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Liu T, Ma Y, Han S, Sun P. Genome-wide investigation of lncRNAs revealed their tight association with gastric cancer. J Cancer Res Clin Oncol 2024; 150:261. [PMID: 38761291 PMCID: PMC11102383 DOI: 10.1007/s00432-024-05790-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 05/07/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND Gastric cancer (GC) is a significant health issue globally, ranking as the fifth most common cancer with over 10,000 new cases reported annually. Long non-coding RNA (lncRNA) has emerged as a critical player in cellular functions, influencing GC's development, growth, metastasis, and prognosis. However, our understanding of lncRNA's role in the pathogenesis of GC remains limited. Therefore, it is particularly important to explore the relationship between lncRNA and gastric cancer. METHODS we conducted a comprehensive analysis of RNA sequencing data from the GEO database and stomach adenocarcinoma (STAD) data from the TCGA database to identify lncRNAs that exhibit altered expression levels in GC and the mechanisms underlying lncRNA-mediated transcription and post-transcriptional regulation were explored. RESULTS This study uncovered 94 lncRNAs with differential expression and, through co-expression analysis, linked these to 1508 differentially expressed genes (DEGs). GO functional enrichment analysis highlighted that these DEGs are involved in critical pathways, such as cell adhesion and the positive regulation of cell migration. By establishing a lncRNA-miRNA-mRNA regulatory network, we found that the ceRNA mechanism, particularly involving RP11-357H14.17 and CTD-2377D24.4, could play a role in GC progression. Experimental validation of selected differentially expressed lncRNAs and mRNAs (including RP11-357H14.17-CLDN1, BBOX1, TRPM2-AS, CLDN1, PLAU, HOXB7) confirmed the RNA-seq results. CONCLUSIONS Overall, our findings highlight the critical role of the lncRNA-mRNA regulatory network in the development and progression of GC, offering potential biomarkers for diagnosis and targets for innovative treatment strategies.
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Affiliation(s)
- Tong Liu
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, 130000, China
| | - Yuedong Ma
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, 130000, China
| | - Shuo Han
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, 130000, China
| | - Pengda Sun
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, 130000, China.
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2
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Hussein R, Abou-Shanab AM, Badr E. A multi-omics approach for biomarker discovery in neuroblastoma: a network-based framework. NPJ Syst Biol Appl 2024; 10:52. [PMID: 38760476 PMCID: PMC11101461 DOI: 10.1038/s41540-024-00371-3] [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: 11/09/2023] [Accepted: 04/16/2024] [Indexed: 05/19/2024] Open
Abstract
Neuroblastoma (NB) is one of the leading causes of cancer-associated death in children. MYCN amplification is a prominent genetic marker for NB, and its targeting to halt NB progression is difficult to achieve. Therefore, an in-depth understanding of the molecular interactome of NB is needed to improve treatment outcomes. Analysis of NB multi-omics unravels valuable insight into the interplay between MYCN transcriptional and miRNA post-transcriptional modulation. Moreover, it aids in the identification of various miRNAs that participate in NB development and progression. This study proposes an integrated computational framework with three levels of high-throughput NB data (mRNA-seq, miRNA-seq, and methylation array). Similarity Network Fusion (SNF) and ranked SNF methods were utilized to identify essential genes and miRNAs. The specified genes included both miRNA-target genes and transcription factors (TFs). The interactions between TFs and miRNAs and between miRNAs and their target genes were retrieved where a regulatory network was developed. Finally, an interaction network-based analysis was performed to identify candidate biomarkers. The candidate biomarkers were further analyzed for their potential use in prognosis and diagnosis. The candidate biomarkers included three TFs and seven miRNAs. Four biomarkers have been previously studied and tested in NB, while the remaining identified biomarkers have known roles in other types of cancer. Although the specific molecular role is yet to be addressed, most identified biomarkers possess evidence of involvement in NB tumorigenesis. Analyzing cellular interactome to identify potential biomarkers is a promising approach that can contribute to optimizing efficient therapeutic regimens to target NB vulnerabilities.
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Affiliation(s)
- Rahma Hussein
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Ahmed M Abou-Shanab
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Eman Badr
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt.
- Faculty of Computers and Artificial Intelligence, Cairo University, Giza, 12613, Egypt.
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3
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Wei J, Ji K, Zhang Y, Zhang J, Wu X, Ji X, Zhou K, Yang X, Lu H, Wang A, Bu Z. Exploration of molecular markers related to chemotherapy efficacy of hepatoid adenocarcinoma of the stomach. Cell Oncol (Dordr) 2024; 47:677-693. [PMID: 37943484 DOI: 10.1007/s13402-023-00892-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2023] [Indexed: 11/10/2023] Open
Abstract
PURPOSE Preoperative neoadjuvant chemotherapy may not improve the prognosis of patients with hepatoid adenocarcinoma of the stomach (HAS), a rare pathological type of gastric cancer. Thus, the study aimed at the genomic and transcriptomic impacts of preoperative chemotherapy on HAS. METHODS Patients with HAS who underwent surgical resection at Peking University Cancer Hospital were retrospectively included in this study. Whole exome sequencing and transcriptome sequencing were performed on pre-chemotherapy, non-chemotherapy and post-chemotherapy samples. We then compared the alterations in molecular markers between the post-chemotherapy and non-chemotherapy groups, and between the chemotherapy-effective and chemotherapy-ineffective groups, respectively. RESULTS A total of 79 tumor samples from 72 patients were collected. Compared to the non-chemotherapy group, the mutation frequencies of several genes were changed after chemotherapy, including TP53. In addition, there was a significant increase in the frequency of frameshift mutations and cytosine transversion to adenine (C > A), appearance of COSMIC signature 6 and 14, and a reduced gene copy number amplification. Interestingly, the same phenomenon was observed in chemotherapy-ineffective patients. In addition, many HAS patients had ERBB2, FGFR2, MET and HGF gene amplification. Moreover, the expression of immune-related genes, especially those related to lymphocyte activation, was down-regulated after chemotherapy. CONCLUSION Chemotherapy is closely associated with changes in the molecular characteristics of HAS. After chemotherapy, at genomic and transcriptome level, many features were altered. These changes may be molecular markers of poor chemotherapeutic efficacy and play an important role in chemoresistance in HAS. In addition, ERBB2, FGFR2, MET and HGF gene amplification may be potential therapeutic targets for HAS.
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Affiliation(s)
- Jingtao Wei
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Ke Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Yue Zhang
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
- The Cardiomyopathy Research Group at Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Beijing, 100037, China
| | - Ji Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Xiaojiang Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Xin Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Kai Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Xuesong Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Hongfeng Lu
- Berry Genomics Corporation, Beijing, 102206, China
| | - Anqiang Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China.
| | - Zhaode Bu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China.
