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Hardwick JP, Song BJ, Rote P, Leahy C, Lee YK, Wolf AR, Diegisser D, Garcia V. The CYP4/20-HETE/GPR75 axis in the progression metabolic dysfunction-associated steatosis liver disease (MASLD) to chronic liver disease. Front Physiol 2025; 15:1497297. [PMID: 39959811 PMCID: PMC11826315 DOI: 10.3389/fphys.2024.1497297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 12/24/2024] [Indexed: 02/18/2025] Open
Abstract
Introduction Metabolic-dysfunction-associated steatosis liver disease (MASLD) is a progressive liver disease from simple steatosis, steatohepatitis, fibrosis, cirrhosis, and hepatocellular carcinoma. Chronic liver diseases (CLDs) can lead to portal hypertension, which is a major cause of complications of cirrhosis. CLDs cause structural alterations across the liver through increased contents of extracellular matrix (ECM), driving dysfunction of liver sinusoidal endothelial cells (LSECs) alongside hepatic stellate cells (HSCs) and activated resident or infiltrating immune cells. Bioactive arachidonic metabolites have diverse roles in the progression of MASLD. Both secreted levels of 20-hydroxyeicosatetraenoic acid (20-HETE) and epoxyeicosatrienoic acid (EET) are elevated in patients with liver cirrhosis. Methods CLD samples were evaluated for changes in free fatty acids (FFA), cholesterol, bilirubin, bile acid, reactive oxygen species (ROD), lipid peroxidation, myeloperoxidase activity and hydroxyproline levels to evaluate the degrees of liver damage and fibrosis. To address the role of the CYP4/20-HETE/GPR75 axis, we measured the amount and the synthesis of 20-HETE in patients with CLD, specifically during the progression of MASLD. Additionally, we evaluated gene expression and protein levels of GPR75, a high-affinity receptor for 20-HETE across CLD patient samples. Results We observed an increase in 20-HETE levels and synthesis during the progression of MASLD. Increased synthesis of 20-HETE correlated with the expression of CYP4A11 genes but not CYP4F2. These results were confirmed by increased P4504A11 protein levels and decreased P4504F2 protein levels during the development and progression of MASLD. The gene expression and protein levels of GPR75, the major receptor for 20-HETE, increased in the progression of MASLD. Interestingly, the CYP4A11 and GPR75 mRNA levels increased in steatohepatitis but dramatically dropped in cirrhosis and then increased in patients with HCC. Also, protein levels of P4504A11 and GPR75 mirrored their mRNA levels. Discussion These results indicate that the CYP4A11 and subsequent GPR75 genes are coordinately regulated in the progression of MASLD and may have multiple roles, including 20-HETE activation of peroxisome proliferator-activated receptor α (PPARα) in steatosis and GPR75 in CLD through either increased cell proliferation or vasoconstriction in portal hypertension during cirrhosis. The abrupt reduction in CYP4A11 and GPR75 in patients with cirrhosis may also be due to increased 20-HETE, serving as a feedback mechanism via GPR75, leading to reduced CYP4A11 and GPR75 gene expression. This work illustrates key correlations associated with the CYP4/20-HETE/GPR75 axis and the progression of liver disease in humans.
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Affiliation(s)
- James P. Hardwick
- Department of Integrative Medical Sciences Liver Focus Group, Northeast Ohio Medical University, Rootstown, OH, United States
| | - Byoung-Joon Song
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, United States
| | - Paul Rote
- Department of Integrative Medical Sciences Liver Focus Group, Northeast Ohio Medical University, Rootstown, OH, United States
| | - Charles Leahy
- Department of Integrative Medical Sciences Liver Focus Group, Northeast Ohio Medical University, Rootstown, OH, United States
| | - Yoon Kwang Lee
- Department of Integrative Medical Sciences Liver Focus Group, Northeast Ohio Medical University, Rootstown, OH, United States
| | - Alexandra Rudi Wolf
- Department of Pharmacology, New York Medical College, Valhalla, NY, United States
| | - Danielle Diegisser
- Department of Pharmacology, New York Medical College, Valhalla, NY, United States
| | - Victor Garcia
- Department of Pharmacology, New York Medical College, Valhalla, NY, United States
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Leow SS, Khoo JS, Lee WK, Hoh CC, Fairus S, Sambanthamurthi R, Hayes KC. RNA-Seq transcriptome profiling of Nile rat livers reveals novel insights on the anti-diabetic mechanisms of Water-Soluble Palm Fruit Extract. J Appl Genet 2024; 65:867-895. [PMID: 38890243 DOI: 10.1007/s13353-024-00880-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 04/08/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024]
Abstract
Water-Soluble Palm Fruit Extract (WSPFE) has been shown to confer anti-diabetic effects in the Nile rat (NR) (Arvicanthis niloticus). Liquid and powder WSPFE both deterred diabetes onset in NRs fed a high-carbohydrate (hiCHO) diet, but the liquid form provided better protection. In this study, NRs were fed either a hiCHO diet or the same diet added with liquid or powder WSPFE. Following feeding of the diets for 8 weeks, random blood glucose levels were measured to categorize NRs as either diabetes-resistant or diabetes-susceptible, based on a cut-off value of 75 mg/dL. Livers were then obtained for Illumina HiSeq 4000 paired end RNA-sequencing (RNA-Seq) and the data were mapped to the reference genome. Consistent with physiological and biochemical parameters, the gene expression data obtained indicated that WSPFE was associated with protection against diabetes. Among hepatic genes upregulated by WSPFE versus controls, were genes related to insulin-like growth factor binding protein, leptin receptor, and processes of hepatic metabolism maintenance, while those downregulated were related to antigen binding, immunoglobulin receptor, inflammation- and cancer-related processes. WSPFE supplementation thus helped inhibit diabetes progression in NRs by increasing insulin sensitivity and reducing both the inflammatory effects of a hiCHO diet and the related DNA-damage compensatory mechanisms contributing to liver disease progression. In addition, the genetic permissiveness of susceptible NRs to develop diabetes was potentially associated with dysregulated compensatory mechanisms involving insulin signaling and oxidative stress over time. Further studies on other NR organs associated with diabetes and its complications are warranted.
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Affiliation(s)
- Soon-Sen Leow
- Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
| | - Jia-Shiun Khoo
- Codon Genomics Sdn Bhd, No. 26, Jalan Dutamas 7, Taman Dutamas Balakong, 43200, Seri Kembangan, Selangor, Malaysia
| | - Wei-Kang Lee
- Codon Genomics Sdn Bhd, No. 26, Jalan Dutamas 7, Taman Dutamas Balakong, 43200, Seri Kembangan, Selangor, Malaysia
| | - Chee-Choong Hoh
- Codon Genomics Sdn Bhd, No. 26, Jalan Dutamas 7, Taman Dutamas Balakong, 43200, Seri Kembangan, Selangor, Malaysia
| | - Syed Fairus
- Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Ravigadevi Sambanthamurthi
- Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
- Academy of Sciences Malaysia, Level 20, West Wing, MATRADE Tower, Jalan Sultan Haji Ahmad Shah, Off Jalan Tuanku Abdul Halim, 50480, Kuala Lumpur, Malaysia
| | - K C Hayes
- Brandeis University, 415 South Street, Waltham, MA, 02454, USA
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Leahy C, Osborne N, Shirota L, Rote P, Lee YK, Song BJ, Yin L, Zhang Y, Garcia V, Hardwick JP. The fatty acid omega hydroxylase genes (CYP4 family) in the progression of metabolic dysfunction-associated steatotic liver disease (MASLD): An RNA sequence database analysis and review. Biochem Pharmacol 2024; 228:116241. [PMID: 38697309 PMCID: PMC11774579 DOI: 10.1016/j.bcp.2024.116241] [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: 02/14/2024] [Revised: 04/21/2024] [Accepted: 04/25/2024] [Indexed: 05/04/2024]
Abstract
Fatty acid omega hydroxylase P450s consist of enzymes that hydroxylate various chain-length saturated and unsaturated fatty acids (FAs) and bioactive eicosanoid lipids. The human cytochrome P450 gene 4 family (CYP4) consists of 12 members that are associated with several human diseases. However, their role in the progression of metabolic dysfunction-associated fatty liver disease (MASLD) remains largely unknown. It has long been thought that the induction of CYP4 family P450 during fasting and starvation prevents FA-related lipotoxicity through FA metabolism to dicarboxylic acids that are chain-shortened in peroxisomes and then transported to the mitochondria for complete oxidation. Several studies have revealed that peroxisome succinate transported to the mitochondria is used for gluconeogenesis during fasting and starvation, and recent evidence suggests that peroxisome acetate can be utilized for lipogenesis and lipid droplet formation as well as epigenetic modification of gene transcription. In addition, omega hydroxylation of the bioactive eicosanoid arachidonic acid to 20-Hydroxyeicosatetraenoic acid (20-HETE) is essential for activating the GPR75 receptor, leading to vasoconstriction and cell proliferation. Several mouse models of diet-induced MASLD have revealed the induction of selective CYP4A members and the suppression of CYP4F during steatosis and steatohepatitis, suggesting a critical metabolic role in the progression of fatty liver disease. Thus, to further investigate the functional roles of CYP4 genes, we analyzed the differential gene expression of 12 members of CYP4 gene family in datasets from the Gene Expression Omnibus (GEO) from patients with steatosis, steatohepatitis, fibrosis, cirrhosis, and hepatocellular carcinoma. We also observed the differential expression of various CYP4 genes in the progression of MASLD, indicating that different CYP4 members may have unique functional roles in the metabolism of specific FAs and eicosanoids at various stages of fatty liver disease. These results suggest that targeting selective members of the CYP4A family is a viable therapeutic approach for treating and managing MASLD.
