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Huang LH, Huang CY, Liu YW, Chien PC, Hsieh TM, Liu HT, Lin HP, Wu CJ, Chuang PC, Hsieh CH. Circadian Rhythm Disruption in Hepatocellular Carcinoma Investigated by Integrated Analysis of Bulk and Single-Cell RNA Sequencing Data. Int J Mol Sci 2024; 25:5748. [PMID: 38891936 PMCID: PMC11171588 DOI: 10.3390/ijms25115748] [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: 04/16/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Circadian rhythms are essential regulators of a multitude of physiological and behavioral processes, such as the metabolism and function of the liver. Circadian rhythms are crucial to liver homeostasis, as the liver is a key metabolic organ accountable for the systemic equilibrium of the body. Circadian rhythm disruption alone is sufficient to cause liver cancer through the maintenance of hepatic metabolic disorder. Although there is evidence linking CRD to hepatocarcinogenesis, the precise cellular and molecular mechanisms that underlie the circadian crosstalk that leads to hepatocellular carcinoma remain unknown. The expression of CRD-related genes in HCC was investigated in this study via bulk RNA transcriptomic analysis and single-cell sequencing. Dysregulated CRD-related genes are predominantly found in hepatocytes and fibroblasts, according to the findings. By using a combination of single-cell RNA sequencing and bulk RNA sequencing analyses, the dysregulated CRD-related genes ADAMTS13, BIRC5, IGFBP3, MARCO, MT2A, NNMT, and PGLYRP2 were identified. The survival analysis using the Kaplan-Meier method revealed a significant correlation between the expression levels of BIRC5 and IGFBP3 and the survival of patients diagnosed with HCC.
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Affiliation(s)
- Lien-Hung Huang
- Department of Trauma Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (L.-H.H.); (C.-Y.H.); (T.-M.H.); (H.-T.L.)
| | - Chun-Ying Huang
- Department of Trauma Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (L.-H.H.); (C.-Y.H.); (T.-M.H.); (H.-T.L.)
| | - Yueh-Wei Liu
- Department of General Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan;
| | - Peng-Chen Chien
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (P.-C.C.); (H.-P.L.); (C.-J.W.)
| | - Ting-Min Hsieh
- Department of Trauma Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (L.-H.H.); (C.-Y.H.); (T.-M.H.); (H.-T.L.)
| | - Hang-Tsung Liu
- Department of Trauma Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (L.-H.H.); (C.-Y.H.); (T.-M.H.); (H.-T.L.)
| | - Hui-Ping Lin
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (P.-C.C.); (H.-P.L.); (C.-J.W.)
| | - Chia-Jung Wu
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (P.-C.C.); (H.-P.L.); (C.-J.W.)
| | - Pei-Chin Chuang
- Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Ching-Hua Hsieh
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (P.-C.C.); (H.-P.L.); (C.-J.W.)
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Ayan D, Cagatay A. Bioinformatic analysis of genetic changes CLOCK, BMAL1, CRY1, CRY2, PER1, PER2, PER3, and NPAS2 proteins in HCC patients. HEPATOLOGY FORUM 2023; 4:108-117. [PMID: 37822309 PMCID: PMC10564247 DOI: 10.14744/hf.2023.2023.0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/30/2023] [Accepted: 06/17/2023] [Indexed: 10/13/2023]
Abstract
Background and Aim Genes related to the circadian rhythm control various biological processes. The aim of this study was to comprehensively investigate the mutational and mRNA profile of core circadian rhythm genes in hepatocellular cancer (HCC) samples. Materials and Methods In this study, the gene profile of a total of 369 patients with HCC was examined over the data obtained from the cancer genome atlas database through-cBioPortal. The effects of mutations on protein were examined by scoring the Polymorphism Phenotyping v2, Mutation Assessor, and SIFT-databases. While the association of genes with other genes was determined with the GeneMANIA-database, the association of expression levels in the genes with overall survival (OS) was evaluated with the Kaplan-Meier Plot database. Results As a result of the analyses, there were a total of 25 mutations. Decreased expression levels of PER1 (1.3e-05), PER3 (p=0.046), and CRY2 (p=1.8e-06) genes were found statistically associated with shorter OS. It was also found that increased expression levels of the PER2 (p=0.045) gene were associated with longer OS, and increased expression levels of the NPAS2 (p=9e-04) gene were associated with shorter OS. Conclusion In particular, changes in the PER1, PER2, CRY2, and NPAS2 genes may provide possible molecular targets in chemotherapy and immunotherapy for HCC patients.
