Targeting Laboratory of Breast Cancer, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Thyroid and Breast Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Fangfang Zhou
- Department of Academician (expert) Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Biological Targeting Laboratory of Breast Cancer, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Anatomy, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Shaoli Xie
- Department of Academician (expert) Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Biological Targeting Laboratory of Breast Cancer, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Thyroid and Breast Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- *Correspondence: Shaoli Xie, , orcid.org/0000-0003-4512-2725
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14
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Yao Y, Guan X, Bao G, Liang J, Li T, Zhong X. Whole-exome sequencing and bioinformatics analysis of a case of non-alpha-fetoprotein-elevated lung hepatoid adenocarcinoma. Front Pharmacol 2022; 13:945038. [PMID: 36091765 PMCID: PMC9462446 DOI: 10.3389/fphar.2022.945038] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/28/2022] [Indexed: 11/21/2022] Open
Abstract
Hepatoid adenocarcinoma of the lung (HAL) is an exceptionally rare malignant tumor with prominent hepatocellular carcinoma (HCC)-like characteristics in organs or tissues outside the liver, while there is no tumor in the liver. Most HAL cases have various degrees of serum alpha-fetoprotein (AFP) levels and exhibit a similar origin and clonal evolution process to HCC. We studied a case of HAL without elevating the AFP level by performing whole-exome sequencing (WES) and bioinformatics analyses after surgical resection. Our results showed mutations in two driver genes, NLRP3 and PBX1, and we identified HNRNPR, TP73, CFAP57, COL11A1, RUSC1, SLC6A9, DISC1, NBPF26, and OR10K1 as potential driver mutation genes in HAL. In addition, 76 significantly mutated genes (SMG) were identified after the statistical test of each mutation type on genes.
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Affiliation(s)
- Yao Yao
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Xiaojiao Guan
- Department of Pathology, Second Affiliated Hospital, China Medical University, Shenyang, China
| | - Guangyao Bao
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Jie Liang
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, Xi’an, China
- *Correspondence: Xinwen Zhong, ; Tian Li,
| | - Xinwen Zhong
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
- *Correspondence: Xinwen Zhong, ; Tian Li,
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15
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Liu J, Yang CQ, Chen Q, Yu TY, Zhang SL, Guo WH, Luo LH, Zhao G, Yin DC, Zhang CY. MiR-4458-loaded gelatin nanospheres target COL11A1 for DDR2/SRC signaling pathway inactivation to suppress the progression of estrogen receptor-positive breast cancer. Biomater Sci 2022; 10:4596-4611. [PMID: 35792605 DOI: 10.1039/d2bm00543c] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
RNA interference is a promising way to treat cancer and the construction of a stable drug delivery system is critically important for its application. Gelatin nanospheres (GNs) comprise a biodegradable drug vehicle with excellent biocompatibility, but there are limited studies on its delivery and role in the stabilization of miRNA and siRNA. Breast cancer is the most diagnosed type of female cancer worldwide. Abnormal miRNA expression is closely related to the occurrence and progression of estrogen receptor-positive (ER+) breast cancer. In this study, miR-4458 was upregulated in ER+ breast cancer and could inhibit MCF-7 cell viability, colony formation, migration, and invasion. Collagen type XI alpha 1 (COL11A1) was identified as a directly interacting protein of miR-4458 and an important component of the extracellular matrix. High COL11A1 expression was positively correlated with poor prognosis, lower overall survival, disease-free survival, and a late tumor-node-metastasis stage. COL11A1 knockdown could inhibit MCF-7 cell migration and invasion. GNs were used to load a miR-4458 mimic or COL11A1 siRNA (si-COL11A1) to achieve sustained and controlled release in xenograft nude mice. Their tumor volume was decreased, tumor cell apoptosis was promoted, and hepatic metastasis was significantly inhibited. Moreover, the DDR2/SRC signaling pathway was inactivated after transfection with the miR-4458 mimic and si-COL11A1. In conclusion, GNs can be potentially used to deliver siRNA or miRNA, and miR-4458 and COL11A1 can be possible targets for ER+ breast cancer treatment.
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Affiliation(s)
- Jie Liu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
| | - Chang-Qing Yang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
| | - Qiang Chen
- State Key Laboratory of Solidification Processing, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Tong-Yao Yu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
| | - Shi-Long Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
| | - Wei-Hong Guo
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
| | - Li-Heng Luo
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
| | - Gang Zhao
- The First Hospital of Jilin University, 130021, Changchun, China.
| | - Da-Chuan Yin
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
| | - Chen-Yan Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
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16
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Wu YH, Chou CY. Collagen XI Alpha 1 Chain, a Novel Therapeutic Target for Cancer Treatment. Front Oncol 2022; 12:925165. [PMID: 35847935 PMCID: PMC9277861 DOI: 10.3389/fonc.2022.925165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/31/2022] [Indexed: 01/13/2023] Open
Abstract
The extracellular matrix (ECM) plays an important role in the progression of cancer. Collagen is the most abundant component in ECM, and is involved in the biological formation of cancer. Although type XI collagen is a minor fibrillar collagen, collagen XI alpha 1 chain (COL11A1) expression has been found to be upregulated in a variety of human cancers including colorectal, esophagus, glioma, gastric, head and neck, lung, ovarian, pancreatic, salivary gland, and renal cancers. High levels of COL11A1 usually predict poor prognosis, owing to its association with angiogenesis, invasion, and drug resistance in cancer. However, little is known about the specific mechanism through which COL11A1 regulates tumor progression. Here, we have organized and summarized recent developments regarding the interactions between COL11A1 and intracellular signaling pathways and selected therapeutic agents targeting COL11A1, as these indicate its potential as a target for treatment of cancers, especially epithelial ovarian cancer.
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Affiliation(s)
- Yi-Hui Wu
- Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan.,Department of Nursing, Min-Hwei Junior College of Health Care Management, Tainan, Taiwan
| | - Cheng-Yang Chou
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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17
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Sun Y, Huang H, Zhan Z, Gao H, Zhang C, Lai J, Cao J, Li C, Chen Y, Liu Z. Berberine inhibits glioma cell migration and invasion by suppressing TGF-β1/COL11A1 pathway. Biochem Biophys Res Commun 2022; 625:38-45. [DOI: 10.1016/j.bbrc.2022.07.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 07/26/2022] [Indexed: 12/01/2022]
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18
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Arolt C, Hoffmann F, Nachtsheim L, Wolber P, Guntinas-Lichius O, Buettner R, von Eggeling F, Quaas A, Klußmann JP. Mutually Exclusive Expression of COL11A1 by CAFs and Tumour Cells in a Large panCancer and a Salivary Gland Carcinoma Cohort. Head Neck Pathol 2022; 16:394-406. [PMID: 34378164 PMCID: PMC9187800 DOI: 10.1007/s12105-021-01370-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/26/2021] [Indexed: 01/06/2023]
Abstract
Procollagen 11A1 (COL11A1) is a central component of the extracellular matrix in many carcinomas, which is considered to be mainly produced by cancer associated fibroblasts (CAFs). As COL11A1 expression correlates with adverse prognosis and is implicated in chemoresistance, it is a promising putative target. For the first time, we used RNA in-situ hybridization to systematically identify the cells that produce COL11A1 in the ten most prevalent carcinoma types, lymphomas (n = 275) and corresponding normal tissue (n = 55; panCancer cohort). Moreover, as most salivary gland carcinomas (SGC) display distinct stromal architectures, we also analysed 110 SGC. The corresponding protein formation of COL11A1 was determined by MALDI-TOF-MS-Imaging. We report that colon, breast and salivary duct carcinomas are highly infiltrated by COL11A1 positive CAFs (CAFsCOL11A1) and might thus be promising candidates for antidesmoplastic or COL11A1-targeted therapies. The amount of CAFsCOL11A1 correlated significantly with tumour grade, tumour stage and nodal spread in the panCancer cohort. Significant associations between CAFsCOL11A1 and vascular invasion, perineural spread and nodal spread were observed in the SGC cohort. Also, we discovered that tumour cells of intercalated duct derived SGC and CAFs produce COL11A1 in a mutually exclusive manner. Our findings represent a novel mode of extracellular matrix production in carcinomas and could be highly relevant in the future. Our findings elucidate the mode of COL11A1 expression in very different carcinoma types and may aid to categorise tumours in the setting of possible future COL11A1-related therapies.