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Affiliation(s)
- Charles Leahy
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA
| | - Nicholas Osborne
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA
| | - Leticia Shirota
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA
| | - Paula Rote
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA
| | - Yoon-Kwang Lee
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA
| | - Byoung-Joon Song
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Liya Yin
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA
| | - Yanqiao Zhang
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA
| | - Victor Garcia
- Department of Pharmacology, New York Medical College, 15 Dana Road Science Building, Rm. 530, Valhalla, NY 10595, USA
| | - James P Hardwick
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA.
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Duan X, Zhang Y, Xu T. CYP4A22 loss-of-function causes a new type of vitamin D-dependent rickets (VDDR1C). J Bone Miner Res 2024; 39:967-979. [PMID: 38847469 DOI: 10.1093/jbmr/zjae084] [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: 10/16/2023] [Revised: 05/08/2024] [Accepted: 06/06/2024] [Indexed: 08/07/2024]
Abstract
Vitamin D-dependent rickets (VDDR) is a group of genetic disorders characterized by early-onset rickets due to deficiency of active vitamin D or a failure to respond to activated vitamin D. VDDR is divided into several subtypes according to the corresponding causative genes. Here we described a new type of autosomal dominant VDDR in a Chinese pedigree. The proband and his mother had severe bone malformations, dentin abnormalities, and lower serum 25 hydroxyvitamin D3 (25[OH]D3) and phosphate levels. The proband slightly responded to a high dose of vitamin D3 instead of a daily low dose of vitamin D3. Whole-exome sequencing, bioinformatic analysis, PCR, and Sanger sequencing identified a nonsense mutation in CYP4A22 (c.900delG). The overexpressed wild-type CYP4A22 mainly localized in endoplasmic reticulum and Golgi apparatus, and synthesized 25(OH)D3 in HepG2 cells. The overexpressed CYP4A22 mutant increased the expression of CYP2R1 and produced little 25(OH)D3 with vitamin D3 supplementation, which was reduced by CYP2R1 siRNA treatment. We concluded that CYP4A22 functions as a new kind of 25-hydroxylases for vitamin D3. Loss-of-function mutations in CYP4A22 lead to a new type of VDDR type 1 (VDDR1C). CYP2R1 and CYP4A22 may have some genetic compensation responding to nonsense-mediated mRNA decay effect of each other.
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Affiliation(s)
- Xiaohong Duan
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Oral Biology, Clinic of Oral Rare Diseases and Genetic Diseases, School of Stomatology, The Fourth Military Medical University, 145 West Changle Road, Xi'an 710032, China
| | - Yanli Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Oral Biology, Clinic of Oral Rare Diseases and Genetic Diseases, School of Stomatology, The Fourth Military Medical University, 145 West Changle Road, Xi'an 710032, China
| | - Taoyun Xu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Oral Biology, Clinic of Oral Rare Diseases and Genetic Diseases, School of Stomatology, The Fourth Military Medical University, 145 West Changle Road, Xi'an 710032, China
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Hossam Abdelmonem B, Abdelaal NM, Anwer EKE, Rashwan AA, Hussein MA, Ahmed YF, Khashana R, Hanna MM, Abdelnaser A. Decoding the Role of CYP450 Enzymes in Metabolism and Disease: A Comprehensive Review. Biomedicines 2024; 12:1467. [PMID: 39062040 PMCID: PMC11275228 DOI: 10.3390/biomedicines12071467] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
Cytochrome P450 (CYP450) is a group of enzymes that play an essential role in Phase I metabolism, with 57 functional genes classified into 18 families in the human genome, of which the CYP1, CYP2, and CYP3 families are prominent. Beyond drug metabolism, CYP enzymes metabolize endogenous compounds such as lipids, proteins, and hormones to maintain physiological homeostasis. Thus, dysregulation of CYP450 enzymes can lead to different endocrine disorders. Moreover, CYP450 enzymes significantly contribute to fatty acid metabolism, cholesterol synthesis, and bile acid biosynthesis, impacting cellular physiology and disease pathogenesis. Their diverse functions emphasize their therapeutic potential in managing hypercholesterolemia and neurodegenerative diseases. Additionally, CYP450 enzymes are implicated in the onset and development of illnesses such as cancer, influencing chemotherapy outcomes. Assessment of CYP450 enzyme expression and activity aids in evaluating liver health state and differentiating between liver diseases, guiding therapeutic decisions, and optimizing drug efficacy. Understanding the roles of CYP450 enzymes and the clinical effect of their genetic polymorphisms is crucial for developing personalized therapeutic strategies and enhancing drug responses in diverse patient populations.
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Affiliation(s)
- Basma Hossam Abdelmonem
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences & Arts (MSA), Giza 12451, Egypt
| | - Noha M. Abdelaal
- Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (N.M.A.); (E.K.E.A.); (A.A.R.)
| | - Eman K. E. Anwer
- Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (N.M.A.); (E.K.E.A.); (A.A.R.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information, Cairo 4411601, Egypt
| | - Alaa A. Rashwan
- Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (N.M.A.); (E.K.E.A.); (A.A.R.)
| | - Mohamed Ali Hussein
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
| | - Yasmin F. Ahmed
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
| | - Rana Khashana
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
| | - Mireille M. Hanna
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
| | - Anwar Abdelnaser
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
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Meng YW, Liu JY. Pathological and pharmacological functions of the metabolites of polyunsaturated fatty acids mediated by cyclooxygenases, lipoxygenases, and cytochrome P450s in cancers. Pharmacol Ther 2024; 256:108612. [PMID: 38369063 DOI: 10.1016/j.pharmthera.2024.108612] [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: 10/30/2023] [Revised: 01/19/2024] [Accepted: 02/05/2024] [Indexed: 02/20/2024]
Abstract
Oxylipins have garnered increasing attention because they were consistently shown to play pathological and/or pharmacological roles in the development of multiple cancers. Oxylipins are the metabolites of polyunsaturated fatty acids via both enzymatic and nonenzymatic pathways. The enzymes mediating the metabolism of PUFAs include but not limited to lipoxygenases (LOXs), cyclooxygenases (COXs), and cytochrome P450s (CYPs) pathways, as well as the down-stream enzymes. Here, we systematically summarized the pleiotropic effects of oxylipins in different cancers through pathological and pharmacological aspects, with specific reference to the enzyme-mediated oxylipins. We discussed the specific roles of oxylipins on cancer onset, growth, invasion, and metastasis, as well as the expression changes in the associated metabolic enzymes and the associated underlying mechanisms. In addition, we also discussed the clinical application and potential of oxylipins and related metabolic enzymes as the targets for cancer prevention and treatment. We found the specific function of most oxylipins in cancers, especially the underlying mechanisms and clinic applications, deserves and needs further investigation. We believe that research on oxylipins will provide not only more therapeutic targets for various cancers but also dietary guidance for both cancer patients and healthy humans.
