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Wu Q, Luo Y, Lin N, Zheng S, Xie X. Prognostic Value and Immune Signatures of Anoikis-related Genes in Breast Cancer. J Immunother 2024:00002371-990000000-00110. [PMID: 38864225 DOI: 10.1097/cji.0000000000000523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/03/2024] [Indexed: 06/13/2024]
Abstract
From databases of the Cancer Genome Atlas (TCGA) and GSE42568, transcriptome data of breast cancer patients was obtained. Then, anoikis-related genes (ANRGs) were identified and constructed a risk score system. As a threshold value, the median risk score was used to stratify patients into low-risk and high-risk groups. Kaplan-Meier analysis was then conducted to evaluate the prognostic ability of the risk score system, which was validated using GSE7390. Furthermore, we identified potential enrichment of function and tumor immune infiltration in the model. Finally, the biological functions of a risk gene (EPB41L4B) in breast cancer were investigated through in vitro experiments. We constructed a risk score system via 9 prognosis ANRGs (CXCL2, EPB41L4B, SLC7A5, SFRP1, SDC1, BHLHE41, SPINT1, KRT15, and CD24). The Kaplan-Meier analysis showed that both TCGA-BRCA (training set) and GSE7390 (testing set) patients with high-risk status had significantly worse survival outcomes. In addition, the calibration plots were in good agreement with the prognosis prediction. Breast cancer patients with immunosuppressive microenvironment could be screened using risk groups since risk scores were correlated negatively with ESTIMATE score, tumor-infiltration lymphocytes, immune checkpoints, and chemotactic factors. Furthermore, cellular viability and cell migration of cancerous breast cells were inhibited and apoptosis was promoted by down-regulation of EPB41L4B gene expression. Based on ANRGs, a 9-gene prognostic model could be developed to predict breast cancer prognosis; moreover, patients of the high-risk group were in an immunosuppressed tumor microenvironment.
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Affiliation(s)
- Qing Wu
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Yang Luo
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
| | - Nan Lin
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Gastrointestinal Surgery, The 900th Hospital of Joint Logistics Support Forces of Chinese PLA, Fuzhou, Fujian Province, China
| | - Shiyao Zheng
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Xianhe Xie
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian Province, China
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
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Bakr S, Brennan K, Mukherjee P, Argemi J, Hernaez M, Gevaert O. Identifying key multifunctional components shared by critical cancer and normal liver pathways via SparseGMM. CELL REPORTS METHODS 2023; 3:100392. [PMID: 36814838 PMCID: PMC9939431 DOI: 10.1016/j.crmeth.2022.100392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/16/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023]
Abstract
Despite the abundance of multimodal data, suitable statistical models that can improve our understanding of diseases with genetic underpinnings are challenging to develop. Here, we present SparseGMM, a statistical approach for gene regulatory network discovery. SparseGMM uses latent variable modeling with sparsity constraints to learn Gaussian mixtures from multiomic data. By combining coexpression patterns with a Bayesian framework, SparseGMM quantitatively measures confidence in regulators and uncertainty in target gene assignment by computing gene entropy. We apply SparseGMM to liver cancer and normal liver tissue data and evaluate discovered gene modules in an independent single-cell RNA sequencing (scRNA-seq) dataset. SparseGMM identifies PROCR as a regulator of angiogenesis and PDCD1LG2 and HNF4A as regulators of immune response and blood coagulation in cancer. Furthermore, we show that more genes have significantly higher entropy in cancer compared with normal liver. Among high-entropy genes are key multifunctional components shared by critical pathways, including p53 and estrogen signaling.
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Affiliation(s)
- Shaimaa Bakr
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
- Stanford Center for Biomedical Informatics Research, Department of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Kevin Brennan
- Stanford Center for Biomedical Informatics Research, Department of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Pritam Mukherjee
- Stanford Center for Biomedical Informatics Research, Department of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Josepmaria Argemi
- Liver Unit, Clinica Universidad de Navarra, Hepatology Program, Center for Applied Medical Research, 31008 Pamplona, Navarra, Spain
| | - Mikel Hernaez
- Center for Applied Medical Research, University of Navarra, 31009 Pamplona, Navarra, Spain
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research, Department of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
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A Genomic Study of Myxomatous Mitral Valve Disease in Cavalier King Charles Spaniels. Animals (Basel) 2020; 10:ani10101895. [PMID: 33081147 PMCID: PMC7602727 DOI: 10.3390/ani10101895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
Cavalier King Charles spaniels (CKCSs) show the earliest onset and the highest incidence of myxomatous mitral valve disease (MMVD). Previous studies have suggested a polygenic inheritance of the disease in this breed and revealed an association with regions on canine chromosomes 13 and 14. Following clinical and echocardiographic examinations, 33 not-directly-related CKCSs were selected and classified as cases (n = 16) if MMVD was present before 5 years of age or as controls (n = 17) if no or very mild MMVD was present after 5 years of age. DNA was extracted from whole blood and genotyped with a Canine 230K SNP BeadChip instrument. Cases and controls were compared with three complementary genomic analyses (Wright's fixation index-FST, cross-population extended haplotype homozygosity-XP-EHH, and runs of homozygosity-ROH) to identify differences in terms of heterozygosity and regions of homozygosity. The top 1% single-nucleotide polymorphisms (SNPs) were selected and mapped, and the genes were thoroughly investigated. Ten consensus genes were found localized on chromosomes 3-11-14-19, partially confirming previous studies. The HEPACAM2, CDK6, and FAH genes, related to the transforming growth factor β (TGF-β) pathway and heart development, also emerged in the ROH analysis. In conclusion, this work expands the knowledge of the genetic basis of MMVD by identifying genes involved in the early onset of MMVD in CKCSs.
