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Wang Q, Gao QC, Wang QC, Wu L, Yu Q, He PF. A compendium of mitochondrial molecular characteristics provides novel perspectives on the treatment of rheumatoid arthritis patients. J Transl Med 2023; 21:561. [PMID: 37608254 PMCID: PMC10463924 DOI: 10.1186/s12967-023-04426-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/06/2023] [Indexed: 08/24/2023] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease that exhibits a high degree of heterogeneity, marked by unpredictable disease flares and significant variations in the response to available treatments. The lack of optimal stratification for RA patients may be a contributing factor to the poor efficacy of current treatment options. The objective of this study is to elucidate the molecular characteristics of RA through the utilization of mitochondrial genes and subsequently construct and authenticate a diagnostic framework for RA. Mitochondrial proteins were obtained from the MitoCarta database, and the R package limma was employed to filter for differentially expressed mitochondrial genes (MDEGs). Metascape was utilized to perform enrichment analysis, followed by an unsupervised clustering algorithm using the ConsensuClusterPlus package to identify distinct subtypes based on MDEGs. The immune microenvironment, biological pathways, and drug response were further explored in these subtypes. Finally, a multi-biomarker-based diagnostic model was constructed using machine learning algorithms. Utilizing 88 MDEGs present in transcript profiles, it was possible to classify RA patients into three distinct subtypes, each characterized by unique molecular and cellular signatures. Subtype A exhibited a marked activation of inflammatory cells and pathways, while subtype C was characterized by the presence of specific innate lymphocytes. Inflammatory and immune cells in subtype B displayed a more modest level of activation (Wilcoxon test P < 0.05). Notably, subtype C demonstrated a stronger correlation with a superior response to biologics such as infliximab, anti-TNF, rituximab, and methotrexate/abatacept (P = 0.001) using the fisher test. Furthermore, the mitochondrial diagnosis SVM model demonstrated a high degree of discriminatory ability in distinguishing RA in both training (AUC = 100%) and validation sets (AUC = 80.1%). This study presents a pioneering analysis of mitochondrial modifications in RA, offering a novel framework for patient stratification and potentially enhancing therapeutic decision-making.
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Affiliation(s)
- Qi Wang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
| | - Qi-Chao Gao
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
| | - Qi-Chuan Wang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Li Wu
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Department of Anesthesiology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
| | - Qi Yu
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- School of Management, Shanxi Medical University, Taiyuan, China
| | - Pei-Feng He
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China.
- School of Management, Shanxi Medical University, Taiyuan, China.
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Sun Y, Bae YE, Zhu J, Zhang Z, Zhong H, Cheng C, Deng Y, Wu C, Wu L. A Splicing Transcriptome-Wide Association Study Identifies Candidate Altered Splicing for Prostate Cancer Risk. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:372-380. [PMID: 37486714 DOI: 10.1089/omi.2023.0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Prostate cancer (PCa) represents a huge public health burden among men. Many susceptibility genetic factors for PCa still remain unknown. In this study, we performed a large splicing transcriptome-wide association study (spTWAS) using three modeling strategies to develop alternative splicing genetic prediction models for identifying novel susceptibility loci and splicing introns for PCa risk by assessing 79,194 cases and 61,112 controls of European ancestry in the PRACTICAL, CRUK, CAPS, BPC3, and PEGASUS consortia. We identified 120 splicing introns of 97 genes showing an association with PCa risk at false discovery rate (FDR)-corrected threshold (FDR <0.05). Of them, 33 genes were enriched in PCa-related diseases and function categories. Fine-mapping analysis suggested that 21 splicing introns of 19 genes were likely causally associated with PCa risk. Thirty-five splicing introns of 34 novel genes were identified to be related to PCa susceptibility for the first time, and 11 of the genes were enriched in a cancer-related network. Our study identified novel loci and splicing introns associated with PCa risk, which can improve our understanding of the etiology of this common malignancy.
