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Song X, Li J, Zhu J, Kong YF, Zhou YH, Wang ZK, Zhang J. Predictors of early colorectal cancer metastasis to lymph nodes: providing rationale for therapy decisions. Front Oncol 2024; 14:1371599. [PMID: 39035744 PMCID: PMC11257837 DOI: 10.3389/fonc.2024.1371599] [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: 01/17/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
With the improvement of national health awareness and the popularization of a series of screening methods, the number of patients with early colorectal cancer is gradually increasing, and accurate prediction of lymph node metastasis of T1 colorectal cancer is the key to determining the optimal therapeutic solutions. Whether patients with T1 colorectal cancer undergoing endoscopic resection require additional surgery and regional lymph node dissection is inconclusive in current guidelines. However, we can be sure that in early colorectal cancer without lymph node metastasis, endoscopic resection alone does not affect the prognosis, and it greatly improves the quality of life and reduces the incidence of surgical complications while preserving organ integrity. Therefore, it is vital to discriminate patients without lymph node metastasis in T1 colorectal cancer, and this requires accurate predictors. This paper briefly explains the significance and shortcomings of traditional pathological factors, then extends and states the new pathological factors, clinical test factors, molecular biomarkers, and the risk assessment models of lymph node metastasis based on artificial intelligence.
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Affiliation(s)
| | | | | | | | | | | | - Jin Zhang
- Department of General Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
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Zhang ZW, Zhang KX, Liao X, Quan Y, Zhang HY. Evolutionary screening of precision oncology biomarkers and its applications in prognostic model construction. iScience 2024; 27:109859. [PMID: 38799582 PMCID: PMC11126775 DOI: 10.1016/j.isci.2024.109859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/15/2024] [Accepted: 04/27/2024] [Indexed: 05/29/2024] Open
Abstract
Biomarker screening is critical for precision oncology. However, one of the main challenges in precision oncology is that the screened biomarkers often fail to achieve the expected clinical effects and are rarely approved by regulatory authorities. Considering the close association between cancer pathogenesis and the evolutionary events of organisms, we first explored the evolutionary feature underlying clinically approved biomarkers, and two evolutionary features of approved biomarkers (Ohnologs and specific evolutionary stages of genes) were identified. Subsequently, we utilized evolutionary features for screening potential prognostic biomarkers in four common cancers: head and neck squamous cell carcinoma, liver hepatocellular carcinoma, lung adenocarcinoma, and lung squamous cell carcinoma. Finally, we constructed an evolution-strengthened prognostic model (ESPM) for cancers. These models can predict cancer patients' survival time across different cancer cohorts effectively and perform better than conventional models. In summary, our study highlights the application potentials of evolutionary information in precision oncology biomarker screening.
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Affiliation(s)
- Zhi-Wen Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Ke-Xin Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Xuan Liao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Yuan Quan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
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Swain IX, Kresak AM. Proteins Involved in Focal Cell Adhesion and Podosome Formation Are Differentially Expressed during Colorectal Tumorigenesis in AOM-Treated Rats. Cancers (Basel) 2024; 16:1678. [PMID: 38730628 PMCID: PMC11083089 DOI: 10.3390/cancers16091678] [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: 04/10/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Colorectal tumorigenesis involves the development of aberrant crypt foci (ACF) or preneoplastic lesions, representing the earliest morphological lesion visible in colon cancer. The purpose of this study was to determine changes in protein expression in carcinogen-induced ACF as they mature and transform into adenomas. Protein expression profiles of azoxymethane (AOM)-induced F344 rat colon ACF and adenomas were compared at four time points, 4 (control), 8, 16, and 24 weeks post AOM administration (n = 9/group), with time points correlating with induction and transformation events. At each time point, micro-dissected ACF and/or adenoma tissues were analyzed across multiple quantitative two-dimensional (2D-DIGE) gels using a Cy-dye labeling technique and a pooled internal standard to quantify expression changes with statistical confidence. Western blot and subsequent network pathway mapping were used to confirm and elucidate differentially expressed (p ≤ 0.05) proteins, including changes in vinculin (Vcl; p = 0.007), scinderin (Scin; p = 0.02), and profilin (Pfn1; p = 0.01), By determining protein expression changes in ACF as they mature and transform into adenomas, a "baseline" of altered regulatory proteins associated with adenocarcinoma development in this model has been elucidated. These data will enable future studies aimed at biomarker identification and understanding the molecular biology of intestinal tumorigenesis and adenocarcinoma maturation under varying intestinal conditions.
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Affiliation(s)
- Ian X. Swain
- Department of Pathology, School of Medicine, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA;
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Zuo Q, Xu Q, Li Z, Luo D, Peng H, Duan Z. TRIM3 inhibits colorectal cancer cell migration and lipid droplet formation by promoting FABP4 degradation. Histol Histopathol 2024; 39:239-250. [PMID: 37212515 DOI: 10.14670/hh-18-627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
This study is to investigate the regulation of TRIM3/FABP4 on colorectal cancer (CRC) cell migration and lipid metabolism. After transfection of HCT116, LoVo, or SW480 cells, the expression of FABP4, TRIM3, N-cadherin, Vimentin, E-cadherin, and lipid droplet (LD) formation-related genes was measured by qRT-PCR or western blot assays. Wound healing and Transwell assays were applied to detect CRC cell migration and invasion abilities. The levels of triglyceride (TG) and total cholesterol (TC) were measured and the formation of LDs was observed. Additionally, the relationship between FABP4 and TRIM3 was confirmed by Co-IP and ubiquitination assays. Furthermore, a liver metastasis model of CRC was established to explore the effect of FABP4 on CRC tumor metastasis in vivo. FABP4 was upregulated in CRC cells. Downregulation of FABP4 or upregulation of TRIM3 resulted in repressed cell migration and invasion, decreased TG and TC levels, and reduced numbers of LDs. In nude mice, knockdown of FABP4 reduced metastatic nodules in the liver. Mechanistically, TRIM3 combined FABP4 and decreased its protein expression by ubiquitination. Overexpressed FABP4 reversed the influence of TRIM3 upregulation on CRC cell migration and LD formation. In conclusion, underexpressed TRIM3 suppressed FABP4 ubiquitination and accelerated CRC cell migration and LD formation.
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Affiliation(s)
- Qi Zuo
- Department of Emergency, The First Hospital of Changsha, Changsha, Hunan, PR China
| | - Qimei Xu
- Department of Pathology, The First Hospital of Changsha, Changsha, Hunan, PR China
| | - Zhen Li
- Department of Pathology, The First Hospital of Changsha, Changsha, Hunan, PR China
| | - Dixian Luo
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, Guangdong, PR China
| | - Hanwu Peng
- Department of Emergency, The First Hospital of Changsha, Changsha, Hunan, PR China
| | - Zhi Duan
- Department of Pathology, The First Hospital of Changsha, Changsha, Hunan, PR China.
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Gaffar S, Aathirah AS. Fatty-Acid-Binding Proteins: From Lipid Transporters to Disease Biomarkers. Biomolecules 2023; 13:1753. [PMID: 38136624 PMCID: PMC10741572 DOI: 10.3390/biom13121753] [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: 10/03/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 12/24/2023] Open
Abstract
Fatty-acid-binding proteins (FABPs) serve a crucial role in the metabolism and transport of fatty acids and other hydrophobic ligands as an intracellular protein family. They are also recognized as a critical mediator in the inflammatory and ischemic pathways. FABPs are found in a wide range of tissues and organs, allowing them to contribute to various disease/injury developments that have not been widely discussed. We have collected and analyzed research journals that have investigated the role of FABPs in various diseases. Through this review, we discuss the findings on the potential of FABPs as biomarkers for various diseases in different tissues and organs, looking at their expression levels and their roles in related diseases according to available literature data. FABPs have been reported to show significantly increased expression levels in various tissues and organs associated with metabolic and inflammatory diseases. Therefore, FABPs are a promising novel biomarker that needs further development to optimize disease diagnosis and prognosis methods along with previously discovered markers.
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Affiliation(s)
- Shabarni Gaffar
- Graduate School, Padjadjaran University, Bandung 40132, Indonesia;
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Sumedang 45363, Indonesia
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Zuo Q, Xu Q, Li Z, Luo D, Peng H, Duan Z. Kruppel-like factor 5 enhances proliferation, lipid droplet formation and oxaliplatin resistance in colorectal cancer by promoting fatty acid binding protein 6 transcription. Anticancer Drugs 2023; 34:1171-1182. [PMID: 37067981 DOI: 10.1097/cad.0000000000001515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Oxaliplatin (OXA) is a standard agent for colorectal cancer (CRC) adjuvant chemotherapy. However, acquired and intrinsic OXA resistance is a primary challenge for CRC treatment. This study investigates the function of the Kruppel-like factor 5/fatty acid binding proteins 6 (KLF5/FABP6) axis in CRC proliferation, lipid droplet formation and OXA resistance. OXA-resistant CRC cell lines were constructed, and FABP6 and KLF5 expression was assessed in parental and OXA-resistant CRC cells. Subsequent to gain- and loss-of-function experiments, CRC cell proliferation was assessed by cell counting kit-8 (CCK-8) and clone formation assays, the intracellular lipid synthesis by oil red O staining and the protein expression of lipid metabolism genes by western blot. OXA resistance of CRC cells was assessed by CCK-8 assay. The binding of KLF5 to FABP6 was analyzed by the dual-luciferase reporter and ChIP assays. A tumorigenicity assay in nude mice was adopted to examine the impact of KLF5 on CRC tumor growth and OXA resistance in vivo . FABP6 and KLF5 expression was high in CRC cell lines. Downregulation of FABP6 or KLF5 restrained CRC cell proliferation and lipid droplet formation in vitro . FABP6 and KLF5 expression was elevated in OXA-resistant CRC cells. Downregulation of FABP6 or KLF5 repressed the OXA resistance of OXA-resistant CRC cells. Mechanistically, KLF5 facilitated the transcription of FABP6. FABP6 overexpression counteracted the suppressive effects of KLF5 downregulation on CRC cell growth, lipid droplet formation and OXA resistance. KLF5 downregulation restrained CRC tumor growth and OXA resistance in vivo . In conclusion, KLF5 knockdown reduced FABP6 transcription to protect against proliferation, lipid droplet formation and OXA resistance in CRC.
