1
|
Sadat Kalaki N, Ahmadzadeh M, Najafi M, Mobasheri M, Ajdarkosh H, Karbalaie Niya MH. Systems biology approach to identify biomarkers and therapeutic targets for colorectal cancer. Biochem Biophys Rep 2024; 37:101633. [PMID: 38283191 PMCID: PMC10821538 DOI: 10.1016/j.bbrep.2023.101633] [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: 08/18/2023] [Revised: 12/24/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024] Open
Abstract
Background Colorectal cancer (CRC), is the third most prevalent cancer across the globe, and is often detected at advanced stage. Late diagnosis of CRC, leave the chemotherapy and radiotherapy as the main options for the possible treatment of the disease which are associated with severe side effects. In the present study, we seek to explore CRC gene expression data using a systems biology framework to identify potential biomarkers and therapeutic targets for earlier diagnosis and treatment of the disease. Methods The expression data was retrieved from the gene expression omnibus (GEO). Differential gene expression analysis was conducted using R/Bioconductor package. The PPI network was reconstructed by the STRING. Cystoscope and Gephi software packages were used for visualization and centrality analysis of the PPI network. Clustering analysis of the PPI network was carried out using k-mean algorithm. Gene-set enrichment based on Gene Ontology (GO) and KEGG pathway databases was carried out to identify the biological functions and pathways associated with gene groups. Prognostic value of the selected identified hub genes was examined by survival analysis, using GEPIA. Results A total of 848 differentially expressed genes were identified. Centrality analysis of the PPI network resulted in identification of 99 hubs genes. Clustering analysis dissected the PPI network into seven interactive modules. While several DEGs and the central genes in each module have already reported to contribute to CRC progression, survival analysis confirmed high expression of central genes, CCNA2, CD44, and ACAN contribute to poor prognosis of CRC patients. In addition, high expression of TUBA8, AMPD3, TRPC1, ARHGAP6, JPH3, DYRK1A and ACTA1 was found to associate with decreased survival rate. Conclusion Our results identified several genes with high centrality in PPI network that contribute to progression of CRC. The fact that several of the identified genes have already been reported to be relevant to diagnosis and treatment of CRC, other highlighted genes with limited literature information may hold potential to be explored in the context of CRC biomarker and drug target discovery.
Collapse
Affiliation(s)
- Niloufar Sadat Kalaki
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
- International Institute of New Sciences (IINS), Tehran, Iran
| | - Mozhgan Ahmadzadeh
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Mohammad Najafi
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Meysam Mobasheri
- Department of Biotechnology, Faculty of Advanced Sciences and Technology, Tehran Islamic Azad University of Medical Sciences, Tehran, Iran
- International Institute of New Sciences (IINS), Tehran, Iran
| | - Hossein Ajdarkosh
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hadi Karbalaie Niya
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
2
|
Zhou S, Abdihamid O, Tan F, Zhou H, Liu H, Li Z, Xiao S, Li B. KIT mutations and expression: current knowledge and new insights for overcoming IM resistance in GIST. Cell Commun Signal 2024; 22:153. [PMID: 38414063 PMCID: PMC10898159 DOI: 10.1186/s12964-023-01411-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/25/2023] [Indexed: 02/29/2024] Open
Abstract
Gastrointestinal stromal tumor (GIST) is the most common sarcoma located in gastrointestinal tract and derived from the interstitial cell of Cajal (ICC) lineage. Both ICC and GIST cells highly rely on KIT signal pathway. Clinically, about 80-90% of treatment-naive GIST patients harbor primary KIT mutations, and special KIT-targeted TKI, imatinib (IM) showing dramatic efficacy but resistance invariably occur, 90% of them was due to the second resistance mutations emerging within the KIT gene. Although there are multiple variants of KIT mutant which did not show complete uniform biologic characteristics, most of them have high KIT expression level. Notably, the high expression level of KIT gene is not correlated to its gene amplification. Recently, accumulating evidences strongly indicated that the gene coding, epigenetic regulation, and pre- or post- protein translation of KIT mutants in GIST were quite different from that of wild type (WT) KIT. In this review, we elucidate the biologic mechanism of KIT variants and update the underlying mechanism of the expression of KIT gene, which are exclusively regulated in GIST, providing a promising yet evidence-based therapeutic landscape and possible target for the conquer of IM resistance. Video Abstract.