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Affiliation(s)
- Yi-Wen Meng
- CNTTI of the Institute of Life Sciences & Department of Anesthesia of the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China; Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Chongqing 400016, China
| | - Jun-Yan Liu
- CNTTI of the Institute of Life Sciences & Department of Anesthesia of the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China; Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Chongqing 400016, China; College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
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Elfakharany HK, Ghoraba HM, Gaweesh KA, Eldeen AAS, Eid AM. Immunohistochemical expression of cytochrome P4A11 (CYP4A11), carbonic anhydrase 9 (CAIX) and Ki67 in renal cell carcinoma; diagnostic relevance and relations to clinicopathological parameters. Pathol Res Pract 2024; 253:155070. [PMID: 38183818 DOI: 10.1016/j.prp.2023.155070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND Cytochrome P4A11 (CYP4A11) is a member of cytochrome p450 family, which is involved in arachidonic acid metabolism that participates in promoting malignant cell proliferation, progression, and angiogenetic capacity. Carbonic Anhydrase 9 (CAIX) is a transmembrane protein that plays an integral part in regulating hypoxia which affects cancer cell metabolism, proliferation and promotes metastasis. The aim of this study was to evaluate the immunohistochemical expression of CYP4A11, CAIX and ki67 in RCC subtypes in relation to clinicopathological parameters and to evaluate the diagnostic significance of CYP4A11 and CAIX in differentiating renal cell carcinoma (RCC) subtypes. MATERIALS AND METHODS one hundred primary RCC cases, collected from Pathology Department, Faculty of Medicine, Tanta University and from private laboratories, were evaluated for immunohistochemical expression of CYP4A11, CAIX and ki67. RESULTS CYP4A11 was expressed in 59% of RCC; with 91.7% sensitivity and 90% specificity in differentiating clear cell and non-clear cell subtypes. CAIX was expressed in 50% of RCC; with 95% sensitivity, 80% specificity. High expression of CYP4A11 was statistically positively associated with higher tumor grade, high expression of CAIX was statistically positively associated with lower tumor grade and absence of necrosis and high ki67 labeling index was significantly associated with clear cell subtype, larger tumor sizes, higher tumor grade, advanced tumor stage, fat invasion and vascular invasion. CONCLUSIONS CYP4A11 and CAIX can be used as diagnostic markers to differentiate clear cell RCC from other subtypes. CYP4A11 is more diagnostically accurate and specific than CAIX. High expression of CYP4A11, low CAIX expression and high ki67 labeling index were related to features of aggressive tumor behavior.
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Sierk M, Ratnayake S, Wagle MM, Chen B, Park B, Wang J, Youkharibache P, Meerzaman D. 3DVizSNP: a tool for rapidly visualizing missense mutations identified in high throughput experiments in iCn3D. BMC Bioinformatics 2023; 24:244. [PMID: 37296383 DOI: 10.1186/s12859-023-05370-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND High throughput experiments in cancer and other areas of genomic research identify large numbers of sequence variants that need to be evaluated for phenotypic impact. While many tools exist to score the likely impact of single nucleotide polymorphisms (SNPs) based on sequence alone, the three-dimensional structural environment is essential for understanding the biological impact of a nonsynonymous mutation. RESULTS We present a program, 3DVizSNP, that enables the rapid visualization of nonsynonymous missense mutations extracted from a variant caller format file using the web-based iCn3D visualization platform. The program, written in Python, leverages REST APIs and can be run locally without installing any other software or databases, or from a webserver hosted by the National Cancer Institute. It automatically selects the appropriate experimental structure from the Protein Data Bank, if available, or the predicted structure from the AlphaFold database, enabling users to rapidly screen SNPs based on their local structural environment. 3DVizSNP leverages iCn3D annotations and its structural analysis functions to assess changes in structural contacts associated with mutations. CONCLUSIONS This tool enables researchers to efficiently make use of 3D structural information to prioritize mutations for further computational and experimental impact assessment. The program is available as a webserver at https://analysistools.cancer.gov/3dvizsnp or as a standalone python program at https://github.com/CBIIT-CGBB/3DVizSNP .
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Affiliation(s)
- Michael Sierk
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, 20852, USA.
| | - Shashikala Ratnayake
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, 20852, USA
| | - Manoj M Wagle
- Faculty of Pharmacy, University of Grenoble Alpes, Grenoble, France
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
- School of Mathematics and Statistics, Faculty of Science, and Computational Systems Biology Group, Children's Medical Research Institute, University of Sydney, Camperdown, NSW, Australia
| | - Ben Chen
- Digital Services and Solutions Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, 20852, USA
| | - Brian Park
- Digital Services and Solutions Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, 20852, USA
| | - Jiyao Wang
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
| | - Philippe Youkharibache
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Daoud Meerzaman
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, 20852, USA
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Gao X, Xu M, Wang H, Xia Z, Sun H, Liu M, Zhao S, Yang F, Niu Z, Gao H, Zhu H, Lu J, Zhou X. Development and validation of a mitochondrial energy metabolism-related risk model in hepatocellular carcinoma. Gene 2023; 855:147133. [PMID: 36565797 DOI: 10.1016/j.gene.2022.147133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/01/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most prevalent cancers and ranks third inmortality. Mitochondria are the energy manufacturers of cells. Disruption of mitochondrial energy metabolism pathways is strongly correlated with the onset and progression of HCC. Aberrant genes in mitochondrial energy metabolism pathways may represent a unique diagnostic and therapeutic targets that act as indicators for HCC. METHODS Gene expression data from 374 HCC patients and 50 controls were acquired from TCGA database. A total of 188 mitochondrial energy metabolism-related genes (MMRGs) were obtained from KEGG PATHWAY database. A total of 368 patients with survival data were randomly split into training and validation groups in a 7: 3 ratio. Prognosis-related MMRGs were selected by univariate Cox and LASSO analyses. Kaplan-Meier and ROC curves were employed to analyze the model precision, whereas the validation set was used for model verification. Furthermore, clinical examinations, immune infiltration analysis, GSVA, and immunotherapy analysis were conducted in the high- and low-risk groups. Finally, the risk model was combined with the clinical variables of HCC patients to perform univariate and multivariate Cox regression analyses to obtain independent risk indicators and draw a nomogram. Therefore, we evaluated the accuracy of the predictions using calibration curves. RESULTS A total of 6032 differentially expressed genes (DEGs) were detected in the HCC and control samples. After overlapping DEGs with 188 MMRGs, 42 mitochondrial energy metabolism-related DEGs (DEMMRGs) were identified. A 17 specific genes-based risk score model of HCC was created, which revealed effectiveness in each TCGA training and validation dataset. Moreover, patients categorized by risk scores exhibited distinct immune infiltration status, immunotherapy responsiveness, and functional properties. Finally, univariate and multivariate Cox regression analyses revealed that risk score and stage T were independent predictive variables. Based on the T stage and risk score, a nomogram for estimating the survival of HCC patients was created. The calibration curves demonstrated that the prediction model had a high level of accuracy. CONCLUSIONS Our study constructed a mitochondrial energy metabolism-related risk model, that may be utilized to anticipate HCC prognosis and represent the immunological microenvironment of HCC.
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Affiliation(s)
- Xin Gao
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Shandong University, 250021 Jinan, China
| | - Mingyue Xu
- Department of Endocrinology, Qilu Hospital of Shandong University, 250012 Jinan, China
| | - Heng Wang
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Shandong University, 250021 Jinan, China
| | - Zhaozhi Xia
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, China
| | - Hongrui Sun
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, China
| | - Meng Liu
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, China
| | - Shuchao Zhao
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, China
| | - Faji Yang
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, China
| | - Zheyu Niu
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, China
| | - Hengjun Gao
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Shandong University, 250021 Jinan, China; Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, China
| | - Huaqiang Zhu
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Shandong University, 250021 Jinan, China; Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, China
| | - Jun Lu
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Shandong University, 250021 Jinan, China; Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, China
| | - Xu Zhou
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Shandong University, 250021 Jinan, China; Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, China.
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10
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Chrabańska M, Szweda-Gandor N, Drozdzowska B. Two Single Nucleotide Polymorphisms in the Von Hippel-Lindau Tumor Suppressor Gene in Patients with Clear Cell Renal Cell Carcinoma. Int J Mol Sci 2023; 24:ijms24043778. [PMID: 36835190 PMCID: PMC9959571 DOI: 10.3390/ijms24043778] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
The most common subtype of renal cell carcinoma (RCC) is clear cell type (ccRCC), which accounts for approximately 75% of cases. von Hippel-Lindau (VHL) gene has been shown to be affected in more than half of ccRCC cases. Two single nucleotide polymorphisms (SNPs) located in VHL gene, rs779805 and rs1642742, are reported to be involved in the occurrence of ccRCC. The aim of this study was to assess their associations with clinicopathologic and immunohistochemical parameters, as well as risk and survival of ccRCC. The study population consisted of 129 patients. No significant differences in genotype or allele frequencies of VHL gene polymorphisms were observed between ccRCC cases and control population, and we have found that our results do not indicate a significant relationship of these SNPs with respect to ccRCC susceptibility. Additionally, we did not observe a significant association of these two SNPs with ccRCC survival. However, our results conclude that rs1642742 and rs779805 in the VHL gene are associated with increased tumor size, which is the most important prognostic indicator of renal cancer. Moreover, our analysis showed that patients with genotype AA of rs1642742 have a trend towards higher likelihood of developing ccRCC within their lifetime, while allele G of rs779805 can have a preventive effect against the development of renal cancer in stage 1. Therefore, these SNPs in VHL may be useful as genetic tumor markers for the molecular diagnostics for ccRCC patients.