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Liu B, Li Y, Xu Y, Xue W, Jin Z. Jian Yun Qing Hua Decoction inhibits malignant behaviors of gastric carcinoma cells via COL12A1 mediated ferroptosis signal pathway. Chin Med 2023; 18:118. [PMID: 37700383 PMCID: PMC10496189 DOI: 10.1186/s13020-023-00799-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/12/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND Jian Yun Qing Hua Decoction (JYQHD), a traditional Chinese medicine decoction, which has been applied in the treatment of gastric cancer (GC). We attempt to confirm the anti-gastric cancer effect of JYQHD and explore the mechanism of JYQHD. METHODS Acute toxicity test was used to understand the toxicity of JYQHD. We studied the expression and prognostic outcome of COL12A1 within GC tissues through the network databases. Using several web-based databases, we analyzed the major components and targets of JYQHD, as well as known therapeutic targets in gastric cancer. The Venn diagram was utilized to obtain the overlapped genes. Lentiviral vector, shRNAs and plasmids, were used to transfect GC cells. Cell counting kit-8 (CCK8), sphere formation, malondialdehyde (MDA), glutathione (GSH), reactive oxygen species (ROS), Fe2+, transmission electron microscopy (TEM), quantitative Real-Time Polymerase Chain Reaction (qRT-PCR), Western-Blot (WB), and immunohistochemical (IHC) assays were employed to investigate the role and mechanism of COL12A1 and JYQHD in GC. RESULTS The results showed that JYQHD was non-toxic and safe. JYQHD inhibited growth and sphere formation ability through inducing the ferroptosis of GC cells, and suppressed the GC cells induced subcutaneous xenograft tumor growth. COL12A1 was highly expressed in gastric cancer tissues, indicating poor prognosis. COL12A1 specifically enhanced GC cell progression and stemness via suppressing ferroptosis. JYQHD down-regulated COL12A1 in order to suppress the stemness of GC cells via inducing ferroptosis. CONCLUSION COL12A1 inhibited ferroptosis and enhanced stemness in GC cells. JYQHD inhibited the development of GC cells by inhibiting cancer cell stemness via the ferroptosis pathway mediated by COL12A1.
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Affiliation(s)
- Baoxinzi Liu
- Department of Medical Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Yu Li
- Department of Medical Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Yuanyuan Xu
- Department of Medical Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Weiwei Xue
- Department of Medical Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China.
| | - Zhichao Jin
- Department of Medical Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China.
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Malvia S, Chintamani C, Sarin R, Dubey US, Saxena S, Bagadi SAR. ABERRANT EXPRESSION OF COL14A1, CELRS3, and CTHRC1 IN BREAST CANCER СELLS. Exp Oncol 2023; 45:28-43. [PMID: 37417284 DOI: 10.15407/exp-oncology.2023.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Collagens, which are the major components of the extracellular matrix involved in the regulation of tumor microenvironment, could be differentially expressed in breast cancer (BC) with different transcriptome profiling. AIM To analyze the transcript level expression of COL1A1, COL5A1, COL10A1, COL11A1, COL12A1, COL14A1, CTHRC1, and CELRS3 genes and the clinical relevance of their differential expression in BC. MATERIALS AND METHODS The transcript level expression of the genes was analyzed using the quantitative real-time PCR (qPCR) in tumor tissue of 60 BC patients. RESULTS Overexpression of COL1A1, COL5A1, COL10A1, COL11A1, COL12A1, CTHRC, and CELRS3 anddown-regulated expression of COL14A1 were observed. COL14A1 down-regulation was associated with aggressive, basal, and Her-2/neu BC subtypes (p = 0.031). Overexpression of CELSR3 was found to be associated with the older age of the patients (> 55 years, p = 0.049). Further analysis with the TCGA BC data set has shown a concordance in the differential expression of the above genes. Furthermore, overexpression of CTHRC1 was associated with poor overall survival (OS), particularly with poor prognosis (p = 0.00042) for the luminal BC subtype. On the other hand, CELSR3 overexpression was associated with mucinous tumors and poor prognosis in post-menopausal women. In silicotarget prediction identified several BC-associated miRNAs and members of miR-154, -515, and -10 families to perform a likely regulatory role in the above ECM genes. CONCLUSION The present study shows that the expression of COL14A1 and CTHRC1 may serve as potential biological markers for the detection of basal BC and the prognosis of survival for patients with the luminal subtype of BC.
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Affiliation(s)
- Shreshtha Malvia
- Tumor Biology Division, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | | | - Ramesh Sarin
- Department of Surgery, Indraprastha Apollo Hospital, New Delhi, 110076, India
| | - Uma S Dubey
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Pilani, Rajasthan, 333031
| | - Sunita Saxena
- Consultant, Department of Health Research, New Delhi, 110001 & Ex-Director National Institute of Pathology-ICMR Safdarjang Hospital Campus
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Darang E, Pezeshkian Z, Mirhoseini SZ, Ghovvati S. Bioinformatics and pathway enrichment analysis identified hub genes and potential biomarker for gastric cancer prognosis. Front Oncol 2023; 13:1187521. [PMID: 37361568 PMCID: PMC10288990 DOI: 10.3389/fonc.2023.1187521] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Gastric cancer is one of the most common cancers in the world. This study aimed to identify genes, biomarkers, and metabolic pathways affecting gastric cancer using bioinformatic analysis and meta-analysis. Methods Datasets containing gene expression profiles of tumor lesions and adjacent non-tumor mucosa samples were downloaded. Common differentially expressed genes between data sets were selected to identify hub genes and further analysis. Gene Expression Profiling and Interactive Analyses (GEPIA) and the Kaplan-Meier method were used to further validate the expression level of genes and plot the overall survivalcurve, respectively. Results and disscussion KEGG pathway analysis showed that the most important pathway was enriched in ECM-receptor interaction. Hub genes includingCOL1A2, FN1, BGN, THBS2, COL5A2, COL6A3, SPARC and COL12A1 wereidentified. The top interactive miRNAs including miR-29a-3p, miR-101-3p,miR-183-5p, and miR-15a-5p targeted the most hub genes. The survival chart showed an increase in mortality in patients with gastric cancer, which shows the importance of the role of these genes in the development of the disease and can be considered candidate genes in the prevention and early diagnosis of gastric cancer.