Collapse
Affiliation(s)
- Shishan Zhou
- Division of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China, Xiangya road 87
| | - Omar Abdihamid
- Garissa Cancer Center, Garissa County Referral Hospital, Kismayu road, Garissa town, P.O BOX, 29-70100, Kenya
| | - Fengbo Tan
- Division of Surgery, Xiangya Hospital, Central South University, China, Hunan, Changsha
| | - Haiyan Zhou
- Division of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Heli Liu
- Division of Surgery, Xiangya Hospital, Central South University, China, Hunan, Changsha
| | - Zhi Li
- Center for Molecular Medicine of Xiangya Hospital, Collaborative Innovation Center for Cancer Medicine, Central South University, Changsha, Hunan, China, 410008
| | - Sheng Xiao
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, 410008, MA, USA
| | - Bin Li
- Division of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China, Xiangya road 87#.
| |
Collapse
|
3
|
Chen C, Xie T, Zhang Y, Wang Y, Yu F, Lin L, Zhang W, Brown BC, Zhang X, Kellems RE, D'Alessandro A, Xia Y. Erythrocyte ENT1-AMPD3 Axis is an Essential Purinergic Hypoxia Sensor and Energy Regulator Combating CKD in a Mouse Model. J Am Soc Nephrol 2023; 34:1647-1671. [PMID: 37725437 PMCID: PMC10561773 DOI: 10.1681/asn.0000000000000195] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 07/05/2023] [Indexed: 09/21/2023] Open
Abstract
SIGNIFICANCE STATEMENT Hypoxia drives kidney damage and progression of CKD. Although erythrocytes respond rapidly to hypoxia, their role and the specific molecules sensing and responding to hypoxia in CKD remain unclear. In this study, we demonstrated in a mouse model that erythrocyte ENT1-AMPD3 is a master energy regulator of the intracellular purinergic hypoxic compensatory response that promotes rapid energy supply from extracellular adenosine, eAMPK-dependent metabolic reprogramming, and O 2 delivery, which combat renal hypoxia and progression of CKD. ENT1-AMPD3-AMPK-BPGM comprise a group of circulating erythroid-specific biomarkers, providing early diagnostic and novel therapeutic targets for CKD. BACKGROUND Hypoxia drives kidney damage and progression of CKD. Although erythrocytes respond rapidly to hypoxia, their role and the specific molecules sensing and responding to hypoxia in CKD remain unclear. METHODS Mice with an erythrocyte-specific deficiency in equilibrative nucleoside transporter 1 ( eEnt1-/- ) and a global deficiency in AMP deaminase 3 ( Ampd3-/- ) were generated to define their function in two independent CKD models, including angiotensin II (Ang II) infusion and unilateral ureteral obstruction (UUO). Unbiased metabolomics, isotopic adenosine flux, and various biochemical and cell culture analyses coupled with genetic studies were performed. Translational studies in patients with CKD and cultured human erythrocytes examined the role of ENT1 and AMPD3 in erythrocyte function and metabolism. RESULTS eEnt1-/- mice display severe renal hypoxia, kidney damage, and fibrosis in both CKD models. The loss of eENT1-mediated adenosine uptake reduces intracellular AMP and thus abolishes the activation of AMPK α and bisphosphoglycerate mutase (BPGM). This results in reduced 2,3-bisphosphoglycerate and glutathione, leading to overwhelming oxidative stress in eEnt1-/- mice. Excess reactive oxygen species (ROS) activates AMPD3, resulting in metabolic reprogramming and reduced O 2 delivery, leading to severe renal hypoxia in eEnt1-/- mice. By contrast, genetic ablation of AMPD3 preserves the erythrocyte adenine nucleotide pool, inducing AMPK-BPGM activation, O 2 delivery, and antioxidative stress capacity, which protect against Ang II-induced renal hypoxia, damage, and CKD progression. Translational studies recapitulated the findings in mice. CONCLUSION eENT1-AMPD3, two highly enriched erythrocyte purinergic components that sense hypoxia, promote eAMPK-BPGM-dependent metabolic reprogramming, O 2 delivery, energy supply, and antioxidative stress capacity, which mitigates renal hypoxia and CKD progression.