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Affiliation(s)
- Christoph Arolt
- Medical Faculty, Institute of Pathology, University of Cologne, Kerpener Straße 62, 50937 Cologne, Germany
| | - Franziska Hoffmann
- Department of Otorhinolaryngology, MALDI Imaging and Innovative Biophotonics, Jena University Hospital, 07747 Jena, Germany
| | - Lisa Nachtsheim
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, 50937 Cologne, Germany
| | - Philipp Wolber
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, 50937 Cologne, Germany
| | - Orlando Guntinas-Lichius
- Department of Otorhinolaryngology, Head and Neck Surgery, Jena University Hospital, 07747 Jena, Germany
| | - Reinhard Buettner
- Medical Faculty, Institute of Pathology, University of Cologne, Kerpener Straße 62, 50937 Cologne, Germany
| | - Ferdinand von Eggeling
- Department of Otorhinolaryngology, Head and Neck Surgery, Jena University Hospital, 07747 Jena, Germany
- MALDI Imaging, Core Unit Proteome Analysis, DFG Core Unit Jena Biophotonic and Imaging, Laboratory (JBIL), Jena University Hospital, 07747 Jena, Germany
| | - Alexander Quaas
- Medical Faculty, Institute of Pathology, University of Cologne, Kerpener Straße 62, 50937 Cologne, Germany
| | - Jens Peter Klußmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, 50937 Cologne, Germany
- Medical Faculty, Centre for Molecular Medicine Cologne (CMMC), University of Cologne, 50937 Cologne, Germany
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19
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Wang H, Zhou H, Ni H, Shen X. COL11A1-Driven Epithelial-Mesenchymal Transition and Stemness of Pancreatic Cancer Cells Induce Cell Migration and Invasion by Modulating the AKT/GSK-3β/Snail Pathway. Biomolecules 2022; 12:391. [PMID: 35327583 PMCID: PMC8945532 DOI: 10.3390/biom12030391] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Collagen type XI α1 (COL11A1) is associated with tumorigenesis and development in many human malignancies. Previous reports indicate that COL11A1 may be a significant diagnostic marker for pancreatic ductal adenocarcinoma (PDAC); however, its biological role in PDAC progression remains unclear. In this study, we investigated the influence of COL11A1 on the invasion and migration abilities of pancreatic cancer cells and explored its potential molecular mechanisms. METHODS Cell migration and invasion were assessed using Transwell assays in pancreatic cancer cells transfected with siCOL11A1 and pCNV3-COL11A1 plasmids. The protein and mRNA expression levels of N-cadherin, E-cadherin, Vimentin, cluster of differentiation (CD)-24, CD44, serine-threonine kinase (AKT), glycogen synthase kinase (GSK)-3β, phospho (p)-AKTSer473, p-GSK-3βSer9, and Snail were analyzed using Western blotting and real-time polymerase chain reaction (PCR). The effect of COL11A1 on cell stemness was tested using flow cytometry and clone formation assays. RESULTS These results demonstrated that COL11A1 significantly promoted the invasion and migration abilities of PDAC cells. Furthermore, COL11A1 facilitated the occurrence of epithelial-mesenchymal transition (EMT) and cell stemness by upregulating the expression levels of p-AKTSer473, p-GSK-3βSer9, and Snail. CONCLUSIONS This study suggests that the activation of the AKT/GSK-3β/Snail signaling pathway induced by COL11A1 plays a major role in the progression of PDAC. Therefore, COL11A1 could serve as a potential target for PDAC treatment.
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Affiliation(s)
- Hui Wang
- Drug Synthesis Laboratory, Tianjin Institute of Medical & Pharmaceutical Sciences, Tianjin 300020, China;
- School of Medicine, Nankai University, Tianjin 300071, China; (H.Z.); (H.N.)
| | - Huichao Zhou
- School of Medicine, Nankai University, Tianjin 300071, China; (H.Z.); (H.N.)
| | - Hong Ni
- School of Medicine, Nankai University, Tianjin 300071, China; (H.Z.); (H.N.)
| | - Xiaohong Shen
- School of Medicine, Nankai University, Tianjin 300071, China; (H.Z.); (H.N.)
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20
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Truong DQ, Ho BT, Chau GC, Truong DK, Pham TTT, Nakagawara A, Bui CB. Collagen XI Alpha 1 (COL11A1) Expression in the Tumor Microenvironment Drives Neuroblastoma Dissemination. Pediatr Dev Pathol 2022; 25:91-98. [PMID: 34460335 DOI: 10.1177/10935266211039200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND Neuroblastoma (NB) is among the most common cancers in children. A highly aggressive form of cancer, NB relies on cells in the microenvironment for dissemination particularly cancer associated fibroblast (CAFs). CAFs synthesise the extracellular matrix to create a scaffold for tumor growth thus enabling the carcinogenesis of NB, Collagen, an abundant scaffold protein produced by CAFs, has been implicated in the creation of an optimal tumor microenvironment, however, the expression profile of collagen within NB is not yet known. METHODS We characterised collagen expression within the tumor-stroma boundary by microarray and confirmed by qRT-PCR and immunohistochemistry. RESULTS The collagen marker, COL11A1, was also upregulated in NB CD45+ cells and SMA+ CAFs. Furthermore, SMA+ CAFs led to neuroblastoma cell invasion in an in vitro co-culture system which was subsequently attenuated by gene silencing COL11A1. Immunohistochemical staining of clinical tumor samples revealed that high COL11A1 expression in the stroma adjacent to tumour site, significantly associated with advanced cancer stages, age ≥18 months, undifferentiated tumor status, relapse and poor overall survival. CONCLUSION Collectively, these results suggest that a COL11A1 signature in the NB microenvironment could represent a novel target for therapeutic intervention.
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Affiliation(s)
| | - Ban Tran Ho
- Department of Paediatric Surgery, Faculty of Medicine, University of medicine and pharmacy at Hochiminh city, Vietnam.,Children Hospital 2, Ho Chi Minh City, Vietnam
| | - Gia-Cac Chau
- School of Medicine, Sungkyunkwan University, Suwon, Korea
| | - Dinh Khai Truong
- Department of Paediatric Surgery, Faculty of Medicine, University of medicine and pharmacy at Hochiminh city, Vietnam.,Children Hospital 2, Ho Chi Minh City, Vietnam
| | | | - Akira Nakagawara
- Division of Innovative Cancer Therapeutics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Chi-Bao Bui
- City Children's Hospital, Ho Chi Minh City, Vietnam.,Vietnam National University Ho Chi Minh city, Ho Chi Minh, Vietnam.,School of Medicine, Ho Chi Minh city, Vietnam
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21
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A Five Collagen-Related Gene Signature to Estimate the Prognosis and Immune Microenvironment in Clear Cell Renal Cell Cancer. Vaccines (Basel) 2021; 9:vaccines9121510. [PMID: 34960256 PMCID: PMC8707639 DOI: 10.3390/vaccines9121510] [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: 11/20/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 11/30/2022] Open
Abstract
Collagen is the main component of the extracellular matrix (ECM) and might play an important role in tumor microenvironments. However, the relationship between collagen and clear cell renal cell cancer (ccRCC) is still not fully clarified. Hence, we aimed to establish a collagen-related signature to predict the prognosis and estimate the tumor immune microenvironment in ccRCC patients. Patients with a high risk score were often correlated with unfavorable overall survival (OS) and an immunosuppressive microenvironment. In addition, the collagen-related genetic signature was highly correlated with clinical pathological features and can be considered as an independent prognostic factor in ccRCC patients. Moreover, GSEA results show that patients with a high risk grade tend to be associated with epithelial–mesenchymal junctions (EMT) and immune responses. In this study, we developed a collagen-related gene signature, which might possess the potential to predict the prognosis and immune microenvironment of ccRCC patients and function as an independent prognostic factor in ccRCC.
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22
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Noël A, Perveen Z, Xiao R, Hammond H, Le Donne V, Legendre K, Gartia MR, Sahu S, Paulsen DB, Penn AL. Mmp12 Is Upregulated by in utero Second-Hand Smoke Exposures and Is a Key Factor Contributing to Aggravated Lung Responses in Adult Emphysema, Asthma, and Lung Cancer Mouse Models. Front Physiol 2021; 12:704401. [PMID: 34912233 PMCID: PMC8667558 DOI: 10.3389/fphys.2021.704401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/19/2021] [Indexed: 12/18/2022] Open
Abstract
Matrix metalloproteinase-12 (Mmp12) is upregulated by cigarette smoke (CS) and plays a critical role in extracellular matrix remodeling, a key mechanism involved in physiological repair processes, and in the pathogenesis of emphysema, asthma, and lung cancer. While cigarette smoking is associated with the development of chronic obstructive pulmonary diseases (COPD) and lung cancer, in utero exposures to CS and second-hand smoke (SHS) are associated with asthma development in the offspring. SHS is an indoor air pollutant that causes known adverse health effects; however, the mechanisms by which in utero SHS exposures predispose to adult lung diseases, including COPD, asthma, and lung cancer, are poorly understood. In this study, we tested the hypothesis that in utero SHS exposure aggravates adult-induced emphysema, asthma, and lung cancer. Methods: Pregnant BALB/c mice were exposed from gestational days 6–19 to either 3 or 10mg/m3 of SHS or filtered air. At 10, 11, 16, or 17weeks of age, female offspring were treated with either saline for controls, elastase to induce emphysema, house-dust mite (HDM) to initiate asthma, or urethane to promote lung cancer. At sacrifice, specific disease-related lung responses including lung function, inflammation, gene, and protein expression were assessed. Results: In the elastase-induced emphysema model, in utero SHS-exposed mice had significantly enlarged airspaces and up-regulated expression of Mmp12 (10.3-fold compared to air-elastase controls). In the HDM-induced asthma model, in utero exposures to SHS produced eosinophilic lung inflammation and potentiated Mmp12 gene expression (5.7-fold compared to air-HDM controls). In the lung cancer model, in utero exposures to SHS significantly increased the number of intrapulmonary metastases at 58weeks of age and up-regulated Mmp12 (9.3-fold compared to air-urethane controls). In all lung disease models, Mmp12 upregulation was supported at the protein level. Conclusion: Our findings revealed that in utero SHS exposures exacerbate lung responses to adult-induced emphysema, asthma, and lung cancer. Our data show that MMP12 is up-regulated at the gene and protein levels in three distinct adult lung disease models following in utero SHS exposures, suggesting that MMP12 is central to in utero SHS-aggravated lung responses.
