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Torshizi Esfahani A, Mohammadpour S, Jalali P, Yaghoobi A, Karimpour R, Torkamani S, Pardakhtchi A, Salehi Z, Nazemalhosseini-Mojarad E. Differential expression of angiogenesis-related genes 'VEGF' and 'angiopoietin-1' in metastatic and EMAST-positive colorectal cancer patients. Sci Rep 2024; 14:10539. [PMID: 38719941 PMCID: PMC11079037 DOI: 10.1038/s41598-024-61000-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Abnormal angiogenesis leads to tumor progression and metastasis in colorectal cancer (CRC). This study aimed to elucidate the association between angiogenesis-related genes, including VEGF-A, ANGPT-1, and ANGPT-2 with both metastatic and microsatellite alterations at selected tetranucleotide repeats (EMAST) subtypes of CRC. We conducted a thorough assessment of the ANGPT-1, ANGPT-2, and VEGF-A gene expression utilizing publicly available RNA sequencing and microarray datasets. Then, the experimental validation was performed in 122 CRC patients, considering their disease metastasis and EMAST+/- profile by using reverse transcription polymerase chain reaction (RT-PCR). Subsequently, a competing endogenous RNA (ceRNA) network associated with these angiogenesis-related genes was constructed and analyzed. The expression level of VEGF-A and ANGPT-2 genes were significantly higher in tumor tissues as compared with normal adjacent tissues (P-value < 0.001). Nevertheless, ANGPT-1 had a significantly lower expression in tumor samples than in normal colon tissue (P-value < 0.01). We identified a significantly increased VEGF-A (P-value = 0.002) and decreased ANGPT-1 (P-value = 0.04) expression in EMAST+ colorectal tumors. Regarding metastasis, a significantly increased VEGF-A and ANGPT-2 expression (P-value = 0.001) and decreased ANGPT-1 expression (P-value < 0.05) were established in metastatic CRC patients. Remarkably, co-expression analysis also showed a strong correlation between ANGPT-2 and VEGF-A gene expressions. The ceRNA network was constructed by ANGPT-1, ANGPT-2, VEGF-A, and experimentally validated miRNAs (hsa-miR-190a-3p, hsa-miR-374c-5p, hsa-miR-452-5p, and hsa-miR-889-3p), lncRNAs (AFAP1-AS1, KCNQ1OT1 and MALAT1), and TFs (Sp1, E2F1, and STAT3). Network analysis revealed that colorectal cancer is amongst the 82 significant pathways. We demonstrated a significant differential expression of VEGF-A and ANGPT-1 in colorectal cancer patients exhibiting the EMAST+ phenotype. This finding provides novel insights into the molecular pathogenesis of colorectal cancer, specifically in EMAST subtypes. Yet, the generalization of in silico findings to EMAST+ colorectal cancer warrants future experimental investigations. In the end, this study proposes that the EMAST biomarker could serve as an additional perspective on CMS4 biology which is well-defined by activated angiogenesis and worse overall survival.
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Affiliation(s)
- Amir Torshizi Esfahani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Mohammadpour
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pooya Jalali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Yaghoobi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Raana Karimpour
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Soha Torkamani
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ali Pardakhtchi
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Zahra Salehi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
- Research Institute for Oncology, Hematology and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands.