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Affiliation(s)
- Magdalena Chrabańska
- Department and Chair of Pathomorphology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
- Correspondence: ; Tel.: +48-663156695
| | - Nikola Szweda-Gandor
- Department and Clinic of Internal Medicine, Diabetology and Nephrology, Medical University of Silesia, 41-800 Zabrze, Poland
| | - Bogna Drozdzowska
- Department and Chair of Pathomorphology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
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11
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Chrabańska M, Rynkiewicz M, Kiczmer P, Drozdzowska B. Does the Immunohistochemical Expression of CD44, MMP-2, and MMP-9 in Association with the Histopathological Subtype of Renal Cell Carcinoma Affect the Survival of Patients with Renal Cancer? Cancers (Basel) 2023; 15:cancers15041202. [PMID: 36831550 PMCID: PMC9954011 DOI: 10.3390/cancers15041202] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 02/17/2023] Open
Abstract
CD44, MMP-2, and MMP-9 are new potential molecular prognostic markers in renal cell carcinoma (RCC). The aim of the study was to analyze whether the expression of CD44, MMP-2, and MMP-9 in association with the histopathological subtype of RCC affects the survival of patients with renal cancer. The study population included 243 clear cell RCC (ccRCC) and 59 non-ccRCC cases. A total of 302 tumors were examined for CD44, MMP2, and MMP9 expression by immunohistochemistry. The expression levels of the proteins were scored by semi-quantitative methods, and the correlation with overall patient survival was verified. We found no significant differences in CD44 expression levels between cc-RCC and non-ccRCC cases; however, significant differences existed in the degree of MMP-2 and MMP-9 expression between cc-RCC and non-ccRCC cases. There was significantly higher MMP expression in non-ccRCC than in ccRCC cases. Univariate Cox regression analysis showed that increased CD44 expression and histopathological subtype of ccRCC were predictors of shorter overall survival. Moreover, MMP-2 overexpression slightly reduced the risk of patient death, while MMP-9 expression did not show an association with patients' survival. However, on multivariate analysis, only the histopathological subtypes of ccRCC and CD44 expression were independent risk factors for patient death.
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12
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Prognostic potential and mechanism of
SORT1
and its co‐expressed genes in hepatocellular carcinoma based on integrative analysis of multiple database. PRECISION MEDICAL SCIENCES 2022. [DOI: 10.1002/prm2.12084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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13
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Chrabańska M, Rynkiewicz M, Kiczmer P, Drozdzowska B. Immunohistochemical Expression of CD44, MMP-2, MMP-9, and Ki-67 as the Prognostic Markers in Non-Clear Cell Renal Cell Carcinomas-A Prospective Cohort Study. J Clin Med 2022; 11:jcm11175196. [PMID: 36079127 PMCID: PMC9457518 DOI: 10.3390/jcm11175196] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
CD44 is the most frequently reported marker of the cancer stem cells in renal cell carcinoma (RCC). Matrix metalloproteinases MMP-2 and MMP-9 are key regulators of tumor invasion and metastasis. The aim of this study was to investigate the clinicopathologic and prognostic values of the immunohistochemical expression of CD44, MMP2, MMP9, and Ki-67 in papillary and chromophobe RCCs. In the case of papillary RCC, MMP-2 expression was positively correlated with patient age (p < 0.05), while CD44 expression was positively correlated with tumor stage (τ = 0.26, p < 0.05). Moreover, CD44 expression positively correlated with MMP-9 (τ = 0.39, p < 0.05). In the case of chromophobe RCC, only Ki-67 expression was negatively correlated with tumor stage (τ = −0.44, p < 0.05). During follow-up, a death was documented in 6 patients with papillary RCC. In these patients, CD44 expression was not a significant factor affecting the overall survival of patients (p > 0.05), whereas there was a positive correlation between increased MMP-9 expression and shorter overall survival (p < 0.05). Taken together, carcinogenesis in papillary RCC is probably dependent on both cancer stem cells and metalloproteinases activity. Expression of CD44 and MMP-9 can significantly improve the prediction of papillary RCC prognosis in the future.
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14
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Kim S, Yeo MK, Kim JS, Kim JY, Kim KH. Elevated CXCL12 in the plasma membrane of locally advanced rectal cancer after neoadjuvant chemoradiotherapy: a potential prognostic marker. J Cancer 2022; 13:162-173. [PMID: 34976180 PMCID: PMC8692683 DOI: 10.7150/jca.64082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 11/10/2021] [Indexed: 02/07/2023] Open
Abstract
Background: Neoadjuvant chemoradiotherapy (nCRT) in locally advanced rectal cancer (LARC) has been shown to improve sphincter preservation and local pelvic control, but the efficacy of nCRT plateaus due to metastasis. CXC chemokine ligand 12 (CXCL12) has a critical impact on cancer development and metastasis. Methods: By investigating public databases containing LARC patient data, CXCL12, CXCR4 and FAPα expression was analyzed via the Tumor Immune Estimation Resource (TIMER) and GSEA. Immunohistochemistry was applied to a total of 121 surgically resected specimens consisting of 61 LARCs after nCRT and 60 LARCs with no nCRT and 16 cases with endoscopic resection of high-grade colorectal adenoma. Results: By investigating public databases containing LARC patient data, CXCL12 expression is correlated with poor prognosis, immune cell infiltration, epithelial- mesenchymal transition, and angiogenesis in LARC. Furthermore, radiation selectively induced CXCL12, CXCR4 and FAPα expression in tumor tissues. Immunohistochemistry results showed that the levels of CXCL12, CXCR4, and FAPα in LARC cells after nCRT were higher than in LARC cells untreated with nCRT (p < 0.001 for each). Elevated levels of CXCL12 in the plasma membrane of LARC cells after nCRT demonstrated an association with the period of freedom from recurrence (FFR) in univariate and multivariate survival analyses (p = 0.005 and p = 0.031, respectively). Conclusions: The expression of CXCL12 may influence the survival and invasive properties of LARC cells during nCRT and promote cancer recurrence. We suggest that CXCL12 expression in the plasma membrane of radioresistant LARC cells may be a predictive factor of recurrence and a viable therapeutic strategy to control radioresistant LARC recurrence.
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Affiliation(s)
- Sup Kim
- Department of Radiation Oncology, Chungnam National University School of Medicine, 288 Munhwa Street, Daejeon 35015, Korea.,Department of Radiation Oncology, Chungnam National University Hospital, 282 Munwha-ro, Daejeon 35015, Korea
| | - Min-Kyung Yeo
- Department of Pathology, Chungnam National University School of Medicine, 266 Munhwa Street, Daejeon 35015, Korea.,Department of Pathology, Chungnam National University Hospital, 282 Munwha-ro, Daejeon 35015, Korea
| | - Jun-Sang Kim
- Department of Radiation Oncology, Chungnam National University School of Medicine, 288 Munhwa Street, Daejeon 35015, Korea.,Department of Radiation Oncology, Chungnam National University Hospital, 282 Munwha-ro, Daejeon 35015, Korea
| | - Ji-Yeon Kim
- Department of Surgery, Division of Colorectal Surgery, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Kyung-Hee Kim
- Department of Pathology, Chungnam National University School of Medicine, 266 Munhwa Street, Daejeon 35015, Korea.,Department of Pathology, Chungnam National University Sejong Hospital, 20 Bodeum 7-ro, Sejong-si 30099, Korea
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15
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Wang J, Wang C, Yang L, Li K. Identification of the critical genes and miRNAs in hepatocellular carcinoma by integrated bioinformatics analysis. Med Oncol 2022; 39:21. [PMID: 34982264 DOI: 10.1007/s12032-021-01622-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is a global health problem with complex etiology and pathogenesis. Microarray data are increasingly being used as a novel and effective method for cancer pathogenesis analysis. An integrative analysis of genes and miRNA for HCC was conducted to unravel the potential prognosis of HCC. Two gene microarray datasets (GSE89377 and GSE101685) and two miRNA expression profiles (GSE112264 and GSE113740) were obtained from Gene Expression Omnibus database. A total of 177 differently expressed genes (DEGs) and 80 differently expressed miRNAs (DEMs) were screened out. Functional enrichment of DEGs was proceeded by Clue GO and these genes were significantly enriched in the chemical carcinogenesis pathway. A protein-protein interaction network was then established on the STRING platform, and ten hub genes (CDC20, TOP2A, ASPM, NCAPG, AURKA, CYP2E1, HMMR, PRC1, TYMS, and CYP4A11) were visualized via Cytoscape software. Then, a miRNA-target network was established to identify the hub dysregulated miRNA. A key miRNA (hsa-miR-124-3p) was filtered. Finally, the miRNA-target-transcription factor network was constructed for hsa-miR-124-3p. The network for hsa-miR-124-3p included two transcription factors (TFs) and five targets. These identified DEGs and DEMs, TFs, targets, and regulatory networks may help advance our understanding of the underlying pathogenesis of HCC.