Collapse
Affiliation(s)
- Changhan Chen
- National Medical Metabolomics International Collaborative Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - TingTing Xie
- National Medical Metabolomics International Collaborative Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of General Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yujin Zhang
- National Medical Metabolomics International Collaborative Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yiyan Wang
- National Medical Metabolomics International Collaborative Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fang Yu
- National Medical Metabolomics International Collaborative Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lizhen Lin
- National Medical Metabolomics International Collaborative Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Weiru Zhang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of General Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Benjamin C. Brown
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xin Zhang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Rodney E. Kellems
- Department of Biochemistry and Molecular Biology, The University of Texas McGovern Medical School at Houston, Houston, Texas
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado
| | - Yang Xia
- National Medical Metabolomics International Collaborative Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| |
Collapse
|
4
|
Kitamura K, Yamamoto T, Ochi H, Suzuki M, Suzuki N, Igawa T, Yoshida T, Futakuchi M, Ogino H, Michiue T. Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis. Sci Rep 2023; 13:13214. [PMID: 37580380 PMCID: PMC10425369 DOI: 10.1038/s41598-023-40193-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/06/2023] [Indexed: 08/16/2023] Open
Abstract
Cancer treatment is still challenging because the disease is often caused by multiple mutations. Although genomic studies have identified many oncogenes and tumor suppressor genes, gene sets involved in tumorigenesis remain poorly understood. Xenopus, a genus of aquatic frogs, is a useful model to identify gene sets because it can be genetically and experimentally analyzed. Here, we analyzed gene expression in tumor tissues of three individuals in Xenopus tropicalis and identified 55 differentially expressed genes (DEGs). Gene ontology (GO) analysis showed that the upregulated genes in the tumor tissues were enriched in GO terms related to the extracellular matrix and collagen fibril organization. Hierarchical clustering showed that the gene expression patterns of tumor tissues in X. tropicalis were comparable to those of human connective, soft, and subcutaneous tissue-derived cancers. Additionally, pathway analysis revealed that these DEGs were associated with multiple pathways, including the extracellular matrix, collagen fibril organization, MET signaling, and keratan sulfate. We also found that the expression tendency of some DEGs that have not been well analyzed in the cancer field clearly determines the prognosis of human cancer patients. This study provides a remarkable reference for future experimental work on X. tropicalis to identify gene sets involved in human cancer.
Collapse
Affiliation(s)
- Kazuki Kitamura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan
| | - Takayoshi Yamamoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan
| | - Haruki Ochi
- Institute for Promotion of Medical Science Research, Faculty of Medicine, Yamagata University, 2-2-2 Iida-Nishi, Yamagata City, Yamagata, 990-9585, Japan
| | - Makoto Suzuki
- Amphibian Research Center, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
| | - Nanoka Suzuki
- Amphibian Research Center, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
| | - Takeshi Igawa
- Amphibian Research Center, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
| | - Tadashi Yoshida
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan
| | - Mitsuru Futakuchi
- Department of Pathology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-Nishi, Yamagata City, Yamagata, 990-9585, Japan
| | - Hajime Ogino
- Amphibian Research Center, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
| | - Tatsuo Michiue
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan.