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Affiliation(s)
- Elham Darang
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, Rasht, Guilan, Iran
| | - Zahra Pezeshkian
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, Rasht, Guilan, Iran
- Research and Development Center (R&D), BioGenTAC Inc., Rasht, Guilan, Iran
| | | | - Shahrokh Ghovvati
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, Rasht, Guilan, Iran
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7
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Charytonowicz D, Brody R, Sebra R. Interpretable and context-free deconvolution of multi-scale whole transcriptomic data with UniCell deconvolve. Nat Commun 2023; 14:1350. [PMID: 36906603 PMCID: PMC10008582 DOI: 10.1038/s41467-023-36961-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/27/2023] [Indexed: 03/13/2023] Open
Abstract
We introduce UniCell: Deconvolve Base (UCDBase), a pre-trained, interpretable, deep learning model to deconvolve cell type fractions and predict cell identity across Spatial, bulk-RNA-Seq, and scRNA-Seq datasets without contextualized reference data. UCD is trained on 10 million pseudo-mixtures from a fully-integrated scRNA-Seq training database comprising over 28 million annotated single cells spanning 840 unique cell types from 898 studies. We show that our UCDBase and transfer-learning models achieve comparable or superior performance on in-silico mixture deconvolution to existing, reference-based, state-of-the-art methods. Feature attribute analysis uncovers gene signatures associated with cell-type specific inflammatory-fibrotic responses in ischemic kidney injury, discerns cancer subtypes, and accurately deconvolves tumor microenvironments. UCD identifies pathologic changes in cell fractions among bulk-RNA-Seq data for several disease states. Applied to lung cancer scRNA-Seq data, UCD annotates and distinguishes normal from cancerous cells. Overall, UCD enhances transcriptomic data analysis, aiding in assessment of cellular and spatial context.
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Affiliation(s)
- Daniel Charytonowicz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel Brody
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Genomics Institute, New York, NY, USA.
- Black Family Stem Cell Institute, New York, NY, USA.
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A novel metabolism-related prognostic gene development and validation in gastric cancer. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2023; 25:447-459. [PMID: 36168087 DOI: 10.1007/s12094-022-02958-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/15/2022] [Indexed: 01/29/2023]
Abstract
BACKGROUND The importance of metabolism-related alterations in the development of gastric cancer (GC) is increasingly recognized. The present study aimed to identify metabolism-related genes to facilitate prognosis of GC patients. METHODS Gene expression datasets and clinical information of GC patients were downloaded from TCGA and GEO databases. We scored the enrichment of human metabolism-related pathways (n = 86) in GC samples by GSV, constructed prognostic risk models using LASSO algorithm and multivariate Cox regression analysis, combined with clinical information to construct a nomogram, and finally cis score algorithm to analyze the abundance of immune-related cells in different subtypes. We used Weka software to screen for prognosis-related marker genes and finally validated the expression of the selected genes in clinical cancer patient tissues. RESULTS We identified that two GC metabolism-related signatures were strongly associated with OS and the levels of immune cell infiltration. Moreover, a survival prediction model for GC was established based on six GC metabolism-related genes. Time-dependent ROC analysis showed good stability of the risk prediction scoring model. The model was successfully validated in an independent ACRG cohort, and the expression trends of key genes were also verified in the GC tissues of patients. DLX1, LTBP2, FGFR1 and MMP2 were highly expressed in the cluster with poorer prognosis while SLC13A2 and SLCO1B3 were highly expressed in the cluster with better prognosis. CONCLUSIONS We identified a risk predictive score model based on six metabolism-related genes related to survival, which may serve as prognostic indicators and potential therapeutic targets for GC.
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Khalid AR, Yasoob TB, Zhang Z, Zhu X, Hang S. Dietary Moringa oleifera leaf powder improves jejunal permeability and digestive function by modulating the microbiota composition and mucosal immunity in heat stressed rabbits. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:80952-80967. [PMID: 35725877 DOI: 10.1007/s11356-022-20737-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Heat stress (HS) has detrimental effects on intestinal health by altering digestive and immune responses in animals. Dietary Moringa oleifera leaf powder (MOLP) has been implicated in ameliorating the impact of HS, but its effects in terms of intestinal function improvement under HS remain poorly characterized. Therefore, the current study investigated the impact of HS and MOLP supplementation on tight junction barriers, intestinal microbiota (jejunal digesta), and differentially expressed genes (DEGs) in jejunal mucosa of heat-stressed rabbits by using the next-generation sequencing techniques. A total of 21 male New Zealand White rabbits (32 weeks old mean body weight of 3318 ± 171 g) were divided into three groups (n = 7/group) as control (CON, 25 °C), heat stress (HS, 35 °C for 7 h daily), and HS with MOLP supplementation (HSM, 35 °C for 7 h daily) gavage at 200 mg/kg body weight per day for 4 weeks. The results indicated that MOLP supplementation increased mRNA expression of tight junction proteins and glutathione transferase activity, while the malonaldehyde concentration was decreased in the jejunal mucosa compared to HS group (P < 0.05). Furthermore, MOLP decreased the concentrations of lipopolysaccharide, pro-inflammatory cytokines, and myeloperoxidase compared with HS group (P < 0.05). Intestinal microbiota analysis revealed that at phyla level, the relative abundance of Bacteroidetes was higher in HSM group compared to CON and HS groups. MOLP supplementation also resulted in higher abundance of putatively health-associated genera such as Christensenellaceae R-7 gut group, Ruminococcaceae NK4A214 group, Ruminococcus 2, Lachnospiraceae NK4A136 group, and Lachnospiraceae unclassified along with higher butyrate levels in HSM group as compared to HS group. The analysis of DEGs revealed that MOLP reversed inflammatory response by downregulation of genes, such as TNFRSF13C, LBP, and COX2 in enriched KEGG pathway of NF-kβ pathway. MOLP supplementation also significantly upregulated the expression of genes in protein digestion and absorption pathway, including PRSS2, LOC100349163, CPA1, CPB1, SLC9A3, SLC1A1, and SLC7A9 in HSM group. Three genes of fibrillar collagens, i.e., COL3A1, COL5A3, and COL12A1 in protein digestion were also down-regulated in HSM group. In conclusion, MOLP supplementation could improve jejunal permeability and digestive function, positively modulate microbiota composition and mucosal immunity in heat-stressed rabbits.
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Affiliation(s)
- Abdur Rauf Khalid
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
| | - Talat Bilal Yasoob
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
| | - Zhen Zhang
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
| | - Xiaofeng Zhu
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
| | - Suqin Hang
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China.
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China.