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Affiliation(s)
- Jun Wang
- School of Biological Food and Environment, Hefei University, Hefei, 230601, China.
| | - Chuyan Wang
- School of Biological Food and Environment, Hefei University, Hefei, 230601, China
| | - Liuqing Yang
- School of Biological Food and Environment, Hefei University, Hefei, 230601, China
| | - Kexin Li
- School of Biological Food and Environment, Hefei University, Hefei, 230601, China
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16
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Song Z, Meng L, He Z, Huang J, Li F, Feng J, Jia Z, Huang Y, Liu W, Liu A, Fang H. LBP Protects Hepatocyte Mitochondrial Function Via the PPAR-CYP4A2 Signaling Pathway in a Rat Sepsis Model. Shock 2021; 56:1066-1079. [PMID: 33988537 DOI: 10.1097/shk.0000000000001808] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To explore the role of LPS binding protein (LBP) in metabolism and optimize sepsis treatment. DESIGN A sepsis model was established by injecting LPS into LBP-/- rats and WT rats and observing changes in the liver over time (0, 1, 6, and 24 h). SETTING Detecting liver inflammation and injury. Optimizing the treatment of sepsis. SUBJECTS WT rats and LBP-/- rats. INTERVENTIONS We established a sepsis model by injecting LPS intravenously. MEASUREMENTS AND MAIN RESULTS First, we induced sepsis in WT and LBP-/- rats with LPS. The rats were sacrificed, and serum and liver samples were collected at 1, 6, and 24 h after LPS injection. We found that the deletion of LBP reduced LPS-induced liver inflammation and injury at 1 and 6 h. Ballooning degeneration was clearly present in LBP-/- rat livers at 24 h after LPS injection. We found that mitochondrial damage and reactive oxygen species (ROS) levels were higher in LBP-/- rat livers than in WT rat livers at 24 h after LPS injection. According to the transcriptomic results, the peroxisome proliferator-activated receptor (PPAR) pathway may be the reason for lesions in LBP-/- rats. To further investigate the function of PPARα in sepsis, we inhibited mTOR with rapamycin and examined mitochondrial injury and ROS levels. The levels of mitochondrial damage and ROS were reduced after LBP-/- rats were pretreated with rapamycin in the context of LPS-induced sepsis. Inhibiting CYP4a2, one of the PPARα-target gene products, reduced the level of LPS-induced ROS in LBP-/- rats. CONCLUSION LBP protects hepatic mitochondria against LPS-induced damage via the LBP-PPARα-CYP4a2 signaling pathway.
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Affiliation(s)
- Zichen Song
- Department of Pathophysiology, Anhui Medical University, Hefei, China
| | - Leilei Meng
- Department of Pathophysiology, Anhui Medical University, Hefei, China
| | - Zhixiang He
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Jing Huang
- Department of Pathophysiology, Anhui Medical University, Hefei, China
| | - Fang Li
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Jingjing Feng
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Zhuoran Jia
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Yue Huang
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Wei Liu
- Department of Clinical Laboratory, Binhu Hospital, Anhui Medical University, Hefei, China
| | - Anding Liu
- Experimental Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haoshu Fang
- Department of Pathophysiology, Anhui Medical University, Hefei, China
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17
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Osborne N, Leahy C, Lee YK, Rote P, Song BJ, Hardwick JP. CYP4V2 fatty acid omega hydroxylase, a druggable target for the treatment of metabolic associated fatty liver disease (MAFLD). Biochem Pharmacol 2021; 195:114841. [PMID: 34798124 DOI: 10.1016/j.bcp.2021.114841] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/10/2021] [Accepted: 11/13/2021] [Indexed: 12/30/2022]
Abstract
Fatty acids are essential in maintaining cellular homeostasis by providing lipids for energy production, cell membrane integrity, protein modification, and the structural demands of proliferating cells. Fatty acids and their derivatives are critical bioactive signaling molecules that influence many cellular processes, including metabolism, cell survival, proliferation, migration, angiogenesis, and cell barrier function. The CYP4 Omega hydroxylase gene family hydroxylate various short, medium, long, and very-long-chain saturated, unsaturated and polyunsaturated fatty acids. Selective members of the CYP4 family metabolize vitamins and biochemicals with long alkyl side chains and bioactive prostaglandins, leukotrienes, and arachidonic acids. It is uncertain of the physiological role of different members of the CYP4 omega hydroxylase gene family in the metabolic control of physiological and pathological processes in the liver. CYP4V2 is a unique member of the CYP4 family. CYP4V2 inactivation in retinal pigment epithelial cells leads to cholesterol accumulation and Bietti's Crystalline Dystrophy (BCD) pathogenesis. This commentary provides information on the role CYP4V2 has in metabolic syndrome and nonalcoholic fatty liver disease progression. This is accomplished by identifying its role in BCD, its control of cholesterol synthesis and lipid droplet formation in C. elegans, and the putative function in cardiovascular disease and gastrointestinal/hepatic pathologies.
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Affiliation(s)
- Nicholas Osborne
- Northeast Ohio Medical Universities, Department of Integrative Medical Sciences, Rootstown, OH 44272, United States
| | - Charles Leahy
- Northeast Ohio Medical Universities, Department of Integrative Medical Sciences, Rootstown, OH 44272, United States
| | - Yoon-Kwang Lee
- Northeast Ohio Medical Universities, Department of Integrative Medical Sciences, Rootstown, OH 44272, United States
| | - Paula Rote
- Internal Medicine University of Minnesota Health Care System, Minneapolis, MN 55455, United States
| | - Byoung-Joon Song
- Section of Molecular Pharmacology and Toxicology, Laboratory of Membrane Biochemistry and Biophysics, 5625 Fishers Lane Room 3N-01, MSC 9410, Bethesda, MD 20892, United States
| | - James P Hardwick
- Northeast Ohio Medical Universities, Department of Integrative Medical Sciences, Rootstown, OH 44272, United States
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18
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Kim S, Joo M, Yeo MK, Cho MJ, Kim JS, Jo EK, Kim JM. Small heterodimer partner as a predictor of neoadjuvant radiochemotherapy response and survival in patients with rectal cancer: A preliminary study. Oncol Lett 2021; 22:708. [PMID: 34457063 PMCID: PMC8358587 DOI: 10.3892/ol.2021.12969] [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: 03/31/2020] [Accepted: 06/16/2021] [Indexed: 11/06/2022] Open
Abstract
Small heterodimer partner (SHP) plays an essential role in the regulation of innate immune and inflammatory responses. The aim of the present study was to identify whether SHP levels are associated with cancer immunology and treatment outcomes in rectal cancer. SHP expression was analyzed via gene set enrichment analysis and the OncoLnc database. In addition, immunohistochemistry and reverse transcription-quantitative PCR analyses were performed on the tissues of patients with locally advanced rectal cancer, and the associations of SHP expression with the clinicopathological and hematological features or treatment response to preoperative radiochemotherapy (pRCT) were analyzed retrospectively. Furthermore, the present study investigated whether SHP expression correlated with immune infiltration levels and immune checkpoint molecules in rectal cancer. The results revealed that low SHP mRNA expression was significantly associated with an inflammatory response and poor prognosis. The nuclear expression of SHP was associated with clinical N stage, neutrophil count, lymphocyte count, neutrophil-lymphocyte ratio and complete pathologic response following pRCT. The low nuclear expression of SHP was associated with poor overall and distant metastasis-free survival (DMFS). In multivariate analysis, the low nuclear expression of SHP was identified as a significant independent prognostic factor for DMFS and a marginally significant prognostic factor for overall survival in rectal cancer. Furthermore, patients with low SHP expression exhibited higher neutrophil and CD8+ T cell infiltration levels and higher PD-L1 expression in rectal adenocarcinoma. These results indicate that SHP may act as an anti-inflammatory mediator via the regulation of systemic and local immune responses in rectal cancer. Moreover, SHP might be useful a potential marker or therapeutic target in rectal cancer.