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2
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Agwa SHA, Elzahwy SS, Hossam N, Yahia YA, Hamady S, Sherif N, Elshazly A, Darwish RM, Hashim JO, Adly MA, Abd Elsamee AM, Shamekh R, Roushdy MMS, Matboli M. Discriminatory power of a circulating multi-noncoding RNA panel in acute coronary syndrome subtypes: Towards precision detection. Int J Biochem Cell Biol 2024; 169:106531. [PMID: 38280541 DOI: 10.1016/j.biocel.2024.106531] [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: 06/22/2023] [Revised: 11/24/2023] [Accepted: 01/18/2024] [Indexed: 01/29/2024]
Abstract
BACKGROUND Acute Coronary Syndrome (ACS) stands as a significant contributor to cardiovascular mortality, necessitating improved diagnostic tools for early detection and tailored therapeutic interventions. Current diagnostic modalities, exhibit limitations in sensitivity and specificity, urging the quest for novel biomarkers to enhance discrimination of the different stages of ACS including unstable angina, Non-ST-segment Elevation Myocardial Infarction (NSTEMI), and ST-segment Elevation Myocardial Infarction (STEMI). METHODS This study investigated the potential of a plasma-circulating multi-noncoding RNA (ncRNA) panel, comprising four miRNAs (miR-182-5p, miR-23a-3p, miR-146a-5p, and miR-183-5p) and three lncRNAs (SNHG15, SNHG5, and RMRP), selected based on their intricate involvement in ACS pathogenesis and signaling pathways regulating post-myocardial infarction (MI) processes. The differential expression of these ncRNAs was validated in sera of ACS patients and healthy controls via real-time polymerase chain reaction (RT-PCR). RESULTS Analysis revealed a marked upregulation of the multi-ncRNAs panel in ACS patients. Notably, miRNA-182-5p and lncRNA-RMRP exhibited exceptional discriminatory power, indicated by the high area under the curve (AUC) values (0.990 and 0.980, respectively). Importantly, this panel displayed superior efficacy in discriminating between STEMI and NSTEMI, outperforming conventional biomarkers like creatine kinase-MB and cardiac troponins. Additionally, the four miRNAs and lncRNA RMRP showcased remarkable proficiency in distinguishing between STEMI and unstable angina. CONCLUSION The findings underscore the promising potential of the multi-ncRNA panel as a robust tool for early ACS detection, and precise differentiation among ACS subtypes, and as a potential therapeutic target.
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Affiliation(s)
- Sara H A Agwa
- Clinical pathology and Molecular Genomics Unit, Medical Ain Shams Research Institute (MASRI), Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt.
| | - Sherif Samir Elzahwy
- Cardiovascular Medicine Department, Faculty of Medicine, Ain Shams University, Cairo 1382, Egypt
| | - Nourhan Hossam
- Medicinal Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt
| | - Yahia A Yahia
- Biochemistry Department, Faculty of Pharmacy, Misr University for Science and Technology, Giza 12566, Egypt
| | - Shaimaa Hamady
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo 11566, Egypt
| | - Nadine Sherif
- Clinical pathology and Molecular Genomics Unit, Medical Ain Shams Research Institute (MASRI), Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt
| | - Ahmed Elshazly
- Cardiovascular Medicine Department, Faculty of Medicine, Ain Shams University, Cairo 1382, Egypt
| | - Reham M Darwish
- Biochemistry and Molecular Genomics Unit, Medical Ain Shams Research Institute (MASRI), Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt
| | - Jomana Osama Hashim
- Biochemistry and Molecular Genomics Unit, Medical Ain Shams Research Institute (MASRI), Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt
| | - Mahmoud Ashraf Adly
- Biochemistry and Molecular Genomics Unit, Medical Ain Shams Research Institute (MASRI), Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt
| | - Aya M Abd Elsamee
- Biochemistry and Molecular Genomics Unit, Medical Ain Shams Research Institute (MASRI), Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt
| | - Rania Shamekh
- Department of Pathology, University of South Florida, Tampa, FL 33620, USA
| | - Marian Maher Salib Roushdy
- Medicinal Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt
| | - Marwa Matboli
- Medicinal Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt.