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Papanicolaou M, Parker AL, Yam M, Filipe EC, Wu SZ, Chitty JL, Wyllie K, Tran E, Mok E, Nadalini A, Skhinas JN, Lucas MC, Herrmann D, Nobis M, Pereira BA, Law AMK, Castillo L, Murphy KJ, Zaratzian A, Hastings JF, Croucher DR, Lim E, Oliver BG, Mora FV, Parker BL, Gallego-Ortega D, Swarbrick A, O'Toole S, Timpson P, Cox TR. Temporal profiling of the breast tumour microenvironment reveals collagen XII as a driver of metastasis. Nat Commun 2022; 13:4587. [PMID: 35933466 PMCID: PMC9357007 DOI: 10.1038/s41467-022-32255-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/22/2022] [Indexed: 01/21/2023] Open
Abstract
The tumour stroma, and in particular the extracellular matrix (ECM), is a salient feature of solid tumours that plays a crucial role in shaping their progression. Many desmoplastic tumours including breast cancer involve the significant accumulation of type I collagen. However, recently it has become clear that the precise distribution and organisation of matrix molecules such as collagen I is equally as important in the tumour as their abundance. Cancer-associated fibroblasts (CAFs) coexist within breast cancer tissues and play both pro- and anti-tumourigenic roles through remodelling the ECM. Here, using temporal proteomic profiling of decellularized tumours, we interrogate the evolving matrisome during breast cancer progression. We identify 4 key matrisomal clusters, and pinpoint collagen type XII as a critical component that regulates collagen type I organisation. Through combining our proteomics with single-cell transcriptomics, and genetic manipulation models, we show how CAF-secreted collagen XII alters collagen I organisation to create a pro-invasive microenvironment supporting metastatic dissemination. Finally, we show in patient cohorts that collagen XII may represent an indicator of breast cancer patients at high risk of metastatic relapse. The distribution and organisation of matrix molecules in the tumour stroma help shape solid tumour progression. Here they perform temporal proteomic profiling of the matrisome during breast cancer progression and show that collagen XII secreted from CAFs provides a pro-invasive microenvironment.
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Affiliation(s)
- Michael Papanicolaou
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Amelia L Parker
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Michelle Yam
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Elysse C Filipe
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Sunny Z Wu
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Jessica L Chitty
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Kaitlin Wyllie
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Emmi Tran
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ellie Mok
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Audrey Nadalini
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Joanna N Skhinas
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Morghan C Lucas
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia
| | - David Herrmann
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Max Nobis
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Brooke A Pereira
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Andrew M K Law
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia
| | - Lesley Castillo
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia
| | - Kendelle J Murphy
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Anaiis Zaratzian
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia
| | - Jordan F Hastings
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia
| | - David R Croucher
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Elgene Lim
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Brian G Oliver
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia.,Woolcock Institute of Medical Research, Respiratory Cellular and Molecular Biology, The University of Sydney, Sydney, NSW, Australia
| | - Fatima Valdes Mora
- Cancer Epigenetic Biology and Therapeutics, Personalised Medicine, Children's Cancer Institute, Sydney, NSW, 2031, Australia.,School of Women's and Children's Health, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Benjamin L Parker
- Metabolic Systems Biology Laboratory, Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - David Gallego-Ortega
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.,School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW, Australia
| | - Alexander Swarbrick
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Sandra O'Toole
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia.,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
| | - Paul Timpson
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia. .,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia. .,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
| | - Thomas R Cox
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney, NSW, Australia. .,Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia. .,School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
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11
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Saito S, Ku CC, Wuputra K, Pan JB, Lin CS, Lin YC, Wu DC, Yokoyama KK. Biomarkers of Cancer Stem Cells for Experimental Research and Clinical Application. J Pers Med 2022; 12:jpm12050715. [PMID: 35629138 PMCID: PMC9147761 DOI: 10.3390/jpm12050715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 12/12/2022] Open
Abstract
The use of biomarkers in cancer diagnosis, therapy, and prognosis has been highly effective over several decades. Studies of biomarkers in cancer patients pre- and post-treatment and during cancer progression have helped identify cancer stem cells (CSCs) and their related microenvironments. These analyses are critical for the therapeutic application of drugs and the efficient targeting and prevention of cancer progression, as well as the investigation of the mechanism of the cancer development. Biomarkers that characterize CSCs have thus been identified and correlated to diagnosis, therapy, and prognosis. However, CSCs demonstrate elevated levels of plasticity, which alters their functional phenotype and appearance by interacting with their microenvironments, in response to chemotherapy and radiotherapeutics. In turn, these changes induce different metabolic adaptations of CSCs. This article provides a review of the most frequently used CSCs and stem cell markers.
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Affiliation(s)
- Shigeo Saito
- Saito Laboratory of Cell Technology, Yaita 329-1571, Japan
- Horus Co., Ltd., Nakano, Tokyo 164-0001, Japan
- Correspondence: (S.S.); (D.-C.W.); (K.K.Y.); Tel.: +886-7312-1001 (ext. 2729) (K.K.Y.); Fax: +886-7313-3849 (K.K.Y.)
| | - Chia-Chen Ku
- Graduate Institute of Medicine, Department of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.K.); (K.W.); (J.-B.P.); (C.-S.L.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Kenly Wuputra
- Graduate Institute of Medicine, Department of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.K.); (K.W.); (J.-B.P.); (C.-S.L.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Jia-Bin Pan
- Graduate Institute of Medicine, Department of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.K.); (K.W.); (J.-B.P.); (C.-S.L.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Chang-Shen Lin
- Graduate Institute of Medicine, Department of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.K.); (K.W.); (J.-B.P.); (C.-S.L.)
| | - Ying-Chu Lin
- School of Dentistry, Department of Dentistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Deng-Chyang Wu
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Correspondence: (S.S.); (D.-C.W.); (K.K.Y.); Tel.: +886-7312-1001 (ext. 2729) (K.K.Y.); Fax: +886-7313-3849 (K.K.Y.)
| | - Kazunari K. Yokoyama
- Graduate Institute of Medicine, Department of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.K.); (K.W.); (J.-B.P.); (C.-S.L.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Correspondence: (S.S.); (D.-C.W.); (K.K.Y.); Tel.: +886-7312-1001 (ext. 2729) (K.K.Y.); Fax: +886-7313-3849 (K.K.Y.)