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Affiliation(s)
- Alexandra Noël
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Zakia Perveen
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Rui Xiao
- Department of Anesthesiology, Columbia University Medical Center, New York, NY, United States
| | - Harriet Hammond
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | | | - Kelsey Legendre
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Manas Ranjan Gartia
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, United States
| | - Sushant Sahu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Daniel B Paulsen
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Arthur L Penn
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
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23
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Kang Z, Zhu J, Sun N, Zhang X, Liang G, Kou Y, Zhu H, Carbonelli C, Sakao Y, Zhang Y. COL11A1 promotes esophageal squamous cell carcinoma proliferation and metastasis and is inversely regulated by miR-335-5p. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1577. [PMID: 34790783 PMCID: PMC8576684 DOI: 10.21037/atm-21-4951] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/21/2021] [Indexed: 12/13/2022]
Abstract
Background Esophagus squamous cell carcinoma (ESCC) is a sort of cancer that occurs in the esophageal epithelial tissue. This study performed integrated bioinformatics analysis of Gene Expression Omnibus (GEO) datasets GSE32424, GSE29968, and GSE130078. Collagen type XI alpha 1 (COL11A1) was identified as the hub gene in ESCC progression. The involvement of COL11A1 in ESCC development was next determined using in vitro functional tests. Methods Hub genes were identified through integrated bioinformatics analysis. The real-time reverse transcription-polymerase chain reaction was implemented for detecting the expression of COL11A1 mRNA in esophageal cancer cells. KYSE-30 cells were transfected using a vector encoding COL11A1. The proliferation of cells was determined using the Cell Counting Kit-8 (CCK-8) assay. Detection of the cell migration and invasion was made through making use of the transwell test. The development of ESCC cells in vivo was evaluated in naked mice. The interplay among COL11A1 and microRNA-335-5p (miR-335-5p) was discovered using a luciferase reporter experiment. Results In vitro studies showed the upregulation of COL11A1 in ESCC cell lines obtained from ESCC patients and upregulation of COL11A1 was correlated with poor disease-free survival of ESCC patients, thereby implying an oncogenic involvement of COL11A1 in ESCC. Overexpression of COL11A1 enhanced the proliferation of ESCC cells, invasion, and migration; whereas COL11A1 knockdown impeded the proliferation of ESCC cells, invasion, and migration. Additionally, miRNA pathway analysis in combination with TargetScan’s online prediction and the luciferase reporter assay suggested miR-335-5p targeting and negatively regulating the COL11A1 3' untranslated region (3'UTR) within ESCC cells. MiR-335-5p overexpression diminished the development of ESCC cells. Additionally, co-expression of COL11A1 ameliorated the repressive influence of miR-335-5p overexpression on the growth and metastasis of ESCC cells. Conclusions Using comprehensive bioinformatics analysis, the current study identified COL11A1 as an oncogene in ESCC. The mechanistic studies indicated that COL11A1 promoted ESCC cell progression and that miR-335-5p negatively regulated the expression of COL11A1 in ESCC.
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Affiliation(s)
- Zheng Kang
- Department of Radiology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jiali Zhu
- Department of Pain Management, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Ning Sun
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaomei Zhang
- Department of Scientific Research, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Geyu Liang
- Key Laboratory of Enviromental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Yingying Kou
- Clinical Pharmacology Base, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Huayun Zhu
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Cristiano Carbonelli
- Department of Medical Sciences, Fondazione IRCCS "Casa Sollievo della Sofferenza", Viale Cappuccini snc, San Giovanni Rotondo, Italy
| | - Yukinori Sakao
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Yan Zhang
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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24
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Identification of Significant Genes in Lung Cancer of Nonsmoking Women via Bioinformatics Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5516218. [PMID: 34671675 PMCID: PMC8523254 DOI: 10.1155/2021/5516218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 08/26/2021] [Indexed: 11/24/2022]
Abstract
Background The aim of this study was to identify potential key genes, proteins, and associated interaction networks for the development of lung cancer in nonsmoking women through a bioinformatics approach. Methods We used the GSE19804 dataset, which includes 60 lung cancer and corresponding paracancerous tissue samples from nonsmoking women, to perform the work. The GSE19804 microarray was downloaded from the GEO database and differentially expressed genes were identified using the limma package analysis in R software, with the screening criteria of p value < 0.01 and ∣log2 fold change (FC) | >2. Results A total of 169 DEGs including 130 upregulated genes and 39 downregulated were selected. Gene Ontology and KEGG pathway analysis were performed using the DAVID website, and protein-protein interaction (PPI) networks were constructed and the hub gene module was screened through STING and Cytoscape. Conclusions We obtained five key genes such as GREM1, MMP11, SPP1, FOSB, and IL33 which were strongly associated with lung cancer in nonsmoking women, which improved understanding and could serve as new therapeutic targets, but their functionality needs further experimental verification.
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25
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Herzog BH, Devarakonda S, Govindan R. Overcoming Chemotherapy Resistance in SCLC. J Thorac Oncol 2021; 16:2002-2015. [PMID: 34358725 DOI: 10.1016/j.jtho.2021.07.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/09/2021] [Accepted: 07/18/2021] [Indexed: 10/20/2022]
Abstract
SCLC is an aggressive form of lung cancer with a very poor prognosis. Although SCLC initially responds very well to platinum-based chemotherapy, it eventually recurs and at recurrence is nearly universally resistant to therapy. In light of the recent advances in understanding regarding the biology of SCLC, we review findings related to SCLC chemotherapy resistance. We discuss the potential clinical implications of recent preclinical discoveries in altered signaling pathways, transcriptional landscapes, metabolic vulnerabilities, and the tumor microenvironment.
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Affiliation(s)
- Brett H Herzog
- Division of Oncology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Alvin J Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri
| | - Siddhartha Devarakonda
- Division of Oncology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Alvin J Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri
| | - Ramaswamy Govindan
- Division of Oncology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Alvin J Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri.
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26
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Song D, Lyu H, Feng Q, Luo J, Li L, Wang X. Subtyping of head and neck squamous cell cancers based on immune signatures. Int Immunopharmacol 2021; 99:108007. [PMID: 34332341 DOI: 10.1016/j.intimp.2021.108007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022]
Abstract
Although head and neck squamous cell cancer (HNSCC) is one of the cancer types in which immune checkpoint inhibitors (ICIs) has achieved a certain success, only a subset of HNSCC patients respond to ICIs. Thus, identification of HNSCC subtypes responsive to ICIs is crucial. Using hierarchical clustering, we identified three subtypes of HNSCC, termed Immunity-H, Immunity-M, and Immunity-L, based on the enrichment scores of 28 immune cells generated by the single-sample gene-set enrichment analysis of transcriptome data. We demonstrated that this subtyping method was stable and producible in four different HNSCC cohorts. Immunity-H had the highest levels of immune infiltrates and PD-L1 expression, lowest levels of stemness, intratumor heterogeneity and genomic instability, and favorable prognosis. In contrast, Immunity-L had the lowest levels of immune infiltrates and PD-L1 expression, highest levels of stemness, intratumor heterogeneity and genomic instability, and unfavorable prognosis. We found that somatic copy number alteration had a significant negative association with anti-tumor immunity in HNSCC, while tumor mutation burden showed no significant association. TP53, COL11A1, NSD1, and PKHD1L1 were more frequently mutated in Immunity-H versus Immunity-L, and their mutations were associated with increased immune signatures in HNSCC. Besides immune-related pathways, many stromal and oncogenic pathways were highly enriched in Immunity-H, including cell adhesion molecules, focal adhesion, ECM-receptor interaction, calcium signaling, MAPK signaling, apoptosis, VEGF signaling, and PPAR signaling. The high levels of PD-L1 expression and immune infiltration in Immunity-H indicate that this subtype responds best to ICIs. Our study recaptures the immunological heterogeneity in HNSCC and provide clinical implications for the immunotherapy of HNSCC.
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Affiliation(s)
- Dandan Song
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Haoyu Lyu
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Qiushi Feng
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Jiangti Luo
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Lin Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China.
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Single-cell analysis reveals the pan-cancer invasiveness-associated transition of adipose-derived stromal cells into COL11A1-expressing cancer-associated fibroblasts. PLoS Comput Biol 2021; 17:e1009228. [PMID: 34283835 PMCID: PMC8323949 DOI: 10.1371/journal.pcbi.1009228] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/30/2021] [Accepted: 06/30/2021] [Indexed: 01/01/2023] Open
Abstract
During the last ten years, many research results have been referring to a particular type of cancer-associated fibroblasts associated with poor prognosis, invasiveness, metastasis and resistance to therapy in multiple cancer types, characterized by a gene expression signature with prominent presence of genes COL11A1, THBS2 and INHBA. Identifying the underlying biological mechanisms responsible for their creation may facilitate the discovery of targets for potential pan-cancer therapeutics. Using a novel computational approach for single-cell gene expression data analysis identifying the dominant cell populations in a sequence of samples from patients at various stages, we conclude that these fibroblasts are produced by a pan-cancer cellular transition originating from a particular type of adipose-derived stromal cells naturally present in the stromal vascular fraction of normal adipose tissue, having a characteristic gene expression signature. Focusing on a rich pancreatic cancer dataset, we provide a detailed description of the continuous modification of the gene expression profiles of cells as they transition from APOD-expressing adipose-derived stromal cells to COL11A1-expressing cancer-associated fibroblasts, identifying the key genes that participate in this transition. These results also provide an explanation to the well-known fact that the adipose microenvironment contributes to cancer progression.
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28
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Liu Z, Lai J, Jiang H, Ma C, Huang H. Collagen XI alpha 1 chain, a potential therapeutic target for cancer. FASEB J 2021; 35:e21603. [PMID: 33999448 DOI: 10.1096/fj.202100054rr] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 11/11/2022]
Abstract
Extracellular matrix (ECM) plays an important role in the progression of cancer. Collagen is the most abundant component in ECM, and it is involved in the biological formation of cancer. Although type XI collagen is a minor fibrillar collagen, collagen XI alpha 1 chain (COL11A1) has been found to be upregulated in a variety of cancers including ovarian cancer, breast cancer, thyroid cancer, pancreatic cancer, non-small-cell lung cancer, and transitional cell carcinoma of the bladder. High levels of COL11A1 usually predict poor prognosis, while COL11A1 is related to angiogenesis, invasion, and drug resistance of cancer. However, little is known about the specific mechanism by which COL11A1 regulates tumor progression. Here, we have organized and summarized the recent developments regarding elucidation of the relationship between COL11A1 and various cancers, as well as the interaction between COL11A1 and intracellular signaling pathways. In addition, we have selected therapeutic agents targeting COL11A1. All these indicate the possibility of using COL11A1 as a target for cancer treatment.