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3
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Arora A, Tsigelny IF, Kouznetsova VL. Laryngeal cancer diagnosis via miRNA-based decision tree model. Eur Arch Otorhinolaryngol 2024; 281:1391-1399. [PMID: 38147113 DOI: 10.1007/s00405-023-08383-1] [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: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023]
Abstract
PURPOSE Laryngeal cancer (LC) is the most common head and neck cancer, which often goes undiagnosed due to the inaccessible nature of current diagnosis methods in some parts of the world. Many recent studies have shown that microRNAs (miRNAs) are crucial biomarkers for a variety of cancers. METHODS In this study, we create a decision tree model for the diagnosis of laryngeal cancer using a created series of miRNA attributes, such as sequence-based characteristics, predicted miRNA target genes, and gene pathways. This series of attributes is extracted from both differentially expressed blood-based miRNAs in laryngeal cancer and random, non-associated with cancer miRNAs. RESULTS Several machine-learning (ML) algorithms were tested in the ML model, and the Hoeffding Tree classifier yields the highest accuracy (86.8%) in miRNAs-based recognition of laryngeal cancer. Furthermore, our model is validated with the independent laryngeal cancer datasets and can accurately diagnose laryngeal cancer with 86% accuracy. We also explored the biological relationships of the attributes used in our model to understand their relationship with cancer proliferation or suppression pathways. CONCLUSION Our study demonstrates that the proposed model and an inexpensive miRNA testing strategy have the potential to serve as an additional method for diagnosing laryngeal cancer.
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Affiliation(s)
- Aarav Arora
- REHS Program, San Diego Supercomputer Center, UC San Diego, La Jolla, CA, USA
| | - Igor F Tsigelny
- San Diego Supercomputer Center, UC San Diego, La Jolla, CA, USA.
- BiAna, La Jolla, CA, USA.
- Department of Neurosciences, UC San Diego, La Jolla, CA, USA.
- CureScience, San Diego, CA, USA.
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, UC San Diego, La Jolla, CA, USA
- BiAna, La Jolla, CA, USA
- CureScience, San Diego, CA, USA
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Fraboulet RM, Si Ahmed Y, Aubry M, Corre S, Galibert MD, Blum Y. Cirscan: a shiny application to identify differentially active sponge mechanisms and visualize circRNA-miRNA-mRNA networks. BMC Bioinformatics 2024; 25:53. [PMID: 38302900 PMCID: PMC10832221 DOI: 10.1186/s12859-024-05668-y] [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: 10/26/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Non-coding RNAs represent a large part of the human transcriptome and have been shown to play an important role in disease such as cancer. However, their biological functions are still incompletely understood. Among non-coding RNAs, circular RNAs (circRNAs) have recently been identified for their microRNA (miRNA) sponge function which allows them to modulate the expression of miRNA target genes by taking on the role of competitive endogenous RNAs (ce-circRNAs). Today, most computational tools are not adapted to the search for ce-circRNAs or have not been developed for the search for ce-circRNAs from user's transcriptomic data. RESULTS In this study, we present Cirscan (CIRcular RNA Sponge CANdidates), an interactive Shiny application that automatically infers circRNA-miRNA-mRNA networks from human multi-level transcript expression data from two biological conditions (e.g. tumor versus normal conditions in the case of cancer study) in order to identify on a large scale, potential sponge mechanisms active in a specific condition. Cirscan ranks each circRNA-miRNA-mRNA subnetwork according to a sponge score that integrates multiple criteria based on interaction reliability and expression level. Finally, the top ranked sponge mechanisms can be visualized as networks and an enrichment analysis is performed to help its biological interpretation. We showed on two real case studies that Cirscan is capable of retrieving sponge mechanisms previously described, as well as identifying potential novel circRNA sponge candidates. CONCLUSIONS Cirscan can be considered as a companion tool for biologists, facilitating their ability to prioritize sponge mechanisms for experimental validations and identifying potential therapeutic targets. Cirscan is implemented in R, released under the license GPL-3 and accessible on GitLab ( https://gitlab.com/geobioinfo/cirscan_Rshiny ). The scripts used in this paper are also provided on Gitlab ( https://gitlab.com/geobioinfo/cirscan_paper ).