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12
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Analysis of Yes-Associated Protein-1 (YAP1) Target Gene Signature to Predict Progressive Breast Cancer. J Clin Med 2022; 11:jcm11071947. [PMID: 35407556 PMCID: PMC8999906 DOI: 10.3390/jcm11071947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/02/2022] [Accepted: 03/29/2022] [Indexed: 02/07/2023] Open
Abstract
Breast cancers are treated according to the ER/PR or HER2 expression and show better survival outcomes with targeted therapy. Triple-negative breast cancers (TNBCs) with a lack of expression of ER/PR and HER2 are treated with systemic therapy with unpredictable responses and outcomes. It is essential to investigate novel markers to identify targeted therapies for TNBC. One such marker is YAP1, a transcription co-activator protein that shows association with poor prognosis of breast cancer. YAP1 transcriptionally regulates the expression of genes that drive the oncogenic phenotypes. Here, we assess a potential YAP target gene signature to predict a progressive subset of breast tumors from METABRIC and TCGA datasets. YAP1 target genes were shortlisted based on expression correlation and concordance with YAP1 expression and significant association with survival outcomes of patients. Hierarchical clustering was performed for the shortlisted genes. The utility of the clustered genes was assessed by survival analysis to identify a recurring subset. Expression of the shortlisted target genes showed significant association with survival outcomes of HER2-positive and TNBC subset in both datasets. The shortlisted genes were verified using an independent dataset. Further validation using IHC can prove the utility of this potential prognostic signature to identify a recurrent subset of HER2-positive and TNBC subtypes.
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13
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Chivu-Economescu M, Necula LG, Matei L, Dragu D, Bleotu C, Sorop A, Herlea V, Dima S, Popescu I, Diaconu CC. Collagen Family and Other Matrix Remodeling Proteins Identified by Bioinformatics Analysis as Hub Genes Involved in Gastric Cancer Progression and Prognosis. Int J Mol Sci 2022; 23:ijms23063214. [PMID: 35328635 PMCID: PMC8950589 DOI: 10.3390/ijms23063214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 02/05/2023] Open
Abstract
Gastric cancer has remained in the top five cancers for over ten years, both in terms of incidence and mortality due to the shortage of biomarkers for disease follow-up and effective therapies. Aiming to fill this gap, we performed a bioinformatics assessment on our data and two additional GEO microarray profiles, followed by a deep analysis of the 40 differentially expressed genes identified. PPI network analysis and MCODE plug-in pointed out nine upregulated hub genes coding for proteins from the collagen family (COL12A1, COL5A2, and COL10A1) or involved in the assembly (BGN) or degradation of collagens (CTHRC1), and also associated with cell adhesion (THBS2 and SPP1) and extracellular matrix degradation (FAP, SULF1). Those genes were highly upregulated at the mRNA and protein level, the increase being correlated with pathological T stages. The high expression of BGN (p = 8 × 10−12), THBS2 (p = 1.2 × 10−6), CTHRC1 (p = 1.1 × 10−4), SULF1 (p = 3.8 × 10−4), COL5A1 (p = 1.3 × 10−4), COL10A1 (p = 5.7 × 10−4), COL12A1 (p = 2 × 10−3) correlated with poor overall survival and an immune infiltrate based especially on immunosuppressive M2 macrophages (p-value range 4.82 × 10−7–1.63 × 10−13). Our results emphasize that these genes could be candidate biomarkers for GC progression and prognosis and new therapeutic targets.
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Affiliation(s)
- Mihaela Chivu-Economescu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania; (L.G.N.); (L.M.); (D.D.); (C.B.); (C.C.D.)
- Correspondence: or ; Tel.: +40-21-324-2592
| | - Laura G. Necula
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania; (L.G.N.); (L.M.); (D.D.); (C.B.); (C.C.D.)
- Faculty of Medicine, Titu Maiorescu University, 040441 Bucharest, Romania; (V.H.); (I.P.)
| | - Lilia Matei
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania; (L.G.N.); (L.M.); (D.D.); (C.B.); (C.C.D.)
| | - Denisa Dragu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania; (L.G.N.); (L.M.); (D.D.); (C.B.); (C.C.D.)
| | - Coralia Bleotu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania; (L.G.N.); (L.M.); (D.D.); (C.B.); (C.C.D.)
| | - Andrei Sorop
- Center of Excellence for Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania; (A.S.); (S.D.)
| | - Vlad Herlea
- Faculty of Medicine, Titu Maiorescu University, 040441 Bucharest, Romania; (V.H.); (I.P.)
- Department of Pathology, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Simona Dima
- Center of Excellence for Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania; (A.S.); (S.D.)
- Center of General Surgery and Liver Transplantation, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Irinel Popescu
- Faculty of Medicine, Titu Maiorescu University, 040441 Bucharest, Romania; (V.H.); (I.P.)
- Center of General Surgery and Liver Transplantation, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Carmen C. Diaconu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania; (L.G.N.); (L.M.); (D.D.); (C.B.); (C.C.D.)
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14
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Somatic mutations in collagens are associated with a distinct tumor environment and overall survival in gastric cancer. BMC Cancer 2022; 22:139. [PMID: 35120467 PMCID: PMC8815231 DOI: 10.1186/s12885-021-09136-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 12/22/2021] [Indexed: 12/11/2022] Open
Abstract
Background Gastric cancer is a heterogeneous disease with poorly understood genetic and microenvironmental factors. Mutations in collagen genes are associated with genetic diseases that compromise tissue integrity, but their role in tumor progression has not been extensively reported. Aberrant collagen expression has been long associated with malignant tumor growth, invasion, chemoresistance, and patient outcomes. We hypothesized that somatic mutations in collagens could functionally alter the tumor extracellular matrix. Methods We used publicly available datasets including The Tumor Cancer Genome Atlas (TCGA) to interrogate somatic mutations in collagens in stomach adenocarcinomas. To demonstrate that collagens were significantly mutated above background mutation rates, we used a moderated Kolmogorov-Smirnov test along with combination analysis with a bootstrap approach to define the background accounting for mutation rates. Association between mutations and clinicopathological features was evaluated by Fisher or chi-squared tests. Association with overall survival was assessed by Kaplan-Meier and the Cox-Proportional Hazards Model. Gene Set Enrichment Analysis was used to interrogate pathways. Immunohistochemistry and in situ hybridization tested expression of COL7A1 in stomach tumors. Results In stomach adenocarcinomas, we identified individual collagen genes and sets of collagen genes harboring somatic mutations at a high frequency compared to background in both microsatellite stable, and microsatellite instable tumors in TCGA. Many of the missense mutations resemble the same types of loss of function mutations in collagenopathies that disrupt tissue formation and destabilize cells providing guidance to interpret the somatic mutations. We identified combinations of somatic mutations in collagens associated with overall survival, with a distinctive tumor microenvironment marked by lower matrisome expression and immune cell signatures. Truncation mutations were strongly associated with improved outcomes suggesting that loss of expression of secreted collagens impact tumor progression and treatment response. Germline collagenopathy variants guided interpretation of impactful somatic mutations on tumors. Conclusions These observations highlight that many collagens, expressed in non-physiologically relevant conditions in tumors, harbor impactful somatic mutations in tumors, suggesting new approaches for classification and therapy development in stomach cancer. In sum, these findings demonstrate how classification of tumors by collagen mutations identified strong links between specific genotypes and the tumor environment. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-09136-1.