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Affiliation(s)
- Sup Kim
- Department of Radiation Oncology, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Mina Joo
- Department of Pathology and Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Min-Kyung Yeo
- Department of Pathology and Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Moon-June Cho
- Department of Radiation Oncology, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Jun-Sang Kim
- Department of Radiation Oncology, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Eun-Kyeong Jo
- Department of Microbiology and Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea.,Infection Control Convergence Research Center, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Jin-Man Kim
- Department of Pathology and Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea.,Infection Control Convergence Research Center, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
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19
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Huo J, Wu L, Zang Y. Development and Validation of a Metabolic-related Prognostic Model for Hepatocellular Carcinoma. J Clin Transl Hepatol 2021; 9:169-179. [PMID: 34007798 PMCID: PMC8111106 DOI: 10.14218/jcth.2020.00114] [Citation(s) in RCA: 4] [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] [Received: 11/14/2020] [Revised: 01/03/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND AND AIMS Growing evidence suggests that metabolic-related genes have a significant impact on the occurrence and development of hepatocellular carcinoma (HCC). However, the prognostic value of metabolic-related genes for HCC has not been fully revealed. METHODS mRNA sequencing and clinical data were obtained from The Cancer Genome Atlas and the GTEx Genotype-Tissue Expression comprehensive database. Differentially expressed metabolic-related genes in tumor tissues (n=374) and normal tissues (n=160) were identified by the Wilcoxon test. Time-dependent receiver operating characteristic curve analysis, univariate multivariate Cox regression analysis and Kaplan-Meier survival analysis were used to evaluate the predictive effectiveness and independence of the prognostic model. Two independent cohorts (International Cancer Genome Consortiums and GSE14520) were applied to verify the prognostic model. RESULTS Our study included a total of 793 patients with HCC. We constructed a risk score consisting of five metabolic-genes (BDH1, RRM2, CYP2C9, PLA2G7, and TXNRD1). For the overall survival rate, the low-risk group had a considerably higher rate than the high-risk group. Univariate and multivariate Cox regression analyses indicated that the risk score was an independent predictor for the prognosis of HCC. CONCLUSIONS We constructed and validated a novel prognostic model, which may provide support for the precise treatment of HCC.
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Affiliation(s)
| | - Liqun Wu
- Correspondence to: Liqun Wu, Liver Disease Center, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, Shandong 266003, China. Tel: +86-18661809789, Fax: +86-532-82913225, E-mail:
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20
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Zhang Q, Xiao Z, Sun S, Wang K, Qian J, Cui Z, Tao T, Zhou J. Integrated Proteomics and Bioinformatics to Identify Potential Prognostic Biomarkers in Hepatocellular Carcinoma. Cancer Manag Res 2021; 13:2307-2317. [PMID: 33732023 PMCID: PMC7959210 DOI: 10.2147/cmar.s291811] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/28/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Liver hepatocellular carcinoma (HCC) is the third most common cause of death by cancer and has a high mortality world-widely. Approximately 75-85% of primary liver cancers are caused by HCC. Uncovering novel genes with prognostic significance would shed light on improving the HCC patient's outcome. OBJECTIVE In this research, we aim to identify novel prognostic biomarkers in hepatocellular carcinoma. METHODS Integrated proteomics and bioinformatics analysis were performed to investigate the expression landscape of prognostic biomarkers in 24 paired HCC patients. RESULTS As a result, eight key genes related to prognosis, including ACADS, HSD17B13, PON3, AMDHD1, CYP2C8, CYP4A11, SLC27A5, CYP2E1, were identified by comparing the weighted gene co-expression network analysis (WGCNA), proteomic differentially expressed genes (DEGs), proteomic turquoise module, The Cancer Genome Atlas (TCGA) cohort DEGs of HCC. Furthermore, we trained and validated eight pivotal genes integrating these independent clinical variables into a nomogram with superior accuracy in predicting progression events, and their lower expression was associated with a higher stage/risk score. The Gene Set Enrichment Analysis (GSEA) further revealed that these key genes showed enrichment in the HCC regulatory pathway. CONCLUSION All in all, we found that these eight genes might be the novel potential prognostic biomarkers for HCC and also provide promising insights into the pathogenesis of HCC at the molecular level.
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Affiliation(s)
- Qifan Zhang
- Division of Hepatobiliopancreatic Surgery, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510515, People’s Republic of China
| | - Zhen Xiao
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People’s Republic of China
| | - Shibo Sun
- Division of Hepatobiliopancreatic Surgery, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510515, People’s Republic of China
| | - Kai Wang
- Division of Hepatobiliopancreatic Surgery, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510515, People’s Republic of China
| | - Jianping Qian
- Division of Hepatobiliopancreatic Surgery, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510515, People’s Republic of China
| | - Zhonglin Cui
- Division of Hepatobiliopancreatic Surgery, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510515, People’s Republic of China
| | - Tao Tao
- Department of Anesthesiology, Central People’s Hospital of Zhanjiang, Zhanjiang, Guangdong Province, 524045, People’s Republic of China
| | - Jie Zhou
- Division of Hepatobiliopancreatic Surgery, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510515, People’s Republic of China
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21
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Zhang R, Mo WJ, Huang LS, Chen JT, Wu WZ, He WY, Feng ZB. Identifying the Prognostic Risk Factors of Synaptojanin 2 and Its Underlying Perturbations Pathways in Hepatocellular Carcinoma. Bioengineered 2021; 12:855-874. [PMID: 33641617 PMCID: PMC8806346 DOI: 10.1080/21655979.2021.1890399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Synaptojanin 2 (SYNJ2) regulates cell proliferation and apoptosis via dephosphorylating plasma membrane phosphoinositides. Aim of this study is to first seek the full-scale expression levels and potential emerging roles of SYNJ2 in hepatocellular carcinoma (HCC). We systematically analyzed SYNJ2 mRNA expression and protein levels in HCC tissues based on large-scale data and in-house immunohistochemistry (IHC). The clinical significance and risk factors for SYNJ2-related HCC cases were identified. A nomogram of prognosis was created and its performance was validated by concordance index (C-index) and shown in calibration plots. Based on the identified differentially coexpressed genes (DCGs) of SYNJ2, enriched annotations and potential pathways were predicted, and the protein interacting networks were mapped. Upregulated SYNJ2 in 3,728 HCC and 3,203 non-HCC tissues were verified and in-house IHC showed higher protein levels of SYNJ2 in HCC tissues. Pathologic T stage was identified as a risk factor. Upregulated mRNA levels and mutated SYNJ2 might cause a poorer outcome. The C-index of the nomogram model constructed by SYNJ2 level, age, gender, TNM classification, grade, and stage was evaluated as 0.643 (95%CI = 0.619–0.668) with well-calibrated plots. A total of 2,533 DCGs were extracted and mainly functioned together with SYNJ2 in metabolic pathways. Possible transcriptional axis of CTCF/POLR2A-SYNJ2/INPP5B (transcription factor-target) in metabolic pathways was discovered based on ChIP-seq datasets. In summary, transcriptional regulatory axis CTCF/POLR2A-SYNJ2 might influence SYNJ2 expression levels. Increased SYNJ2 expression level could be utilized for predicting HCC prognosis and potentially accelerates the occurrence and development of HCC via metabolic perturbations pathways.