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Affiliation(s)
- Yanfa Sun
- College of Life Science, Longyan University, Longyan, P.R. China
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan, P.R. China
- Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan, P.R. China
| | - Ye Eun Bae
- Department of Statistics, Florida State University, Tallahassee, Florida, USA
| | - Jingjing Zhu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Zichen Zhang
- Department of Statistics, Florida State University, Tallahassee, Florida, USA
| | - Hua Zhong
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Chunmei Cheng
- College of Life Science, Longyan University, Longyan, P.R. China
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Chong Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
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3
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Shen Y, Wang X, Ni Z, Xu S, Qiu S, Zheng W, Zhang J. Identification of acetyl-CoA carboxylase alpha as a prognostic and targeted candidate for hepatocellular carcinoma. Clin Transl Oncol 2023:10.1007/s12094-023-03137-1. [PMID: 36976490 DOI: 10.1007/s12094-023-03137-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/26/2023] [Indexed: 03/29/2023]
Abstract
PURPOSE The de novo lipogenesis has been a longstanding observation in hepatocellular carcinoma (HCC). However, the prognostic value and carcinogenic roles of the enzyme Acetyl-CoA carboxylase alpha (ACACA) in HCC remains unknown. METHODS The proteins with remarkable prognostic significance were screened out from The Cancer Proteome Atlas Portal (TCPA) database. Furthermore, the expression characteristics and prognostic value of ACACA were evaluated in multiple databases and the local HCC cohort. The loss-of-function assays were performed to uncover the potential roles of ACACA in steering malignant behaviors of HCC cells. The underlying mechanisms were conjectured by bioinformatics and validated in HCC cell lines. RESULTS ACACA was identified as a crucial factor of HCC prognosis. Bioinformatics analyses showed that HCC patients with higher expression of ACACA protein or mRNA levels had poor prognosis. Knockdown of ACACA remarkably crippled the proliferation, colony formation, migration, invasion, epithelial-mesenchymal transition (EMT) process of HCC cells and induced the cell cycle arrest. Mechanistically, ACACA might facilitate the malignant phenotypes of HCC through aberrant activation of Wnt/β-catenin signaling pathway. In addition, ACACA expression was associated with the dilute infiltration of immune cells including plasmacytoid DC (pDC) and cytotoxic cells by utilization of relevant database analysis. CONCLUSION ACACA could be a potential biomarker and molecular target for HCC.
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Affiliation(s)
- Yiping Shen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Xin Wang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Zhiyu Ni
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Shiyu Xu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Shi Qiu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Wenjie Zheng
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China.
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China.
| | - Jie Zhang
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China.
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Zhang M, Liao X, Ji G, Fan X, Wu Q. High Expression of COA6 Is Related to Unfavorable Prognosis and Enhanced Oxidative Phosphorylation in Lung Adenocarcinoma. Int J Mol Sci 2023; 24:ijms24065705. [PMID: 36982777 PMCID: PMC10056783 DOI: 10.3390/ijms24065705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Abstract
Mitochondrial metabolism plays an important role in the occurrence and development of cancers. Cytochrome C oxidase assembly factor six (COA6) is essential in mitochondrial metabolism. However, the role of COA6 in lung adenocarcinoma (LUAD) remains unknown. Here we report that the expression of COA6 mRNA and protein were upregulated in LUAD tissues compared with lung normal tissues. We found that COA6 had high sensitivity and specificity to distinguish LUAD tissues from normal lung tissues shown by a receiver operating characteristic (ROC) curve. In addition, our univariate and multivariate Cox regression analysis indicated that COA6 was an independent unfavorable prognostic factor for LUAD patients. Furthermore, our survival analysis and nomogram showed that a high expression of COA6 mRNA was related to the short overall survival (OS) of LUAD patients. Notably, our weighted correlation network analysis (WGCNA) and functional enrichment analysis revealed that COA6 may participate in the development of LUAD by affecting mitochondrial oxidative phosphorylation (OXPHOS). Importantly, we demonstrated that depletion of COA6 could decrease the mitochondrial membrane potential (MMP), nicotinamide adenine dinucleotide (NAD) + hydrogen (H) (NADH), and adenosine triphosphate (ATP) production in LUAD cells (A549 and H1975), hence inhibiting the proliferation of these cells in vitro. Together, our study strongly suggests that COA6 is significantly associated with the prognosis and OXPHOS in LUAD. Hence, COA6 is highly likely a novel prognostic biomarker and therapeutic target of LUAD.