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Affiliation(s)
| | - Qimei Xu
- Department of Pathology, The First Hospital of Changsha, Changsha, Hunan
| | - Zhen Li
- Department of Pathology, The First Hospital of Changsha, Changsha, Hunan
| | - Dixian Luo
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, Guangdong 518052, People's Republic of China
| | | | - Zhi Duan
- Department of Pathology, The First Hospital of Changsha, Changsha, Hunan
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Nimptsch K, Aleksandrova K, Pham TT, Papadimitriou N, Janke J, Christakoudi S, Heath A, Olsen A, Tjønneland A, Schulze MB, Katzke V, Kaaks R, van Guelpen B, Harbs J, Palli D, Macciotta A, Pasanisi F, Yohar SMC, Guevara M, Amiano P, Grioni S, Jakszyn PG, Figueiredo JC, Samadder NJ, Li CI, Moreno V, Potter JD, Schoen RE, Um CY, Weiderpass E, Jenab M, Gunter MJ, Pischon T. Prospective and Mendelian randomization analyses on the association of circulating fatty acid binding protein 4 (FABP-4) and risk of colorectal cancer. BMC Med 2023; 21:391. [PMID: 37833736 PMCID: PMC10576353 DOI: 10.1186/s12916-023-03104-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Fatty acid binding protein 4 (FABP-4) is a lipid-binding adipokine upregulated in obesity, which may facilitate fatty acid supply for tumor growth and promote insulin resistance and inflammation and may thus play a role in colorectal cancer (CRC) development. We aimed to investigate the association between circulating FABP-4 and CRC and to assess potential causality using a Mendelian randomization (MR) approach. METHODS The association between pre-diagnostic plasma measurements of FABP-4 and CRC risk was investigated in a nested case-control study in 1324 CRC cases and the same number of matched controls within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. A two-sample Mendelian randomization study was conducted based on three genetic variants (1 cis, 2 trans) associated with circulating FABP-4 identified in a published genome-wide association study (discovery n = 20,436) and data from 58,131 CRC cases and 67,347 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium, Colorectal Cancer Transdisciplinary Study, and Colon Cancer Family Registry. RESULTS In conditional logistic regression models adjusted for potential confounders including body size, the estimated relative risk, RR (95% confidence interval, CI) per one standard deviation, SD (8.9 ng/mL) higher FABP-4 concentration was 1.01 (0.92, 1.12) overall, 0.95 (0.80, 1.13) in men and 1.09 (0.95, 1.25) in women. Genetically determined higher FABP-4 was not associated with colorectal cancer risk (RR per FABP-4 SD was 1.10 (0.95, 1.27) overall, 1.03 (0.84, 1.26) in men and 1.21 (0.98, 1.48) in women). However, in a cis-MR approach, a statistically significant association was observed in women (RR 1.56, 1.09, 2.23) but not overall (RR 1.23, 0.97, 1.57) or in men (0.99, 0.71, 1.37). CONCLUSIONS Taken together, these analyses provide no support for a causal role of circulating FABP-4 in the development of CRC, although the cis-MR provides some evidence for a positive association in women, which may deserve to be investigated further.
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Affiliation(s)
- Katharina Nimptsch
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany.
| | - Krasimira Aleksandrova
- Department Epidemiological Methods and Etiological Research, Leibniz Institute for Prevention Research and Epidemiology, Bremen, Germany
- Faculty of Human and Health Sciences, University of Bremen, Bremen, Germany
| | - Thu Thi Pham
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Charité - Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Berlin, Germany
| | - Nikos Papadimitriou
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Jürgen Janke
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Biobank Technology Platform, Berlin, Germany
| | - Sofia Christakoudi
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Inflammation Biology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Alicia Heath
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Anja Olsen
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Public Health, University of Århus, Århus, Denmark
| | - Anne Tjønneland
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nutehtal, Germany
- Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Verena Katzke
- Department of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rudolf Kaaks
- Department of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bethany van Guelpen
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Justin Harbs
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Domenico Palli
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy
| | - Alessandra Macciotta
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Fabrizio Pasanisi
- Dipartimento di Medicina Clinica e Chirurgia, Federico II University, Naples, Italy
| | - Sandra Milena Colorado Yohar
- Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca, Murcia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Research Group on Demography and Health, National Faculty of Public Health, University of Antioquia, Medellín, Colombia
| | - Marcela Guevara
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Instituto de Salud Pública de Navarra, Pamplona, 31003, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, 31008, Spain
| | - Pilar Amiano
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Ministry of Health of the Basque Government, Sub Directorate for Public Health and Addictions of Gipuzkoa, San Sebastian, Spain
- Epidemiology of Chronic and Communicable Diseases Group, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Sara Grioni
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, 20133, Italy
| | - Paula Gabriela Jakszyn
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Programme, Catalan Institute of Oncology (ICO-IDIBELL), Barcelona, Spain
- Blanquerna School of Health Sciences, Ramon Llull University, Barcelona, Spain
| | - Jane C Figueiredo
- Cedars-Sinai Medical Center Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
| | - N Jewel Samadder
- Division of Gastroenterology and Hepatology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Phoenix, AZ, USA
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Victor Moreno
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona (UB), L'Hospitalet de Llobregat, Barcelona, Spain
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Caroline Y Um
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Elisabete Weiderpass
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Mazda Jenab
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Marc J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Tobias Pischon
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Charité - Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Berlin, Germany
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Biobank Technology Platform, Berlin, Germany
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Li Z, Yuan F, Liu X, Wei J, Liu T, Li W, Li C. Establishment and validation of a ferroptosis-related signature predicting prognosis and immunotherapy effect in colon cancer. Front Oncol 2023; 13:1201616. [PMID: 37287923 PMCID: PMC10243598 DOI: 10.3389/fonc.2023.1201616] [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: 04/06/2023] [Accepted: 04/25/2023] [Indexed: 06/09/2023] Open
Abstract
Background Ferroptosis, a novel form of regulating cell death, is related to various cancers. However, the role of ferroptosis-related genes (FRGs) on the occurrence and development of colon cancer (CC) needs to be further elucidated. Method CC transcriptomic and clinical data were downloaded from TCGA and GEO databases. The FRGs were obtained from the FerrDb database. The consensus clustering was performed to identify the best clusters. Then, the entire cohort was randomly divided into the training and testing cohorts. Univariate Cox, LASSO regression and multivariate Cox analyses were used to construct a novel risk model in training cohort. The testing and the merged cohorts were performed to validate the model. Moreover, CIBERSORT algorithm analyze TIME between high- and low- risk groups. The immunotherapy effect was evaluated by analyzing the TIDE score and IPS between high- and low- risk groups. Lastly, RT-qPCR were performed to analyze the expression of the three prognostic genes, and the 2-years OS and DFS between the high- and low- risk groups of 43 clinical CC samples to further validate the value of the risk model. Results SLC2A3, CDKN2A, and FABP4 were identified to construct a prognostic signature. Kaplan-Meier survival curves showed that OS between the high- and low-risk groups were statistically significant (pmerged<0.001, ptraining<0.001, ptesting<0.001). TIDE score and IPS were higher in the high-risk group (pTIDE<0.005, pDysfunction<0.005, pExclusion<0.001, pmAb-CTLA-4 = 3e-08, pmAb-PD-1 = 4.1e-10). The clinical samples were divided into high- and low- risk groups according to the risk score. There was a statistical difference in DFS (p=0.0108). Conclusion This study established a novel prognostic signature and provided more insight into the immunotherapy effect of CC.
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Affiliation(s)
- Zhufeng Li
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Fang Yuan
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xin Liu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Jianming Wei
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Tong Liu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Weidong Li
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Chuan Li
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
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Wang J, Millstein J, Yang Y, Stintzing S, Arai H, Battaglin F, Kawanishi N, Soni S, Zhang W, Mancao C, Cremolini C, Liu T, Heinemann V, Falcone A, Shen L, Lenz HJ. Impact of genetic variants involved in the lipid metabolism pathway on progression free survival in patients receiving bevacizumab-based chemotherapy in metastatic colorectal cancer: a retrospective analysis of FIRE-3 and MAVERICC trials. EClinicalMedicine 2023; 57:101827. [PMID: 36816347 PMCID: PMC9932345 DOI: 10.1016/j.eclinm.2023.101827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Antiangiogenic drug (AAD)-triggered oxygen and nutrient depletion through suppression of angiogenesis switches glucose-dependent to lipid-dependent metabolism. Blocking fatty acid oxidation can enhance AAD-mediated anti-tumor effects in colorectal cancer (CRC). Therefore, we hypothesised that genetic variants in the lipid metabolism pathway may predict clinical outcomes [overall response rate (ORR), overall survival (OS) and progression-free survival (PFS)] in metastatic CRC (mCRC) patients receiving bevacizumab-based first-line treatment. METHODS Genomic DNA from blood samples of patients enrolled in FIRE-3 (a global, randomised, open-label, phase 3 trial, between 2007-6-23 and 2012-9-19, discovery cohort: FOLFIRI/bevacizumab arm, n = 107; control cohort: FOLFIRI/cetuximab arm, n = 129) and MAVERICC (a global, randomised, open-label, phase II study, between 2011-8 and 2015-7, in United States, Canada, Estonia, Ireland, Switzerland, Norway, and Portugal. Validation cohort: FOLFIRI/bevacizumab arm, n = 163) trials, was genotyped using the OncoArray-500 K beadchip panel. The impact on OS and PFS of 17 selected SNPs in 7 genes involved in the lipid metabolism pathway (CD36, FABP4, LPCAT1/2, CPT1A, FASN, ACACA) was analysed using Kaplan-Meier curves, the log-rank test for univariate analyses and likelihood ratio tests of Cox proportional hazards regression parameters for multivariable analyses. ORR and SNP associations were evaluated using Chi-square or Fisher's exact tests. FINDINGS In the discovery cohort, patients with FASN rs4485435 any C allele (n = 21) showed significantly shorter PFS (median PFS: 8.69 vs 13.48 months) compared to carriers of G/G (n = 62) in multivariable (HR = 2.87; 95%CI 1.4-5.9; p = 0.00675) analysis. These data were confirmed in the validation cohort in multivariable analysis (HR = 2.07, 95%CI: 1.15-3.74; p = 0.02), but no association was observed in the cetuximab cohort of FIRE-3. In the comparison of bevacizumab vs cetuximab arm in FIRE-3, a significant interaction was shown with FASN rs4485435 (p = 0.017) on PFS. INTERPRETATION Our study demonstrates for the first time, to our knowledge, that FASN polymorphisms may predict outcome of bevacizumab-based treatment in patients with mCRC. These findings support a possible role of the lipid metabolism pathway in contributing to resistance to anti-VEGF treatment. FUNDING This work was supported by the National Cancer Institute [P30CA 014089 to H.-J.L.], Gloria Borges WunderGlo Foundation, Dhont Family Foundation, Victoria and Philip Wilson Research Fund, San Pedro Peninsula Cancer Guild, Ming Hsieh Research Fund, Eddie Mahoney Memorial Research Fund, Shanghai Sailing Program (22YF1407000), China National Postdoctoral Program for Innovative Talents (BX20220084), China Postdoctoral Science Foundation (2022M710768), National Natural Science Foundation of China (82202892).
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Key Words
- 3' UTR, 3′ untranslated regions
- ACACA, acetyl-coA carboxylase
- ADD, antiangiogenic drug
- AIM, ancestry informative markers
- Bevacizumab
- Biomarker
- CEU, Utah residents with Northern and Western European ancestry from the CEPH collection
- CORECT, Colorectal Cancer Transdisciplinary
- CPT1A, carnitine palmitoyl transferase 1A
- CRC, colorectal cancer
- Colorectal cancer
- ECOG PS, Eastern Cooperative Oncology Group performance status
- FAO, fatty acids β-oxidation
- FASN, fatty acid synthase
- LPCAT1, lysolecithin acyltransferase 1
- LPCAT2, lysolecithin acyltransferase 2
- Lipid metabolism
- MAF, minor allele frequency
- MUFA, monounsaturated fatty acids
- ORR, overall response rate
- OS, overall survival
- PFS, progression-free survival
- SNP, single nucleotide polymorphisms
- mCRC, metastatic colorectal cancer
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Affiliation(s)
- Jingyuan Wang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Xuhui District, Shanghai, 200032, China
- Division of Medical Oncology, Norris Comprehensive Cancer Centre, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China
- Cancer Centre, Zhongshan Hospital Fudan University, Xuhui District, Shanghai, 200032, China
| | - Joshua Millstein
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Yan Yang
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Sebastian Stintzing
- Department of Hematology, Oncology and Cancer Immunology (CCM), Charité- Universitaetsmedizin Berlin, Germany
| | - Hiroyuki Arai
- Division of Medical Oncology, Norris Comprehensive Cancer Centre, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Centre, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Natsuko Kawanishi
- Division of Medical Oncology, Norris Comprehensive Cancer Centre, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Centre, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Wu Zhang
- Division of Medical Oncology, Norris Comprehensive Cancer Centre, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christoph Mancao
- Oncology Biomarker Development, Genentech Inc., Basel, Switzerland
| | | | - Tianshu Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Xuhui District, Shanghai, 200032, China
| | - Volker Heinemann
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Alfredo Falcone
- Department of Translational Medicine, University of Pisa, Italy
| | - Lin Shen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Centre, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Corresponding author. Division of Medical Oncology, Norris Comprehensive Cancer Centre, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA, 90033, USA.