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Affiliation(s)
- Ziqiang Liu
- Department of Neurosurgery, the First Hospital of Jilin University, Changchun, China
| | - Jiacheng Lai
- Department of Neurosurgery, the First Hospital of Jilin University, Changchun, China
| | - Heng Jiang
- Department of Neurosurgery, the First Hospital of Jilin University, Changchun, China
| | - Chengyuan Ma
- Department of Neurosurgery, the First Hospital of Jilin University, Changchun, China
| | - Haiyan Huang
- Department of Neurosurgery, the First Hospital of Jilin University, Changchun, China
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29
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Zhang Y, Fu Y. Comprehensive Analysis and Identification of an Immune-Related Gene Signature with Prognostic Value for Prostate Cancer. Int J Gen Med 2021; 14:2931-2942. [PMID: 34234523 PMCID: PMC8254424 DOI: 10.2147/ijgm.s321319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/14/2021] [Indexed: 12/27/2022] Open
Abstract
Background The tumor microenvironment (TME) has recently been proven to play a crucial role in the development and prognosis of tumors. However, the current knowledge on the potential of the TME in prostate cancer (PCa) remains scarce. Purpose This study aims to elucidate the value of TME-related genes for PCa prognosis by integrative bioinformatics analysis. Materials and Methods We downloaded the immune and stromal scores of PCa samples via the ESTIMATE and correlated these scores to clinicopathological characteristics and recurrence-free survival (RFS) of patients. Based on these scores, the TME-related differentially expressed genes were identified for functional enrichment analysis. Cox regression analyses were performed to identify prognostic genes and establish a predictive risk model. Moreover, gene set enrichment analysis (GSEA) was performed to evaluate the relationship between risk score and immune pathway. Results The stromal and immune scores were associated with clinicopathological characteristics and RFS in PCa patients. In total, 238 intersecting differentially expressed genes were identified. Functional enrichment analysis further revealed that these genes dramatically participated in the immune-related pathways. The immune-related risk model was built with C-type lectin domain containing 7A (CLEC7A) and collagen type XI alpha 1 chain (COL11A1) using Cox regression analyses. Kaplan–Meier survival analysis showed that the expression levels of CLEC7A and COL11A1 were significantly associated with the RFS. Further, the RFS time in high-risk group was significantly shorter than that in low-risk group. The areas under the curve for the risk model in predicting 3- and 5-year RFS rates were 0.694 and 0.731, respectively. GSEA suggested that immunosuppression existed in high-risk PCa patients. Conclusion CLEC7A and COL11A1 were selected to build a predictive risk model, which may help clinicians to assess the prognosis of PCa patients and select appropriate targets for immunotherapy.
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Affiliation(s)
- Yongrui Zhang
- Department of Urology, The First Hospital of Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Yaowen Fu
- Department of Urology, The First Hospital of Jilin University, Changchun, 130021, Jilin, People's Republic of China
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30
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Li X, He Z, Zhang J, Han Y. Identification of crucial noncoding RNAs and mRNAs in hypertrophic scars via RNA sequencing. FEBS Open Bio 2021; 11:1673-1684. [PMID: 33932142 PMCID: PMC8167876 DOI: 10.1002/2211-5463.13167] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/04/2021] [Accepted: 04/14/2021] [Indexed: 12/22/2022] Open
Abstract
Hypertrophic scarring (HS) is a dermal fibroproliferative disorder characterized by excessive deposition of collagen and other extracellular matrix components. The aim of this study is to explore crucial long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) associated with HS and provide a better understanding of the molecular mechanism of HS. To investigate the lncRNA, circRNA and mRNA expression profiles, we performed RNA sequencing of human HS and normal skin tissues. After the identification of differentially expressed mRNAs (DEmRNAs), lncRNAs (DElncRNAs) and circRNAs (DEcircRNAs), we performed functional enrichment of DEmRNAs. Further on, we constructed DElncRNA/DEcircRNA–DEmRNA coexpression networks and competing endogenous RNA regulatory networks, and performed functional analyses of the DEmRNAs in the constructed networks. In total, 487 DEmRNAs, 92 DElncRNAs and 17 DEcircRNAs were identified. DEmRNAs were significantly enriched in processes such as collagen fibril organization, extracellular matrix–receptor interaction and the phosphatidylinositol 3‐kinase (PI3K)–Akt signaling pathway. In addition, we detected 580 DElncRNA–DEmRNA and 505 DEcircRNA–DEmRNA coexpression pairs. The competing endogenous RNA network contained 18 circRNA–microRNA (miRNA) pairs, 18 lncRNA–miRNA pairs and 409 miRNA–mRNA pairs, including 10 circRNAs, 5 lncRNAs, 15 miRNAs and 160 mRNAs. We concluded that MIR503HG/hsa‐miR‐204‐3p/ACAN, MIR503HG/hsa‐miR‐431‐5p/TNFRSF9, MEG3/hsa‐miR‐6884‐5p/ADAMTS14, AC000035.1‐ADAMTS14 and hsa_circ_0069865‐COMP/ADAM12 interaction pairs may play a central role in HS.
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Affiliation(s)
- Xiaodong Li
- Department of Burn and Plastic Surgery, The 980st Hospital of the PLA Joint Logistics Support Force, Shijiazhuang, China.,Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zeliang He
- Department of Burn and Plastic Surgery, The 980st Hospital of the PLA Joint Logistics Support Force, Shijiazhuang, China
| | - Julei Zhang
- Department of Burn and Plastic Surgery, The 980st Hospital of the PLA Joint Logistics Support Force, Shijiazhuang, China
| | - Yan Han
- Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
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31
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Pöschel A, Beebe E, Kunz L, Amini P, Guscetti F, Malbon A, Markkanen E. Identification of disease-promoting stromal components by comparative proteomic and transcriptomic profiling of canine mammary tumors using laser-capture microdissected FFPE tissue. Neoplasia 2021; 23:400-412. [PMID: 33794398 PMCID: PMC8042244 DOI: 10.1016/j.neo.2021.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 02/08/2023] Open
Abstract
Cancer-associated stroma (CAS) profoundly influences progression of tumors including mammary carcinoma (mCA). Canine simple mCA represent relevant models of human mCA, notably also with respect to CAS. While transcriptomic changes in CAS of mCA are well described, it remains unclear to what extent these translate to the protein level. Therefore, we sought to gain insight into the proteomic changes in CAS and compare them with transcriptomic changes in the same tissue. To this end, we analyzed CAS and matched normal stroma using laser-capture microdissection (LCM) and LC-MS/MS in a cohort of 14 formalin-fixed paraffin embedded (FFPE) canine mCAs that we had previously characterized using LCM-RNAseq. Our results reveal clear differences in protein abundance between CAS and normal stroma, which are characterized by changes in the extracellular matrix, the cytoskeleton, and cytokines such as TNF. The proteomics- and RNAseq-based analyses of LCM-FFPE show a substantial degree of correlation, especially for the most deregulated targets and a comparable activation of pathways. Finally, we validate transcriptomic upregulation of LTBP2, IGFBP2, COL6A5, POSTN, FN1, COL4A1, COL12A1, PLOD2, COL4A2, and IGFBP7 in CAS on the protein level and demonstrate their adverse prognostic value for human breast cancer. Given the relevance of canine mCA as a model for the human disease, our analysis substantiates these targets as disease-promoting stromal components with implications for breast cancer in both species.
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Affiliation(s)
- Amiskwia Pöschel
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Erin Beebe
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Laura Kunz
- Functional Genomics Center Zürich, ETH Zürich/University of Zurich, Zurich, Switzerland
| | - Parisa Amini
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Franco Guscetti
- Institute of Veterinary Pathology Vetsuisse Faculty, University of Zurich, Zürich, Switzerland
| | - Alexandra Malbon
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute Easter Bush Campus, Midlothian, Scotland
| | - Enni Markkanen
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
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32
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Shi Y, Chang D, Li W, Zhao F, Ren X, Hou B. Identification of core genes and clinical outcomes in tumors originated from endoderm (gastric cancer and lung carcinoma) via bioinformatics analysis. Medicine (Baltimore) 2021; 100:e25154. [PMID: 33761685 PMCID: PMC10545272 DOI: 10.1097/md.0000000000025154] [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: 02/16/2020] [Revised: 11/30/2020] [Accepted: 02/23/2021] [Indexed: 12/24/2022] Open
Abstract
ABSTRACT During last decade, bioinformatics analysis has provided an effective way to study the relationship between various genes and biological processes. In this study, we aimed to identify potential core candidate genes and underlying mechanisms of progression of lung and gastric carcinomas which both originated from endoderm. The expression profiles, GSE54129 (gastric carcinoma) and GSE27262 (lung carcinoma), were collected from GEO database. One hundred eleven patients with gastric carcinoma and 21 health people were included in this research. Meanwhile, there were 25 lung carcinoma patients. Then, 75 differentially expressed genes were selected via GEO2R online tool and Venn software, including 31 up-regulated genes and 44 down-regulated genes. Next, we used Database for Annotation, Visualization, and Integrated Discovery and Metascpe software to analyze Kyoto Encyclopedia of Gene and Genome pathway and gene ontology. Furthermore, Cytoscape software and MCODE App were performed to construct complex of these differentially expressed genes . Twenty core genes were identified, which mainly enriched in extracellular matrix-receptor interaction, focal adhesion, and PI3K-Akt pathway (P < .01). Finally, the significant difference of gene expression between cancer tissues and normal tissues in both lung and gastric carcinomas was examined by Gene Expression Profiling Interactive Analysis database. Twelve candidate genes with positive statistical significance (P < .01), COMP CTHRC1 COL1A1 SPP1 COL11A1 COL10A1 CXCL13 CLDN3 CLDN1 matrix metalloproteinases 7 ADAM12 PLAU, were picked out to further analysis. The Kaplan-Meier plotter website was applied to examine relationship among these genes and clinical outcomes. We found 4 genes (ADAM12, SPP1, COL1A1, COL11A1) were significantly associated with poor prognosis in both lung and gastric carcinoma patients (P < .05). In conclusion, these candidate genes may be potential therapeutic targets for cancer treatment.