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Affiliation(s)
- Ming Zhang
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macao 999078, China
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Xiaohua Liao
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macao 999078, China
| | - Guanxu Ji
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macao 999078, China
| | - Xianming Fan
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Correspondence: (X.F.); (Q.W.); Tel.: +86-139-8276-9572 (X.F.); +853-8897-2708 (Q.W.)
| | - Qiang Wu
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macao 999078, China
- Correspondence: (X.F.); (Q.W.); Tel.: +86-139-8276-9572 (X.F.); +853-8897-2708 (Q.W.)
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Brane A, Arora I, Tollefsbol TO. Peripubertal Nutritional Prevention of Cancer-Associated Gene Expression and Phenotypes. Cancers (Basel) 2023; 15:674. [PMID: 36765634 PMCID: PMC9913820 DOI: 10.3390/cancers15030674] [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: 12/16/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023] Open
Abstract
Breast cancer (BC) is a nearly ubiquitous malignancy that effects the lives of millions worldwide. Recently, nutritional prevention of BC has received increased attention due to its efficacy and ease of application. Chief among chemopreventive compounds are plant-based substances known as dietary phytochemicals. Sulforaphane (SFN), an epigenetically active phytochemical found in cruciferous vegetables, has shown promise in BC prevention. In addition, observational studies suggest that the life stage of phytochemical consumption may influence its anticancer properties. These life stages, called critical periods (CPs), are associated with rapid development and increased susceptibility to cellular damage. Puberty, a CP in which female breast tissue undergoes proliferation and differentiation, is of particular interest for later-life BC development. However, little is known about the importance of nutritional chemoprevention to CPs. We sought to address this by utilizing two estrogen receptor-negative [ER(-)] transgenic mouse models fed SFN-containing broccoli sprout extract during the critical period of puberty. We found that this treatment resulted in a significant decrease in tumor incidence and weight, as well as an increase in tumor latency. Further, we found significant alterations in the long-term expression of cancer-associated genes, including p21, p53, and BRCA2. Additionally, our transcriptomic analyses identified expressional changes in many cancer-associated genes, and bisulfite sequencing revealed that the antiproliferation-associated gene Erich4 was both hypomethylated and overexpressed in our experimental group. Our study indicates that dietary interventions during the CP of puberty may be important for later-life ER(-) BC prevention and highlights potential important genetic and epigenetic targets for treatment and study of the more deadly variants of BC.
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Affiliation(s)
- Andrew Brane
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Itika Arora
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Trygve O. Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Integrative Center for Aging Research, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- University Wide Microbiome Center, University of Alabama Birmingham, Birmingham, AL 35294, USA
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Ma X, Sun L. Construction and Validation of Protein Expression-related Prognostic Models in Clear Cell Renal Cell Carcinoma. J Cancer 2023; 14:793-808. [PMID: 37056387 PMCID: PMC10088890 DOI: 10.7150/jca.81915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/19/2023] [Indexed: 04/15/2023] Open
Abstract
Objective: To construct a prognostic evaluation model for clear cell renal cell carcinoma (ccRCC) patients using bioinformatics method and to screen potential drugs for ccRCC. Methods: ccRCC RNA sequencing data, clinical data, and protein expression data were downloaded from the TCGA database. Univariate Cox and Lasso regression analyses were performed on the combined data to screen out the proteins related to the prognosis, and they were included in a multivariate Cox proportional hazard model. The patients were divided into high and low-risk groups for a survival difference analysis. The predictive power of the model was evaluated on the basis of overall survival, progression-free survival, independent prognostic, clinically relevant receiver operating characteristic (ROC) curve, C-index, principal component, and clinical data statistics analyses. GSEA enrichment and immune function correlation analyses were performed. The samples were divided into different subtypes based on the expression of the risk proteins, and survival analysis of the subtypes was performed. The risk-related protein and RNA sequencing data were analyzed to screen out sensitive drugs with significant differences between the high and low-risk groups. Results: A total of 469 ccRCC-related proteins were screened, of which 13 proteins with independent prognostic significance were screened by univariate Cox, Lasso, and multivariate Cox regression analyses to construct the prognostic model. The sensitivity and accuracy of the model in predicting the survival of patients with ccRCC were high (1 year: 0.811, 3 years: 0.783, 5 years: 0.777). The 13 proteins were closely related to immunity, and the model proteins were different between kidney and tumor tissues according to the HPA database. The samples were divided into three subtypes, and there were obvious clinical characteristics of the three subtypes in the grade and T, N and M stages. According to the IC50 values, CGP-60474, vinorelbine, doxorubicin, etoposide, FTI-277, JQ12, OSU-03012, pyrimethamine, and other drugs were more sensitive in the high-risk group. Conclusions: A prognostic model of protein expression in ccRCC was successfully constructed, which had good predictive ability for the prognosis of ccRCC patients. The ccRCC-related proteins in the model can be used as targets for studying the pathogenesis and targeted therapy.