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Affiliation(s)
- Rose-Marie Fraboulet
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Genetique et Developpement de Rennes) - UMR 6290, ERL U1305, Equipe Labellisée Ligue Nationale contre le Cancer, 35000, Rennes, France
| | - Yanis Si Ahmed
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Genetique et Developpement de Rennes) - UMR 6290, ERL U1305, Equipe Labellisée Ligue Nationale contre le Cancer, 35000, Rennes, France
| | - Marc Aubry
- INSERM, OSS (Oncogenesis Stress Signaling), UMR-S 1242, CLCC Eugene Marquis, Univ Rennes 1, 35000, Rennes, France
| | - Sebastien Corre
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Genetique et Developpement de Rennes) - UMR 6290, ERL U1305, Equipe Labellisée Ligue Nationale contre le Cancer, 35000, Rennes, France
| | - Marie-Dominique Galibert
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Genetique et Developpement de Rennes) - UMR 6290, ERL U1305, Equipe Labellisée Ligue Nationale contre le Cancer, 35000, Rennes, France
- Department of Molecular Genetics and Genomics, Hospital University of Rennes (CHU Rennes), 35000, Rennes, France
| | - Yuna Blum
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Genetique et Developpement de Rennes) - UMR 6290, ERL U1305, Equipe Labellisée Ligue Nationale contre le Cancer, 35000, Rennes, France.
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Chuang TD, Ton N, Rysling S, Boos D, Khorram O. The Effect of Race/Ethnicity and MED12 Mutation on the Expression of Long Non-Coding RNAs in Uterine Leiomyoma and Myometrium. Int J Mol Sci 2024; 25:1307. [PMID: 38279317 PMCID: PMC10816284 DOI: 10.3390/ijms25021307] [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: 12/16/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
The objective of this study was to elucidate the expression of long non-coding RNA (lncRNA) in leiomyomas (Lyo) and paired myometrium (Myo) and explore the impact of race and MED12 mutation. Fold change analysis (Lyo/paired Myo) indicated the expression of 63 lncRNAs was significantly altered in the mutated group but not in the non-mutated Lyo. Additionally, 65 lncRNAs exhibited an over 1.5-fold change in the Black but not the White group. Fifteen differentially expressed lncRNAs identified with next-generation sequencing underwent qRT-PCR confirmation. Compared with Myo, the expression of TPTEP1, PART1, RPS10P7, MSC-AS1, SNHG12, CA3-AS1, LINC00337, LINC00536, LINC01436, LINC01449, LINC02433, and LINC02624 was significantly higher, while the expression of ZEB2-AS1, LINC00957, and LINC01186 was significantly lower. Comparison of normal Myo with diseased Myo showed significant differences in the expression of several lncRNAs. Analysis based on race and Lyo MED12 mutation status indicated a significantly higher expression of RPS10P7, SNHG12, LINC01449, LINC02433, and LINC02624 in Lyo from Black patients. The expression of TPTEP1, PART1, RPS10P7, MSC-AS1, LINC00337, LINC00536, LINC01436, LINC01449, LINC02433, and LINC02624 was higher, while LINC01186 was significantly lower in the MED12-mutated group. These results indicate that Lyo are characterized by aberrant lncRNA expression, which is further impacted by race and Lyo MED12 mutation status.
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Affiliation(s)
- Tsai-Der Chuang
- Department of Obstetrics and Gynecology, Harbor-UCLA Medical Center, Torrance, CA 90502, USA;
- The Lundquist Institute for Biomedical Innovation, Torrance, CA 90502, USA; (N.T.); (S.R.); (D.B.)
| | - Nhu Ton
- The Lundquist Institute for Biomedical Innovation, Torrance, CA 90502, USA; (N.T.); (S.R.); (D.B.)
| | - Shawn Rysling
- The Lundquist Institute for Biomedical Innovation, Torrance, CA 90502, USA; (N.T.); (S.R.); (D.B.)
| | - Drake Boos
- The Lundquist Institute for Biomedical Innovation, Torrance, CA 90502, USA; (N.T.); (S.R.); (D.B.)
| | - Omid Khorram
- Department of Obstetrics and Gynecology, Harbor-UCLA Medical Center, Torrance, CA 90502, USA;
- The Lundquist Institute for Biomedical Innovation, Torrance, CA 90502, USA; (N.T.); (S.R.); (D.B.)