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.
| |
Collapse
|
5
|
Dong W, Wong KHY, Liu Y, Levy-Sakin M, Hung WC, Li M, Li B, Jin SC, Choi J, Lopez-Giraldez F, Vaka D, Poon A, Chu C, Lao R, Balamir M, Movsesyan I, Malloy MJ, Zhao H, Kwok PY, Kane JP, Lifton RP, Pullinger CR. Whole-exome sequencing reveals damaging gene variants associated with hypoalphalipoproteinemia. J Lipid Res 2022; 63:100209. [PMID: 35460704 PMCID: PMC9126845 DOI: 10.1016/j.jlr.2022.100209] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/02/2022] Open
Abstract
Low levels of high density lipoprotein-cholesterol (HDL-C) are associated with an elevated risk of arteriosclerotic coronary heart disease. Heritability of HDL-C levels is high. In this research discovery study, we used whole-exome sequencing to identify damaging gene variants that may play significant roles in determining HDL-C levels. We studied 204 individuals with a mean HDL-C level of 27.8 ± 6.4 mg/dl (range: 4-36 mg/dl). Data were analyzed by statistical gene burden testing and by filtering against candidate gene lists. We found 120 occurrences of probably damaging variants (116 heterozygous; four homozygous) among 45 of 104 recognized HDL candidate genes. Those with the highest prevalence of damaging variants were ABCA1 (n = 20), STAB1 (n = 9), OSBPL1A (n = 8), CPS1 (n = 8), CD36 (n = 7), LRP1 (n = 6), ABCA8 (n = 6), GOT2 (n = 5), AMPD3 (n = 5), WWOX (n = 4), and IRS1 (n = 4). Binomial analysis for damaging missense or loss-of-function variants identified the ABCA1 and LDLR genes at genome-wide significance. In conclusion, whole-exome sequencing of individuals with low HDL-C showed the burden of damaging rare variants in the ABCA1 and LDLR genes is particularly high and revealed numerous occurrences in HDL candidate genes, including many genes identified in genome-wide association study reports. Many of these genes are involved in cancer biology, which accords with epidemiologic findings of the association of HDL deficiency with increased risk of cancer, thus presenting a new area of interest in HDL genomics.
Collapse
Affiliation(s)
- Weilai Dong
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Karen H Y Wong
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Youbin Liu
- Department of Cardiology, The Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Michal Levy-Sakin
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Wei-Chien Hung
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Mo Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jungmin Choi
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | | | - Dedeepya Vaka
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Annie Poon
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Catherine Chu
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Richard Lao
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Melek Balamir
- Department of Internal Medicine, Istanbul University, Istanbul, Turkey
| | - Irina Movsesyan
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Mary J Malloy
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, CA, USA; Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, CA, USA; Department of Dermatology, University of California, San Francisco, CA, USA
| | - John P Kane
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Clive R Pullinger
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA; Physiological Nursing, University of California, San Francisco, CA, USA.