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Affiliation(s)
| | - Libin Sun
- ✉ Corresponding author: Libin Sun, Department of Urology, Affiliated First Hospital of Shanxi Medical University, 85 South Jiefang Rd, Taiyuan, Shanxi Province, 030001, China. Tel: +86-15698579398; Email address:
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Acetyl-CoA carboxylase 1 depletion suppresses de novo fatty acid synthesis and mitochondrial β-oxidation in castration-resistant prostate cancer cells. J Biol Chem 2022; 299:102720. [PMID: 36410440 PMCID: PMC9771725 DOI: 10.1016/j.jbc.2022.102720] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 11/11/2022] [Accepted: 11/12/2022] [Indexed: 11/21/2022] Open
Abstract
Cancer cells, including those of prostate cancer (PCa), often hijack intrinsic cell signaling to reprogram their metabolism. Part of this reprogramming includes the activation of de novo synthesis of fatty acids that not only serve as building blocks for membrane synthesis but also as energy sources for cell proliferation. However, how de novo fatty acid synthesis contributes to PCa progression is still poorly understood. Herein, by mining public datasets, we discovered that the expression of acetyl-CoA carboxylase alpha (ACACA), which encodes acetyl-CoA carboxylase 1 (ACC1), was highly expressed in human PCa. In addition, patients with high ACACA expression had a short disease-free survival time. We also reported that depletion of ACACA reduced de novo fatty acid synthesis and PI3K/AKT signaling in the human castration-resistant PCa (CRPC) cell lines DU145 and PC3. Furthermore, depletion of ACACA downregulates mitochondrial beta-oxidation, resulting in mitochondrial dysfunction, a reduction in ATP production, an imbalanced NADP+/NADPhydrogen(H) ratio, increased reactive oxygen species, and therefore apoptosis. Reduced exogenous fatty acids by depleting lipid or lowering serum supplementation exacerbated both shRNA depletion and pharmacological inhibition of ACACA-induced apoptosis in vitro. Collectively, our results suggest that inhibition of ectopic ACACA, together with suppression of exogenous fatty acid uptake, can be a novel strategy for treating currently incurable CRPC.
