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Zhang X, Zhang Y, Liu Q, Zeng A, Song L. Glycolysis-associated lncRNAs in cancer energy metabolism and immune microenvironment: a magic key. Front Immunol 2024; 15:1456636. [PMID: 39346921 PMCID: PMC11437524 DOI: 10.3389/fimmu.2024.1456636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 08/27/2024] [Indexed: 10/01/2024] Open
Abstract
The dependence of tumor cells on glycolysis provides essential energy and raw materials for their survival and growth. Recent research findings have indicated that long chain non-coding RNAs (LncRNAs) have a key regulatory function in the tumor glycolytic pathway and offer new opportunities for cancer therapy. LncRNAs are analogous to a regulatory key during glycolysis. In this paper, we review the mechanisms of LncRNA in the tumor glycolytic pathway and their potential therapeutic strategies, including current alterations in cancer-related energy metabolism with lncRNA mediating the expression of key enzymes, lactate production and transport, and the mechanism of interaction with transcription factors, miRNAs, and other molecules. Studies targeting LncRNA-regulated tumor glycolytic pathways also offer the possibility of developing new therapeutic strategies. By regulating LncRNA expression, the metabolic pathways of tumor cells can be interfered with to inhibit tumor growth and metastasis, thus affecting the immune and drug resistance mechanisms of tumor cells. In addition, lncRNAs have the capacity to function as molecular markers and target therapies, thereby contributing novel strategies and approaches to the field of personalized cancer therapy and prognosis evaluation. In conclusion, LncRNA, as key molecules regulating the tumor glycolysis pathway, reveals a new mechanism of abnormal metabolism in cancer cells. Future research will more thoroughly investigate the specific mechanisms of LncRNA glycolysis regulation and develop corresponding therapeutic strategies, thereby fostering new optimism for the realization of precision medicine.
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Affiliation(s)
- Xi Zhang
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yunchao Zhang
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Qiong Liu
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Anqi Zeng
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, Sichuan, China
| | - Linjiang Song
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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2
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Xiao F, Wang Z, Qiao L, Zhang X, Wu N, Wang J, Yu X. Application of PARP inhibitors combined with immune checkpoint inhibitors in ovarian cancer. J Transl Med 2024; 22:778. [PMID: 39169400 PMCID: PMC11337781 DOI: 10.1186/s12967-024-05583-z] [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: 06/02/2024] [Accepted: 08/04/2024] [Indexed: 08/23/2024] Open
Abstract
The advent of polyadenosine diphosphate ribose polymerase inhibitors (PARPi) has brought about significant changes in the field of ovarian cancer treatment. However, in 2022, Rucaparib, Olaparib, and Niraparib, had their marketing approval revoked for third-line and subsequent therapies due to an increased potential for adverse events. Consequently, the exploration of new treatment modalities remains imperative. Recently, the integration of PARPi with immune checkpoint inhibitors (ICIs) has emerged as a potential remedy option within the context of ovarian cancer. This article offers a comprehensive examination of the mechanisms and applications of PARPi and ICIs in the treatment of ovarian cancer. It synthesizes the existing evidence supporting their combined use and discusses key considerations that merit attention in ongoing development efforts.
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Affiliation(s)
- Fen Xiao
- Department of Basic Medical Sciences, School of Medicine, Hunan Normal University, Changsha, China
- Hunan Gynecological Tumor Clinical Research Center; Hunan Key Laboratory of Cancer Metabolism; Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - ZhiBin Wang
- Hunan Gynecological Tumor Clinical Research Center; Hunan Key Laboratory of Cancer Metabolism; Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Liu Qiao
- Department of Basic Medical Sciences, School of Medicine, Hunan Normal University, Changsha, China
- Hunan Gynecological Tumor Clinical Research Center; Hunan Key Laboratory of Cancer Metabolism; Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Xiu Zhang
- Hunan Gynecological Tumor Clinical Research Center; Hunan Key Laboratory of Cancer Metabolism; Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - NaYiYuan Wu
- Hunan Gynecological Tumor Clinical Research Center; Hunan Key Laboratory of Cancer Metabolism; Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.
| | - Jing Wang
- Hunan Gynecological Tumor Clinical Research Center; Hunan Key Laboratory of Cancer Metabolism; Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.
| | - Xing Yu
- Department of Basic Medical Sciences, School of Medicine, Hunan Normal University, Changsha, China.
- Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China.
- Research Center of Reproduction and Translational Medicine of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China.
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China.
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3
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Bouzari B, Chugaeva UY, Karampoor S, Mirzaei R. Immunometabolites in viral infections: Action mechanism and function. J Med Virol 2024; 96:e29807. [PMID: 39037069 DOI: 10.1002/jmv.29807] [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: 01/18/2024] [Revised: 05/10/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024]
Abstract
The interplay between viral pathogens and host metabolism plays a pivotal role in determining the outcome of viral infections. Upon viral detection, the metabolic landscape of the host cell undergoes significant changes, shifting from oxidative respiration via the tricarboxylic acid (TCA) cycle to increased aerobic glycolysis. This metabolic shift is accompanied by elevated nutrient accessibility, which is vital for cell function, development, and proliferation. Furthermore, depositing metabolites derived from fatty acids, TCA intermediates, and amino acid catabolism accelerates the immunometabolic transition, facilitating pro-inflammatory and antimicrobial responses. Immunometabolites refer to small molecules involved in cellular metabolism regulating the immune response. These molecules include nutrients, such as glucose and amino acids, along with metabolic intermediates and signaling molecules adenosine, lactate, itaconate, succinate, kynurenine, and prostaglandins. Emerging evidence suggests that immunometabolites released by immune cells establish a complex interaction network within local niches, orchestrating and fine-tuning immune responses during viral diseases. However, our current understanding of the immense capacity of metabolites to convey essential cell signals from one cell to another or within cellular compartments remains incomplete. Unraveling these complexities would be crucial for harnessing the potential of immunometabolites in therapeutic interventions. In this review, we discuss specific immunometabolites and their mechanisms of action in viral infections, emphasizing recent findings and future directions in this rapidly evolving field.
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Affiliation(s)
- Behnaz Bouzari
- Department of Pathology, Firouzgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Uliana Y Chugaeva
- Department of Pediatric, Preventive Dentistry and Orthodontics, Institute of Dentistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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4
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Kerro Dego O, Vidlund J. Staphylococcal mastitis in dairy cows. Front Vet Sci 2024; 11:1356259. [PMID: 38863450 PMCID: PMC11165426 DOI: 10.3389/fvets.2024.1356259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
Bovine mastitis is one of the most common diseases of dairy cattle. Even though different infectious microorganisms and mechanical injury can cause mastitis, bacteria are the most common cause of mastitis in dairy cows. Staphylococci, streptococci, and coliforms are the most frequently diagnosed etiological agents of mastitis in dairy cows. Staphylococci that cause mastitis are broadly divided into Staphylococcus aureus and non-aureus staphylococci (NAS). NAS is mainly comprised of coagulase-negative Staphylococcus species (CNS) and some coagulase-positive and coagulase-variable staphylococci. Current staphylococcal mastitis control measures are ineffective, and dependence on antimicrobial drugs is not sustainable because of the low cure rate with antimicrobial treatment and the development of resistance. Non-antimicrobial effective and sustainable control tools are critically needed. This review describes the current status of S. aureus and NAS mastitis in dairy cows and flags areas of knowledge gaps.
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Affiliation(s)
- Oudessa Kerro Dego
- Department of Animal Science, University of Tennessee, Knoxville, TN, United States
| | - Jessica Vidlund
- Department of Animal Science, University of Tennessee, Knoxville, TN, United States
- East Tennessee AgResearch and Education Center-Little River Animal and Environmental Unit, University of Tennessee, Walland, TN, United States
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5
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Noonong K, Chatatikun M, Surinkaew S, Kotepui M, Hossain R, Bunluepuech K, Noothong C, Tedasen A, Klangbud WK, Imai M, Kawakami F, Kubo M, Kitagawa Y, Ichikawa H, Kanekura T, Sukati S, Somsak V, Udomwech L, Ichikawa T, Nissapatorn V, Tangpong J, Indo HP, Majima HJ. Mitochondrial oxidative stress, mitochondrial ROS storms in long COVID pathogenesis. Front Immunol 2023; 14:1275001. [PMID: 38187378 PMCID: PMC10766822 DOI: 10.3389/fimmu.2023.1275001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024] Open
Abstract
Significance This review discusses the coronavirus disease 2019 (COVID-19) pathophysiology in the context of diabetes and intracellular reactions by COVID-19, including mitochondrial oxidative stress storms, mitochondrial ROS storms, and long COVID. Recent advances The long COVID is suffered in ~10% of the COVID-19 patients. Even the virus does not exist, the patients suffer the long COVID for even over a year, This disease could be a mitochondria dysregulation disease. Critical issues Patients who recover from COVID-19 can develop new or persistent symptoms of multi-organ complications lasting weeks or months, called long COVID. The underlying mechanisms involved in the long COVID is still unclear. Once the symptoms of long COVID persist, they cause significant damage, leading to numerous, persistent symptoms. Future directions A comprehensive map of the stages and pathogenetic mechanisms related to long COVID and effective drugs to treat and prevent it are required, which will aid the development of future long COVID treatments and symptom relief.