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Affiliation(s)
- Rui Zhang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Wei-Jia Mo
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Lan-Shan Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Ji-Tian Chen
- Department of Pathology, People's Hospital of Ling Shan, Ling Shan, Guangxi Zhuang Autonomous Region, China
| | - Wei-Zi Wu
- Department of Pathology, People's Hospital of Ling Shan, Ling Shan, Guangxi Zhuang Autonomous Region, China
| | - Wei-Ying He
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Zhen-Bo Feng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
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22
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Liu L, Wang B, Han Q, Zhen C, Li J, Qu X, Wang F, Kong X, Zheng L. Bioinformatic Analysis to Identify a Multi-mRNA Signature for the Prediction of Metastasis in Hepatocellular Carcinoma. DNA Cell Biol 2020; 39:2028-2039. [PMID: 33147069 DOI: 10.1089/dna.2020.5513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) with metastasis indicates worse prognosis for patients. However, the current methods are insufficient to accurately predict HCC metastasis at early stage. Based on the expression profiles of three Gene Expression Omnibus datasets, the differentially expressed genes associated with HCC metastasis were screened by online analytical tool GEO2R and weighted gene co-expression network analysis. Second, a risk score model including 27-mRNA was established by univariate Cox regression analyses, time-dependent ROC curves and least absolute shrinkage and selection operator Cox regression analysis. Then, we validated the model in cohort The Cancer Genome Atlas-liver hepatocellular carcinoma and analyzed the functions and key signaling pathways of the genes associated with the risk score model. According to the risk score model, patients were divided into two subgroups (high risk and low risk groups). The metastasis rate between two subgroups was significantly different in training cohort (p < 0.0001, hazard ratio [HR]: 10.3, confidence interval [95% CI]: 6.827-15.55) and external validation cohort (p = 0.0008, HR: 1.768, 95% CI: 1.267-2.467). Multivariable analysis showed that the risk score model was superior to and independent of other clinical factors (such as tumor stage, tumor size, and other parameters) in predicting early HCC metastasis. Moreover, the risk score model could predict the overall survival of patients with HCC. Finally, most of 27-mRNA were enriched in exosome and membrane bounded organelle, and these were involved in transportation and metabolic biological process. Protein-protein interaction network analysis showed most of these genes might be key genes affecting the progression of HCC. In addition, 3 genes of 27-mRNA were also differentially expressed in peripheral blood mononuclear cell. In conclusion, by using two combined methods and a broader of HCC datasets, our study provided reliable and superior predictive model for HCC metastases, which will facilitate individual medical management for these high metastatic risk HCC patients.
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Affiliation(s)
- Longgen Liu
- Institute of Hepatology, The Third People's Hospital of Changzhou, Jiangsu, P.R. China
| | - Bingrui Wang
- Department of Tumor Interventional Oncology, Renji South Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, P.R. China
| | - Qiucheng Han
- Department of Liver Diseases, Central Laboratory, ShuGuang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, P.R. China
| | - Chao Zhen
- Department of Tumor Interventional Oncology, Renji South Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, P.R. China
| | - Jichang Li
- Department of Tumor Interventional Oncology, Renji South Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, P.R. China
| | - Xiaoye Qu
- Department of Tumor Interventional Oncology, Renji South Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, P.R. China
| | - Fang Wang
- Department of Liver Diseases, Central Laboratory, ShuGuang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, P.R. China
| | - Xiaoni Kong
- Department of Liver Diseases, Central Laboratory, ShuGuang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, P.R. China
| | - Liming Zheng
- Institute of Hepatology, The Third People's Hospital of Changzhou, Jiangsu, P.R. China
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23
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Nekvindova J, Mrkvicova A, Zubanova V, Hyrslova Vaculova A, Anzenbacher P, Soucek P, Radova L, Slaby O, Kiss I, Vondracek J, Spicakova A, Bohovicova L, Fabian P, Kala Z, Palicka V. Hepatocellular carcinoma: Gene expression profiling and regulation of xenobiotic-metabolizing cytochromes P450. Biochem Pharmacol 2020; 177:113912. [PMID: 32173367 DOI: 10.1016/j.bcp.2020.113912] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 03/10/2020] [Indexed: 12/18/2022]
Abstract
Hepatocellular carcinoma (HCC) remains a highly prevalent and deadly disease, being among the top causes of cancer-related deaths worldwide. Despite the fact that the liver is the major site of biotransformation, studies on drug metabolizing enzymes in HCC are scarce. It is known that malignant transformation of hepatocytes leads to a significant alteration of their metabolic functions and overall deregulation of gene expression. Advanced stages of the disease are thus frequently associated with liver failure, and severe alteration of drug metabolism. However, the impact of dysregulation of metabolic enzymes on therapeutic efficacy and toxicity in HCC patients is largely unknown. Here we demonstrate a significant down-regulation in European Caucasian patients of cytochromes P450 (CYPs), the major xenobiotic-metabolizing enzymes, in HCC tumour samples as compared to their surrounding non-cancerous (reference) tissue. Moreover, we report for the first time the association of the unique CYP profiles with specific transcriptome changes, and interesting correlations with expression levels of nuclear receptors and with the histological grade of the tumours. Integrated analysis has suggested certain co-expression profiles of CYPs with lncRNAs that need to be further characterized. Patients with large tumours with down-regulated CYPs could be more vulnerable to drug toxicity; on the other hand, such tumours would eliminate drugs more slowly and should be more sensitive to pharmacotherapy (except in the case of pro-drugs where activation is necessary).
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Affiliation(s)
- Jana Nekvindova
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Czech Republic.
| | - Alena Mrkvicova
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Czech Republic; Department of Medical Biochemistry, Charles University, Faculty of Medicine in Hradec Kralove, Czech Republic.
| | - Veronika Zubanova
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Czech Republic.
| | - Alena Hyrslova Vaculova
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
| | - Pavel Anzenbacher
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic.
| | - Pavel Soucek
- Center for Toxicology and Health Safety, National Institute of Public Health, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.
| | - Lenka Radova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Department of Biology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic.
| | - Igor Kiss
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute and Masaryk University, Brno, Czech Republic.
| | - Jan Vondracek
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
| | - Alena Spicakova
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic.
| | - Lucia Bohovicova
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute and Masaryk University, Brno, Czech Republic.
| | - Pavel Fabian
- Department of Oncological and Experimental Pathology, Cancer Institute, Brno, Czech Republic.
| | - Zdenek Kala
- Department of Surgery, University Hospital Brno, Czech Republic.
| | - Vladimir Palicka
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Czech Republic.
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Singh U, Hur M, Dorman K, Wurtele ES. MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets. Nucleic Acids Res 2020; 48:e23. [PMID: 31956905 PMCID: PMC7039010 DOI: 10.1093/nar/gkz1209] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/05/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
The diverse and growing omics data in public domains provide researchers with tremendous opportunity to extract hidden, yet undiscovered, knowledge. However, the vast majority of archived data remain unused. Here, we present MetaOmGraph (MOG), a free, open-source, standalone software for exploratory analysis of massive datasets. Researchers, without coding, can interactively visualize and evaluate data in the context of its metadata, honing-in on groups of samples or genes based on attributes such as expression values, statistical associations, metadata terms and ontology annotations. Interaction with data is easy via interactive visualizations such as line charts, box plots, scatter plots, histograms and volcano plots. Statistical analyses include co-expression analysis, differential expression analysis and differential correlation analysis, with significance tests. Researchers can send data subsets to R for additional analyses. Multithreading and indexing enable efficient big data analysis. A researcher can create new MOG projects from any numerical data; or explore an existing MOG project. MOG projects, with history of explorations, can be saved and shared. We illustrate MOG by case studies of large curated datasets from human cancer RNA-Seq, where we identify novel putative biomarker genes in different tumors, and microarray and metabolomics data from Arabidopsis thaliana. MOG executable and code: http://metnetweb.gdcb.iastate.edu/ and https://github.com/urmi-21/MetaOmGraph/.
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Affiliation(s)
- Urminder Singh
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Manhoi Hur
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Karin Dorman
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
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25
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Kim S, Kim JM, Lee HJ, Lim JS, Seong IO, Kim KH. Alteration of CYP4A11 expression in renal cell carcinoma: diagnostic and prognostic implications. J Cancer 2020; 11:1478-1485. [PMID: 32047554 PMCID: PMC6995385 DOI: 10.7150/jca.36438] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 12/01/2019] [Indexed: 01/08/2023] Open
Abstract
Background: Cytochrome P-450 4A11 (CYP4A11) and peroxisome proliferator-activated receptor-α (PPARα) are expressed at high levels in renal proximal tubules, and upregulation of CYP4A11 protein levels is known to be influenced by PPAR agonists. The goal of this study was to evaluate the clinicopathological role of CYP4A11 expression in renal cell carcinoma (RCC). Methods: We performed immunohistochemical analysis of CYP4A11, CYP4A22 and PPARα and correlated the results with the clinicopathological features of RCC (n=139). Reverse transcription digital droplet polymerase chain reaction (RT-ddPCR) against CYP4A11 and CYP4A22 was also performed. Results: CYP4A11 mRNA expression levels were higher in non-neoplastic kidney tissues than in matched tumor tissues in 12 matched pairs of freshly frozen primary clear-cell RCC (ccRCC) and nontumor tissue (p=0.002). Immunohistochemical staining showed that CYP4A11 expression was significantly lower in ccRCC than in non-ccRCCs, including papillary, chromophobe, and unclassified RCCs (p<0.001). CYP4A11 expression was associated with PPARα expression, males and high nuclear histologic grades (p=0.001, p=0.018 and p<0.001). Univariate and multivariate analyses revealed that CYP4A11 expression was correlated with short overall survival (p=0.007 and p=0.010). Conclusion: These findings suggest that CYP4A11 expression is a potential poor prognostic factor of RCC. The considerable decrease in CYP4A11 expression is a predictive diagnostic factor of ccRCC, and CYP4A11 metabolism in ccRCC might be different from that in non-ccRCCs.