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at University of California, Los Angeles, CA 90024, USA
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Jin Z, Sheng J, Hu Y, Zhang Y, Wang X, Huang Y. Shining a spotlight on m6A and the vital role of RNA modification in endometrial cancer: a review. Front Genet 2023; 14:1247309. [PMID: 37886684 PMCID: PMC10598767 DOI: 10.3389/fgene.2023.1247309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
RNA modifications are mostly dynamically reversible post-transcriptional modifications, of which m6A is the most prevalent in eukaryotic mRNAs. A growing number of studies indicate that RNA modification can finely tune gene expression and modulate RNA metabolic homeostasis, which in turn affects the self-renewal, proliferation, apoptosis, migration, and invasion of tumor cells. Endometrial carcinoma (EC) is the most common gynecologic tumor in developed countries. Although it can be diagnosed early in the onset and have a preferable prognosis, some cases might develop and become metastatic or recurrent, with a worse prognosis. Fortunately, immunotherapy and targeted therapy are promising methods of treating endometrial cancer patients. Gene modifications may also contribute to these treatments, as is especially the case with recent developments of new targeted therapeutic genes and diagnostic biomarkers for EC, even though current findings on the relationship between RNA modification and EC are still very limited, especially m6A. For example, what is the elaborate mechanism by which RNA modification affects EC progression? Taking m6A modification as an example, what is the conversion mode of methylation and demethylation for RNAs, and how to achieve selective recognition of specific RNA? Understanding how they cope with various stimuli as part of in vivo and in vitro biological development, disease or tumor occurrence and development, and other processes is valuable and RNA modifications provide a distinctive insight into genetic information. The roles of these processes in coping with various stimuli, biological development, disease, or tumor development in vivo and in vitro are self-evident and may become a new direction for cancer in the future. In this review, we summarize the category, characteristics, and therapeutic precis of RNA modification, m6A in particular, with the purpose of seeking the systematic regulation axis related to RNA modification to provide a better solution for the treatment of EC.
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Affiliation(s)
- Zujian Jin
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Jingjing Sheng
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yingying Hu
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yu Zhang
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Xiaoxia Wang
- Reproductive Medicine Center, School of Medicine, The Fourth Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang, China
| | - Yiping Huang
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
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Holubekova V, Loderer D, Grendar M, Mikolajcik P, Kolkova Z, Turyova E, Kudelova E, Kalman M, Marcinek J, Miklusica J, Laca L, Lasabova Z. Differential gene expression of immunity and inflammation genes in colorectal cancer using targeted RNA sequencing. Front Oncol 2023; 13:1206482. [PMID: 37869102 PMCID: PMC10586664 DOI: 10.3389/fonc.2023.1206482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 08/24/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction Colorectal cancer (CRC) is a heterogeneous disease caused by molecular changes, as driver mutations, gene methylations, etc., and influenced by tumor microenvironment (TME) pervaded with immune cells with both pro- and anti-tumor effects. The studying of interactions between the immune system (IS) and the TME is important for developing effective immunotherapeutic strategies for CRC. In our study, we focused on the analysis of expression profiles of inflammatory and immune-relevant genes to identify aberrant signaling pathways included in carcinogenesis, metastatic potential of tumors, and association of Kirsten rat sarcoma virus (KRAS) gene mutation. Methods A total of 91 patients were enrolled in the study. Using NGS, differential gene expression analysis of 11 tumor samples and 11 matching non-tumor controls was carried out by applying a targeted RNA panel for inflammation and immunity genes containing 475 target genes. The obtained data were evaluated by the CLC Genomics Workbench and R library. The significantly differentially expressed genes (DEGs) were analyzed in Reactome GSA software, and some selected DEGs were used for real-time PCR validation. Results After prioritization, the most significant differences in gene expression were shown by the genes TNFRSF4, IRF7, IL6R, NR3CI, EIF2AK2, MIF, CCL5, TNFSF10, CCL20, CXCL11, RIPK2, and BLNK. Validation analyses on 91 samples showed a correlation between RNA-seq data and qPCR for TNFSF10, RIPK2, and BLNK gene expression. The top differently regulated signaling pathways between the studied groups (cancer vs. control, metastatic vs. primary CRC and KRAS positive and negative CRC) belong to immune system, signal transduction, disease, gene expression, DNA repair, and programmed cell death. Conclusion Analyzed data suggest the changes at more levels of CRC carcinogenesis, including surface receptors of epithelial or immune cells, its signal transduction pathways, programmed cell death modifications, alterations in DNA repair machinery, and cell cycle control leading to uncontrolled proliferation. This study indicates only basic molecular pathways that enabled the formation of metastatic cancer stem cells and may contribute to clarifying the function of the IS in the TME of CRC. A precise identification of signaling pathways responsible for CRC may help in the selection of personalized pharmacological treatment.