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Affiliation(s)
- Yewen Shi
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Affiliated Hospital of Xi’an Jiaotong University
| | - Dongmin Chang
- Department of Surgical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University
| | - Wenhan Li
- Department of Surgical Oncology, Shaanxi Provincial People's Hospital
- The Third Affiliated Hospital, the School of Medicine Xi’an Jiaotong University
| | - FengYu Zhao
- Department of Surgical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University
| | - Xiaoyong Ren
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Affiliated Hospital of Xi’an Jiaotong University
| | - Bin Hou
- The Third Affiliated Hospital, the School of Medicine Xi’an Jiaotong University
- Department of Thoracic Surgery, Shaanxi Provincial People's Hospital, Xi’an, Shaanxi, China
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33
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Zhang J, Zhang J, Wang F, Xu X, Li X, Guan W, Men T, Xu G. Overexpressed COL5A1 is correlated with tumor progression, paclitaxel resistance, and tumor-infiltrating immune cells in ovarian cancer. J Cell Physiol 2021; 236:6907-6919. [PMID: 33655494 DOI: 10.1002/jcp.30350] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/02/2021] [Accepted: 02/17/2021] [Indexed: 01/19/2023]
Abstract
Ovarian cancer (OC) remains the leading cause of cancer-related death among gynecological cancers. The present study examined the role of collagen type V alpha 1 (COL5A1) and the characteristics of COL5A1 as an oncogenic protein in OC. The association of COL5A1 with paclitaxel (PTX)-resistance and stemness in OC was also studied and the multidatabase and big data analyses of the prognostic value, coexpression network, genetic alterations, and tumor-infiltrating immune cells of COL5A1 were elucidated. We found that COL5A1 expression was high in OC cells and tissues. Knockdown of COL5A1 inhibited the proliferation and migration of OC cells. Further study also showed that COL5A1 was overexpressed in PTX-resistant OC cells compared to respective PTX-sensitive cells. Additionally, COL5A1 was more enriched in OC stem cell-like cells. Silencing COL5A1 expression decreased the OC cell resistance to PTX and inhibited the ability of OC-spheroid formation. Survival analysis predicted that the elevated COL5A1 expression was associated with a worse survival outcome and correlated to the tumor stage of OC patients. The estimating relative subsets of RNA transcripts (CIBERSORT) algorithm analysis also unveiled the correlation of several tumor-infiltrating immune cells with the expression of COL5A1. Taken together, our data demonstrate that COL5A1 is a biomarker to predict OC progression and PTX-resistance and represents a promising target for OC treatment.
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Affiliation(s)
- Jinguo Zhang
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jihong Zhang
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, Shanghai, China
| | - Fanchen Wang
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaolin Xu
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xin Li
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wencai Guan
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, Shanghai, China
| | - Ting Men
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, Shanghai, China
| | - Guoxiong Xu
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, China
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34
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Kumar A, Nayakanti DS, Mangalaparthi KK, Gopinath V, Reddy NVN, Govindan K, Voolapalli G, Kumar P, Kumar LD. Quantitative proteome profiling stratifies fibroepithelial lesions of the breast. Oncotarget 2021; 12:507-518. [PMID: 33747363 PMCID: PMC7939526 DOI: 10.18632/oncotarget.27889] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/26/2021] [Indexed: 11/25/2022] Open
Abstract
Breast fibroepithelial lesions (FELs) include heterogeneous pathological tumors, involving indolent fibroadenoma (FAD) to potentially aggressive phyllodes tumors (PTs). The current grading system remains unreliable in differentiating these tumors due to histological heterogeneity and lack of appropriate markers to monitor the sudden and unpredictable malignant transformation of PTs. Thus, there exists an imminent need for a marker-based diagnostic approach to augment the conventional histological platform that could lead to accurate diagnosis and distinction of FELs. The high- throughput quantitative proteomic analysis suggested that FAD and PTs form distinct clusters away from borderline and malignant though there exist marked differences between them. Interestingly, over-expression of extracellular matrices (ECM) related proteins and epithelial-mesenchymal transition (EMT) markers in borderline PTs led us to hypothesize a model of deposition and degradation leading to ECM remodeling and EMT acquisition triggering its malignant transformation. We also identified three candidate biomarkers such as MUCL1, HTRA1, and VEGDF uniquely expressed in FAD, borderline, and malignant PTs, respectively, which were further validated using immunohistochemistry. The present work shed light on a brief mechanistic framework of PTs aggressive nature and present potential biomarkers to differentiate overlapping FELs that would be of practical utility in augmenting existing diagnosis and disease management for this rare tumor.
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Affiliation(s)
- Aviral Kumar
- Cancer Biology, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India.,Authors share equal first authorship
| | - David S Nayakanti
- Institute of Bioinformatics, Discoverer Building International Tech Park, Whitefield, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.,Authors share equal first authorship
| | - Kiran K Mangalaparthi
- Institute of Bioinformatics, Discoverer Building International Tech Park, Whitefield, Bangalore, 560066, India.,Authors share equal second authorship
| | - Veena Gopinath
- Cancer Biology, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India.,Authors share equal second authorship
| | | | - Krishna Govindan
- Department of Pathology, Government Medical College, Thiruvananthapuram, Kerala, 695011, India
| | - Geeta Voolapalli
- Department of Surgery and Pathology, Gandhi Hospital, Secunderabad, 500025, India
| | - Prashant Kumar
- Institute of Bioinformatics, Discoverer Building International Tech Park, Whitefield, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Lekha Dinesh Kumar
- Cancer Biology, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
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35
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Nallanthighal S, Heiserman JP, Cheon DJ. Collagen Type XI Alpha 1 (COL11A1): A Novel Biomarker and a Key Player in Cancer. Cancers (Basel) 2021; 13:935. [PMID: 33668097 PMCID: PMC7956367 DOI: 10.3390/cancers13050935] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/17/2022] Open
Abstract
Collagen type XI alpha 1 (COL11A1), one of the three alpha chains of type XI collagen, is crucial for bone development and collagen fiber assembly. Interestingly, COL11A1 expression is increased in several cancers and high levels of COL11A1 are often associated with poor survival, chemoresistance, and recurrence. This review will discuss the recent discoveries in the biological functions of COL11A1 in cancer. COL11A1 is predominantly expressed and secreted by a subset of cancer-associated fibroblasts, modulating tumor-stroma interaction and mechanical properties of extracellular matrix. COL11A1 also promotes cancer cell migration, metastasis, and therapy resistance by activating pro-survival pathways and modulating tumor metabolic phenotype. Several inhibitors that are currently being tested in clinical trials for cancer or used in clinic for other diseases, can be potentially used to target COL11A1 signaling. Collectively, this review underscores the role of COL11A1 as a promising biomarker and a key player in cancer.
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Affiliation(s)
| | | | - Dong-Joo Cheon
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, USA; (S.N.); (J.P.H.)
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36
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Patra R, Das NC, Mukherjee S. Exploring the Differential Expression and Prognostic Significance of the COL11A1 Gene in Human Colorectal Carcinoma: An Integrated Bioinformatics Approach. Front Genet 2021; 12:608313. [PMID: 33597969 PMCID: PMC7882494 DOI: 10.3389/fgene.2021.608313] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 01/14/2021] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer is one of the most common cancers of humans and the second highest in cancer-related death. Genes used as prognostic biomarkers play an imperative role in cancer detection and may direct the development of appropriate therapeutic strategies. Collagen type XI alpha 1 (COL11A1) is a minor fibrillary collagen that has an essential role in the regulation of cell division, differentiation, proliferation, migration, growth, and apoptosis of intestinal and colon cells. The present study seeks to evaluate the significance of the COL11A1 gene in the progression of colorectal cancer in humans across the various parameters using advanced bioinformatics approaches. The application of various databases and servers like ONCOMINE, UALCAN, and GEPIA were accessed for analyzing the differential expression of the COLL11A1 gene and its relative influence over the survival of the transformed subjects. In addition, oncogenomics of COL11A1 gene, mutations associated with this gene and interacting partners of the gene in the context of oncogenesis were studied using COSMIC, cBioPortal, GeneMANIA, and NetworkAnalyst. Our experimental data indicate that the COL11A1 gene is overexpressed in the transformed tissues across the various clinicopathological parameters reduces the probability of survival in both overall and disease-specific survival cases. Mutational studies imply that it can induce perturbations in various signaling pathways viz. RTK-RAS-PI3K, Wnt, TGF-β, and TP53 pathways influencing cancer development. Also, a positive association and correlation amongst the THBS2, COL10A1, COL5A2, and COL1A2 genes were observed, which most likely to contribute to the upregulation of carcinogenesis. Conclusively, this comprehensive study indicates the COL11A1 gene to be a significant contributor in the etiology of colorectal cancer, henceforth this gene can be considered as a prognostic biomarker for the conception of diagnostic and therapeutic strategies against colorectal cancer in the near future.
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Affiliation(s)
- Ritwik Patra
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, India
| | - Nabarun Chandra Das
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, India
| | - Suprabhat Mukherjee
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, India
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Martins Cavaco AC, Dâmaso S, Casimiro S, Costa L. Collagen biology making inroads into prognosis and treatment of cancer progression and metastasis. Cancer Metastasis Rev 2021; 39:603-623. [PMID: 32447477 DOI: 10.1007/s10555-020-09888-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Progression through dissemination to tumor-surrounding tissues and metastasis development is a hallmark of cancer that requires continuous cell-to-cell interactions and tissue remodeling. In fact, metastization can be regarded as a tissue disease orchestrated by cancer cells, leading to neoplastic colonization of new organs. Collagen is a major component of the extracellular matrix (ECM), and increasing evidence suggests that it has an important role in cancer progression and metastasis. Desmoplasia and collagen biomarkers have been associated with relapse and death in cancer patients. Despite the increasing interest in ECM and in the desmoplastic process in tumor microenvironment as prognostic factors and therapeutic targets in cancer, further research is required for a better understanding of these aspects of cancer biology. In this review, published evidence correlating collagen with cancer prognosis is retrieved and analyzed, and the role of collagen and its fragments in cancer pathophysiology is discussed.