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Affiliation(s)
- Kunwadee Noonong
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
- Research Excellence Center for Innovation and Health Products (RECIHP), School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
| | - Moragot Chatatikun
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
- Center of Excellence Research for Melioidosis and Microorganisms, Walailak University, Nakhon Si Thammarat, Thailand
| | - Sirirat Surinkaew
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
- Center of Excellence Research for Melioidosis and Microorganisms, Walailak University, Nakhon Si Thammarat, Thailand
| | - Manas Kotepui
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
| | - Rahni Hossain
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
| | | | - Chanittha Noothong
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
| | - Aman Tedasen
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
- Research Excellence Center for Innovation and Health Products (RECIHP), School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
| | - Wiyada Kwanhian Klangbud
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
- Research Excellence Center for Innovation and Health Products (RECIHP), School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
| | - Motoki Imai
- Department of Molecular Diagnostics, School of Allied Health Sciences, Kitasato University, Sagamihara, Japan
- Regenerative Medicine and Cell Design Research Facility, School of Allied Health Sciences, Kitasato University, Sagamihara, Japan
| | - Fumitaka Kawakami
- Regenerative Medicine and Cell Design Research Facility, School of Allied Health Sciences, Kitasato University, Sagamihara, Japan
- Department of Regulation Biochemistry, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan
- Department of Health Administration, School of Allied Health Sciences, Kitasato University, Sagamihara, Japan
| | - Makoto Kubo
- Regenerative Medicine and Cell Design Research Facility, School of Allied Health Sciences, Kitasato University, Sagamihara, Japan
- Division of Microbiology, School of Allied Health Sciences, Kitasato University, Sagamihara, Japan
- Department of Environmental Microbiology, Graduate School of Medical Sciences, Kitasato University, Sagamihara, Japan
| | - Yoshimasa Kitagawa
- Oral Diagnosis and Medicine, Division of Oral Pathobiological Science, Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan
| | - Hiroshi Ichikawa
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Takuro Kanekura
- Department of Dermatology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Suriyan Sukati
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
| | - Voravuth Somsak
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
- Research Excellence Center for Innovation and Health Products (RECIHP), School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
| | - Lunla Udomwech
- School of Medicine, Walailak University, Nakhon Si Thammarat, Thailand
| | - Takafumi Ichikawa
- Regenerative Medicine and Cell Design Research Facility, School of Allied Health Sciences, Kitasato University, Sagamihara, Japan
- Department of Regulation Biochemistry, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
- Research Excellence Center for Innovation and Health Products (RECIHP), School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
| | - Jitbanjong Tangpong
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
- Research Excellence Center for Innovation and Health Products (RECIHP), School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
| | - Hiroko P. Indo
- Department of Oncology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Amanogawa Galaxy Astronomy Research Center, Kagoshima University Graduate School of Engineering, Kagoshima, Japan
| | - Hideyuki J. Majima
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
- Research Excellence Center for Innovation and Health Products (RECIHP), School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
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6
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Sun Q, Wang H, Liu H. Identification of long non-coding RNA MSTRG.5748.1 and MSTRG.7894.1 from Megalobrama amblycephala and their potential roles in innate immunity. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108949. [PMID: 37453493 DOI: 10.1016/j.fsi.2023.108949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/08/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Megalobrama amblycephala is one of the most economically important freshwater fish in China, and the bacterial septicemia caused by Aeromonas hydrophila is a serious threat to the breeding industry of M. amblycephala. Unfortunately, the characterization of long noncoding RNA (lncRNA) in response to A. hydrophila infection has not been performed in M. amblycephala. To better understand the biological significance of lncRNA in the immune system, we identified two lncRNA, named MSTRG.5748.1 and MSTRG.7894.1, as playing critical roles in the antibacterial response of M. amblycephala. After separating the nucleus and cytoplasm of the hepatocytes from M. amblycephala, cellular localization of MSTRG.5748.1 and MSTRG.7894.1 was performed to predict their functions. The results showed that MSTRG.5748.1 was mainly expressed in the nucleus, suggesting that its functions