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NEAGU MONICA, CARUNTU CONSTANTIN, CONSTANTIN CAROLINA, BODA DANIEL, ZURAC SABINA, SPANDIDOS DEMETRIOSA, TSATSAKIS ARISTIDISM. Chemically induced skin carcinogenesis: Updates in experimental models (Review). Oncol Rep 2016; 35:2516-28. [PMID: 26986013 PMCID: PMC4811393 DOI: 10.3892/or.2016.4683] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/16/2016] [Indexed: 02/06/2023] Open
Abstract
Skin cancer is one of the most common malignancies affecting humans worldwide, and its incidence is rapidly increasing. The study of skin carcinogenesis is of major interest for both scientific research and clinical practice and the use of in vivo systems may facilitate the investigation of early alterations in the skin and of the mechanisms involved, and may also lead to the development of novel therapeutic strategies for skin cancer. This review outlines several aspects regarding the skin toxicity testing domain in mouse models of chemically induced skin carcinogenesis. There are important strain differences in view of the histological type, development and clinical evolution of the skin tumor, differences reported decades ago and confirmed by our hands‑on experience. Using mouse models in preclinical testing is important due to the fact that, at the molecular level, common mechanisms with human cutaneous tumorigenesis are depicted. These animal models resemble human skin cancer development, in that genetic changes caused by carcinogens and pro‑inflammatory cytokines, and simultaneous inflammation sustained by pro‑inflammatory cytokines and chemokines favor tumor progression. Drugs and environmental conditions can be tested using these animal models. keeping in mind the differences between human and rodent skin physiology.
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Affiliation(s)
- MONICA NEAGU
- 'Victor Babes' National Institute of Pathology, Bucharest 050096, Romania
- Faculty of Biology, University of Bucharest, Bucharest 76201, Romania
| | - CONSTANTIN CARUNTU
- Department of Physiology, 'Carol Davila' University of Medicine and Pharmacy, Bucharest 050474, Romania
- Department of Dermatology, 'Prof. N. Paulescu' National Institute of Diabetes, Nutrition and Metabolic Diseases, Bucharest 79811, Romania
| | | | - DANIEL BODA
- Department of Dermatology, 'Prof. N. Paulescu' National Institute of Diabetes, Nutrition and Metabolic Diseases, Bucharest 79811, Romania
| | - SABINA ZURAC
- Department of Pathology, 'Colentina' Clinical Hospital, Bucharest 72202, Romania
| | - DEMETRIOS A. SPANDIDOS
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion 71409, Greece
| | - ARISTIDIS M. TSATSAKIS
- Department of Forensic Sciences and Toxicology, Medical School, University of Crete, Heraklion 71003, Greece
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Genome-Wide Association Study of Staphylococcus aureus Carriage in a Community-Based Sample of Mexican-Americans in Starr County, Texas. PLoS One 2015; 10:e0142130. [PMID: 26569114 PMCID: PMC4646511 DOI: 10.1371/journal.pone.0142130] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/16/2015] [Indexed: 02/07/2023] Open
Abstract
Staphylococcus aureus is the number one cause of hospital-acquired infections. Understanding host pathogen interactions is paramount to the development of more effective treatment and prevention strategies. Therefore, whole exome sequence and chip-based genotype data were used to conduct rare variant and genome-wide association analyses in a Mexican-American cohort from Starr County, Texas to identify genes and variants associated with S. aureus nasal carriage. Unlike most studies of S. aureus that are based on hospitalized populations, this study used a representative community sample. Two nasal swabs were collected from participants (n = 858) 11–17 days apart between October 2009 and December 2013, screened for the presence of S. aureus, and then classified as either persistent, intermittent, or non-carriers. The chip-based and exome sequence-based single variant association analyses identified 1 genome-wide significant region (KAT2B) for intermittent and 11 regions suggestively associated with persistent or intermittent S. aureus carriage. We also report top findings from gene-based burden analyses of rare functional variation. Notably, we observed marked differences between signals associated with persistent and intermittent carriage. In single variant analyses of persistent carriage, 7 of 9 genes in suggestively associated regions and all 5 top gene-based findings are associated with cell growth or tight junction integrity or are structural constituents of the cytoskeleton, suggesting that variation in genes associated with persistent carriage impact cellular integrity and morphology.