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Óvilo C, Trakooljul N, Núñez Y, Hadlich F, Murani E, Ayuso M, García-Contreras C, Vázquez-Gómez M, Rey AI, Garcia F, García-Casco JM, López-Bote C, Isabel B, González-Bulnes A, Wimmers K, Muñoz M. SNP discovery and association study for growth, fatness and meat quality traits in Iberian crossbred pigs. Sci Rep 2022; 12:16361. [PMID: 36180572 PMCID: PMC9525691 DOI: 10.1038/s41598-022-20817-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/19/2022] [Indexed: 11/22/2022] Open
Abstract
Iberian pigs and its crosses are produced to obtain high-quality meat products. The objective of this work was to evaluate a wide panel of DNA markers, selected by biological and functional criteria, for association with traits related to muscle growth, fatness, meat quality and metabolism. We used 18 crossbred Iberian pigs with divergent postnatal growth patterns for whole genome sequencing and SNP discovery, with over 13 million variants being detected. We selected 1023 missense SNPs located on annotated genes and showing different allele frequencies between pigs with makerdly different growth patterns. We complemented this panel with 192 candidate SNPs obtained from literature mining and from muscle RNAseq data. The selected markers were genotyped in 480 Iberian × Duroc pigs from a commercial population, in which phenotypes were obtained, and an association study was performed for the 1005 successfully genotyped SNPs showing segregation. The results confirmed the effects of several known SNPs in candidate genes (such as LEPR, ACACA, FTO, LIPE or SCD on fatness, growth and fatty acid composition) and also disclosed interesting effects of new SNPs in less known genes such as LRIG3, DENND1B, SOWAHB, EPHX1 or NFE2L2 affecting body weight, average daily gain and adiposity at different ages, or KRT10, NLE1, KCNH2 or AHNAK affecting fatness and FA composition. The results provide a valuable basis for future implementation of marker-assisted selection strategies in swine and contribute to a better understanding of the genetic architecture of relevant traits.
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Affiliation(s)
- C Óvilo
- Departamento Mejora Genética Animal, INIA-CSIC, Madrid, Spain.
| | - N Trakooljul
- Research Institute for Farm Animal Biology, FBN, Dummerstorf, Germany
| | - Y Núñez
- Departamento Mejora Genética Animal, INIA-CSIC, Madrid, Spain
| | - F Hadlich
- Research Institute for Farm Animal Biology, FBN, Dummerstorf, Germany
| | - E Murani
- Research Institute for Farm Animal Biology, FBN, Dummerstorf, Germany
| | - M Ayuso
- CoPeD, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - C García-Contreras
- Department of Nutrition and Sustainable Animal Production, CSIC, Granada, Spain
| | | | - A I Rey
- Departamento de Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | - F Garcia
- Departamento Mejora Genética Animal, INIA-CSIC, Madrid, Spain
| | | | - C López-Bote
- Departamento de Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | - B Isabel
- Departamento de Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | - A González-Bulnes
- Facultad de Medicina Veterinaria, Universidad Cardenal Herrera-CEU, Valencia, Spain
| | - K Wimmers
- Research Institute for Farm Animal Biology, FBN, Dummerstorf, Germany
| | - M Muñoz
- Departamento Mejora Genética Animal, INIA-CSIC, Madrid, Spain
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Elkady G, Chen Y, Hu C, Chen J, Chen X, Guo A. MicroRNA Profile of MA-104 Cell Line Associated With the Pathogenesis of Bovine Rotavirus Strain Circulated in Chinese Calves. Front Microbiol 2022; 13:854348. [PMID: 35516441 PMCID: PMC9062783 DOI: 10.3389/fmicb.2022.854348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Bovine rotavirus (BRV) causes massive economic losses in the livestock industry worldwide. Elucidating the pathogenesis of BRV would help in the development of more effective measures to control BRV infection. The MA-104 cell line is sensitive to BRV and is thereby a convenient tool for determining BRV–host interactions. Thus far, the role of the microRNAs (miRNAs) of MA-104 cells during BRV infection is still ambiguous. We performed Illumina RNA sequencing analysis of the miRNA libraries of BRV-infected and mock-infected MA-104 cells at different time points: at 0 h post-infection (hpi) (just after 90 min of adsorption) and at 6, 12, 24, 36, and 48 hpi. The total clean reads obtained from BRV-infected and uninfected cells were 74,701,041 and 74,184,124, respectively. Based on these, 579 were categorized as known miRNAs and 144 as novel miRNAs. One hundred and sixty differentially expressed (DE) miRNAs in BRV-infected cells in comparison with uninfected MA-104 cells were successfully investigated, 95 of which were upregulated and 65 were downregulated. The target messenger RNAs (mRNAs) of the DE miRNAs were examined by bioinformatics analysis. Functional annotation of the target genes with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) suggested that these genes mainly contributed to biological pathways, endocytosis, apoptotic process, trans-Golgi membrane, and lysosome. Pathways such as the mammalian target of rapamycin (mTOR) (mml-miR-486-3p and mml-miR-197-3p), nuclear factor kappa B (NF-κB) (mml-miR-204-3p and novel_366), Rap1 (mml-miR-127-3p), cAMP (mml-miR-106b-3p), mitogen-activated protein kinase (MAPK) (mml-miR-342-5p), T-cell receptor signaling (mml-miR-369-5p), RIG-I-like receptor signaling (mml-miR-504-5p), AMP-activated protein kinase (AMPK) (mml-miR-365-1-5p), and phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt) signaling (mml-miR-299-3p) were enriched. Moreover, real-time quantitative PCR (qPCR) verified the expression profiles of 23 selected DE miRNAs, which were consistent with the results of deep sequencing, and the 28 corresponding target mRNAs were mainly of regulatory pathways of the cellular machinery and immune importance, according to the bioinformatics analysis. Our study is the first to report a novel approach that uncovers the impact of BRV infection on the miRNA expressions of MA-104 cells, and it offers clues for identifying potential candidates for antiviral or vaccine strategies.