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10
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Ghosh A, Ghosh A, Sinha A, Mathai S, Bhaumik J, Mukhopadhyay A, Maitra A, Biswas NK, Majumder PP, Sengupta S. Identification of HPV16 positive cervical cancer subsets characterized by divergent immune and oncogenic phenotypes with potential implications for immunotherapy. Tumour Biol 2023; 45:55-69. [PMID: 37599552 DOI: 10.3233/tub-220035] [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] [Indexed: 08/22/2023] Open
Abstract
BACKGROUND Cervical cancers (CaCx), like many other cancer types, portray high molecular heterogeneity that affects response to therapy, including immunotherapy. In India and other developing countries, CaCx mortality rates are very high because women report to the clinics with advanced cancers in absence of organized screening programs. This calls for implementation of newer therapeutic regimens for CaCx, like immunotherapy, which is again not used commonly in such countries. OBJECTIVE Therefore, we focused on dissecting tumour immune heterogeneity, if any, identify immune gene-based biomarkers of heterogeneity and subsets of such cancers with the potential for immunotherapy. We also attempted to characterize the cancer-associated phenotypes of such subsets, including viral load, to decipher the relationship of tumour immunogenicity with oncogenicity. METHODS Employing RNA-seq analysis of 44 HPV16 positive CaCx patients, immune subtypes were identified by unsupervised hierarchical clustering of global immune-gene expression profiles. Proportions of tumor infiltrating immune cells in the tumor milieu were estimated, employing Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT), using gene expression data from RNA-seq. The oncogenic phenotypes of the immune subtypes of CaCx were deciphered through differential gene expression (DEGs) and pathway enrichment analysis. Viral load was estimated through TaqMan-based qRT-PCR analysis. RESULTS Analysis revealed the presence of two immune subtypes of CaCx, A (26/44; 59.09%) and B (18/44; 40.90%). Compared to Subtype-A, Subtype-B portrayed overexpression of immune genes and high infiltration of immune cells, specifically CD8+ T cells (p < 0.0001). Besides, a significant correlation between PD-1 and PD-L1 co-expression among Subtype-B, as opposed to Subtype-A, confirmed the interactive roles of these immune checkpoint molecules in Subtype B. Stepwise discriminant analysis pin-pointed ten immune-genes that could classify 100% of the patients significantly (p < 0.0001) into the two immune subtypes and serve as potential biomarkers of CaCx immunity. Differential gene expression analysis between the subtypes unveiled that Subtype-B was more biologically aggressive than Subtype-A, reflecting loss of structural integrity and promotion of cancer progression. The viral load was significantly lower in Subtype-B (average viral load = 10.74/100 ng of genomic DNA) compared to Subtype-A (average viral load = 14.29/100 ng of genomic DNA). Thus viral load and the ten-gene panel underscore their association with immunogenicity and oncogenicity. CONCLUSION Our study provides strong evidence that only a subset, about 41% of HPV16 positive CaCx patients in India, portray immune enrichment of the tumor milieu coupled with aggressive phenotypes. Such subtypes are therefore likely to benefit through checkpoint molecule-based or tumor infiltrating lymphocyte-based immunotherapy, which could be a leap forward in tackling aggressive forms of such CaCx in India and other developing countries.
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Affiliation(s)
- Abhisikta Ghosh
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Arnab Ghosh
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Abarna Sinha
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Sonia Mathai
- Tata Medical Center, Kolkata, West Bengal, India
| | | | - Asima Mukhopadhyay
- Kolkata Gynecological Oncology Trials and Translational Research Group, Kolkata, West Bengal, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Nidhan K Biswas
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Partha P Majumder
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Sharmila Sengupta
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
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11
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Su X, Jin M, Xu C, Gao Y, Yang Y, Qi H, Zhang Q, Yang X, Ya W, Zhang Y, Yang R. FABP4 in Paneth cells regulates antimicrobial protein expression to reprogram gut microbiota. Gut Microbes 2022; 14:2139978. [PMID: 36519446 PMCID: PMC9635462 DOI: 10.1080/19490976.2022.2139978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Antimicrobial proteins possess a broad spectrum of bactericidal activity and play an important role in shaping the composition of gut microbiota, which is related to multiple diseases such as metabolic syndrome. However, it is incompletely known for the regulation of defensin expression in the gut Paneth cells. Here, we found that FABP4 in the Paneth cells of gut epithelial cells and organoids can downregulate the expression of defensins. FABP4fl/flpvillinCreT mice were highly resistance to Salmonella Typhimurium (S.T) infection and had increased bactericidal ability to pathogens. The FABP4-mediated downregulation of defensins is through degrading PPARγ after K48 ubiquitination. We also demonstrate that high-fat diet (HFD)-mediated downregulation of defensins is through inducing a robust FABP4 in Paneth cells. Firmicutes/Bacteroidetes (F/B) ratio in FABP4fl/flpvillinCreT mice is lower than control mice, which is opposite to that in mice fed HFD, indicating that FABP4 in the Paneth cells could reprogram gut microbiota. Interestingly, FABP4-mediated downregulation of defensins in Paneth cells not only happens in mice but also in human. A better understanding of the regulation of defensins, especially HFD-mediated downregulation of defensin in Paneth cells will provide insights into factor(s) underlying modern diseases.Abbreviations: FABP4: Fatty acid binding protein 4; S. T: Salmonella Typhimurium; HFD: High-fat diet; Defa: α-defensin; 930 HD5: Human α-defensin 5; HD6: Human α-defensin 6; F/B: Firmicutes/Bacteroidetes; SFB: Segmental filamentous bacteria; AMPs: Antimicrobial peptides; PPARγ: Peroxisome proliferator-activated receptor γ; P-PPAR: Phosphorylated PPAR; Dhx15: DEAD-box helicase 15; 935 EGF: Epidermal growth factor; ENR: Noggin and R-spondin 1; CFU: Colony forming unit; Lyz1: Lysozyme 1; Saa1: Serum amyoid A 1; Pla2g2a: Phospholipase A2, group IIA; MMP-7: Matrix metalloproteinase; AU-PAGE: Acid-urea polyacrylamide gel electrophoresis; PA: Palmitic 940 acid; GPR40: G-protein-coupled receptor; GF: Germ-free; EGF: Epidermal growth factor; LP: Lamina propria; KO: Knock out; WT: Wild-type.
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Affiliation(s)
- Xiaomin Su
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China
| | - Mengli Jin
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Chen Xu
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China
| | - Yunhuan Gao
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Yazheng Yang
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Houbao Qi
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Qianjing Zhang
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Xiaorong Yang
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Wang Ya
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China
| | - Yuan Zhang
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Rongcun Yang
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China,CONTACT Rongcun Yang Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin300071, China
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12
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Hoxha M, Zappacosta B. A review on the role of fatty acids in colorectal cancer progression. Front Pharmacol 2022; 13:1032806. [PMID: 36578540 PMCID: PMC9791100 DOI: 10.3389/fphar.2022.1032806] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
Colorectal cancer (CRC) is the third leading cause of mortality in cancer patients. The role of fatty acids (FA) and their metabolism in cancer, particularly in CRC raises a growing interest. In particular, dysregulation of synthesis, desaturation, elongation, and mitochondrial oxidation of fatty acids are involved. Here we review the current evidence on the link between cancer, in particular CRC, and fatty acids metabolism, not only to provide insight on its pathogenesis, but also on the development of novel biomarkers and innovative pharmacological therapies that are based on FAs dependency of cancer cells.
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Yang J, Liu X, Shao Y, Zhou H, Pang L, Zhu W. Diagnostic, Prognostic, and Immunological Roles of FABP4 in Pancancer: A Bioinformatics Analysis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:3764914. [PMID: 36532833 PMCID: PMC9754845 DOI: 10.1155/2022/3764914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/15/2022] [Accepted: 11/20/2022] [Indexed: 08/27/2023]
Abstract
BACKGROUND Fatty acid binding protein 4 (FABP4) is mainly involved in the regulation of systemic metabolism through various lipid signaling pathways. Metabolic reprogramming is one of the important factors in the development and progression of cancer. It has been recently reported that FABP4 is closely related to the development of cancer and may be involved in tumor invasion and metastasis. METHODS In this study, we explored the expression pattern of FABP4 in pancancer through TCGA and CPTAC. Using TCGA, Kaplan-Meier Plotter, and STRING databases, to explore its diagnostic and prognostic value, and function through GO/KEGG and GSEA. Then, using the TIMER2.0 database, we investigated the correlation between FABP4 expression and immune infiltration in cancers, especially stomach adenocarcinomas (STAD) and colorectal adenocarcinoma (COADREAD). RESULTS Compared with normal tissues, the expression of FABP4 in more than 10 tumor tissues was lower (p < 0.05). Through the receiver operating characteristic (ROC) curve, the diagnostic value was found higher in colorectal cancer, breast cancer, thyroid cancer, and lung cancer, with the area under the curve (AUC) > 0.9. Through the K-M curve, FABP4 was found to correlate to the prognosis of various cancers. The results of gastric cancer and colorectal cancer are consistent. The low-expression group has a better prognosis than the high-expression group, and the expression of FABP4 in the early T and N stages of gastrointestinal tumors is lower. FABP4 highly expressed gene set is mostly enriched in extracellular matrix degradation and cell adhesion functions. Gastrointestinal tumors with high expression of FABP4 may have more immunosuppressive effects on macrophages and have a worse prognosis. CONCLUSION FABP4 can be used as a diagnostic and prognostic biomarker in pancancer, and its high expression in gastrointestinal tumors suggests poor prognosis. This may be correlated to the immune infiltration of macrophages and epithelial-mesenchymal transition.