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Affiliation(s)
- Ana C Martins Cavaco
- Luis Costa Lab, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Sara Dâmaso
- Serviço de Oncologia, Hospital de Santa Maria-CHULN, 1649-028, Lisboa, Portugal
| | - Sandra Casimiro
- Luis Costa Lab, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Luís Costa
- Luis Costa Lab, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisboa, Portugal.
- Serviço de Oncologia, Hospital de Santa Maria-CHULN, 1649-028, Lisboa, Portugal.
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38
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Mutant collagen COL11A1 enhances cancerous invasion. Oncogene 2021; 40:6299-6307. [PMID: 34584216 PMCID: PMC8566234 DOI: 10.1038/s41388-021-02013-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/17/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023]
Abstract
Collagens are the most abundant proteins in the body and comprise the basement membranes and stroma through which cancerous invasion occurs; however, a pro-neoplastic function for mutant collagens is undefined. Here we identify COL11A1 mutations in 66 of 100 cutaneous squamous cell carcinomas (cSCCs), the second most common U.S. cancer, concentrated in a triple helical region known to produce trans-dominant collagens. Analysis of COL11A1 and other collagen genes found that they are mutated across common epithelial malignancies. Knockout of mutant COL11A1 impairs cSCC tumorigenesis in vivo. Compared to otherwise genetically identical COL11A1 wild-type tissue, gene-edited mutant COL11A1 skin is characterized by induction of β1 integrin targets and accelerated neoplastic invasion. In mosaic tissue, mutant COL11A1 cells enhanced invasion by neighboring wild-type cells. These results suggest that specific collagens are commonly mutated in cancer and that mutant collagens may accelerate this process.
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Chen D, Qin Y, Dai M, Li L, Liu H, Zhou Y, Qiu C, Chen Y, Jiang Y. BGN and COL11A1 Regulatory Network Analysis in Colorectal Cancer (CRC) Reveals That BGN Influences CRC Cell Biological Functions and Interacts with miR-6828-5p. Cancer Manag Res 2020; 12:13051-13069. [PMID: 33376399 PMCID: PMC7764722 DOI: 10.2147/cmar.s277261] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
Purpose We explored specific expression profiles of BGN and COL11A1 genes and studied their biological functions in CRC using bioinformatics tools. Patients and Methods A total of 68 pairs of cancer and non-cancerous tissues from CRC patients were enrolled in this study. Methods we used in this articles including: qRT-PCR, Western blot analysis, ELISA, GO and KEGG regulatory network analysis, tumor infiltration, luciferase reporter-based protein and etc. Results According to The Cancer Genome Atlas (TCGA) data, BGN and COL11A1 expression levels were significantly higher in CRC patient samples than in samples from healthy controls. Moreover, levels were much higher in late-stage CRC than in early-stage disease, warranting evaluation of these genes as CRC prognostic biomarkers. Subsequently, qRT-PCR, Western blot analysis, and ELISA results obtained from analyses of CRC cells, tissues, and patient sera aligned with TCGA results. GO and KEGG regulatory network analysis revealed BGN- and COL11A1-associated genes that were functionally related to extracellular matrix (ECM) receptor pathway activation, with transcription factor genes RELA and NFKB1 positively associated with BGN expression and CEBPZ and SIRT1 with COL11A1 expression. Meanwhile, BGN and COL11A1 expression were separately and significantly correlated to tumor infiltration by six immune cell types. Additionally, kinase genes PLK1 and LYN appeared to be downstream targets of differentially expressed BGN and COL11A1, respectively. In addition, the expression of PLK1 mRNA was down-regulated while BGN was down-regulated. Finally, BGN effects on CRC cell proliferation, cycle, apoptosis, invasion, and migration were studied using molecular biological methods, including luciferase reporter-based protein analysis, qRT-PCR, and Western blot results, which revealed that miR-6828-5p may regulate BGN expression. Conclusion We speculate that the use of BGN and COL11A1 as CRC biomarkers would improve CRC staging, while also providing several novel targets for use in the development of more effective CRC treatments.
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Affiliation(s)
- Danqi Chen
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong, People's Republic of China
| | - Ying Qin
- Department of Gastrointestinal Surgery, Shenzhen Second People's Hospital, Shenzhen, Guangdong, People's Republic of China
| | - Mengmeng Dai
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong, People's Republic of China
| | - Lulu Li
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong, People's Republic of China
| | - Hongpeng Liu
- Department of Gastrointestinal Surgery, Shenzhen Second People's Hospital, Shenzhen, Guangdong, People's Republic of China
| | - Yaoyao Zhou
- National & Local United Engineering Laboratory for Personalized Anti-Tumor Drugs, Shenzhen Kivita Innovative Drug Discovery Institute, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong, People's Republic of China
| | - Cheng Qiu
- National & Local United Engineering Laboratory for Personalized Anti-Tumor Drugs, Shenzhen Kivita Innovative Drug Discovery Institute, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong, People's Republic of China
| | - Yan Chen
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong, People's Republic of China
| | - Yuyang Jiang
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong, People's Republic of China.,School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, People's Republic of China
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40
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Arauz RF, Byun JS, Tandon M, Sinha S, Kuhn S, Taylor S, Zingone A, Mitchell KA, Pine SR, Gardner K, Perez-Stable EJ, Napoles AM, Ryan BM. Whole-Exome Profiling of NSCLC Among African Americans. J Thorac Oncol 2020; 15:1880-1892. [PMID: 32931935 PMCID: PMC7704928 DOI: 10.1016/j.jtho.2020.08.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Lung cancer incidence is higher among African Americans (AAs) compared with European Americans (EAs) in the United States, especially among men. Although significant progress has been made profiling the genomic makeup of lung cancer in EAs, AAs continue to be underrepresented. Our objective was to chart the genome-wide landscape of somatic mutations in lung cancer tumors from AAs. METHODS In this study, we used the whole-exome sequencing of 82 tumor and noninvolved tissue pairs from AAs. Patients were selected from an ongoing case-control study conducted by the National Cancer Institute and the University of Maryland. RESULTS Among all samples, we identified 178 significantly mutated genes (p < 0.05), five of which passed the threshold for false discovery rate (p < 0.1). In lung adenocarcinoma (LUAD) tumors, mutation rates in STK11 (p = 0.05) and RB1 (p = 0.008) were significantly higher in AA LUAD tumors (25% and 13%, respectively) compared with The Cancer Genome Atlas EA samples (14% and 4%, respectively). In squamous cell carcinomas, mutation rates in STK11 (p = 0.002) were significantly higher among AA (8%) than EA tumors from The Cancer Genome Atlas (1%). Integrated somatic mutation data with CIBERSORT (Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts) data analysis revealed LUAD tumors from AAs carrying STK11 mutations have decreased interferon signaling. CONCLUSIONS Although a considerable degree of the somatic mutation landscape is shared between EAs and AAs, discrete differences in mutation frequency in potentially important oncogenes and tumor suppressors exist. A better understanding of the molecular basis of lung cancer in AA patients and leveraging this information to guide clinical interventions may help reduce disparities.
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Affiliation(s)
- Rony F Arauz
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Jung S Byun
- Division of Intramural Research, National Institute on Minority Health and Health Disparities, Bethesda, Maryland; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Mayank Tandon
- CCR Collaborative Bioinformatics Resource CCBR, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Sanju Sinha
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland; Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Skyler Kuhn
- CCR Collaborative Bioinformatics Resource CCBR, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Sheryse Taylor
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Adriana Zingone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Khadijah A Mitchell
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Sharon R Pine
- Departments of Pharmacology and Medicine, Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Kevin Gardner
- National Institute of Minority Health and Health Disparities, Bethesda, Maryland; Department of Pathology and Cell Biology, Columbia University Medical Center, Columbia University, New York, New York
| | | | - Anna M Napoles
- National Institute of Minority Health and Health Disparities, Bethesda, Maryland
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.
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Tan GF, Goh S, Lim AH, Liu W, Lee JY, Rajasegaran V, Sam XX, Tay TKY, Selvarajan S, Ng CCY, Teh BT, Chan JY. Bizarre giant cells in human angiosarcoma exhibit chemoresistance and contribute to poor survival outcomes. Cancer Sci 2020; 112:397-409. [PMID: 33164299 PMCID: PMC7780052 DOI: 10.1111/cas.14726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/31/2020] [Accepted: 11/04/2020] [Indexed: 11/28/2022] Open
Abstract
Giant cells (GC) are a poorly understood subset of tumor cells that have been increasingly recognized as a potential contributor to tumor heterogeneity and treatment resistance. We aimed to characterize the biological and clinical significance of GC in angiosarcoma, an aggressive rare cancer of endothelial origin. Archival angiosarcoma samples were examined for the presence of GC and compared with clinicopathological as well as NanoString gene expression data. GC were examined in angiosarcoma cell lines MOLAS and ISOHAS using conventional and electron microscopy, single cell whole genome profiling, and other assays. In the cell lines, GC represented a rare population of mitotically active, non–senescent CD31+ cells, and shared similar genomic profiles with regular‐sized cells, consistent with a malignant endothelial phenotype. GC remained viable and persisted in culture following exposure to paclitaxel and doxorubicin. In patient samples, GC were present in 24 of 58 (41.4%) cases. GC was correlated with poorer responses to chemotherapy (25.0% vs 73.3%, P = 0.0213) and independently contributed to worse overall survival outcomes (hazard ratio 2.20, 95% confidence interval 1.17‐4.15, P = 0.0142). NanoString profiling revealed overexpression of genes, including COL11A1, STC1, and ERO1A, accompanied by upregulation of immune‐related metabolic stress and metastasis/matrix remodeling pathways in GC‐containing tumors. In conclusion, GC may contribute to chemoresistance and poor prognosis in angiosarcoma.