| |
Collapse
|
6
|
Yi R, Xie L, Wang X, Shen C, Chen X, Qiao L. Multi-Omic Profiling of Multi-Biosamples Reveals the Role of Amino Acid and Nucleotide Metabolism in Endometrial Cancer. Front Oncol 2022; 12:861142. [PMID: 35574395 PMCID: PMC9099206 DOI: 10.3389/fonc.2022.861142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/01/2022] [Indexed: 11/15/2022] Open
Abstract
Background Endometrial cancer (EC) is one of the most common gynecological cancers. The traditional diagnosis of EC relies on histopathology, which, however, is invasive and may arouse tumor spread. There have been many studies aiming to find the metabolomic biomarkers of EC to improve the early diagnosis of cancer in a non-invasive or minimally invasive way, which can also provide valuable information for understanding the disease. However, most of these studies only analyze a single type of sample by metabolomics, and cannot provide a comprehensive view of the altered metabolism in EC patients. Our study tries to gain a pathway-based view of multiple types of samples for understanding metabolomic disorders in EC by combining metabolomics and proteomics. Methods Forty-four EC patients and forty-three controls were recruited for the research. We collected endometrial tissue, urine, and intrauterine brushing samples. Untargeted metabolomics and untargeted proteomics were both performed on the endometrial tissue samples, while only untargeted metabolomics was performed on the urine and intrauterine brushing samples. Results By integrating the differential metabolites and proteins between EC patients and controls detected in the endometrial tissue samples, we identified several EC-related significant pathways, such as amino acid metabolism and nucleotide metabolism. The significance of these pathways and the potential of metabolite biomarker-based diagnosis were then further verified by using urine and intrauterine brushing samples. It was found that the regulation of metabolites involved in the significant pathways showed similar trends in the intrauterine brushings and the endometrial tissue samples, while opposite trends in the urine and the endometrial tissue samples. Conclusions With multi-omics characterization of multi-biosamples, the metabolomic changes related to EC are illustrated in a pathway-based way. The network of altered metabolites and related proteins provides a comprehensive view of altered metabolism in the endometrial tissue samples. The verification of these critical pathways by using urine and intrauterine brushing samples provides evidence for the possible non-invasive or minimally invasive biopsy for EC diagnosis in the future.
Collapse
Affiliation(s)
- Runqiu Yi
- Department of Chemistry, Shanghai Stomatological Hospital, and Obstetrics and Gynecology Hospital of Fudan University, Fudan University, Shanghai, China
| | - Liying Xie
- Department of Chemistry, Shanghai Stomatological Hospital, and Obstetrics and Gynecology Hospital of Fudan University, Fudan University, Shanghai, China
| | | | | | - Xiaojun Chen
- Department of Chemistry, Shanghai Stomatological Hospital, and Obstetrics and Gynecology Hospital of Fudan University, Fudan University, Shanghai, China
- *Correspondence: Liang Qiao, ; Xiaojun Chen,
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, and Obstetrics and Gynecology Hospital of Fudan University, Fudan University, Shanghai, China
- *Correspondence: Liang Qiao, ; Xiaojun Chen,
| |
Collapse
|
7
|
Abstract
Perturbations in metabolic processes are associated with diseases such as obesity, type 2 diabetes mellitus, certain infections and some cancers. A resurgence of interest in creatine biology is developing, with new insights into a diverse set of regulatory functions for creatine. This resurgence is primarily driven by technological advances in genetic engineering and metabolism as well as by the realization that this metabolite has key roles in cells beyond the muscle and brain. Herein, we highlight the latest advances in creatine biology in tissues and cell types that have historically received little attention in the field. In adipose tissue, creatine controls thermogenic respiration and loss of this metabolite impairs whole-body energy expenditure, leading to obesity. We also cover the various roles that creatine metabolism has in cancer cell survival and the function of the immune system. Renewed interest in this area has begun to showcase the therapeutic potential that lies in understanding how changes in creatine metabolism lead to metabolic disease.
Collapse
Affiliation(s)
- Lawrence Kazak
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada.
- Department of Biochemistry, McGill University, Montreal, QC, Canada.
| | - Paul Cohen
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
8
|
Yun JW, Lee S, Ryu D, Park S, Park WY, Joung JG, Jeong J. Biomarkers Associated with Tumor Heterogeneity in Prostate Cancer. Transl Oncol 2018; 12:43-48. [PMID: 30265975 PMCID: PMC6161410 DOI: 10.1016/j.tranon.2018.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/09/2018] [Accepted: 09/09/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND: Prostate cancers exhibit intratumor heterogeneity (ITH), like other cancer types. The ITH may affect diverse phenotypes such as treatment response, drug resistance, and clinical outcomes. It is crucial to consider ITH to understand tumorigenesis. METHODS: Genomic and transcriptomic profiles of prostate cancer patients were investigated to determine which markers are correlated with the degree of tumor heterogeneity. In addition, the correlation between the immune activity and clonality of tumors was examined. RESULTS: Tumor heterogeneity across all prostate cancer samples was variable. However, ITH events were dependent on genomic and clinical features. Interestingly, prostate-specific antigen score increased in tumors with multiple subclones, indicating high-grade tumor heterogeneity. On the other hand, CD8-positive T-cell activation decreased in highly heterogeneous tumors. Intriguingly, PTEN deletion was prominently enriched in high heterogeneity groups, with a strong association with heterozygous loss. Expression of major genes including PTEN, CDC42EP5, RNLS, GP2, NETO2, and AMPD3 was closely related to tumor heterogeneity in association with PTEN deletion. CONCLUSIONS: In prostate cancer, ITH, a potential factor affecting tumor progression, is associated with PTEN deletion and cytotoxic T cell inactivation.