are mostly to regulate the expression of downstream genes through epistasis and transcription. MSTRG.7894.1 existed in both the nucleus and cytoplasm, which indicated that it has many regulatory modes. qPCR analysis showed that MSTRG.5748.1 and MSTRG.7894.1 were expressed in the immune-related organs of M. amblycephala, and significantly changed in the liver after A. hydrophila infection. RNA-seq analysis revealed that differentially expressed genes (DEGs) were mainly enriched in antigen processing and presentation via MHC class I, RIG-I-like receptor (RLR) signaling pathway, and IFN-related pathway, and a large number of pathway-related genes were significantly regulated after lncRNA overexpression in muscle cell of M. amblycephala. Overexpression of MSTRG.5748.1 and MSTRG.7894.1 significantly inhibited the expression of STING and IFN, significantly upregulated muscle cell viability, and promoted cell proliferation by targeting STING and IFN.
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Affiliation(s)
- Qianhui Sun
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair / Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education / Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Huanling Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair / Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education / Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Hong Liu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair / Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education / Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, 430070, China.
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7
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Li J, Wang Y, Deng H, Li S, Qiu HJ. Cellular metabolism hijacked by viruses for immunoevasion: potential antiviral targets. Front Immunol 2023; 14:1228811. [PMID: 37559723 PMCID: PMC10409484 DOI: 10.3389/fimmu.2023.1228811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023] Open
Abstract
Cellular metabolism plays a central role in the regulation of both innate and adaptive immunity. Immune cells utilize metabolic pathways to modulate the cellular differentiation or death. The intricate interplay between metabolism and immune response is critical for maintaining homeostasis and effective antiviral activities. In recent years, immunometabolism induced by viral infections has been extensively investigated, and accumulating evidence has indicated that cellular metabolism can be hijacked to facilitate viral replication. Generally, virus-induced changes in cellular metabolism lead to the reprogramming of metabolites and metabolic enzymes in different pathways (glucose, lipid, and amino acid metabolism). Metabolic reprogramming affects the function of immune cells, regulates the expression of immune molecules and determines cell fate. Therefore, it is important to explore the effector molecules with immunomodulatory properties, including metabolites, metabolic enzymes, and other immunometabolism-related molecules as the antivirals. This review summarizes the relevant advances in the field of metabolic reprogramming induced by viral infections, providing novel insights for the development of antivirals.
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Affiliation(s)
| | | | | | - Su Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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8
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Vasilopoulou C, McDaid-McCloskey SL, McCluskey G, Duguez S, Morris AP, Duddy W. Genome-Wide Gene-Set Analysis Identifies Molecular Mechanisms Associated with ALS. Int J Mol Sci 2023; 24:4021. [PMID: 36835433 PMCID: PMC9966913 DOI: 10.3390/ijms24044021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal late-onset motor neuron disease characterized by the loss of the upper and lower motor neurons. Our understanding of the molecular basis of ALS pathology remains elusive, complicating the development of efficient treatment. Gene-set analyses of genome-wide data have offered insight into the biological processes and pathways of complex diseases and can suggest new hypotheses regarding causal mechanisms. Our aim in this study was to identify and explore biological pathways and other gene sets having genomic association to ALS. Two cohorts of genomic data from the dbGaP repository were combined: (a) the largest available ALS individual-level genotype dataset (N = 12,319), and (b) a similarly sized control cohort (N = 13,210). Following comprehensive quality control pipelines, imputation and meta-analysis, we assembled a large European descent ALS-control cohort of 9244 ALS cases and 12,795 healthy controls represented by genetic variants of 19,242 genes. Multi-marker analysis of genomic annotation (MAGMA) gene-set analysis was applied to an extensive collection of 31,454 gene sets from the molecular signatures database (MSigDB). Statistically significant associations were observed for gene sets related to immune response, apoptosis, lipid metabolism, neuron differentiation, muscle cell function, synaptic plasticity and development. We also report novel interactions between gene sets, suggestive of mechanistic overlaps. A manual meta-categorization and enrichment mapping approach is used to explore the overlap of gene membership between significant gene sets, revealing a number of shared mechanisms.