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Affiliation(s)
- Grace Fangmin Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore City, Singapore
| | - Shane Goh
- Integrated Genomics Platform, National Cancer Centre Singapore, Singapore City, Singapore
| | - Abner Herbert Lim
- Integrated Genomics Platform, National Cancer Centre Singapore, Singapore City, Singapore
| | - Wei Liu
- Integrated Genomics Platform, National Cancer Centre Singapore, Singapore City, Singapore
| | - Jing Yi Lee
- Integrated Genomics Platform, National Cancer Centre Singapore, Singapore City, Singapore
| | - Vikneswari Rajasegaran
- Integrated Genomics Platform, National Cancer Centre Singapore, Singapore City, Singapore
| | - Xin Xiu Sam
- Department of Anatomical Pathology, Singapore General Hospital, Singapore City, Singapore
| | - Timothy Kwang Yong Tay
- Department of Anatomical Pathology, Singapore General Hospital, Singapore City, Singapore
| | | | - Cedric Chuan-Young Ng
- Integrated Genomics Platform, National Cancer Centre Singapore, Singapore City, Singapore
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore City, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore City, Singapore.,Institute of Molecular and Cell Biology, Singapore City, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore City, Singapore.,Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore City, Singapore
| | - Jason Yongsheng Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore City, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore City, Singapore.,Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore City, Singapore
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42
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Ribeiro IP, Esteves L, Anjo SI, Marques F, Barroso L, Manadas B, Carreira IM, Melo JB. Proteomics-based Predictive Model for the Early Detection of Metastasis and Recurrence in Head and Neck Cancer. Cancer Genomics Proteomics 2020; 17:259-269. [PMID: 32345667 DOI: 10.21873/cgp.20186] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND/AIM Head and neck squamous cell carcinoma (HNSCC) presents high morbidity, an overall poor prognosis and survival, and a compromised quality of life of the survivors. Early tumor detection, prediction of its behavior and prognosis as well as the development of novel therapeutic strategies are urgently needed for a more successful HNSCC management. MATERIALS AND METHODS In this study, a proteomics analysis of HNSCC tumor and non-tumor samples was performed and a model to predict the risk of recurrence and metastasis development was built. RESULTS This predictive model presented good accuracy (>80%) and comprises as variables the tumor staging along with DHB12, HMGB3 and COBA1 proteins. Differences at the intensity levels of these proteins were correlated with the development of metastasis and recurrence as well as with patient's survival. CONCLUSION The translation of proteomic predictive models to routine clinical practice may contribute to a more precise and individualized clinical management of the HNSCC patients, reducing recurrences and improving patients' quality of life. The capability of generalization of this proteomic model to predict the recurrence and metastases development should be evaluated and validated in other HNSCC populations.
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Affiliation(s)
- Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Luísa Esteves
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Sandra Isabel Anjo
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Francisco Marques
- iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Stomatology Unit, Coimbra Hospital and University Centre, CHUC, EPE, Coimbra, Portugal.,Department of Dentistry, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Leonor Barroso
- Maxillofacial Surgery Department, Coimbra Hospital and University Centre, CHUC, EPE, Coimbra, Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,CNC.IBILI, Group of Aging and Brain Diseases: Advanced Diagnosis and Biomarkers, Coimbra, Portugal
| | - Joana Barbosa Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal .,iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,CNC.IBILI, Group of Aging and Brain Diseases: Advanced Diagnosis and Biomarkers, Coimbra, Portugal
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43
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Tu H, Li J, Lin L, Wang L. COL11A1 Was Involved in Cell Proliferation, Apoptosis and Migration in Non-Small Cell Lung Cancer Cells. J INVEST SURG 2020; 34:664-669. [PMID: 33148075 DOI: 10.1080/08941939.2019.1672839] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Type XI collagen (COL11A1) was reported to associate with malignancy in several cancer types, whereas its role in lung cancer is not fully understood. Therefore, the present study aimed to explore the expression level and biological role of COL11A1 in lung cancer cells. METHODS Gene Expression Omnibus (GEO) database containing 6 lung cancer tissues and normal lung tissues was used to identify potential aberrantly expressed genes. The expression of COL11A1, apoptosis related genes, cell cycle related genes and migration associated genes at the protein level were evaluated by western blot and at the mRNA level was determined by real-time PCR in lung cancer cell lines. Furthermore, the expression of COL11A1 was silenced by siRNA, and cell viability was detected by Cell counting kit-8 (CCK-8) assay. Moreover, cell apoptosis and cell cycle were determined by flow cytometry. In addition, transwell and wound-healing assay were applied to determine cell migration ability. RESULTS GEO analysis suggests that COL11A1 was highly expressed in patients with lung cancer, which was consistent with the results in lung cancer cell lines. COL11A1 knockdown in lung cancer cells significantly lowered the colony formation ability, augmented cell apoptosis rate and elevated the expression of cleaved caspase-3, cleaved caspase-9, Bax, P21 and the expression of Bcl-2, CyclinD1, CDK2 and CDK-4 was significantly downregulated (all p < 0.05). Moreover, post-COL11A1 knockdown, the cell wound-healing and migration ability was significantly impaired, which also supported by the upregulation of E-Cadherin and downregulation of N-Cadherin, Vimentin and Snail (all p < 0.05). Furthermore, we also found that COL11A1 knockdown decreased the expression of p-AKT, p-PI3K and p-ERK. CONCLUSION The present study revealed that COL11A1 may contribute to the malignancy and involve in the pathogenesis of lung cancer.
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Affiliation(s)
- Hongbin Tu
- Department of Integrated Traditional Chinese and Western Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jing Li
- Department of Integrated Traditional Chinese and Western Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lei Lin
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lixin Wang
- Department of Integrated Traditional Chinese and Western Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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Luan M, Song F, Qu S, Meng X, Ji J, Duan Y, Sun C, Si H, Zhai H. Multi-omics integrative analysis and survival risk model construction of non-small cell lung cancer based on The Cancer Genome Atlas datasets. Oncol Lett 2020; 20:58. [PMID: 32863893 PMCID: PMC7435128 DOI: 10.3892/ol.2020.11919] [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: 04/27/2019] [Accepted: 04/20/2020] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is a major cause of cancer-associated mortality worldwide. However, the association between multi-omics data and survival in lung cancer is not fully understood. The present study investigated the performance of the methylation survival risk model in multi-platform integrative molecular subtypes and aimed to identify copy number (CN) variations and mutations that are associated with survival risk. The present study analyzed 439 lung adenocarcinoma cases based on DNA methylation, RNA, microRNA (miRNA), DNA copy number and mutations from The Cancer Genome Atlas datasets. First, six cancer subtypes were identified using integrating DNA methylation, RNA, miRNA and DNA copy number data. The least absolute shrinkage and selection operator (LASSO) regression algorithm was used to extract methylation sites of survival model and calculate the methylation-based survival risk indices for all patients. Survival for patients in the high-risk group was significantly lower compared with that for patients in the low-risk group (P<0.05). The present study also assessed methylation-based survival risks of the six subtypes and analyzed the association between survival risk and non-silent mutation rate, number of segments, fraction of segments altered, aneuploidy score, number of segments with loss of heterozygosity (LOH), fraction of segments with LOH and homologous repair deficiency. Finally, the specific copy number regions and mutant genes associated with the different subtypes were identified (P<0.01). Chromosome regions 17q24.3 and 11p15.5 were identified as those with the most survival risk-associated copy number variation regions, while a total of 29 mutant genes were significantly associated with survival (P<0.01).
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Affiliation(s)
- Mingyuan Luan
- School of Basic Medicine, Qingdao University Medical College, Qingdao, Shandong 266071, P.R. China
| | - Fucheng Song
- Department of Public Health, Qingdao University Medical College, Qingdao, Shandong 266071, P.R. China
| | - Shuyuan Qu
- School of Basic Medicine, Qingdao University Medical College, Qingdao, Shandong 266071, P.R. China
| | - Xi Meng
- Department of Public Health, Qingdao University Medical College, Qingdao, Shandong 266071, P.R. China
| | - Junjie Ji
- School of Basic Medicine, Qingdao University Medical College, Qingdao, Shandong 266071, P.R. China
| | - Yunbo Duan
- Institute for Computational Science and Engineering, Laboratory of New Fibrous Materials and Modern Textile State Key Laboratory, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Changgang Sun
- Department of Cancer Center, Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong 262699, P.R. China
| | - Hongzong Si
- Department of Public Health, Qingdao University Medical College, Qingdao, Shandong 266071, P.R. China
- Institute for Computational Science and Engineering, Laboratory of New Fibrous Materials and Modern Textile State Key Laboratory, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Honglin Zhai
- Department of Chemistry, Lanzhou University, Lanzhou, Gansu 730000, P.R. China
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45
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Carratt SA, Kovalchuk N, Ding X, Van Winkle LS. Metabolism and Lung Toxicity of Inhaled Naphthalene: Effects of Postnatal Age and Sex. Toxicol Sci 2020; 170:536-548. [PMID: 31020322 DOI: 10.1093/toxsci/kfz100] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Human exposure to naphthalene (NA), an acute lung toxicant and possible human carcinogen, is primarily through inhalation. Acute lung toxicity and carcinogenesis are thought to be related because the target sites for both are similar. To understand susceptibility of the developing lung to cytotoxicity of inhaled NA, we exposed neonatal (7 days), juvenile (3 weeks), and adult mice to 5 or 10 ppm NA vapor for 4 h. We measured vacuolated airway epithelium morphometrically, quantified NA and NA-glutathione levels in plasma and lung, and quantified gene expression in microdissected airways. NA inhalation caused airway epithelial cytotoxicity at all ages, in both sexes. Contrary to a previous study that showed the greatest airway epithelial cytotoxicity in neonatal mice following intraperitoneal NA injection, we observed the most extensive airway epithelial toxicity in older, juvenile, animals exposed to NA by inhalation. Juvenile female animals were the most susceptible. Furthermore, NA inhalation in juvenile animals resulted in damage to conducting airway Club cells that was greater in proximal versus distal airways. We also found NA tissue burden and metabolism differed by age. Gene expression pathway analysis was consistent with the premise that female juvenile mice are more predisposed to damage; DNA damage and cancer pathways were upregulated. Our data demonstrate special susceptibility of young, juvenile mice to NA inhalation-induced cytotoxicity, highlight the importance of route of exposure and airway location in toxicity of chemicals in the developing lung, and provide metabolic and molecular insights for further identification of mechanisms underlying age and sex differences in NA toxicity.