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Affiliation(s)
- Jing Yang
- Oncology Center, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Wujiang, Jiangsu 215228, China
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xiaojing Liu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
- Department of Radiotherapy, The Friendship Hospital of Ily Kazak Autonomous Prefecture, Ily, Xinjiang 835000, China
| | - Yueqin Shao
- Oncology Center, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Wujiang, Jiangsu 215228, China
| | - Hong Zhou
- Oncology Center, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Wujiang, Jiangsu 215228, China
| | - Lijun Pang
- Oncology Center, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Wujiang, Jiangsu 215228, China
| | - Wei Zhu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
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14
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Sun M, Ji X, Xie M, Chen X, Zhang B, Luo X, Feng Y, Liu D, Wang Y, Li Y, Liu B, Xia L, Huang W. Identification of necroptosis-related subtypes, development of a novel signature, and characterization of immune infiltration in colorectal cancer. Front Immunol 2022; 13:999084. [PMID: 36544770 PMCID: PMC9762424 DOI: 10.3389/fimmu.2022.999084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Necroptosis, a type of programmed cell death, has recently been extensively studied as an important pathway regulating tumor development, metastasis, and immunity. However, the expression patterns of necroptosis-related genes (NRGs) in colorectal cancer (CRC) and their potential roles in the tumor microenvironment (TME) have not been elucidated. Methods We explored the expression patterns of NRGs in 1247 colorectal cancer samples from genetics and transcriptional perspective. Based on a consensus clustering algorithm, we identified NRG molecular subtypes and gene subtypes, respectively. Furthermore, we constructed a necroptosis-related signature for predicting overall survival time and verified the predictive ability of the model. Using the ESTIMATE, CIBERSORT, and ssGSEA algorithms, we assessed the association between the above subtypes, scores and immune infiltration. Results Most NRGs were differentially expressed between CRC tissues and normal tissues. We found that distinct subtypes exhibited different NRGs expression, patients' prognosis, immune checkpoint gene expression, and immune infiltration characteristics. The scores calculated from the necroptosis-related signature can be used to classify patients into high-risk and low-risk groups, with the high-risk group corresponding to reduced immune cell infiltration and immune function, and a greater risk of immune dysfunction and immune escape. Discussion Our comprehensive analysis of NRGs in CRC demonstrated their potential role in clinicopathological features, prognosis, and immune infiltration in the TME. These findings help us deepen our understanding of NRGs and the tumor microenvironment landscape, and lay a foundation for effectively assessing patient outcomes and promoting more effective immunotherapy.
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Affiliation(s)
- Mengyu Sun
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoyu Ji
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Meng Xie
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoping Chen
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, China
| | - Bixiang Zhang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, China
| | - Xiangyuan Luo
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yangyang Feng
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Danfei Liu
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yijun Wang
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Bifeng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Limin Xia
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wenjie Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, China
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Lin ZH, Zhang J, Zhuang LK, Xin YN, Xuan SY. Establishment of a Prognostic Model for Hepatocellular Carcinoma Based on Bioinformatics and the Role of NR6A1 in the Progression of HCC. J Clin Transl Hepatol 2022; 10:901-912. [PMID: 36304495 PMCID: PMC9547269 DOI: 10.14218/jcth.2022.00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND AND AIMS Generally acceptable prognostic models for hepatocellular carcinoma (HCC) are not available. This study aimed to establish a prognostic model for HCC by identifying immune-related differentially expressed genes (IR-DEGs) and to investigate the potential role of NR6A1 in the progression of HCC. METHODS Bioinformatics analysis using The Cancer Genome Atlas and ImmPort databases was used to identify IR-DEGs. Lasso Cox regression and multivariate Cox regression analysis were used to establish a prognostic model of HCC. Kaplan-Meier analysis and the receiver operating characteristic (ROC) curves were used to evaluate the performance of the prognostic model, which was further verified in the International Cancer Genome Consortium (ICGC) database. Gene set enrichment analysis was used to explore the potential pathways of NR6A1. Cell counting kit 8, colony formation, wound healing, and Transwell migration assays using Huh7 cells, and tumor formation models in nude mice were conducted. RESULTS A prognostic model established based on ten identified IR-DEGs including HSPA4, FABP6, MAPT, NDRG1, APLN, IL17D, LHB, SPP1, GLP1R, and NR6A1, effectively predicted the prognosis of HCC patients, was confirmed by the ROC curves and verified in ICGC database. NR6A1 expression was significantly up-regulated in HCC patients, and NR6A1 was significantly associated with a low survival rate. Gene set enrichment analysis showed the enrichment of cell cycle, mTOR, WNT, and ERBB signaling pathways in patients with high NR6A1 expression. NR6A1 promoted cell proliferation, invasiveness, migration, and malignant tumor formation and growth in vitro and in vivo. CONCLUSIONS An effective prognostic model for HCC, based on a novel signature of 10 immune-related genes, was established. NR6A1 was up-regulated in HCC and was associated with a poor prognosis of HCC. NR6A1 promoted cell proliferation, migration, and growth of HCC, most likely through the cell cycle, mTOR, WNT, and ERBB signaling pathways.
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Affiliation(s)
- Zhong-Hua Lin
- College of Medicine and Pharmaceutics, Ocean University of China, Qingdao, Shandong, China
- Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao, Shandong, China
| | - Jie Zhang
- Medical College, Qingdao University, Qingdao, Shandong, China
| | - Li-Kun Zhuang
- Clinical Research Center, Qingdao Municipal Hospital, Qingdao University, Qingdao, Shandong, China
| | - Yong-Ning Xin
- College of Medicine and Pharmaceutics, Ocean University of China, Qingdao, Shandong, China
- Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao, Shandong, China
- Correspondence to: Yong-Ning Xin, College of Medicine and Pharmaceutics, Ocean University of China, Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao, Shandong, China. ORCID: https://orcid.org/0000-0002-3692-7655. Tel: +86-532-82789463, Fax: +86-532-85968434, E-mail: ; Shi-Ying Xuan, College of Medicine and Pharmaceutics, Ocean University of China, Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao, Shandong, China. Tel: +86-532-82789463, Fax: +86-532-85968434, E-mail:
| | - Shi-Ying Xuan
- College of Medicine and Pharmaceutics, Ocean University of China, Qingdao, Shandong, China
- Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao, Shandong, China
- Correspondence to: Yong-Ning Xin, College of Medicine and Pharmaceutics, Ocean University of China, Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao, Shandong, China. ORCID: https://orcid.org/0000-0002-3692-7655. Tel: +86-532-82789463, Fax: +86-532-85968434, E-mail: ; Shi-Ying Xuan, College of Medicine and Pharmaceutics, Ocean University of China, Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao, Shandong, China. Tel: +86-532-82789463, Fax: +86-532-85968434, E-mail:
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Hermawan A, Putri H. Bioinformatics analysis reveals the potential target of rosiglitazone as an antiangiogenic agent for breast cancer therapy. BMC Genom Data 2022; 23:72. [PMID: 36114448 PMCID: PMC9482259 DOI: 10.1186/s12863-022-01086-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 09/06/2022] [Indexed: 11/19/2022] Open
Abstract
Background Several studies have demonstrated the antitumor activity of rosiglitazone (RGZ) in cancer cells, including breast cancer cells. However, the molecular targets of RGZ in the inhibition of angiogenesis in breast cancer cells remain unclear. This study aimed to explore the potential targets of RGZ in inhibiting breast cancer angiogenesis using bioinformatics-based analysis. Results Venn diagram analysis revealed 29 TR proteins. KEGG pathway enrichment analysis demonstrated that TR regulated the adipocytokine, AMPK, and PPAR signaling pathways. Oncoprint analysis showed genetic alterations in FABP4 (14%), ADIPOQ (2.9%), PPARG (2.8%), PPARGC1A (1.5%), CD36 (1.7%), and CREBBP (11%) in patients with breast cancer in a TCGA study. The mRNA levels of FABP4, ADIPOQ, PPARG, CD36, and PPARGC1A were significantly lower in patients with breast cancer than in those without breast cancer. Analysis of gene expression using bc-GenExMiner showed that the mRNA levels of FABP, ADIPOQ, PPARG, CD36, PPARGC1A, and CREBBP were significantly lower in basal-like and triple-negative breast cancer (TNBC) cells than in non-basal-like and non-TNBC cells. In general, the protein levels of these genes were low, except for that of CREBBP. Patients with breast cancer who had low mRNA levels of FABP4, ADIPOQ, PPARG, and PPARGC1A had lower overall survival rates than those with high mRNA levels, which was supported by the overall survival related to DNA methylation. Correlation analysis of immune cell infiltration with TR showed a correlation between TR and immune cell infiltration, highlighting the potential of RGZ for immunotherapy. Conclusion This study explored the potential targets of RGZ as antiangiogenic agents in breast cancer therapy and highlighted FABP4, ADIPOQ, PPARG, PPARGC1A, CD36, and CREBBP as potential targets of RGZ. These findings require further validation to explore the potential of RGZ as an antiangiogenic agent. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01086-2. Recent studies have focused on the development of indirect angiogenesis inhibitors. Bioinformatics-based identification of potential rosiglitazone target genes to inhibit breast cancer angiogenesis. FABP4, ADIPOQ, PPARG, PPARGC1A, CD36, and CREBBP are potential targets of rosiglitazone.
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Liao Y, Weng J, Chen L, Hu N, Yuan X, Wang J, He F, Cai Y, Huang Q, Wang J, Huang L. Comprehensive analysis of SLC43A2 on the tumor immune microenvironment and prognosis of liver hepatocellular carcinoma. Front Genet 2022; 13:911378. [PMID: 36186480 PMCID: PMC9523210 DOI: 10.3389/fgene.2022.911378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/04/2022] [Indexed: 12/05/2022] Open
Abstract
Background: Tumor cells outcompete T cells for methionine via overexpressing SLC43A2, causing T cells exhaustion. We explored the influence of SLC43A2 on tumor immune microenvironment (TIME), immune-related genes (IRGs) and the prognosis of liver hepatocellular carcinoma (LIHC) patients. Methods: The TCGA-LIHC dataset (n = 374) and the ICGC-LIRI-JP-LIHC (n = 231) datasets were used as training and validation cohort, respectively. IRGs were obtained from ImmPort. Statistical analyses were performed using R (V 4.0.5). Online databases such as GEPIA, GSCALite, the Kaplan–Meier plotter, KEGG, TIMER2, and CMap were used for differential expression, immune infiltration, functional enrichment, survival, and drug-induced gene perturbation analysis. Results: SLC43A2 expression was higher in LIHC, correlated with worse survival, but could not predict prognosis of LIHC separately (AUC = 0.467). SLC43A2 positively correlated with immune exhaustion markers (all p < 0.001) and with increased infiltration of Tregs, macrophages and myeloid-derived suppressor cells (MDSC) (all p < 0.05). SLC43A2 may regulate 120 IRGs. A prognostic risk score model was developed using the TCGA-LIHC cohort and validated by the ICGC-LIRI-JP cohort. Arachidonic acid, SB-202190 and guanethidine were identified as possible immunomodulators pharmacologically targeting SLC43A2 in LIHC. Conclusion: SLC43A2 may create suppressive tumor microenvironment and regulate related IRGs, thus affecting the prognosis of LIHC. Arachidonic acid, SB-202190, and guanethidine may be worthy of further study as immunomodulators on SLC43A2.