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15
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Liu B, Ma X, Ha W. Identification of Potential Prognostic Biomarkers Associated With Macrophage M2 Infiltration in Gastric Cancer. Front Genet 2022; 12:827444. [PMID: 35111208 PMCID: PMC8802722 DOI: 10.3389/fgene.2021.827444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/30/2021] [Indexed: 11/18/2022] Open
Abstract
Gastric cancer is a common cancer afflicting people worldwide. Although incremental progress has been achieved in gastric cancer research, the molecular mechanisms underlying remain unclear. In this study, we conducted bioinformatics methods to identify prognostic marker genes associated with gastric cancer progression. Three hundred and twenty-seven overlapping DEGs were identified from three GEO microarray datasets. Functional enrichment analysis revealed that these DEGs are involved in extracellular matrix organization, tissue development, extracellular matrix–receptor interaction, ECM-receptor interaction, PI3K-Akt signaling pathway, focal adhesion, and protein digestion and absorption. A protein–protein interaction network (PPI) was constructed for the DEGs in which 25 hub genes were obtained. Furthermore, the turquoise module was identified to be significantly positively coexpressed with macrophage M2 infiltration by weighted gene coexpression network analysis (WGCNA). Hub genes of COL1A1, COL4A1, COL12A1, and PDGFRB were overlapped in both PPI hub gene list and the turquoise module with significant association with the prognosis in gastric cancer. Moreover, functional analysis demonstrated that these hub genes play pivotal roles in cancer cell proliferation and invasion. The investigation of the gene markers can help deepen our understanding of the molecular mechanisms of gastric cancer. In addition, these genes may serve as potential prognostic biomarkers for gastric cancer diagnosis.
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Affiliation(s)
- Baohong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- *Correspondence: Baohong Liu,
| | - Xueting Ma
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Wei Ha
- Department of Radiology, Affiliated Hospital of Gansu University of Traditional Chinese Medicine, Lanzhou, China
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16
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Wu H, Wang H, Jiang Z, Chen Y. Identification of Three Core Secretome Genes Associated with Immune Infiltration in High Tumor Mutation Burden Across 14 Major Solid Tumors. Int J Gen Med 2021; 14:6755-6767. [PMID: 34703282 PMCID: PMC8527654 DOI: 10.2147/ijgm.s333141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/23/2021] [Indexed: 12/27/2022] Open
Abstract
Background Secretome genes, encoding proteins secreted from the cell, are involved in the tumor immune response and correlated with levels of tumor mutation burden (TMB) in multiple tumors. This study aimed to identify core secretome genes and their potential association with immunomodulators and immune infiltration in high TMB groups across 14 major solid tumors through bioinformatics analysis. Methods Multi-omics data for 14 major solid tumors were downloaded from The Cancer Genome Atlas (TCGA) database. Patients were divided into high TMB (TMB-high) and low TMB (TMB-low) groups using the median TMB values for each of the solid tumors. The CIBERSORT algorithm was conducted to estimate the proportion of 22 tumor-infiltrating immune cells (TIICs). Kaplan-Meier analysis and the log-rank test were utilized to screened prognosis-related genes. The correlations between core secretome genes and TIICs were analyzed using Spearman correlation coefficients. Results In TMB-high groups, multi-omics data analysis revealed that secretome genes were strongly associated with clinical characteristics, and 65 prognosis-related secretome genes were screened. Among the prognosis-related genes, 21 core secretome genes were identified, and strongly associated with five types of TIICs, namely activated NK cells, follicular helper T cells, CD8 T cells, and macrophages M0 and M2. Notably, three secretome genes (ADAMTS12, COL12A1, and COL5A2) were significantly related to immunomodulators and TIICs in multiple solid tumors. In addition, 12 core secretome genes were significantly differentially expressed between responding and non-responding patients receiving immunotherapy. Furthermore, core secretome genes may be involved in the PI3K/AKT signaling pathway. Conclusion We examined the prognostic significance of secretome genes and their potential association with immunomodulators and immune infiltration across 14 major solid tumors. In summary, three secretome genes (ADAMTS12, COL12A1, and COL5A2) may be pivotal mediators of immune infiltration in TMB-high patients, which may help to identify patients who could benefit from immunotherapy.
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Affiliation(s)
- Huan Wu
- Department of Medical Laboratory, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, People's Republic of China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, People's Republic of China
| | - Hanchu Wang
- The Second Clinical Medical College, Jinan University, Guangzhou, People's Republic of China
| | - Zhenyou Jiang
- Department of Microbiology and Immunology, College of Basic Medicine and Public Hygiene, Jinan University, Guangzhou, People's Republic of China
| | - Yue Chen
- Department of Medical Laboratory, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, People's Republic of China
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17
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Gatti G, Vilardo L, Musa C, Di Pietro C, Bonaventura F, Scavizzi F, Torcinaro A, Bucci B, Saporito R, Arisi I, De Santa F, Raspa M, Guglielmi L, D’Agnano I. Role of Lamin A/C as Candidate Biomarker of Aggressiveness and Tumorigenicity in Glioblastoma Multiforme. Biomedicines 2021; 9:biomedicines9101343. [PMID: 34680461 PMCID: PMC8533312 DOI: 10.3390/biomedicines9101343] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 12/11/2022] Open
Abstract
Nuclear lamina components have long been regarded as scaffolding proteins, forming a dense fibrillar structure necessary for the maintenance of the nucleus shape in all the animal kingdom. More recently, mutations, aberrant localisation and deregulation of these proteins have been linked to several diseases, including cancer. Using publicly available data we found that the increased expression levels of the nuclear protein Lamin A/C correlate with a reduced overall survival in The Cancer Genome Atlas Research Network (TCGA) patients affected by glioblastoma multiforme (GBM). We show that the expression of the LMNA gene is linked to the enrichment of cancer-related pathways, particularly pathways related to cell adhesion and cell migration. Mimicking the modulation of LMNA in a GBM preclinical cancer model, we confirmed both in vitro and in vivo that the increased expression of LMNA is associated with an increased aggressiveness and tumorigenicity. In addition, delving into the possible mechanism behind LMNA-induced GBM aggressiveness and tumorigenicity, we found that the mTORC2 component, Rictor, plays a central role in mediating these effects.