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Affiliation(s)
- Gehad Elkady
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
- Benha University, Benha, Egypt
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Changmin Hu
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Jianguo Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Xi Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Aizhen Guo,
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10
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Fidelito G, Watt MJ, Taylor RA. Personalized Medicine for Prostate Cancer: Is Targeting Metabolism a Reality? Front Oncol 2022; 11:778761. [PMID: 35127483 PMCID: PMC8813754 DOI: 10.3389/fonc.2021.778761] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/21/2021] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer invokes major shifts in gene transcription and metabolic signaling to mediate alterations in nutrient acquisition and metabolic substrate selection when compared to normal tissues. Exploiting such metabolic reprogramming is proposed to enable the development of targeted therapies for prostate cancer, yet there are several challenges to overcome before this becomes a reality. Herein, we outline the role of several nutrients known to contribute to prostate tumorigenesis, including fatty acids, glucose, lactate and glutamine, and discuss the major factors contributing to variability in prostate cancer metabolism, including cellular heterogeneity, genetic drivers and mutations, as well as complexity in the tumor microenvironment. The review draws from original studies employing immortalized prostate cancer cells, as well as more complex experimental models, including animals and humans, that more accurately reflect the complexity of the in vivo tumor microenvironment. In synthesizing this information, we consider the feasibility and potential limitations of implementing metabolic therapies for prostate cancer management.
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Affiliation(s)
- Gio Fidelito
- Department of Anatomy & Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Matthew J. Watt
- Department of Anatomy & Physiology, The University of Melbourne, Melbourne, VIC, Australia
- *Correspondence: Renea A. Taylor, ; Matthew J. Watt,
| | - Renea A. Taylor
- Department of Physiology, Biomedicine Discovery Institute, Cancer Program, Monash University, Melbourne, VIC, Australia
- Prostate Cancer Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- *Correspondence: Renea A. Taylor, ; Matthew J. Watt,
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Chen CL, Lin CY, Kung HJ. Targeting Mitochondrial OXPHOS and Their Regulatory Signals in Prostate Cancers. Int J Mol Sci 2021; 22:13435. [PMID: 34948229 PMCID: PMC8708687 DOI: 10.3390/ijms222413435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Increasing evidence suggests that tumor development requires not only oncogene/tumor suppressor mutations to drive the growth, survival, and metastasis but also metabolic adaptations to meet the increasing energy demand for rapid cellular expansion and to cope with the often nutritional and oxygen-deprived microenvironment. One well-recognized strategy is to shift the metabolic flow from oxidative phosphorylation (OXPHOS) or respiration in mitochondria to glycolysis or fermentation in cytosol, known as Warburg effects. However, not all cancer cells follow this paradigm. In the development of prostate cancer, OXPHOS actually increases as compared to normal prostate tissue. This is because normal prostate epithelial cells divert citrate in mitochondria for the TCA cycle to the cytosol for secretion into seminal fluid. The sustained level of OXPHOS in primary tumors persists in progression to an advanced stage. As such, targeting OXPHOS and mitochondrial activities in general present therapeutic opportunities. In this review, we summarize the recent findings of the key regulators of the OXPHOS pathway in prostate cancer, ranging from transcriptional regulation, metabolic regulation to genetic regulation. Moreover, we provided a comprehensive update of the current status of OXPHOS inhibitors for prostate cancer therapy. A challenge of developing OXPHOS inhibitors is to selectively target cancer mitochondria and spare normal counterparts, which is also discussed.