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Affiliation(s)
- Yan Liao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- The Reproductive Medical Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Junmei Weng
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lian Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Nan Hu
- Department of Neurology and Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Beijing, China
| | - Xun Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jianhua Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Feng He
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yixin Cai
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qin Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jianing Wang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liu Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- *Correspondence: Liu Huang,
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An Immune-Related Prognostic Risk Model in Colon Cancer by Bioinformatics Analysis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:3640589. [PMID: 36065262 PMCID: PMC9440785 DOI: 10.1155/2022/3640589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022]
Abstract
Colon cancer is one of the leading malignancies with poor prognosis worldwide. Immune cell infiltration has a potential prognostic value for colon cancer. This study aimed to establish an immune-related prognostic risk model for colon cancer by bioinformatics analysis. A total of 1670 differentially expressed genes (DEGs), including 177 immune-related genes, were identified from The Cancer Genome Atlas (TCGA) dataset. A prognostic risk model was constructed based on six critical immune-related genes (C-X-C motif chemokine ligand 1 (CXCL1), epiregulin (EREG), C-C motif chemokine ligand 24 (CCL24), fatty acid binding protein 4 (FABP4), tropomyosin 2 (TPM2), and semaphorin 3G (SEMA3G)). This model was validated using the microarray dataset GSE35982. In addition, Cox regression analysis showed that age and clinical stage were correlated with prognostic risk scores. Kaplan–Meier survival analysis showed that high risk scores correlated with low survival probabilities in patients with colon cancer. Downregulated TPM2, FABP4, and SEMA3G levels were positively associated with the activated mast cells, monocytes, and macrophages M2. Upregulated CXCL1 and EREG were positively correlated with macrophages M1 and activated T cells CD4 memory, respectively. Based on these results, we can conclude that the proposed prognostic risk model presents promising novel signatures for the diagnosis and prognosis prediction of colon cancer. This model may provide therapeutic benefits for the development of immunotherapy for colon cancer.
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Fatty Acid-Binding Proteins: Their Roles in Ischemic Stroke and Potential as Drug Targets. Int J Mol Sci 2022; 23:ijms23179648. [PMID: 36077044 PMCID: PMC9455833 DOI: 10.3390/ijms23179648] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Stroke is among the leading causes of death and disability worldwide. However, despite long-term research yielding numerous candidate neuroprotective drugs, there remains a lack of effective neuroprotective therapies for ischemic stroke patients. Among the factors contributing to this deficiency could be that single-target therapy is insufficient in addressing the complex and extensive mechanistic basis of ischemic brain injury. In this context, lipids serve as an essential component of multiple biological processes and play important roles in the pathogenesis of numerous common neurological diseases. Moreover, in recent years, fatty acid-binding proteins (FABPs), a family of lipid chaperone proteins, have been discovered to be involved in the onset or development of several neurodegenerative diseases, including Alzheimer’s and Parkinson’s disease. However, comparatively little attention has focused on the roles played by FABPs in ischemic stroke. We have recently demonstrated that neural tissue-associated FABPs are involved in the pathological mechanism of ischemic brain injury in mice. Here, we review the literature published in the past decade that has reported on the associations between FABPs and ischemia and summarize the relevant regulatory mechanisms of FABPs implicated in ischemic injury. We also propose candidate FABPs that could serve as potential therapeutic targets for ischemic stroke.
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Sun N, Zhao X. Therapeutic Implications of FABP4 in Cancer: An Emerging Target to Tackle Cancer. Front Pharmacol 2022; 13:948610. [PMID: 35899119 PMCID: PMC9310032 DOI: 10.3389/fphar.2022.948610] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Metabolic reprogramming is an emerging hallmark of tumor cells. In order to survive in nutrient-deprived environment, tumor cells rewire their metabolic phenotype to provide sufficient energy and build biomass to sustain their transformed state and promote malignant behaviors. Fatty acid uptake and trafficking is an essential part of lipid metabolism within tumor cells. Fatty acid-binding proteins (FABPs), which belongs to a family of intracellular lipid-binding protein, can bind hydrophobic ligands to regulate lipid trafficking and metabolism. In particular, adipocyte fatty acid binding protein (FABP4), one of the most abundant members, has been found to be upregulated in many malignant solid tumors, and correlated with poor prognosis. In multiple tumor types, FABP4 is critical for tumor proliferation, metastasis and drug resistance. More importantly, FABP4 is a crucial driver of malignancy not only by activating the oncogenic signaling pathways, but also rewiring the metabolic phenotypes of tumor cells to satisfy their enhanced energy demand for tumor development. Thus, FABP4 serves as a tumor-promoting molecule in most cancer types, and may be a promising therapeutic target for cancer treatment.
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Affiliation(s)
- Naihui Sun
- Department of Anesthesiology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xing Zhao
- Department of Pediatrics, The First Affiliated Hospital of China Medical University, Shenyang, China
- *Correspondence: Xing Zhao,
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21
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Basak S, Mallick R, Banerjee A, Pathak S, Duttaroy AK. Cytoplasmic fatty acid-binding proteins in metabolic diseases and cancers. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:143-174. [PMID: 36088074 DOI: 10.1016/bs.apcsb.2022.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cytoplasmic fatty acid-binding proteins (FABPs) are multipurpose proteins that can modulate lipid fluxes, trafficking, signaling, and metabolism. FABPs regulate metabolic and inflammatory pathways, its inhibition can improve type 2 diabetes mellitus and atherosclerosis. In addition, FABPs are involved in obesity, metabolic disease, cardiac dysfunction, and cancers. FABPs are promising tissue biomarkers in solid tumors for diagnostic and/or prognostic targets for novel therapeutic strategies. The signaling responsive elements of FABPs and determinants of FABP-mediated functions may be exploited in preventing or treating these diseases.
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Affiliation(s)
- Sanjay Basak
- Molecular Biology Division, ICMR-National Institute of Nutrition, Indian Council of Medical Research, Hyderabad, India
| | - Rahul Mallick
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Finland
| | - Antara Banerjee
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai, India
| | - Surajit Pathak
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai, India
| | - Asim K Duttaroy
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
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22
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Shi L, Guo R, Chen Z, Jiao R, Zhang S, Xiong X. Analysis of immune related gene expression profiles and immune cell components in patients with Barrett esophagus. Sci Rep 2022; 12:9209. [PMID: 35654816 PMCID: PMC9163054 DOI: 10.1038/s41598-022-13200-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 05/23/2022] [Indexed: 12/02/2022] Open
Abstract
Barrett's esophagus (BE) is a well-known precancerous condition of esophageal adenocarcinoma. However, the immune cells and immune related genes involved in BE development and progression are not fully understood. Therefore, our study attempted to investigate the roles of immune cells and immune related genes in BE patients. The raw gene expression data were downloaded from the GEO database. The limma package in R was used to screen differentially expressed genes (DEGs). Then we performed the least absolute shrinkage and selection operator (LASSO) and random forest (RF) analyses to screen key genes. The proportion of infiltrated immune cells was evaluated using the CIBERSORT algorithm between BE and normal esophagus (NE) samples. The spearman index was used to show the correlations of immune genes and immune cells. Receiver operating characteristic (ROC) curves were used to assess the diagnostic value of key genes in BE. A total of 103 differentially expressed immune-related genes were identified between BE samples and normal samples. Then, 7 genes (CD1A, LTF, FABP4, PGC, TCF7L2, INSR,SEMA3C) were obtained after Lasso analysis and RF modeling. CIBERSORT analysis revealed that resting CD4 T memory cells and gamma delta T cells were present at significantly lower levels in BE samples. Moreover, plasma cell and regulatory T cells were present at significantly higher levels in BE samples than in NE samples. INSR had the highest AUC values in ROC analysis. We identified 7 immune related genes and 4 different immune cells in our study, that may play vital roles in the occurrence and development of BE. Our findings improve the understanding of the molecular mechanisms of BE.
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Affiliation(s)
- Lin Shi
- Department of Gastroenterology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Renwei Guo
- Department of Gastroenterology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Zhuo Chen
- Department of Gastroenterology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Ruonan Jiao
- Department of Gastroenterology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Shuangshuang Zhang
- Department of Gastroenterology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Xuanxuan Xiong
- Department of Gastroenterology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China.
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Ding Z, Zhang C, Zhang B, Li Q. Unraveling the Proteomic Landscape of Intestinal Epithelial Cell-Derived Exosomes in Mice. Front Physiol 2022; 13:773671. [PMID: 35283765 PMCID: PMC8905357 DOI: 10.3389/fphys.2022.773671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/14/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose This study aimed to identify the biological functions of small intestine intestinal epithelial cell derived exosomes (IEC-Exos) and further distinguished the difference proteins in IEC-Exos between ileum and jejunum related to function of the digestive system and occurrence of several diseases. Materials and Methods IECs of Male C57BL/6J mice were isolated. IEC-Exos were extracted from jejunum and ileum epithelial cell culture fluid by ultracentrifugation. In addition, isobaric tags for relative and absolute quantitation (iTRAQ) combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to detect IEC-Exo proteins and conduct biological information analysis. Results The results showed that compared with jejunum IEC-Exos from ileum IEC-Exos, there were 393 up-regulated proteins and 346 down-regulated proteins. IECs-Exos, especially derived from jejunum, were rich in angiotensin-converting enzyme 2 (ACE2). The highly expressed proteins from ileum IEC-Exos were mostly enriched in genetic information processing pathways, which mainly mediate the processes of bile acid transport, protein synthesis and processing modification. In contrast, the highly expressed proteins from jejunum IEC-Exos were mainly enriched in metabolic pathways involved in sugar, fatty acid, amino acid, drug, and bone metabolism, etc. The differentially expressed proteins between ileum and jejunum IEC-Exos were not only related to the function of the digestive system but also closely related to the occurrence of infectious diseases, endocrine diseases and osteoarthritis, etc. Conclusion IEC-Exos there were many differentially expressed proteins between ileum and jejunum, which played different roles in regulating intestinal biological functions. ACE2, the main host cell receptor of SARS-CoV-2, was highly expressed in IEC-Exos, which indicated that IEC-Exos may be a potential route of SARS-CoV-2 infection.
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Affiliation(s)
- Zhenyu Ding
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Cuiyu Zhang
- Department of Physiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Baokun Zhang
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Qin Li
- Department of Physiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
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Jacobsen GE, Fernández I, Quintero MA, Santander AM, Pignac-Kobinger J, Damas OM, Deshpande AR, Kerman DH, Ban Y, Gao Z, Silva TC, Wang L, Beecham AH, McCauley JL, Burgueño JF, Abreu MT. Lamina Propria Phagocyte Profiling Reveals Targetable Signaling Pathways in Refractory Inflammatory Bowel Disease. GASTRO HEP ADVANCES 2022; 1:380-392. [PMID: 36061955 PMCID: PMC9438737 DOI: 10.1016/j.gastha.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Gillian E. Jacobsen
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, Florida
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
- Medical Scientist Training Program, Miller School of Medicine, University of Miami, Miami, Florida
| | - Irina Fernández
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - Maria A. Quintero
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - Ana M. Santander
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - Judith Pignac-Kobinger
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - Oriana M. Damas
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - Amar R. Deshpande
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - David H. Kerman
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - Yuguang Ban
- Biostatistics and Bioinformatics Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Zhen Gao
- Biostatistics and Bioinformatics Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Tiago C. Silva
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, Florida
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, Florida
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Ashley H. Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Jacob L. McCauley
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Juan F. Burgueño
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - Maria T. Abreu
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, Florida
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
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Li Y, Li Y, Xia Z, Zhang D, Chen X, Wang X, Liao J, Yi W, Chen J. Identification of a novel immune signature for optimizing prognosis and treatment prediction in colorectal cancer. Aging (Albany NY) 2021; 13:25518-25549. [PMID: 34898475 PMCID: PMC8714135 DOI: 10.18632/aging.203771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/22/2021] [Indexed: 04/11/2023]
Abstract
BACKGROUND Globally, colorectal cancer (CRC) is one of the most lethal malignant diseases. However, the currently approved therapeutic options for CRC failed to acquire satisfactory treatment efficacy. Tailoring therapeutic strategies for CRC individuals can provide new insights into personalized prediction approaches and thus maximize clinical benefits. METHODS In this study, a multi-step process was used to construct an immune-related genes (IRGs) based signature leveraging the expression profiles and clinical characteristics of CRC from the Gene Expression Omnibus (GEO) database and the Cancer Genome Atlas (TCGA) database. An integrated immunogenomic analysis was performed to determine the association between IRGs with prognostic significance and cancer genotypes in the tumor immune microenvironment (TIME). Moreover, we performed a comprehensive in silico therapeutics screening to identify agents with subclass-specific efficacy. RESULTS The established signature was shown to be a promising biomarker for evaluating clinical outcomes in CRC. The immune risk score as calculated by this classifier was significantly correlated with over-riding malignant phenotypes and immunophenotypes. Further analyses demonstrated that CRCs with low immune risk scores achieved better therapeutic benefits from immunotherapy, while AZD4547, Cytochalasin B and S-crizotinib might have potential therapeutic implications in the immune risk score-high CRCs. CONCLUSIONS Overall, this IRGs-based signature not only afforded a useful tool for determining the prognosis and evaluating the TIME features of CRCs, but also shed new light on tailoring CRCs with precise treatment.