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Affiliation(s)
- Giuliana Gatti
- Department of Biotechnology and Translational Medicine, University of Milan, 20129 Milan, Italy;
| | - Laura Vilardo
- Institute for Biomedical Technologies (ITB), CNR, 20054 Segrate, Italy; (L.V.); (C.M.)
| | - Carla Musa
- Institute for Biomedical Technologies (ITB), CNR, 20054 Segrate, Italy; (L.V.); (C.M.)
| | - Chiara Di Pietro
- Institute of Biochemistry and Cell Biology (IBBC), CNR, 00015 Monterotondo, Italy; (C.D.P.); (F.B.); (F.S.); (A.T.); (F.D.S.); (M.R.)
| | - Fabrizio Bonaventura
- Institute of Biochemistry and Cell Biology (IBBC), CNR, 00015 Monterotondo, Italy; (C.D.P.); (F.B.); (F.S.); (A.T.); (F.D.S.); (M.R.)
| | - Ferdinando Scavizzi
- Institute of Biochemistry and Cell Biology (IBBC), CNR, 00015 Monterotondo, Italy; (C.D.P.); (F.B.); (F.S.); (A.T.); (F.D.S.); (M.R.)
| | - Alessio Torcinaro
- Institute of Biochemistry and Cell Biology (IBBC), CNR, 00015 Monterotondo, Italy; (C.D.P.); (F.B.); (F.S.); (A.T.); (F.D.S.); (M.R.)
| | - Barbara Bucci
- UOC Clinical Pathology, San Pietro Hospital FBF, 00189 Rome, Italy; (B.B.); (R.S.)
| | - Raffaele Saporito
- UOC Clinical Pathology, San Pietro Hospital FBF, 00189 Rome, Italy; (B.B.); (R.S.)
| | - Ivan Arisi
- Bioinformatics Facility, European Brain Research Institute (EBRI) “Rita Levi Montalcini”, 00161 Rome, Italy;
| | - Francesca De Santa
- Institute of Biochemistry and Cell Biology (IBBC), CNR, 00015 Monterotondo, Italy; (C.D.P.); (F.B.); (F.S.); (A.T.); (F.D.S.); (M.R.)
| | - Marcello Raspa
- Institute of Biochemistry and Cell Biology (IBBC), CNR, 00015 Monterotondo, Italy; (C.D.P.); (F.B.); (F.S.); (A.T.); (F.D.S.); (M.R.)
| | - Loredana Guglielmi
- Institute for Biomedical Technologies (ITB), CNR, 20054 Segrate, Italy; (L.V.); (C.M.)
- Correspondence: (L.G.); (I.D.)
| | - Igea D’Agnano
- Institute for Biomedical Technologies (ITB), CNR, 20054 Segrate, Italy; (L.V.); (C.M.)
- Correspondence: (L.G.); (I.D.)
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Abstract
Although the probiotic Lactobacillus acidophilus LA14 is used worldwide, its effect on liver diseases remains unelucidated. Here, 32 rats were divided into four groups, gavaged with L. acidophilus LA14 (3 × 109 CFU) or phosphate-buffered saline for 7 days, and then intraperitoneally injected with d-galactosamine or saline. After 24 h, blood, liver, ileum, and feces samples were collected for liver injury, inflammation, intestinal barrier, gut microbiota, metabolome, and transcriptome analyses. Pretreatment with L. acidophilus LA14 alleviated the d-galactosamine-induced elevation of serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), and bile acids; mitigated the histological injury to the liver and gut; and suppressed the inflammatory cytokines macrophage inflammatory protein 1α (MIP-1α), MIP-3α, and MCP-1. L. acidophilus LA14 also ameliorated the d-galactosamine-induced dysbiosis of the gut microbiota and metabolism, such as the enrichment of Bacteroides sp. strain dnLKV3 and the depletion of Streptococcus, butanoic acid, and N-acetyl-d-glucosamine. The underlying mechanism of L. acidophilus LA14 included prevention of not only the d-galactosamine-induced upregulation of infection- and tumor-related pathways but also the d-galactosamine-induced downregulation of antioxidation-related pathways during this process, as reflected by the liver transcriptome and proteome analyses. Furthermore, the administration of L. acidophilus LA14 to healthy rats did not alter the tested liver indicators but significantly enriched the beneficial Lactobacillus and Bifidobacterium species, promoted metabolism and regulated pathways to improve immunity. The ability of L. acidophilus LA14 to alleviate liver injury was further confirmed with an acetaminophen-induced mouse model. These results might provide a reference for future studies on the application of L. acidophilus LA14 for the prevention of liver injury. IMPORTANCE The probiotic Lactobacillus acidophilus LA14 is widely used, but its effect on liver diseases has not been elucidated. We explored the protective effect of L. acidophilus LA14 on the liver using rats with d-galactosamine-induced liver injury. Pretreatment with L. acidophilus LA14 alleviated the d-galactosamine-induced elevation of serum ALT, AST, ALP, and bile acids, mitigated the histological injury to the liver and gut, and suppressed the inflammatory cytokines MIP-1α, MIP-3α, and MCP-1. These effects were correlated with the modulations of the gut microbiome, metabolome, and hepatic gene expression induced by L. acidophilus LA14. Moreover, the ability of L. acidophilus LA14 to alleviate liver injury was further confirmed with an acetaminophen-induced mouse model. These results might provide a reference for future studies on the application of L. acidophilus LA14 for the prevention of liver injury.