Collapse
Affiliation(s)
- Jae Won Yun
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea; Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul 06351, Republic of Korea
| | - Soomin Lee
- Center for Health Promotion, Samsung Medical Center, Seoul, Republic of Korea
| | - Daeun Ryu
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Semi Park
- Center for Health Promotion, Samsung Medical Center, Seoul, Republic of Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea; Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul 06351, Republic of Korea; Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea.
| | - Jeongyun Jeong
- Center for Health Promotion, Samsung Medical Center, Seoul, Republic of Korea.
| |
Collapse
|
9
|
Zhu K, Li K, Yuan DW, Xu G, Kang L, Dang CX, Zhang Y. Clinicopathological and Prognostic Significance of Expression of B-Cell-Specific Moloney Murine Leukemia Virus Insertion Site 1 (BMI-1) Gene and Protein in Gastrointestinal Stromal Tumors. Med Sci Monit 2018; 24:6414-6421. [PMID: 30209248 PMCID: PMC6149236 DOI: 10.12659/msm.909443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 05/08/2018] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Gastrointestinal stromal tumor (GIST) is an uncommon visceral sarcoma that arises predominantly in the gastrointestinal tract. Since GISTs are encountered infrequently and inflexible to traditional therapy, the aim of the present study was to explore the correlation of B-cell-specific Moloney murine leukemia virus insertion site 1 (BMI-1) mRNA and BMI-1 protein levels with the clinicopathological characteristics and prognosis significance of GISTs. MATERIAL AND METHODS GIST tissues and normal tissues were collected from 156 patients who had undergone surgical treatment. RT-qPCR and immunohistochemistry were used to measure the BMI-1 mRNA and protein levels in GIST tissues and normal tissues. Univariate survival analysis was used for determination of the factors that affect prognosis of GIST patients. Cox proportional hazards model was plotted to determine the independent risk factors for prognosis of GIST patients. RESULTS The BMI-1 mRNA and protein levels in GIST tissues were higher than those in normal tissues. BMI-1 mRNA and positive protein levels were correlated with the National Institutes of Health (NIH) risk grade, tumor diameter and infiltration, and metastasis. There was a short survival period for the patients with a positive protein level and a high mRNA level of BMI-1. The site of primary tumor, tumor diameter, NIH risk grade, infiltration, and metastasis, as well as BMI-1 mRNA and protein levels were independent risk factors for prognosis of GIST patients. CONCLUSIONS Taken together, these findings suggest there might be a relationship between BMI-1 mRNA and protein levels, and clinicopathological characteristics, including NIH risk grade, tumor size as well as infiltration and metastasis, of GIST patients. In addition, BMI-1 mRNA and protein levels were identified as independent risk factors for prognosis of GIST patients.