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Affiliation(s)
- Yan Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yiyi Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zijin Xia
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Dun Zhang
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xiaomei Chen
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Xinyu Wang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jing Liao
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Wei Yi
- Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jun Chen
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Engineering and Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
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Liu H, Zhao F, Zhang K, Zhao J, Wang Y. Investigating the growth performance, meat quality, immune function and proteomic profiles of plasmal exosomes in Lactobacillus plantarum-treated broilers with immunological stress. Food Funct 2021; 12:11790-11807. [PMID: 34761788 DOI: 10.1039/d1fo01936h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Exosomes are extracellular membranous nanovesicles that carry functional molecules to mediate cell-to-cell communication. To date, whether probiotics improve the immune function of broilers by plasmal exosome cargo is unclear. In this study, 300 broilers were allocated to three treatments: control diet (CON group), control diet + dexamethasone injection (DEX group), and control diet containing 1 × 108 cfu g-1 P8 + DEX injection (P8 + DEX group). The growth performance, meat quality and immune function of plasma and jejunal mucosa were detected. Exosomes were isolated from the plasma and characterized. Then, the exosome protein profile was determined by proteomic analysis. Correlation analyses between the exosomal proteins and growth performance, meat quality, immune function were performed. Lastly, the related protein levels were verified by multiple reaction monitoring (MRM). Results showed that P8 treatment increased the growth performance, meat quality and immune function of DEX-induced broilers with immunological stress. Moreover, the average diameters, cup-shaped morphology and expressed exosomal proteins confirmed that the isolated extracellular vesicles were exosomes. A total of 784 proteins were identified in the exosomes; among which, 126 differentially expressed proteins (DEPs) were found between the DEX and CON groups and 102 DEPs were found between the P8 + DEX and DEX groups. Gene ontology analysis indicated that DEPs between the DEX and CON groups are mainly involved in the metabolic process, cellular anatomical entity, cytoplasm, etc. DEPs between the P8 + DEX and DEX groups are mainly involved in the multicellular organismal process, response to stimulus, cytoplasm, etc. Pathway analysis revealed that most of the DEPs between the DEX and CON groups participated in the ECM-receptor interaction, focal adhesion, regulation of actin cytoskeleton, etc. Most of the DEPs between the P8 + DEX and DEX groups participated in the ErbB and PPAR signaling pathways. Moreover, many DEPs were correlated with the altered parameters of growth performance, meat quality and immunity in P8-treated broilers. MRM further revealed that the upregulated FABP6 and EPCAM in the DEX group were decreased by P8 + DEX treatment, and the downregulated C1QTNF3 in the DEX group was increased by P8 + DEX treatment. In conclusion, our findings demonstrated that P8 may promote the immune function, growth performance and meat quality of broilers with immunological stress by regulating the plasma exosomal proteins, especially the proteins of FABP6, EPCAM and C1QTNF3 and the pathway of PPAR (ILK/FABP6).
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Affiliation(s)
- Huawei Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
| | - Fan Zhao
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
| | - Kai Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
| | - Jinshan Zhao
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
| | - Yang Wang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
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Pai FC, Huang HW, Tsai YL, Tsai WC, Cheng YC, Chang HH, Chen Y. Inhibition of FABP6 Reduces Tumor Cell Invasion and Angiogenesis through the Decrease in MMP-2 and VEGF in Human Glioblastoma Cells. Cells 2021; 10:2782. [PMID: 34685761 PMCID: PMC8534568 DOI: 10.3390/cells10102782] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 12/05/2022] Open
Abstract
Malignant glioma is one of the most lethal cancers with rapid progression, high recurrence, and poor prognosis in the central nervous system. Fatty acid-binding protein 6 (FABP6) is a bile acid carrier protein that is overexpressed in colorectal cancer. This study aimed to assess the involvement of FABP6 expression in the progression of malignant glioma. Immunohistochemical analysis revealed that FABP6 expression was higher in glioma than in normal brain tissue. After the knockdown of FABP6, a decrease in the migration and invasion abilities of glioma cells was observed. The phosphorylation of the myosin light chain was inhibited, which may be associated with migration ability. Moreover, expression levels of invasion-related proteins, matrix metalloproteinase-2 (MMP-2) and cathepsin B, were reduced. Furthermore, tube formation was inhibited in the human umbilical vein endothelial cells with a decreased concentration of vascular endothelial growth factor (VEGF) in the conditioned medium after the knockdown of FABP6. The phosphorylation of the extracellular signal-regulated kinase (ERK), c-Jun NH2-terminal kinase (JNK), and p65 were also decreased after FABP6 reduction. Finally, the bioluminescent images and immunostaining of MMP-2, cluster of differentiation 31 (CD31), and the VEGF receptor 1 (VEGFR1) revealed attenuated tumor progression in the combination of the FABP6-knocked-down and temozolomide (TMZ)-treated group in an orthotopic xenograft mouse tumor model. This is the first study that revealed the impact of FABP6 on the invasion, angiogenesis, and progression of glioma. The results of this study show that FABP6 may be a potential therapeutic target combined with TMZ for malignant gliomas.
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Affiliation(s)
- Feng-Cheng Pai
- Department of Emergency Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 11490, Taiwan;
| | - Hsiang-Wei Huang
- Department of Biology and Anatomy, National Defense Medical Center, Taipei 11490, Taiwan; (H.-W.H.); (Y.-C.C.)
| | - Yu-Ling Tsai
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei 11490, Taiwan; (Y.-L.T.); (W.-C.T.)
| | - Wen-Chiuan Tsai
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei 11490, Taiwan; (Y.-L.T.); (W.-C.T.)
| | - Yu-Chen Cheng
- Department of Biology and Anatomy, National Defense Medical Center, Taipei 11490, Taiwan; (H.-W.H.); (Y.-C.C.)
| | - Hsin-Han Chang
- Department of Biology and Anatomy, National Defense Medical Center, Taipei 11490, Taiwan; (H.-W.H.); (Y.-C.C.)
| | - Ying Chen
- Department of Biology and Anatomy, National Defense Medical Center, Taipei 11490, Taiwan; (H.-W.H.); (Y.-C.C.)
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Prayugo FB, Kao TJ, Anuraga G, Ta HDK, Chuang JY, Lin LC, Wu YF, Wang CY, Lee KH. Expression Profiles and Prognostic Value of FABPs in Colorectal Adenocarcinomas. Biomedicines 2021; 9:1460. [PMID: 34680577 PMCID: PMC8533171 DOI: 10.3390/biomedicines9101460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 01/04/2023] Open
Abstract
Colorectal cancer (CRC) is one of the world's leading causes of cancer-related deaths; thus, it is important to detect it as early as possible. Obesity is thought to be linked to a large rise in the CRC incidence as a result of bad dietary choices, such as a high intake of animal fats. Fatty acid-binding proteins (FABPs) are a set of molecules that coordinate intracellular lipid responses and are highly associated with metabolism and inflammatory pathways. There are nine types of FABP genes that have been found in mammals, which are FABP1-7, FABP9, and FABP12. Each FABP gene has its own roles in different organs of the body; hence, each one has different expression levels in different cancers. The roles of FABP family genes in the development of CRC are still poorly understood. We used a bioinformatics approach to examine FABP family gene expression profiles using the Oncomine, GEPIA, PrognoScan, STRING, cBioPortal, MetaCore, and TIMER platforms. Results showed that the FABP6 messenger (m)RNA level is overexpressed in CRC cells compared to normal cells. The overexpression of FABP6 was found to be related to poor prognosis in CRC patients' overall survival. The immunohistochemical results in the Human Protein Atlas showed that FABP1 and FABP6 exhibited strong staining in CRC tissues. An enrichment analysis showed that high expression of FABP6 was significantly correlated with the role of microRNAs in cell proliferation in the development of CRC through the insulin-like growth factor (IGF) signaling pathway. FABP6 functions as an intracellular bile-acid transporter in the ileal epithelium. We looked at FABP6 expression in CRC since bile acids are important in the carcinogenesis of CRC. In conclusion, high FABP6 expression is expected to be a potential biomarker for detecting CRC at the early stage.
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Affiliation(s)
- Fidelia Berenice Prayugo
- International Master/PhD Program in Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (L.-C.L.)
| | - Tzu-Jen Kao
- The PhD Program for Neural Regenerative Medicine, Taipei Medical University, Taipei 11031, Taiwan; (T.-J.K.); (J.-Y.C.)
- Research Center of Neuroscience, Taipei Medical University, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Gangga Anuraga
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (L.-C.L.)
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, East Java, Indonesia
| | - Hoang Dang Khoa Ta
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (L.-C.L.)
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Jian-Ying Chuang
- The PhD Program for Neural Regenerative Medicine, Taipei Medical University, Taipei 11031, Taiwan; (T.-J.K.); (J.-Y.C.)
- Research Center of Neuroscience, Taipei Medical University, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Li-Chia Lin
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (L.-C.L.)
| | - Yung-Fu Wu
- National Defense Medical Center, Department of Medical Research, School of Medicine, Tri-Service General Hospital, Taipei 11490, Taiwan;
| | - Chih-Yang Wang
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (L.-C.L.)
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Kuen-Haur Lee
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (L.-C.L.)
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
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Luo M, Lin Y, Liang R, Li Y, Ge L. Clinical Significance of the HHLA2 Protein in Hepatocellular Carcinoma and the Tumor Microenvironment. J Inflamm Res 2021; 14:4217-4228. [PMID: 34483677 PMCID: PMC8409601 DOI: 10.2147/jir.s324336] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022] Open
Abstract
Background The protein “human endogenous retrovirus H long terminal repeat-associating 2” (HHLA2), a member of the B7 family, has been linked to cancer progression and immune responses. However, its functional role in hepatocellular carcinoma (HCC) remains unknown. Methods Bioinformatics was used to examine the potential roles of HHLA2 in HCC and the molecular pathways involved. Expression of HHLA2 and PD-L1 as well as the density of tumor-infiltrating lymphocytes (TILs) in tumoral areas were evaluated by immunohistochemistry and hematoxylin-eosin staining of 202 resected human HCC samples. Potential correlations of HHLA2 expression with pathological characteristics or prognosis of HCC patients were explored. Different types of immune microenvironment in HCC were defined based on HHLA2 expression and TIL density. Results High HHLA2 levels in HCC correlated with more advanced clinical cancer stage (P = 0.040), multiple tumors (P = 0.044), poor tumor differentiation (P = 0.048), microvascular invasion (P = 0.011) and hepatic capsule invasion (P = 0.047). HHLA2 levels correlated significantly with density of TILs, but not with PD-L1 levels. High HHLA2 levels were associated with worse prognosis. Intermediate and high TIL densities were independent predictors of better prognosis. Tumor microenvironments with type I (HHLA2 - high TILs +) or type IV (HHLA2 - low TILs +) were associated with better prognosis. Conclusion HHLA2 level can independently predict worse prognosis and affect the tumor microenvironment in HCC, which may help guide immunotherapy against the cancer.