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Affiliation(s)
- Sup Kim
- Department of Radiation Oncology, Chungnam National University Hospital, Daejeon, South Korea
| | - Jin Man Kim
- Department of Pathology/Medical Science, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Hyo Jin Lee
- Division of Hematology/Oncology, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Jae Sung Lim
- Department of Urology, Chungnam National University School of Medicine, Daejeon, South Korea
| | - In-Ock Seong
- Department of Pathology/Medical Science, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Kyung-Hee Kim
- Department of Pathology/Medical Science, Chungnam National University School of Medicine, Daejeon, South Korea
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26
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Lee YM, Kim JM, Lee HJ, Seong IO, Kim KH. Immunohistochemical expression of CD44, matrix metalloproteinase2 and matrix metalloproteinase9 in renal cell carcinomas. Urol Oncol 2019; 37:742-748. [PMID: 31053527 DOI: 10.1016/j.urolonc.2019.04.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/16/2019] [Indexed: 12/24/2022]
Abstract
PURPOSE The aim of our study was to investigate the clinicopathologic values of the expression of CD44, matrix metalloproteinase (MMP)2, and MMP9 in renal cell carcinoma (RCC). PATIENTS AND METHODS A total of 107 clear cell RCCs (ccRCCs) and 32 nonclear cell RCCs (non-ccRCCs) were examined for CD44, MMP2, and MMP9 expression by immunohistochemistry. The membrane and cytoplasmic expression levels of the 3 proteins were scored by semiquantitative methods, and the correlations of the 3 proteins with clinicopathological parameters were verified. RESULTS The expression levels of CD44, MMP2, and MMP9 were positively correlated with nuclear grade (grade 1-2 vs. grade 3-4) (P = 0.003, P < 0.001 and P < 0.001, respectively) in the ccRCCs, while in the non-ccRCCs, only CD44 expression was correlated with higher nuclear grade (grade 1-3 vs. grade 4) (P = 0.001). Furthermore, CD44 expression in ccRCCs and non-ccRCCs was correlated with shorter overall survival in the univariate analyses (P < 0.001 and P = 0.015, respectively). In the multivariate analysis, which accounted for age, sex, nuclear grade, and pathologic stage, CD44 expression was an independent predictor of shorter overall survival only in ccRCCs. Correlations among the 3 proteins were all positive in ccRCCs, but in non-ccRCCs, only MMP2 and MMP9 were positively correlated. CONCLUSION CD44 expression may play an important role in the progression of both ccRCC and non-ccRCC. CD44 expression in ccRCC may be associated with elevated MMP2 and MMP9 expression levels, which is in contrast to non-ccRCC. The different correlations between CD44, MMP2, and MMP9 in ccRCC and non-ccRCC can be useful in understanding the mechanisms of carcinogenesis and stratifying patients for therapeutic purposes.
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Affiliation(s)
- Yong-Moon Lee
- Department of Pathology, Dankook University, School of Medicine, Cheonan, South Korea
| | - Jin Man Kim
- Department of Pathology/Medical science, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Hyo Jin Lee
- Division of Hematology/Oncology, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, South Korea
| | - In-Ock Seong
- Department of Pathology/Medical science, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Kyung-Hee Kim
- Department of Pathology/Medical science, Chungnam National University School of Medicine, Daejeon, South Korea.
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27
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APEX1 Expression as a Potential Diagnostic Biomarker of Clear Cell Renal Cell Carcinoma and Hepatobiliary Carcinomas. J Clin Med 2019; 8:jcm8081151. [PMID: 31375000 PMCID: PMC6723795 DOI: 10.3390/jcm8081151] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 12/28/2022] Open
Abstract
Apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APEX1) has been known to play key roles in DNA repair, the regulation of diverse transcriptional activity, and cellular responses to redox activity. This study aimed to examine serum APEX1 (s-APEX1) expression as a possible screening biomarker for clear cell renal cell carcinoma (ccRCC), hepatocellular carcinoma (HCC), and proximal and distal cholangiocarcinoma (CC). A total of 216 frozen serum samples were collected from 39 healthy control cases, 32 patients with ≥58 copies/mL of hepatitis B viral DNA (HBV DNA (+)), 40 ccRCC cases, 59 HCC cases, and 46 CC cases. The serum samples were examined for s-APEX1 concentration by enzyme-linked immunosorbent assay. The association of APEX1 expression with clinicopathological characteristics was also studied by immunohistochemical staining in 106 ccRCC, 131 HCC, and 32 intrahepatic CC cases. The median s-APEX1 concentrations of the HCC, CC, ccRCC, healthy control, and HBV DNA (+) groups were 0.294, 0.710, 0.474, 0.038, and 2.384 ng/mL, respectively (p < 0.001). Univariate and multivariate analyses revealed that increased cytoplasmic APEX1 expression led to a shorter disease-free survival period in HCC and CC cases. We suggest that the s-APEX1 level could be a potential diagnostic biomarker of ccRCC, HCC, and CC. Additionally, cytoplasmic APEX1 expression in cancer cells could be used to predict relapses in patients with HCC or CC.
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28
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Lin JT, Chan TC, Li CF, Huan SKH, Tian YF, Liang PI, Pan CT, Shiue YL. Downregulation of the cytochrome P450 4B1 protein confers a poor prognostic factor in patients with urothelial carcinomas of upper urinary tracts and urinary bladder. APMIS 2019; 127:170-180. [PMID: 30803053 DOI: 10.1111/apm.12939] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/11/2019] [Indexed: 12/15/2022]
Abstract
The objective of this study was to examine the expression level of cytochrome P450 4B1 (CYP4B1) protein and its clinical significance in specimens from patients with urothelial carcinomas (UC) including upper tract urothelial carcinoma (UTUC, n = 340) and urinary bladder urothelial carcinoma (UBUC, n = 295). Data mining on public domains identified five potential candidate transcripts which were downregulated in advanced UBUCs, indicating that it might implicate in UC progression. Immunohistochemistry was performed to analyze the CYP4B1 protein levels on 635 tissues from UC patients retrospectively. Immunoexpression of CYP4B1 was further estimated using the H-score method. Correlations between CYP4B1 H-score and important clinicopathological factors, as well as the significance of CYP4B1 expression level for disease-specific and metastasis-free survivals were evaluated. In UTUCs and UBUCs, 118 (34.7%) and 92 (31.2%) patients, respectively, were identified to be of CYP4B1 downregulation. The CYP4B1 expression level was found to be associated with several clinicopathological factors and patient survivals. Downregulation of CYP4B1 protein was correlated to advanced primary tumor (p < 0.001), nodal metastasis (p < 0.001), high histological grade (p = 0.001), vascular invasion (p < 0.001), perineural invasion (p = 0.017) and mitotic rate (p = 0.036) in UTUCs and/or UBUCs. Low CYP4B1 protein level independently predicted inferior disease-specific (p = 0.009; p < 0.001) and metastasis-free (p = 0.035; p < 0.001) survivals in UTUC and UBUC patients. Our findings showed that downregulation of CYP4B1 protein level is an independent unfavorable prognosticator. Loss of the CYP4B1 gene expression may play an important role in UC progression.
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Affiliation(s)
- Jen-Tai Lin
- Division of Urology, Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Ti-Chun Chan
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
- Department of Medical Research, Chi-Mei Medical Center, Tainan, Taiwan
| | - Chien-Feng Li
- Department of Pathology, Chi-Mei Medical Center, Tainan, Taiwan
- Department of Biotechnology, Southern Taiwan University of Science and Technology, Tainan, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
- Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Steven K H Huan
- Department of Medical Research, Chi-Mei Medical Center, Tainan, Taiwan
| | - Yu-Feng Tian
- Division of Colorectal Surgery, Department of Surgery, Chi-Mei Medical Center, Tainan, Taiwan
- Department of Health and Nutrition, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
| | - Peir-In Liang
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Cheng-Tang Pan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yow-Ling Shiue
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan
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