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Chen S, Gao C, Yu T, Qu Y, Xiao GG, Huang Z. Bioinformatics Analysis of a Prognostic miRNA Signature and Potential Key Genes in Pancreatic Cancer. Front Oncol 2021; 11:641289. [PMID: 34094925 PMCID: PMC8174116 DOI: 10.3389/fonc.2021.641289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/31/2021] [Indexed: 12/11/2022] Open
Abstract
Background In this study, miRNAs and their critical target genes related to the prognosis of pancreatic cancer were screened based on bioinformatics analysis to provide targets for the prognosis and treatment of pancreatic cancer. Methods R software was used to screen differentially expressed miRNAs (DEMs) and genes (DEGs) downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, respectively. A miRNA Cox proportional hazards regression model was constructed based on the miRNAs, and a miRNA prognostic model was generated. The target genes of the prognostic miRNAs were predicted using TargetScan and miRDB and then intersected with the DEGs to obtain common genes. The functions of the common genes were subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses. A protein-protein interaction (PPI) network of the common genes was constructed with the STRING database and visualized with Cytoscape software. Key genes were also screened with the MCODE and cytoHubba plug-ins of Cytoscape. Finally, a prognostic model formed by the key gene was also established to help evaluate the reliability of this screening process. Results A prognostic model containing four downregulated miRNAs (hsa-mir-424, hsa-mir-3613, hsa-mir-4772 and hsa-mir-126) related to the prognosis of pancreatic cancer was constructed. A total of 118 common genes were enriched in two KEGG pathways and 33 GO functional annotations, including extracellular matrix (ECM)-receptor interaction and cell adhesion. Nine key genes related to pancreatic cancer were also obtained: MMP14, ITGA2, THBS2, COL1A1, COL3A1, COL11A1, COL6A3, COL12A1 and COL5A2. The prognostic model formed by nine key genes also possessed good prognostic ability. Conclusions The prognostic model consisting of four miRNAs can reliably predict the prognosis of patients with pancreatic cancer. In addition, the screened nine key genes, which can also form a reliable prognostic model, are significantly related to the occurrence and development of pancreatic cancer. Among them, one novel miRNA (hsa-mir-4772) and two novel genes (COL12A1 and COL5A2) associated with pancreatic cancer have great potential to be used as prognostic factors and therapeutic targets for this tumor.
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Affiliation(s)
- Shuoling Chen
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China.,The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Chang Gao
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Tianyang Yu
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Yueyang Qu
- School of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian, China
| | - Gary Guishan Xiao
- School of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian, China
| | - Zunnan Huang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
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Memon RA, Wei S, Siegal GP. Some Reactive Lesions of Bone Are Probably Neoplasms: A Review. Arch Pathol Lab Med 2021; 146:60-69. [PMID: 33946096 DOI: 10.5858/arpa.2020-0817-ra] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— A number of fibro-osseous and osteocartilaginous lesions, especially common in the small bones of hand and feet, pose a diagnostic challenge and have historically been thought to be reactive lesions. However, modern molecular techniques when supplementing clinical, radiographic, and histologic evaluation suggest they may, in fact, be neoplasms. OBJECTIVE.— To review the clinical presentation and histopathologic, molecular, and radiologic features of selective bone lesions, focusing most specifically on subungual exostosis, florid reactive periostitis, and bizarre periosteal osteochondromatous proliferation. DATA SOURCES.— Literature review and personal experience are the source of this review. CONCLUSIONS.— Some lesions previously thought to be reactive are locally aggressive and demonstrate reproducible molecular abnormalities, and thus may be neoplasms. Although most common in the bones of the fingers and toes, these lesions also occur in long and other bones. The clinical presentations, radiologic appearances, and histopathologic features often overlap, making the diagnosis challenging, and these lesions may require molecular evaluation to maximize accurate prognostication.
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Affiliation(s)
- Raima A Memon
- From the Departments of Pathology & Genetics, University of Alabama at Birmingham
| | - Shi Wei
- From the Departments of Pathology & Genetics, University of Alabama at Birmingham
| | - Gene P Siegal
- From the Departments of Pathology & Genetics, University of Alabama at Birmingham
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21
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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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Identification of Core Prognosis-Related Candidate Genes in Chinese Gastric Cancer Population Based on Integrated Bioinformatics. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8859826. [PMID: 33381592 PMCID: PMC7748906 DOI: 10.1155/2020/8859826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 12/29/2022]
Abstract
Background Gastric cancer (GC) is one of the leading causes of cancer-related mortality worldwide. There are great geographical differences in the incidence of GC, and somatic mutation rates of driver genes are also different. The present study is aimed at screening core prognosis-related candidate genes in Chinese gastric cancer population based on integrated bioinformatics for the early diagnosis and prognosis of GC. Methods In the present study, the differentially expressed genes (DEGs) in GC were identified using four microarray datasets from the Gene Expression Omnibus (GEO) database. The samples of these datasets were all from China. Functional enrichment analysis of DEGs was conducted to evaluate the underlying molecular mechanisms involved in GC. Protein-protein interaction (PPI) network and cytoHubba were performed to determine hub genes associated with GC. Gene Expression Profiling Interactive Analysis (GEPIA) and Human Protein Atlas (HPA) were performed to validate the hub genes. Results A total of 240 DEGs were obtained through the RRA method, including 80 upregulated genes and 160 downregulated genes. Upregulated genes were mainly enriched in extracellular matrix organization, extracellular matrix, and extracellular matrix structural constituent. The downregulated genes were mainly enriched in digestion, extracellular space, and oxidoreductase activity. The KEGG pathway enrichment analysis showed that the upregulated genes were mainly associated with ECM-receptor interaction, focal adhesion, and PI3K-Akt signaling pathway. And downregulated genes were mainly associated with the metabolism of xenobiotics by cytochrome P450, metabolic pathways, and gastric acid secretion. The transcriptional and translational expression levels of the genes including COL1A1, COL5A2, COL12A1, and VCAN were higher in GC tissues than normal tissues. Conclusion A total of four genes including COL1A1, COL5A2, COL12A1, and VCAN were considered potential GC biomarkers in the Chinese population. And ECM-receptor interaction, focal adhesion, and PI3K-Akt signaling pathway were revealed to be important mechanisms of GC. Our findings provide novel insights into the occurrence and progression of GC in the Chinese population.
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The Extracellular Matrix: An Accomplice in Gastric Cancer Development and Progression. Cells 2020; 9:cells9020394. [PMID: 32046329 PMCID: PMC7072625 DOI: 10.3390/cells9020394] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 02/07/2023] Open
Abstract
The extracellular matrix (ECM) is a dynamic and highly organized tissue structure, providing support and maintaining normal epithelial architecture. In the last decade, increasing evidence has emerged demonstrating that alterations in ECM composition and assembly strongly affect cellular function and behavior. Even though the detailed mechanisms underlying cell-ECM crosstalk are yet to unravel, it is well established that ECM deregulation accompanies the development of many pathological conditions, such as gastric cancer. Notably, gastric cancer remains a worldwide concern, representing the third most frequent cause of cancer-associated deaths. Despite increased surveillance protocols, patients are usually diagnosed at advanced disease stages, urging the identification of novel diagnostic biomarkers and efficient therapeutic strategies. In this review, we provide a comprehensive overview regarding expression patterns of ECM components and cognate receptors described in normal gastric epithelium, pre-malignant lesions, and gastric carcinomas. Important insights are also discussed for the use of ECM-associated molecules as predictive biomarkers of the disease or as potential targets in gastric cancer.
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