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Affiliation(s)
- Christina Vasilopoulou
- Personalised Medicine Centre, School of Medicine, Ulster University, Londonderry BT47 6SB, UK
| | | | - Gavin McCluskey
- Personalised Medicine Centre, School of Medicine, Ulster University, Londonderry BT47 6SB, UK
| | - Stephanie Duguez
- Personalised Medicine Centre, School of Medicine, Ulster University, Londonderry BT47 6SB, UK
| | - Andrew P. Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, University of Manchester, Manchester M13 9PT, UK
| | - William Duddy
- Personalised Medicine Centre, School of Medicine, Ulster University, Londonderry BT47 6SB, UK
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9
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Liu J, Ji Q, Cheng F, Chen D, Geng T, Huang Y, Zhang J, He Y, Song T. The lncRNAs involved in regulating the RIG-I signaling pathway. Front Cell Infect Microbiol 2022; 12:1041682. [PMID: 36439216 PMCID: PMC9682092 DOI: 10.3389/fcimb.2022.1041682] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/21/2022] [Indexed: 09/23/2023] Open
Abstract
Understanding the targets and interactions of long non-coding RNAs (lncRNAs) related to the retinoic acid-inducible gene-I (RIG-I) signaling pathway is essential for developing interventions, which would enable directing the host inflammatory response regulation toward protective immunity. In the RIG-I signaling pathway, lncRNAs are involved in the important processes of ubiquitination, phosphorylation, and glycolysis, thus promoting the transport of the interferon regulatory factors 3 and 7 (IRF3 and IRF7) and the nuclear factor kappa B (NF-κB) into the nucleus, and activating recruitment of type I interferons (IFN-I) and inflammatory factors to the antiviral action site. In addition, the RIG-I signaling pathway has recently been reported to contain the targets of coronavirus disease-19 (COVID-19)-related lncRNAs. The molecules in the RIG-I signaling pathway are directly regulated by the lncRNA-microRNAs (miRNAs)-messenger RNA (mRNA) axis. Therefore, targeting this axis has become a novel strategy for the diagnosis and treatment of cancer. In this paper, the studies on the regulation of the RIG-I signaling pathway by lncRNAs during viral infections and cancer are comprehensively analyzed. The aim is to provide a solid foundation of information for conducting further detailed studies on lncRNAs and RIG-I in the future and also contribute to clinical drug development.
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Affiliation(s)
- Jing Liu
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Qinglu Ji
- School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Feng Cheng
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Dengwang Chen
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Tingting Geng
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Yueyue Huang
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Jidong Zhang
- Department of Immunology, Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, China
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Yuqi He
- School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Tao Song
- Department of Immunology, Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, China
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, China
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10
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Hu C, Xu Y, Li F, Mi W, Yu H, Wang X, Wen X, Chen S, Li X, Xu Y, Zhang Y. Identifying and characterizing drug sensitivity-related lncRNA-TF-gene regulatory triplets. Brief Bioinform 2022; 23:6675752. [PMID: 36007239 PMCID: PMC9487635 DOI: 10.1093/bib/bbac366] [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: 04/13/2022] [Revised: 06/19/2022] [Accepted: 08/06/2022] [Indexed: 11/15/2022] Open
Abstract
Recently, many studies have shown that lncRNA can mediate the regulation of TF-gene in drug sensitivity. However, there is still a lack of systematic identification of lncRNA-TF-gene regulatory triplets for drug sensitivity. In this study, we propose a novel analytic approach to systematically identify the lncRNA-TF-gene regulatory triplets related to the drug sensitivity by integrating transcriptome data and drug sensitivity data. Totally, 1570 drug sensitivity-related lncRNA-TF-gene triplets were identified, and 16 307 relationships were formed between drugs and triplets. Then, a comprehensive characterization was performed. Drug sensitivity-related triplets affect a variety of biological functions including drug response-related pathways. Phenotypic similarity analysis showed that the drugs with many shared triplets had high similarity in their two-dimensional structures and indications. In addition, Network analysis revealed the diverse regulation mechanism of lncRNAs in different drugs. Also, survival analysis indicated that lncRNA-TF-gene triplets related to the drug sensitivity could be candidate prognostic biomarkers for clinical applications. Next, using the random walk algorithm, the results of which we screen therapeutic drugs for patients across three cancer types showed high accuracy in the drug-cell line heterogeneity network based on the identified triplets. Besides, we developed a user-friendly web interface-DrugSETs (http://bio-bigdata.hrbmu.edu.cn/DrugSETs/) available to explore 1570 lncRNA-TF-gene triplets relevant with 282 drugs. It can also submit a patient’s expression profile to predict therapeutic drugs conveniently. In summary, our research may promote the study of lncRNAs in the drug resistance mechanism and improve the effectiveness of treatment.