Collapse
Affiliation(s)
- Kun Zhu
- Department of Oncology Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, P.R. China
| | - Kang Li
- Department of Oncology Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, P.R. China
| | - Da-Wei Yuan
- Department of Oncology Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, P.R. China
| | - Gang Xu
- Department of Oncology Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, P.R. China
| | - Li Kang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, P.R. China
| | - Cheng-Xue Dang
- Department of Oncology Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, P.R. China
| | - Yong Zhang
- Department of Oncology Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, P.R. China
| |
Collapse
|
10
|
Luo Y, Zeng B, Zeng L, Du X, Li B, Huo R, Liu L, Wang H, Dong M, Pan J, Zheng P, Zhou C, Wei H, Xie P. Gut microbiota regulates mouse behaviors through glucocorticoid receptor pathway genes in the hippocampus. Transl Psychiatry 2018; 8:187. [PMID: 30194287 PMCID: PMC6128920 DOI: 10.1038/s41398-018-0240-5] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 06/19/2018] [Accepted: 07/14/2018] [Indexed: 12/20/2022] Open
Abstract
Gut microbiota has an important role in the immune system, metabolism, and digestion, and has a significant effect on the nervous system. Recent studies have revealed that abnormal gut microbiota induces abnormal behaviors, which may be associated with the hypothalamic-pituitary-adrenal (HPA) axis. Therefore, we investigated the behavioral changes in germ-free (GF) mice by behavioral tests, quantified the basal serum cortisol levels, and examined glucocorticoid receptor pathway genes in hippocampus using microarray analysis followed by real-time PCR validation, to explore the molecular mechanisms by which the gut microbiota influences the host's behaviors and brain function. Moreover, we quantified the basal serum cortisol levels and validated the differential genes in an Escherichia coli-derived lipopolysaccharide (LPS) treatment mouse model and fecal "depression microbiota" transplantation mouse model by real-time PCR. We found that GF mice showed antianxiety- and antidepressant-like behaviors, whereas E. coli LPS-treated mice showed antidepressant-like behavior, but did not show antianxiety-like behavior. However, "depression microbiota" recipient mice exhibited anxiety- and depressive-like behaviors. In addition, six glucocorticoid receptor pathway genes (Slc22a5, Aqp1, Stat5a, Ampd3, Plekhf1, and Cyb561) were upregulated in GF mice, and of these only two (Stat5a and Ampd3) were upregulated in LPS-treated mice, whereas the shared gene, Stat5a, was downregulated in "depression microbiota" recipient mice. Furthermore, basal serum cortisol levels were decreased in E. coli LPS-treated mice but not in GF mice and "depression microbiota" recipient mice. These results indicated that the gut microbiota may lead to behavioral abnormalities in mice through the downstream pathway of the glucocorticoid receptor. Herein, we proposed a new insight into the molecular mechanisms by which gut microbiota influence depressive-like behavior.
Collapse
Affiliation(s)
- Yuanyuan Luo
- 0000 0000 8653 0555grid.203458.8Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, 400016 China ,Chongqing Key Laboratory of Neurobiology, Chongqing, 400016 China ,0000 0000 8653 0555grid.203458.8Department of Neurology, Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160 China
| | - Benhua Zeng
- 0000 0004 1760 6682grid.410570.7Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing, 400038 China
| | - Li Zeng
- 0000 0000 8653 0555grid.203458.8Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, 400016 China ,grid.412461.4Department of Nephrology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010 China
| | - Xiangyu Du
- 0000 0000 8653 0555grid.203458.8Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, 400016 China ,Chongqing Key Laboratory of Neurobiology, Chongqing, 400016 China
| | - Bo Li
- 0000 0000 8653 0555grid.203458.8Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, 400016 China ,Chongqing Key Laboratory of Neurobiology, Chongqing, 400016 China ,0000 0004 0369 313Xgrid.419897.aKey Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), Chongqing, China
| | - Ran Huo
- 0000 0000 8653 0555grid.203458.8Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, 400016 China ,Chongqing Key Laboratory of Neurobiology, Chongqing, 400016 China ,0000 0004 0369 313Xgrid.419897.aKey Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), Chongqing, China
| | - Lanxiang Liu