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Affiliation(s)
- Veronika Holubekova
- Laboratory of Genomics and Prenatal Diagnostics, Biomedical Center in Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Dusan Loderer
- Laboratory of Genomics and Prenatal Diagnostics, Biomedical Center in Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Marian Grendar
- Laboratory of Bioinformatics and Biostatistics, Biomedical Center in Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Peter Mikolajcik
- Clinic of Surgery and Transplant Center, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, Martin, Slovakia
| | - Zuzana Kolkova
- Laboratory of Genomics and Prenatal Diagnostics, Biomedical Center in Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Eva Turyova
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Eva Kudelova
- Clinic of Surgery and Transplant Center, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, Martin, Slovakia
| | - Michal Kalman
- Department of Pathological Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, Slovakia
| | - Juraj Marcinek
- Department of Pathological Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, Slovakia
| | - Juraj Miklusica
- Clinic of Surgery and Transplant Center, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, Martin, Slovakia
| | - Ludovit Laca
- Clinic of Surgery and Transplant Center, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, Martin, Slovakia
| | - Zora Lasabova
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
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Thakur A, Liang L, Banerjee S, Zhang K. Single-Cell Transcriptomics Reveals Evidence of Endothelial Dysfunction in the Brains of COVID-19 Patients with Implications for Glioblastoma Progression. Brain Sci 2023; 13:brainsci13050762. [PMID: 37239234 DOI: 10.3390/brainsci13050762] [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: 04/01/2023] [Revised: 04/25/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Endothelial dysfunction is implicated in various inflammatory diseases such as ischemic stroke, heart attack, organ failure, and COVID-19. Recent studies have shown that endothelial dysfunction in the brain is attributed to excessive inflammatory responses caused by the SARS-CoV-2 infection, leading to increased permeability of the blood-brain barrier and consequently neurological damage. Here, we aim to examine the single-cell transcriptomic landscape of endothelial dysfunction in COVID-19 and its implications for glioblastoma (GBM) progression. METHODS Single-cell transcriptome data GSE131928 and GSE159812 were obtained from the gene expression omnibus (GEO) to analyze the expression profiles of key players in innate immunity and inflammation between brain endothelial dysfunction caused by COVID-19 and GBM progression. RESULTS Single-cell transcriptomic analysis of the brain of COVID-19 patients revealed that endothelial cells had undergone significant transcriptomic changes, with several genes involved in immune responses and inflammation upregulated. Moreover, transcription factors were observed to modulate this inflammation, including interferon-regulated genes. CONCLUSIONS The results indicate a significant overlap between COVID-19 and GBM in the context of endothelial dysfunction, suggesting that there may be an endothelial dysfunction link connecting severe SARS-CoV-2 infection in the brain to GBM progression.
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Affiliation(s)
- Abhimanyu Thakur
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation-CAS Limited, Hong Kong 999077, China
| | - Lifan Liang
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, USA
| | - Sourav Banerjee
- Department of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Kui Zhang
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400716, China
- Cancer Centre, Medical Research Institute, Southwest University, Chongqing 400716, China
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