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Affiliation(s)
- Min Luo
- Department of Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, People's Republic of China
| | - Yan Lin
- Department of Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, People's Republic of China
| | - Rong Liang
- Department of Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, People's Republic of China
| | - Yongqiang Li
- Department of Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, People's Republic of China
| | - Lianying Ge
- Department of Endoscopy, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, People's Republic of China
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Investigating the Mechanism of Scutellariae barbata Herba in the Treatment of Colorectal Cancer by Network Pharmacology and Molecular Docking. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:3905367. [PMID: 34381520 PMCID: PMC8352706 DOI: 10.1155/2021/3905367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/11/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022]
Abstract
Background Colorectal cancer (CRC) is one of the most common gastrointestinal tumors, which accounts for approximately 10% of all diagnosed cancers and cancer deaths worldwide per year. Scutellariae barbatae Herba (SBH) is one of the most frequently used traditional Chinese medicine (TCM) in the treatment of CRC. Although many experiments have been carried out to explain the mechanisms of SBH, the mechanisms of SBH have not been illuminated fully. Thus, we constructed a network pharmacology and molecular docking to investigate the mechanisms of SBH. Methods We adopted active constituent prescreening, target predicting, protein-protein interaction (PPI) analysis, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, differentially expressed gene analysis, and molecular docking to establish a system pharmacology database of SBH against CRC. Results A total of 64 active constituents of SBH were obtained and 377 targets were predicted, and the result indicated that quercetin, luteolin, wogonin, and apigenin were the main active constituents of SBH. Glucocorticoid receptor (NR3C1), pPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (PIK3CA), cellular tumor antigen p53 (TP53), transcription factor AP-1 (JUN), mitogen-activated protein kinase 1 (MAPK1), Myc protooncogene protein (MYC), cyclin-dependent kinase 1 (CDK1), and broad substrate specificity ATP-binding cassette transporter ABCG2 (ABCG2) were the major targets of SBH in the treatment of CRC. GO analysis illustrated that the core biological process regulated by SBH was the regulation of the cell cycle. Thirty pathways were presented and 8 pathways related to CRC were involved. Molecular docking presented the binding details of 3 key targets with 6 active constituents. Conclusions The mechanisms of SBH against CRC depend on the synergistic effect of multiple active constituents, multiple targets, and multiple pathways.
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Zhang Y, Zhao X, Li Y, Wang Y, Chen M. Association between the omentin-1 gene rs2274907 A>T polymorphism and colorectal cancer in the Chinese Han population: a case-control study. J Int Med Res 2021; 49:3000605211006522. [PMID: 33823642 PMCID: PMC8033482 DOI: 10.1177/03000605211006522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE To explore the relationship between the omentin-1 gene rs2274907 A>T polymorphism and colorectal cancer (CRC) in the Chinese Han population. METHODS rs2274907 A>T was assessed by PCR-restriction fragment length polymorphism analysis. Plasma omentin-1 expression from 358 patients with CRC and 286 healthy controls was analyzed by enzyme-linked immunosorbent assay. CRC and control groups were divided into subgroups according to the body mass index (BMI) threshold of 25 kg/m2. RESULTS No significant differences were observed between CRC and control groups in terms of genotype or allele frequencies of rs2274907 A>T. Compared with individuals with BMI <25 kg/m2 and the rs2274907 TT genotype, those with AA+AT genotypes and BMI ≥25 kg/m2 had a 3.027-fold increased risk of CRC. A significant tendency toward a higher stage of colorectal adenocarcinomas and depth of invasion was observed in individuals with the rs2274907 AA genotype compared with other genotypes. CONCLUSIONS The omentin-1 gene rs2274907 A>T polymorphism does not seem to play a critical role in the development of CRC in the Chinese Han population, but an interaction between the rs2274907 A allele and BMI may increase the CRC risk. The rs2274907 AA genotype is a potential biomarker for CRC stage progression.
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Affiliation(s)
- Yaqin Zhang
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Xiaotong Zhao
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Peoples Republic of China
| | - Yongxiang Li
- Division of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Youmin Wang
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Peoples Republic of China
| | - Mingwei Chen
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Peoples Republic of China.,Institute of Traditional Chinese Medicine Diabetes Prevention, Anhui Academy of Traditional Chinese Medicine, Hefei, People's Republic of China
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Baczewska M, Bojczuk K, Kołakowski A, Dobroch J, Guzik P, Knapp P. Obesity and Energy Substrate Transporters in Ovarian Cancer-Review. Molecules 2021; 26:1659. [PMID: 33809784 PMCID: PMC8002293 DOI: 10.3390/molecules26061659] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 01/12/2023] Open
Abstract
Ovarian cancer is the seventh most common cancer in women. It is characterized by a high mortality rate because of its aggressiveness and advanced stage at the time of diagnosis. It is a nonhomogenous group of neoplasms and, of which the molecular basics are still being investigated. Nowadays, the golden standard in the treatment is debulking cytoreductive surgery combined with platinum-based chemotherapy. We have presented the interactions and the resulting perspectives between fatty acid transporters, glucose transporters and ovarian cancer cells. Studies have shown the association between a lipid-rich environment and cancer progression, which suggests the use of correspondent transporter inhibitors as promising chemotherapeutic agents. This review summarizes preclinical and clinical studies highlighting the role of fatty acid transport proteins and glucose transporters in development, growth, metastasizing and its potential use in targeted therapies of ovarian cancer.
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Affiliation(s)
- Marta Baczewska
- Department of Gynecology and Gynecological Oncology, Medical University of Białystok, 15-089 Bialystok, Poland; (K.B.); (A.K.); (J.D.); (P.K.)
| | - Klaudia Bojczuk
- Department of Gynecology and Gynecological Oncology, Medical University of Białystok, 15-089 Bialystok, Poland; (K.B.); (A.K.); (J.D.); (P.K.)
| | - Adrian Kołakowski
- Department of Gynecology and Gynecological Oncology, Medical University of Białystok, 15-089 Bialystok, Poland; (K.B.); (A.K.); (J.D.); (P.K.)
| | - Jakub Dobroch
- Department of Gynecology and Gynecological Oncology, Medical University of Białystok, 15-089 Bialystok, Poland; (K.B.); (A.K.); (J.D.); (P.K.)
| | - Paweł Guzik
- Clinical Department of Gynecology and Obstetrics, City Hospital, 35-241 Rzeszów, Poland;
| | - Paweł Knapp
- Department of Gynecology and Gynecological Oncology, Medical University of Białystok, 15-089 Bialystok, Poland; (K.B.); (A.K.); (J.D.); (P.K.)
- University Oncology Center, University Clinical Hospital in Białystok, 15-276 Białystok, Poland
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Zengin T, Önal-Süzek T. Comprehensive Profiling of Genomic and Transcriptomic Differences between Risk Groups of Lung Adenocarcinoma and Lung Squamous Cell Carcinoma. J Pers Med 2021; 11:154. [PMID: 33672117 PMCID: PMC7926392 DOI: 10.3390/jpm11020154] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 12/17/2022] Open
Abstract
Lung cancer is the second most frequently diagnosed cancer type and responsible for the highest number of cancer deaths worldwide. Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) are subtypes of non-small-cell lung cancer which has the highest frequency of lung cancer cases. We aimed to analyze genomic and transcriptomic variations including simple nucleotide variations (SNVs), copy number variations (CNVs) and differential expressed genes (DEGs) in order to find key genes and pathways for diagnostic and prognostic prediction for lung adenocarcinoma and lung squamous cell carcinoma. We performed a univariate Cox model and then lasso-regularized Cox model with leave-one-out cross-validation using The Cancer Genome Atlas (TCGA) gene expression data in tumor samples. We generated 35- and 33-gene signatures for prognostic risk prediction based on the overall survival time of the patients with LUAD and LUSC, respectively. When we clustered patients into high- and low-risk groups, the survival analysis showed highly significant results with high prediction power for both training and test datasets. Then, we characterized the differences including significant SNVs, CNVs, DEGs, active subnetworks, and the pathways. We described the results for the risk groups and cancer subtypes separately to identify specific genomic alterations between both high-risk groups and cancer subtypes. Both LUAD and LUSC high-risk groups have more downregulated immune pathways and upregulated metabolic pathways. On the other hand, low-risk groups have both up- and downregulated genes on cancer-related pathways. Both LUAD and LUSC have important gene alterations such as CDKN2A and CDKN2B deletions with different frequencies. SOX2 amplification occurs in LUSC and PSMD4 amplification in LUAD. EGFR and KRAS mutations are mutually exclusive in LUAD samples. EGFR, MGA, SMARCA4, ATM, RBM10, and KDM5C genes are mutated only in LUAD but not in LUSC. CDKN2A, PTEN, and HRAS genes are mutated only in LUSC samples. The low-risk groups of both LUAD and LUSC tend to have a higher number of SNVs, CNVs, and DEGs. The signature genes and altered genes have the potential to be used as diagnostic and prognostic biomarkers for personalized oncology.
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Affiliation(s)
- Talip Zengin
- Department of Molecular Biology and Genetics, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey;
- Department of Bioinformatics, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey
| | - Tuğba Önal-Süzek
- Department of Bioinformatics, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey
- Department of Computer Engineering, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey
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Zhang Y, Zhang W, Xia M, Xie Z, An F, Zhan Q, Tian W, Zhu T. High expression of FABP4 in colorectal cancer and its clinical significance. J Zhejiang Univ Sci B 2021; 22:136-145. [PMID: 33615754 DOI: 10.1631/jzus.b2000366] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
OBJECTIVES To investigate the relationship between the fatty acid-binding protein 4 (FABP4) and colorectal cancer (CRC). METHODS Using an enzyme-linked immunosorbent assay (ELISA), we measured the expression of FABP4 in plasma of 50 patients who underwent surgery for CRC from October 2017 to May 2018 and 50 healthy controls. The content of the visceral fat area (VFA) as seen with abdominal computed tomography (CT) scanning was measured by ImageJ software. The expression levels of FABP4, E-cadherin, and Snail proteins in CRC and adjacent tissues were determined by immunohistochemistry. RESULTS The mean concentration of plasma FABP4 of CRC patients was higher than that of the control group (22.46 vs. 9.82 ng/mL; P<0.05). The concentration of plasma FABP4 was related to the tumor, node, metastatis (TNM) stage and lymph node metastasis and was independent of age, body mass index (BMI), tumor size and location, and the degree of differentiation of CRC. The concentration of plasma FABP4 was positively correlated with high VFA and lipoprotein-a (LPA) (P<0.05); but it was not correlated with total cholesterol (TG), total triglyceride (TC), low-density lipoprotein (LDL), high-density lipoprotein (HDL), or apolipoprotein AI (Apo-AI). The expression of FABP4 protein in CRC tissues was positively correlated with the degree of CRC differentiation, tumor stage, and lymph node metastasis. The level of FABP4 protein was negatively correlated with E-cadherin protein (r=-0.3292, P=0.0196) and positively correlated with Snail protein (r=0.5856, P<0.0001). CONCLUSIONS High LPA and VFA were risk factors for increased plasma FABP4 in CRC patients. FABP4 protein was highly expressed in CRC tissues and associated with TNM stage, differentiation, and lymph node metastasis of CRC. The level of FABP4 in CRC tissue was correlated with E-cadherin and Snail expression, suggesting that FABP4 may promote CRC progression related to epithelial-mesenchymal transition (EMT).