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Affiliation(s)
- Chia-Lin Chen
- Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; (C.-L.C.); (C.-Y.L.)
| | - Ching-Yu Lin
- Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; (C.-L.C.); (C.-Y.L.)
| | - Hsing-Jien Kung
- Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; (C.-L.C.); (C.-Y.L.)
- Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 110, Taiwan
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County 350, Taiwan
- Comprehensive Cancer Center, Department of Biochemistry and Molecular Medicine, University of California at Davis, Sacramento, CA 95817, USA
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12
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Multi-Omic Approaches to Breast Cancer Metabolic Phenotyping: Applications in Diagnosis, Prognosis, and the Development of Novel Treatments. Cancers (Basel) 2021; 13:cancers13184544. [PMID: 34572770 PMCID: PMC8470181 DOI: 10.3390/cancers13184544] [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: 07/19/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022] Open
Abstract
Breast cancer (BC) is characterized by high disease heterogeneity and represents the most frequently diagnosed cancer among women worldwide. Complex and subtype-specific gene expression alterations participate in disease development and progression, with BC cells known to rewire their cellular metabolism to survive, proliferate, and invade. Hence, as an emerging cancer hallmark, metabolic reprogramming holds great promise for cancer diagnosis, prognosis, and treatment. Multi-omics approaches (the combined analysis of various types of omics data) offer opportunities to advance our understanding of the molecular changes underlying metabolic rewiring in complex diseases such as BC. Recent studies focusing on the combined analysis of genomics, epigenomics, transcriptomics, proteomics, and/or metabolomics in different BC subtypes have provided novel insights into the specificities of metabolic rewiring and the vulnerabilities that may guide therapeutic development and improve patient outcomes. This review summarizes the findings of multi-omics studies focused on the characterization of the specific metabolic phenotypes of BC and discusses how they may improve clinical BC diagnosis, subtyping, and treatment.
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Chen J, Zhan Y, Zhang R, Chen B, Huang J, Li C, Zhang W, Wang Y, Gao Y, Zheng J, Li Y. A New Prognostic Risk Signature of Eight Ferroptosis-Related Genes in the Clear Cell Renal Cell Carcinoma. Front Oncol 2021; 11:700084. [PMID: 34249761 PMCID: PMC8267866 DOI: 10.3389/fonc.2021.700084] [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: 04/25/2021] [Accepted: 06/10/2021] [Indexed: 01/03/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common renal cell carcinoma and has poor prognosis in the locally advanced stage. Ferroptosis, a relatively new type of cell death, has gained significant attention in recent years. This study aimed to explore the prognostic value of ferroptosis-related genes (FRGs) in ccRCC. In this study, 50 differentially expressed FRGs between ccRCC and adjacent normal kidney tissues were identified, 26 of them correlated with overall survival (OS) (P <0.05). Eight optimal FRGs were selected by Lasso regression and multivariate Cox regression analysis, and used to construct a new prognostic risk signature to predict the prognosis of ccRCC patients. In addition, the signature passed the validation of prognostic survival analyses by a significant margin, and the risk score was identified as an independent prognostic marker via Cox regression analyses. Further studies indicated that the signature was significantly correlated with immune cell infiltration. Moreover, the levels of eight FRGs were examined in ccRCC. Collectively, the 8-FRG prognostic risk signature helps the clinicians predict the prognosis and OS of the patients, and standardize prognostic assessments.
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Affiliation(s)
- Ji Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yating Zhan
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Rongrong Zhang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Bo Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Junting Huang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chunxue Li
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenjie Zhang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yajing Wang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuxiang Gao
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianjian Zheng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yeping Li
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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