- 0000 0000 8653 0555grid.203458.8Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, 400016 China ,Chongqing Key Laboratory of Neurobiology, Chongqing, 400016 China ,grid.452206.7Department of Neurology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042 China
| | - Haiyang Wang
- 0000 0000 8653 0555grid.203458.8Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, 400016 China ,Chongqing Key Laboratory of Neurobiology, Chongqing, 400016 China
| | - Meixue Dong
- 0000 0000 8653 0555grid.203458.8Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, 400016 China ,Chongqing Key Laboratory of Neurobiology, Chongqing, 400016 China ,grid.452206.7Department of Neurology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042 China
| | - Junxi Pan
- 0000 0000 8653 0555grid.203458.8Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, 400016 China ,Chongqing Key Laboratory of Neurobiology, Chongqing, 400016 China ,0000 0004 0369 313Xgrid.419897.aKey Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), Chongqing, China
| | - Peng Zheng
- 0000 0000 8653 0555grid.203458.8Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, 400016 China ,Chongqing Key Laboratory of Neurobiology, Chongqing, 400016 China ,grid.452206.7Department of Neurology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042 China
| | - Chanjuan Zhou
- 0000 0000 8653 0555grid.203458.8Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, 400016 China ,Chongqing Key Laboratory of Neurobiology, Chongqing, 400016 China
| | - Hong Wei
- Chongqing Key Laboratory of Neurobiology, Chongqing, 400016, China.
| | - Peng Xie
- Chongqing Key Laboratory of Neurobiology, Chongqing, 400016, China. .,Department of Neurology, Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160, China. .,Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), Chongqing, China. .,Department of Neurology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, China. .,South Australian Health and Medical Research Institute, Mind and Brain Theme, and Flinders University, Adelaide, SA, Australia.
| |
Collapse
|
11
|
Kwan STC, King JH, Grenier JK, Yan J, Jiang X, Roberson MS, Caudill MA. Maternal Choline Supplementation during Normal Murine Pregnancy Alters the Placental Epigenome: Results of an Exploratory Study. Nutrients 2018; 10:nu10040417. [PMID: 29597262 PMCID: PMC5946202 DOI: 10.3390/nu10040417] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 12/14/2022] Open
Abstract
The placental epigenome regulates processes that affect placental and fetal development, and could be mediating some of the reported effects of maternal choline supplementation (MCS) on placental vascular development and nutrient delivery. As an extension of work previously conducted in pregnant mice, the current study sought to explore the effects of MCS on various epigenetic markers in the placenta. RNA and DNA were extracted from placentas collected on embryonic day 15.5 from pregnant mice fed a 1X or 4X choline diet, and were subjected to genome-wide sequencing procedures or mass-spectrometry-based assays to examine placental imprinted gene expression, DNA methylation patterns, and microRNA (miRNA) abundance. MCS yielded a higher (fold change = 1.63-2.25) expression of four imprinted genes (Ampd3, Tfpi2, Gatm and Aqp1) in the female placentas and a lower (fold change = 0.46-0.62) expression of three imprinted genes (Dcn, Qpct and Tnfrsf23) in the male placentas (false discovery rate (FDR) ≤ 0.05 for both sexes). Methylation in the promoter regions of these genes and global placental DNA methylation were also affected (p ≤ 0.05). Additionally, a lower (fold change = 0.3; Punadjusted = 2.05 × 10-4; FDR = 0.13) abundance of miR-2137 and a higher (fold change = 1.25-3.92; p < 0.05) expression of its target genes were detected in the 4X choline placentas. These data demonstrate that the placental epigenome is responsive to maternal choline intake during murine pregnancy and likely mediates some of the previously described choline-induced effects on placental and fetal outcomes.
Collapse
Affiliation(s)
| | - Julia H King
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA.
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA.
| | - Jian Yan
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA.
| | - Xinyin Jiang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA.
- Department of Health and Nutrition Sciences, Brooklyn College, Brooklyn, NY 11210, USA.
| | - Mark S Roberson
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA.
| | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA.
| |
Collapse
|