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Affiliation(s)
- Yan Zhang
- Department of Gastroenterology, the Second Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Wenjia Zhang
- Department of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi 214023, China
| | - Min Xia
- Department of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi 214023, China.
| | - Zhujun Xie
- Department of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi 214023, China
| | - Fangmei An
- Department of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi 214023, China
| | - Qiang Zhan
- Department of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi 214023, China
| | - Wenying Tian
- Department of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi 214023, China
| | - Tianyue Zhu
- Department of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi 214023, China
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D’Anneo A, Bavisotto CC, Gammazza AM, Paladino L, Carlisi D, Cappello F, de Macario EC, Macario AJL, Lauricella M. Lipid chaperones and associated diseases: a group of chaperonopathies defining a new nosological entity with implications for medical research and practice. Cell Stress Chaperones 2020; 25:805-820. [PMID: 32856199 PMCID: PMC7591661 DOI: 10.1007/s12192-020-01153-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/16/2020] [Accepted: 08/10/2020] [Indexed: 02/08/2023] Open
Abstract
Fatty acid-binding proteins (FABPs) are lipid chaperones assisting in the trafficking of long-chain fatty acids with functions in various cell compartments, including oxidation, signaling, gene-transcription regulation, and storage. The various known FABP isoforms display distinctive tissue distribution, but some are active in more than one tissue. Quantitative and/or qualitative changes of FABPs are associated with pathological conditions. Increased circulating levels of FABPs are biomarkers of disorders such as obesity, insulin resistance, cardiovascular disease, and cancer. Deregulated expression and malfunction of FABPs can result from genetic alterations or posttranslational modifications and can be pathogenic. We have assembled the disorders with abnormal FABPs as chaperonopathies in a distinct nosological entity. This entity is similar but separate from that encompassing the chaperonopathies pertaining to protein chaperones. In this review, we discuss the role of FABPs in the pathogenesis of metabolic syndrome, cancer, and neurological diseases. We highlight the opportunities for improving diagnosis and treatment that open by encompassing all these pathological conditions within of a coherent nosological group, focusing on abnormal lipid chaperones as biomarkers of disease and etiological-pathogenic factors.
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Affiliation(s)
- Antonella D’Anneo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), Laboratory of Biochemistry, University of Palermo, 90127 Palermo, Italy
| | - Celeste Caruso Bavisotto
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Institute of Anatomy, University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Antonella Marino Gammazza
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Institute of Anatomy, University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Letizia Paladino
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Institute of Anatomy, University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Daniela Carlisi
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Institute of Biochemistry, University of Palermo, 90127 Palermo, Italy
| | - Francesco Cappello
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Institute of Anatomy, University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Everly Conway de Macario
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore-Institute of Marine and Environmental Technology (IMET), Baltimore, MD 21202 USA
| | - Alberto J. L. Macario
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore-Institute of Marine and Environmental Technology (IMET), Baltimore, MD 21202 USA
| | - Marianna Lauricella
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Institute of Biochemistry, University of Palermo, 90127 Palermo, Italy
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Hermanowicz JM, Kwiatkowska I, Pawlak D. Important players in carcinogenesis as potential targets in cancer therapy: an update. Oncotarget 2020; 11:3078-3101. [PMID: 32850012 PMCID: PMC7429179 DOI: 10.18632/oncotarget.27689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
The development of cancer is a problem that has accompanied mankind for years. The growing number of cases, emerging drug resistance, and the need to reduce the serious side effects of pharmacotherapy are forcing scientists to better understand the complex mechanisms responsible for the initiation, promotion, and progression of the disease. This paper discusses the modulation of the particular stages of carcinogenesis by selected physiological factors, including: acetylcholine (ACh), peroxisome proliferator-activated receptors (PPAR), fatty acid-binding proteins (FABPs), Bruton's tyrosine kinase (Btk), aquaporins (AQPs), insulin-like growth factor-2 (IGF-2), and exosomes. Understanding their role may contribute to the development of more effective and safer therapies based on new binding sites.
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Affiliation(s)
- Justyna Magdalena Hermanowicz
- Department of Pharmacodynamics, Medical University of Bialystok, Mickiewicza, Bialystok, Poland
- Department of Clinical Pharmacy, Medical University of Bialystok, Mickiewicza, Bialystok, Poland
| | - Iwona Kwiatkowska
- Department of Pharmacodynamics, Medical University of Bialystok, Mickiewicza, Bialystok, Poland
| | - Dariusz Pawlak
- Department of Pharmacodynamics, Medical University of Bialystok, Mickiewicza, Bialystok, Poland
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Liñares-Blanco J, Munteanu CR, Pazos A, Fernandez-Lozano C. Molecular docking and machine learning analysis of Abemaciclib in colon cancer. BMC Mol Cell Biol 2020; 21:52. [PMID: 32640984 PMCID: PMC7346626 DOI: 10.1186/s12860-020-00295-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/24/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The main challenge in cancer research is the identification of different omic variables that present a prognostic value and personalised diagnosis for each tumour. The fact that the diagnosis is personalised opens the doors to the design and discovery of new specific treatments for each patient. In this context, this work offers new ways to reuse existing databases and work to create added value in research. Three published signatures with significante prognostic value in Colon Adenocarcinoma (COAD) were indentified. These signatures were combined in a new meta-signature and validated with main Machine Learning (ML) and conventional statistical techniques. In addition, a drug repurposing experiment was carried out through Molecular Docking (MD) methodology in order to identify new potential treatments in COAD. RESULTS The prognostic potential of the signature was validated by means of ML algorithms and differential gene expression analysis. The results obtained supported the possibility that this meta-signature could harbor genes of interest for the prognosis and treatment of COAD. We studied drug repurposing following a molecular docking (MD) analysis, where the different protein data bank (PDB) structures of the genes of the meta-signature (in total 155) were confronted with 81 anti-cancer drugs approved by the FDA. We observed four interactions of interest: GLTP - Nilotinib, PTPRN - Venetoclax, VEGFA - Venetoclax and FABP6 - Abemaciclib. The FABP6 gene and its role within different metabolic pathways were studied in tumour and normal tissue and we observed the capability of the FABP6 gene to be a therapeutic target. Our in silico results showed a significant specificity of the union of the protein products of the FABP6 gene as well as the known action of Abemaciclib as an inhibitor of the CDK4/6 protein and therefore, of the cell cycle. CONCLUSIONS The results of our ML and differential expression experiments have first shown the FABP6 gene as a possible new cancer biomarker due to its specificity in colonic tumour tissue and no expression in healthy adjacent tissue. Next, the MD analysis showed that the drug Abemaciclib characteristic affinity for the different protein structures of the FABP6 gene. Therefore, in silico experiments have shown a new opportunity that should be validated experimentally, thus helping to reduce the cost and speed of drug screening. For these reasons, we propose the validation of the drug Abemaciclib for the treatment of colon cancer.
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Affiliation(s)
- Jose Liñares-Blanco
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, CITIC, Campus Elviña s/n, A Coruña, 15071, Spain
| | - Cristian R Munteanu
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, CITIC, Campus Elviña s/n, A Coruña, 15071, Spain.,Grupo de Redes de Neuronas Artificiales y Sistemas Adaptativos. Imagen Médica y Diagnóstico Radiológico (RNASA-IMEDIR). Instituto de Investigación Biomédica de A Coruña (INIBIC). Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas. Universidade da Coruña (UDC), Xubias de arriba, 84, A Coruña, 15006, Spain
| | - Alejandro Pazos
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, CITIC, Campus Elviña s/n, A Coruña, 15071, Spain.,Grupo de Redes de Neuronas Artificiales y Sistemas Adaptativos. Imagen Médica y Diagnóstico Radiológico (RNASA-IMEDIR). Instituto de Investigación Biomédica de A Coruña (INIBIC). Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas. Universidade da Coruña (UDC), Xubias de arriba, 84, A Coruña, 15006, Spain
| | - Carlos Fernandez-Lozano
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, CITIC, Campus Elviña s/n, A Coruña, 15071, Spain. .,Grupo de Redes de Neuronas Artificiales y Sistemas Adaptativos. Imagen Médica y Diagnóstico Radiológico (RNASA-IMEDIR). Instituto de Investigación Biomédica de A Coruña (INIBIC). Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas. Universidade da Coruña (UDC), Xubias de arriba, 84, A Coruña, 15006, Spain.
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Guo L, Yang G, Kang Y, Li S, Duan R, Shen L, Jiang W, Qian B, Yin Z, Liang T. Construction and Analysis of a ceRNA Network Reveals Potential Prognostic Markers in Colorectal Cancer. Front Genet 2020; 11:418. [PMID: 32457800 PMCID: PMC7228005 DOI: 10.3389/fgene.2020.00418] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/02/2020] [Indexed: 01/15/2023] Open
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide and is derived from an accumulation of genetic and epigenetic changes. This study explored potential prognostic markers in CRC via the construction and in-depth analysis of a competing endogenous RNA (ceRNA) network, which was generated through a three-step process. First, we screened candidate hub genes in CRC as the primary gene markers to survey their related regulatory non-coding RNAs, miRNAs. Second, the interacting miRNAs were used to search for associated lncRNAs. Thus, candidate RNAs were first constructed into ceRNA networks based on close associations with miRNAs. Further analysis at the isomiR level was also performed for each miRNA locus to understand the detailed expression patterns of the multiple variants. Finally, RNAs were performed an in-depth analysis of expression correlations, which contributed to further screening and validation of potential RNAs with close correlations to each other. Using this approach, nine hub genes, 13 related miRNAs, and 29 candidate lncRNAs were collected and used to construct the ceRNA network. Further in-depth analysis identified the MFAP5-miR-200b-3p-AC005154.6 axis as a potential prognostic marker in CRC. MFAP5 and miR-200b-3p have previously been reported to play important roles in tumorigenesis. These RNAs showed potential prognostic values, and the combination of them may have more sensitivity than using them alone. In conclusion, MFAP5, miR-200b-3p, and AC005154.6 may have potential prognostic value in CRC and may provide a prognostic reference for this patient population.
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Affiliation(s)
- Li Guo
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Guowei Yang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Yihao Kang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Sunjing Li
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Rui Duan
- School of Life Science, Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing, China
| | - Lulu Shen
- School of Life Science, Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing, China
| | - Wenwen Jiang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Bowen Qian
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Zibo Yin
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Tingming Liang
- School of Life Science, Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing, China.,Changzhou Institute of Innovation & Development, Nanjing Normal University, Nanjing, China
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