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Affiliation(s)
- Sarah A Carratt
- Center for Health and the Environment, University of California Davis, Davis, California 95616
| | - Nataliia Kovalchuk
- Wadsworth Center, New York State Department of Health, Albany, New York 12201.,Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721
| | - Xinxin Ding
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721.,College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, New York 12203
| | - Laura S Van Winkle
- Center for Health and the Environment, University of California Davis, Davis, California 95616.,Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, California 95616
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Bourgot I, Primac I, Louis T, Noël A, Maquoi E. Reciprocal Interplay Between Fibrillar Collagens and Collagen-Binding Integrins: Implications in Cancer Progression and Metastasis. Front Oncol 2020; 10:1488. [PMID: 33014790 PMCID: PMC7461916 DOI: 10.3389/fonc.2020.01488] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/13/2020] [Indexed: 12/14/2022] Open
Abstract
Cancers are complex ecosystems composed of malignant cells embedded in an intricate microenvironment made of different non-transformed cell types and extracellular matrix (ECM) components. The tumor microenvironment is governed by constantly evolving cell-cell and cell-ECM interactions, which are now recognized as key actors in the genesis, progression and treatment of cancer lesions. The ECM is composed of a multitude of fibrous proteins, matricellular-associated proteins, and proteoglycans. This complex structure plays critical roles in cancer progression: it functions as the scaffold for tissues organization and provides biochemical and biomechanical signals that regulate key cancer hallmarks including cell growth, survival, migration, differentiation, angiogenesis, and immune response. Cells sense the biochemical and mechanical properties of the ECM through specialized transmembrane receptors that include integrins, discoidin domain receptors, and syndecans. Advanced stages of several carcinomas are characterized by a desmoplastic reaction characterized by an extensive deposition of fibrillar collagens in the microenvironment. This compact network of fibrillar collagens promotes cancer progression and metastasis, and is associated with low survival rates for cancer patients. In this review, we highlight how fibrillar collagens and their corresponding integrin receptors are modulated during cancer progression. We describe how the deposition and alignment of collagen fibers influence the tumor microenvironment and how fibrillar collagen-binding integrins expressed by cancer and stromal cells critically contribute in cancer hallmarks.
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Affiliation(s)
| | | | | | | | - Erik Maquoi
- Laboratory of Tumor and Development Biology, GIGA-Cancer, University of Liège, Liège, Belgium
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47
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Fibroblast Growth Factor-14 Acts as Tumor Suppressor in Lung Adenocarcinomas. Cells 2020; 9:cells9081755. [PMID: 32707902 PMCID: PMC7466013 DOI: 10.3390/cells9081755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/25/2022] Open
Abstract
Investigation of the molecular dynamics in lung cancer is crucial for the development of new treatment strategies. Fibroblast growth factor (FGF) 14 belongs to the FGF family, which might play a crucial role in cancer progression. We analyzed lung adenocarcinoma (LUAC) patients samples and found that FGF14 was downregulated, correlating with reduced survival and oncogenic mutation status. FGF14 overexpression in lung cancer cell lines resulted in decreased proliferation, colony formation, and migration, as well as increased expression of epithelial markers and a decreased expression of mesenchymal markers, indicating a mesenchymal to epithelial transition in vitro. We verified these findings using small interfering RNA against FGF14 and further confirmed the suppressive effect of FGF14 in a NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ immunodeficient xenograft tumor model. Moreover, FGF14 overexpressing tumor cell RNA sequencing data suggests that genes affected by FGF14 were related to the extracellular matrix, playing a role in proliferation and migration. Notably, newly identified FGF14 target genes, adenosine deaminase RNA specific B1 (ADARB1), collagen and calcium-binding epidermal growth factor domain-containing protein 1 (CCBE1), α1 chain of collagen XI (COL11A1), and mucin 16 (MUC16) expression was negatively correlated with overall survival when FGF14 was downregulated in LUAC. These findings led us to suggest that FGF14 regulates proliferation and migration in LUAC.
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48
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Lv Z, Lei T. Systematical identifications of prognostic meaningful lung adenocarcinoma subtypes and the underlying mutational and expressional characters. BMC Cancer 2020; 20:56. [PMID: 31987030 PMCID: PMC6983970 DOI: 10.1186/s12885-019-6462-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/15/2019] [Indexed: 01/10/2023] Open
Abstract
Background Lung adenocarcinoma (LUAD) is one of the most common cancer types, threatening the human health around the world. However, the high heterogeneity and complexity of LUAD limit the benefits of targeted therapies. This study aimed to identify the key prognosis impacting genes and relevant subtypes for LUAD. Methods We recognized significant mutations and prognosis-relevant genes based on the omics data of 515 LUAD samples from The Cancer Genome Atlas. Mutation significance was estimated by MutSigCV. Prognosis analysis was based on the cox proportional hazards regression (Coxph) model. Specifically, the Coxph model was combined with a causal regulatory network to help reveal which genes play master roles among numerous prognosis impacting genes. Based on expressional profiles of the master genes, LUAD patients were clustered into different sub-types by a consensus clustering method and the importance of master genes were further evaluated by random forest. Results Significant mutations did not influence the prognosis directly. However, a collection of prognosis relevant genes were recognized, where 75 genes like GAPDH and GGA2 which are involved in mTOR signaling, lysosome or other key pathways are further identified as the master ones. Interestingly, the master gene expressions help separate LUAD patients into two sub-types displaying remarkable differences in expressional profiles, prognostic outcomes and genomic mutations in certain genes, like SMARCA4 and COL11A1. Meanwhile, the subtypes were re-discovered from two additional LUAD cohorts based on the top-10 important master genes. Conclusions This study can promote precision treatment of LUAD by providing a comprehensive description on the key prognosis-relevant genes and an alternative way to classify LUAD subtypes.
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Affiliation(s)
- Zhenyang Lv
- The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People's Republic of China
| | - Ting Lei
- The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People's Republic of China.
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49
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Galván JA, Wiprächtiger J, Slotta-Huspenina J, Feith M, Ott K, Kröll D, Seiler CA, Langer R. Immunohistochemical analysis of the expression of cancer-associated fibroblast markers in esophageal cancer with and without neoadjuvant therapy. Virchows Arch 2019; 476:725-734. [PMID: 31828432 DOI: 10.1007/s00428-019-02714-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/22/2019] [Accepted: 11/03/2019] [Indexed: 12/15/2022]
Abstract
Esophageal carcinoma (EC) is one of the most aggressive human malignancies with high rates of resistance to conventional anticancer treatment. Cancer-associated fibroblasts (CAFs) are an important part of the tumor microenvironment and associated with tumor progression. COL11A1, SPARC, and CD90 have been identified as rather specific CAF markers, with COL11A1 expression particularly shown to influence response to chemotherapy. We investigated the impact of CAFs in esophageal cancer with a special focus on response to neoadjuvant treatment (nTX). Two collections of esophageal carcinomas were investigated: 164 cases treated with primary resection and 256 cases receiving nTX before resection. The expression of CAF markers was determined using next-generation tissue microarray (ngTMA®) technology and immunohistochemistry. The presence of COL11A1 and SPARC in fibroblasts within both primary resected cases and nTX-treated cases was associated with unfavorable clinicopathological variables such as higher (y)pT category and lymphatic invasion (p<0.001 each). The presence of COL11A1-positive CAFs was associated with worse overall survival in primary resected cases (HR: 2.162, p = 0.004, CI 95% 1.275-3.686). While in tumors showing regression after nTX, COL11A1-positive CAFs were detected less frequently, SPARC-positive CAFs were enriched after nTX, in both responding and non-responding patients (p < 0.001). Our results support the concept of CAFs as an important factor of tumor promotion and maintenance in EC. The population of CAFs increases with tumor progression and decreases, partly depending on the subtype, after regression following nTX. CAFs may serve as potential target for future therapeutic approaches for these highly aggressive tumors.
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Affiliation(s)
- José A Galván
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland.
| | - Julia Wiprächtiger
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | | | - Marcus Feith
- Department of Surgery, Klinikum Rechts der Isar, Technische Universität München, München, Germany
| | - Katja Ott
- Department of Surgery, RoMED Klinikum, Rosenheim, Germany
| | - Dino Kröll
- Department of Visceral Surgery and Medicine, University Hospital of Bern, University of Bern, Bern, Switzerland
| | - Christian A Seiler
- Department of Visceral Surgery and Medicine, University Hospital of Bern, University of Bern, Bern, Switzerland
| | - Rupert Langer
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
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50
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A Toolbox for Functional Analysis and the Systematic Identification of Diagnostic and Prognostic Gene Expression Signatures Combining Meta-Analysis and Machine Learning. Cancers (Basel) 2019; 11:cancers11101606. [PMID: 31640282 PMCID: PMC6827106 DOI: 10.3390/cancers11101606] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 02/06/2023] Open
Abstract
The identification of biomarker signatures is important for cancer diagnosis and prognosis. However, the detection of clinical reliable signatures is influenced by limited data availability, which may restrict statistical power. Moreover, methods for integration of large sample cohorts and signature identification are limited. We present a step-by-step computational protocol for functional gene expression analysis and the identification of diagnostic and prognostic signatures by combining meta-analysis with machine learning and survival analysis. The novelty of the toolbox lies in its all-in-one functionality, generic design, and modularity. It is exemplified for lung cancer, including a comprehensive evaluation using different validation strategies. However, the protocol is not restricted to specific disease types and can therefore be used by a broad community. The accompanying R package vignette runs in ~1 h and describes the workflow in detail for use by researchers with limited bioinformatics training.
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