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Neagu M, Constantin C, Dumitrascu GR, Lupu AR, Caruntu C, Boda D, Zurac S. Inflammation markers in cutaneous melanoma - edgy biomarkers for prognosis. Discoveries (Craiova) 2015; 3:e38. [PMID: 32309563 PMCID: PMC6941591 DOI: 10.15190/d.2015.30] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
There is a fine balance between inflammation and tumorigenesis. While environmentally induced inflammatory condition can precede a malignant transformation, in other cases an oncogenic change of unknown origin can induce an inflammatory microenvironment that promotes the development of tumors. Regardless of its origin, maintaining the inflammation milieu has many tumor-promoting effects. As a result, inflammation can aid the proliferation and survival of malignant cells, can promote angiogenesis and metastasis, can down-regulate innate/adaptive immune responses, and can alter responses to hormones and chemotherapeutic agents. There is an abundance of studies unveiling molecular pathways of cancer-related inflammation; this wealth of information brings new insights into biomarkers domain in the diagnosis and treatment improvement pursue.
In cutaneous tissue there is an established link between tissue damage, inflammation, and cancer development. Inflammation is a self-limiting process in normal healthy physiological conditions, while tumorigenesis is a complex mechanism of constitutive pathway activation. Once more, in cutaneous melanoma, there is an unmet need for inflammatory biomarkers that could improve prognostication. Targeting inflammation and coping with the phenotypic plasticity of melanoma cells represent rational strategies to specifically interfere with metastatic progression. We have shown that there is a prototype of intratumor inflammatory infiltrate depicting a good prognosis, infiltrate that is composed of numerous T cells CD3+, Langerhans cells, few/absent B cells CD20+ and few/absent plasma cells. Circulating immune cells characterized by phenotype particularities are delicately linked to the stage melanoma is diagnosed in. Hence circulatory immune sub-populations, with activated or suppressor phenotype would give the physician a more detailed immune status of the patient. A panel of tissue/circulatory immune markers can complete the immune status, can add value to the overall prognostic of the patient and, as a result direct/redirect the therapy choice. The future lies within establishing low-cost, affordable/available, easily reproducible assays that will complete the pre-clinical parameters of the patient.
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Affiliation(s)
- Monica Neagu
- Immunobiology Laboratory, "Victor Babes" National Institute of Pathology and Biomedical Sciences, Bucharest, Romania.,Faculty of Biochemistry, University of Bucharest, Romania
| | - Carolina Constantin
- Immunobiology Laboratory, "Victor Babes" National Institute of Pathology and Biomedical Sciences, Bucharest, Romania
| | - Georgiana Roxana Dumitrascu
- Immunobiology Laboratory, "Victor Babes" National Institute of Pathology and Biomedical Sciences, Bucharest, Romania
| | - Andreea Roxana Lupu
- Immunobiology Laboratory, "Victor Babes" National Institute of Pathology and Biomedical Sciences, Bucharest, Romania
| | - Constantin Caruntu
- Immunobiology Laboratory, "Victor Babes" National Institute of Pathology and Biomedical Sciences, Bucharest, Romania.,Dermatology Research Laboratory, "Carol Davila" University of Medicine & Pharmacy, Bucharest, Romania
| | - Daniel Boda
- Dermatology Research Laboratory, "Carol Davila" University of Medicine & Pharmacy, Bucharest, Romania
| | - Sabina Zurac
- Department of Pathology, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania.,Colentina University Hospital, Bucharest, Romania
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Glasbey JC, Sanders AJ, Bosanquet DC, Ruge F, Harding KG, Jiang WG. Expression of Hepatocyte Growth Factor-Like Protein in Human Wound Tissue and Its Biological Functionality in Human Keratinocytes. Biomedicines 2015; 3:110-123. [PMID: 28536402 PMCID: PMC5344237 DOI: 10.3390/biomedicines3010110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 09/29/2014] [Accepted: 01/27/2015] [Indexed: 01/04/2023] Open
Abstract
human keratinocyte model, may indicate a role for HGFl in active wound healing.