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Affiliation(s)
- Congxue Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yingqi Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Feng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Wanqi Mi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - He Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xinran Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xin Wen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shuaijun Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou 571199, China
| | - Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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11
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Interferon Signaling-Dependent Contribution of Glycolysis to Rubella Virus Infection. Pathogens 2022; 11:pathogens11050537. [PMID: 35631058 PMCID: PMC9146913 DOI: 10.3390/pathogens11050537] [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: 03/21/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
Interferons (IFNs) are an essential part of innate immunity and contribute to adaptive immune responses. Here, we employed a loss-of-function analysis with human A549 respiratory epithelial cells with a knockout (KO) of the type I IFN receptor (IFNAR KO), either solely or together with the receptor of type III IFN (IFNAR/IFNLR1 KO). The course of rubella virus (RuV) infection on the IFNAR KO A549 cells was comparable to the control A549. However, on the IFNAR/IFNLR1 KO A549 cells, both genome replication and the synthesis of viral proteins were significantly enhanced. The generation of IFN β during RuV infection was influenced by type III IFN signaling. In contrast to IFNAR KO A549, extracellular IFN β was not detected on IFNAR/IFNLR1 KO A549. The bioenergetic profile of RuV-infected IFNAR/IFNLR1 KO A549 cells generated by extracellular flux analysis revealed a significant increase in glycolysis, whereas mitochondrial respiration was comparable between all three cell types. Moreover, the application of the glucose analogue 2-deoxy-D-glucose (2-DG) significantly increased viral protein synthesis in control A549 cells, while no effect was noted on IFNAR/IFNLR KO A549. In conclusion, we identified a positive signaling circuit of type III IFN signaling on the generation of IFN β during RuV infection and an IFN signaling-dependent contribution of glycolysis to RuV infection. This study on epithelial A549 cells emphasizes the interaction between glycolysis and antiviral IFN signaling and notably, the antiviral activity of type III IFNs against RuV infection, especially in the absence of both type I and III IFN signaling, the RuV replication cycle was enhanced.
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12
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Yang Y, Li M, Ma Y, Ye W, Si Y, Zheng X, Liu H, Cheng L, Zhang L, Zhang H, Zhang X, Lei Y, Shen L, Zhang F, Ma H. LncRNA NEAT1 Potentiates SREBP2 Activity to Promote Inflammatory Macrophage Activation and Limit Hantaan Virus Propagation. Front Microbiol 2022; 13:849020. [PMID: 35495674 PMCID: PMC9044491 DOI: 10.3389/fmicb.2022.849020] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/10/2022] [Indexed: 11/17/2022] Open
Abstract
As the global prototypical zoonotic hantavirus, Hantaan virus (HTNV) is prevalent in Asia and is the leading causative agent of severe hemorrhagic fever with renal syndrome (HFRS), which has profound morbidity and mortality. Macrophages are crucial components of the host innate immune system and serve as the first line of defense against HTNV infection. Previous studies indicated that the viral replication efficiency in macrophages determines hantavirus pathogenicity, but it remains unknown which factor manipulates the macrophage activation pattern and the virus-host interaction process. Here, we performed the transcriptomic analysis of HTNV-infected mouse bone marrow-derived macrophages and identified the long noncoding RNA (lncRNA) nuclear enriched abundant transcript 1 (NEAT1), especially the isoform NEAT1-2, as one of the lncRNAs that is differentially expressed at the early phase. Based on coculture experiments, we revealed that silencing NEAT1-2 hinders inflammatory macrophage activation and facilitates HTNV propagation, while enhancing NEAT1-2 transcription effectively restrains viral replication. Furthermore, sterol response element binding factor-2 (SREBP2), which controls the cholesterol metabolism process, was found to stimulate macrophages by promoting the production of multiple inflammatory cytokines upon HTNV infection. NEAT1-2 could potentiate SREBP2 activity by upregulating Srebf1 expression and interacting with SREBP2, thus stimulating inflammatory macrophages and limiting HTNV propagation. More importantly, we demonstrated that the NEAT1-2 expression level in patient monocytes was negatively correlated with viral load and HFRS disease progression. Our results identified a function and mechanism of action for the lncRNA NEAT1 in heightening SREBP2-mediated macrophage activation to restrain hantaviral propagation and revealed the association of NEAT1 with HFRS severity.