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Affiliation(s)
- James C Glasbey
- Cardiff China Medical Research Collaborative (CCMRC), Cardiff University-Peking University Cancer Institute, Cardiff University-Capital Medical University Joint Centre Biomedical Research, Cardiff University School of Medicine, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK.
- Department of Wound Healing and Welsh Wound Innovation Centre, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK.
| | - Andrew J Sanders
- Cardiff China Medical Research Collaborative (CCMRC), Cardiff University-Peking University Cancer Institute, Cardiff University-Capital Medical University Joint Centre Biomedical Research, Cardiff University School of Medicine, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK.
| | - David C Bosanquet
- Cardiff China Medical Research Collaborative (CCMRC), Cardiff University-Peking University Cancer Institute, Cardiff University-Capital Medical University Joint Centre Biomedical Research, Cardiff University School of Medicine, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK.
- Department of Wound Healing and Welsh Wound Innovation Centre, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK.
| | - Fiona Ruge
- Cardiff China Medical Research Collaborative (CCMRC), Cardiff University-Peking University Cancer Institute, Cardiff University-Capital Medical University Joint Centre Biomedical Research, Cardiff University School of Medicine, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK.
- Department of Wound Healing and Welsh Wound Innovation Centre, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK.
| | - Keith G Harding
- Department of Wound Healing and Welsh Wound Innovation Centre, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK.
| | - Wen G Jiang
- Cardiff China Medical Research Collaborative (CCMRC), Cardiff University-Peking University Cancer Institute, Cardiff University-Capital Medical University Joint Centre Biomedical Research, Cardiff University School of Medicine, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK.
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Kasuya A, Tokura Y. Attempts to accelerate wound healing. J Dermatol Sci 2014; 76:169-72. [PMID: 25468357 DOI: 10.1016/j.jdermsci.2014.11.001] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 11/10/2014] [Accepted: 11/10/2014] [Indexed: 12/23/2022]
Abstract
Wound healing is a well-orchestrated process, where numerous factors are activated or inhibited in a sequence of steps. Immediately after the infliction of damage, the repair of wound stars. The initial step is an inflammatory change with activation of innate immunity, which is followed by proliferation phase, including fibroplasia, angiogenesis and re-epithelialization. Pathological impairment of wound healing process may lead to persistent ulceration as seen in diabetic patients. Various signaling pathways are involved in wound healing. TGFβ/Smad pathway is a representative and well known to participate in fibroplasia, however, its comprehensive effect on wound healing is controversial. Experimental and clinical remedies have been being tried to promote wound healing. Advancement of cell engineering allows us to use stem cells and living skin equivalents.
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Affiliation(s)
- Akira Kasuya
- Department of Dermatology, Hamamatsu University School of Medicine, Japan.
| | - Yoshiki Tokura
- Department of Dermatology, Hamamatsu University School of Medicine, Japan
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Bosanquet DC, Ye L, Harding KG, Jiang WG. FERM family proteins and their importance in cellular movements and wound healing (review). Int J Mol Med 2014; 34:3-12. [PMID: 24820650 DOI: 10.3892/ijmm.2014.1775] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 03/10/2014] [Indexed: 11/06/2022] Open
Abstract
Motility is a requirement for a number of biological processes, including embryonic development, neuronal development, immune responses, cancer progression and wound healing. Specific to wound healing is the migration of endothelial cells, fibroblasts and other key cellular players into the wound space. Aberrations in wound healing can result in either chronic wounds or abnormally healed wounds. The protein 4.1R, ezrin, radixin, moesin (FERM) superfamily consists of over 40 proteins all containing a three lobed N-terminal FERM domain which binds a variety of cell-membrane associated proteins and lipids. The C-terminal ends of these proteins typically contain an actin-binding domain (ABD). These proteins therefore mediate the linkage between the cell membrane and the actin cytoskeleton, and are involved in cellular movements and migration. Certain FERM proteins have been shown to promote cancer metastasis via this very mechanism. Herein we review the effects of a number of FERM proteins on wound healing and cancer. We show how these proteins typically aid wound healing through their effects on increasing cellular migration and movements, but also typically promote metastasis in cancer. We conclude that FERM proteins play important roles in cellular migration, with markedly different outcomes in the context of cancer and wound healing.
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Affiliation(s)
- David C Bosanquet
- Departments of Surgery and Wound Healing, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XW, UK
| | - Lin Ye
- Departments of Surgery and Wound Healing, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XW, UK
| | - Keith G Harding
- Departments of Surgery and Wound Healing, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XW, UK
| | - Wen G Jiang
- Departments of Surgery and Wound Healing, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XW, UK
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