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Affiliation(s)
- Yongheng Yang
- College of Life Sciences, Northwest University, Xi'an, China.,Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Mengyun Li
- College of Life Sciences, Northwest University, Xi'an, China.,Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Yongtao Ma
- Department of Emergency, Children's Hospital of Kaifeng City, Kaifeng, China
| | - Wei Ye
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Yue Si
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Xuyang Zheng
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China.,Department of Infectious Diseases, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - He Liu
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Linfeng Cheng
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Liang Zhang
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Hui Zhang
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Xijing Zhang
- Department of Anesthesiology and Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Yingfeng Lei
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Lixin Shen
- College of Life Sciences, Northwest University, Xi'an, China
| | - Fanglin Zhang
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Hongwei Ma
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China.,Department of Anesthesiology and Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
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13
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Jia L, Wang J, Luoreng Z, Wang X, Wei D, Yang J, Hu Q, Ma Y. Progress in Expression Pattern and Molecular Regulation Mechanism of LncRNA in Bovine Mastitis. Animals (Basel) 2022; 12:ani12091059. [PMID: 35565486 PMCID: PMC9105470 DOI: 10.3390/ani12091059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Bovine mastitis is an inflammatory disease of the mammary glands that causes serious harm to cow health and huge economic losses. Susceptibility or resistance to mastitis in individual cows is mainly determined by genetic factors, including coding genes and non-coding genes. Long non-coding RNAs (lncRNAs) are non-coding RNA molecules with a length of more than 200 nucleotides (nt) that have recently been discovered. They can regulate a variety of diseases of humans and animals, especially the immune response and inflammatory disease process. This paper reviews the role of long non-coding RNA (lncRNA) in inflammatory diseases, emphasizes on the latest research progress of lncRNA expression and the molecular regulatory mechanism in bovine mastitis, and looks forward to the research and application prospect of lncRNA in bovine mastitis, intending to provide a reference for scientific researchers to systematically understand this research field. Abstract Bovine mastitis is an inflammatory disease caused by pathogenic microbial infection, trauma, or other factors. Its morbidity is high, and it is difficult to cure, causing great harm to the health of cows and the safety of dairy products. Susceptibility or resistance to mastitis in individual cows is mainly determined by genetic factors, including coding genes and non-coding genes. Long non-coding RNAs (lncRNAs) are a class of endogenous non-coding RNA molecules with a length of more than 200 nucleotides (nt) that have recently been discovered. They can regulate the immune response of humans and animals on three levels (transcription, epigenetic modification, and post-transcription), and are widely involved in the pathological process of inflammatory diseases. Over the past few years, extensive findings revealed basic roles of lncRNAs in inflammation, especially bovine mastitis. This paper reviews the expression pattern and mechanism of long non-coding RNA (lncRNA) in inflammatory diseases, emphasizes on the latest research progress of the lncRNA expression pattern and molecular regulatory mechanism in bovine mastitis, analyzes the molecular regulatory network of differentially expressed lncRNAs, and looks forward to the research and application prospect of lncRNA in bovine mastitis, laying a foundation for molecular breeding and the biological therapy of bovine mastitis.
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Affiliation(s)
- Li Jia
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Jinpeng Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Zhuoma Luoreng
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
- Correspondence: (Z.L.); (X.W.)
| | - Xingping Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
- Correspondence: (Z.L.); (X.W.)
| | - Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Jian Yang
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Qichao Hu
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Yun Ma
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
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