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Affiliation(s)
- Durmus Ayan
- Department of Medical Biochemistry, Nigde Training and Research Hospital, Nigde, Turkiye
- Department of Medical Biochemistry, Nigde Omer Halisdemir University, School of Medicine, Nigde, Turkiye
| | - Ak Cagatay
- Nigde Training and Research Hospital, Department of Gastroenterology, Nigde, Turkiye
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Miro C, Docimo A, Barrea L, Verde L, Cernea S, Sojat AS, Marina LV, Docimo G, Colao A, Dentice M, Muscogiuri G. "Time" for obesity-related cancer: The role of the circadian rhythm in cancer pathogenesis and treatment. Semin Cancer Biol 2023; 91:99-109. [PMID: 36893964 DOI: 10.1016/j.semcancer.2023.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/21/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023]
Abstract
The circadian rhythm is regulated by an intrinsic time-tracking system, composed both of a central and a peripheral clock, which influences the cycles of activities and sleep of an individual over 24 h. At the molecular level, the circadian rhythm begins when two basic helix-loop-helix/Per-ARNT-SIM (bHLH-PAS) proteins, BMAL-1 and CLOCK, interact with each other to produce BMAL-1/CLOCK heterodimers in the cytoplasm. The BMAL-1/CLOCK target genes encode for the repressor components of the clock, cryptochrome (Cry1 and Cry2) and the Period proteins (Per1, Per2 and Per3). It has been recently demonstrated that the disruption of circadian rhythm is associated with an increased risk of developing obesity and obesity-related diseases. In addition, it has been demonstrated that the disruption of the circadian rhythm plays a key role in tumorigenesis. Further, an association between the circadian rhythm disruptions and an increased incidence and progression of several types of cancer (e.g., breast, prostate, colorectal and thyroid cancer) has been found. As the perturbation of circadian rhythm has adverse metabolic consequences (e.g., obesity) and at the same time tumor promoter functions, this manuscript has the aim to report how the aberrant circadian rhythms affect the development and prognosis of different types of obesity-related cancers (breast, prostate, colon rectal and thyroid cancer) focusing on both human studies and on molecular aspects.
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Affiliation(s)
- Caterina Miro
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131 Naples, Italy
| | - Annamaria Docimo
- Dipartimento di Medicina Clinica e Chirurgia, Unità di Endocrinologia, Diabetologia ed Andrologia, Università Federico II, Naples, Italy
| | - Luigi Barrea
- Dipartimento di Scienze Umanistiche, Università Telematica Pegaso, 80143 Naples, Italy
| | - Ludovica Verde
- Department of Public Health, University of Federico II, 80131 Naples, Italy
| | - Simona Cernea
- George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mures/Internal Medicine I, Târgu Mureş, Romania; Diabetes, Nutrition and Metabolic Diseases Outpatient Unit, Emergency County Clinical Hospital, Târgu Mureş, Romania
| | - Antoan Stefan Sojat
- National Centre for Infertility and Endocrinology of Gender, Clinic for Endocrinology Diabetes and Metabolic Diseases, University Clinical Centre of Serbia, Serbia
| | - Ljiljana V Marina
- National Centre for Infertility and Endocrinology of Gender, Clinic for Endocrinology Diabetes and Metabolic Diseases, University Clinical Centre of Serbia, Serbia
| | - Giovanni Docimo
- Department of Medical and Advanced Surgical Sciences, University of Campania "Luigi Vanvitelli", 80131 Naples, Italy
| | - Annamaria Colao
- Dipartimento di Medicina Clinica e Chirurgia, Unità di Endocrinologia, Diabetologia ed Andrologia, Università Federico II, Naples, Italy; UNESCO Chair "Education for Health and Sustainable Development", University of Naples "Federico II", Naples, Italy
| | - Monica Dentice
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131 Naples, Italy
| | - Giovanna Muscogiuri
- Dipartimento di Medicina Clinica e Chirurgia, Unità di Endocrinologia, Diabetologia ed Andrologia, Università Federico II, Naples, Italy; UNESCO Chair "Education for Health and Sustainable Development", University of Naples "Federico II", Naples, Italy.
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Gao W, Li R, Ye M, Zhang L, Zheng J, Yang Y, Wei X, Zhao Q. The circadian clock has roles in mesenchymal stem cell fate decision. Stem Cell Res Ther 2022; 13:200. [PMID: 35578353 PMCID: PMC9109355 DOI: 10.1186/s13287-022-02878-0] [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: 11/29/2021] [Accepted: 04/26/2022] [Indexed: 02/08/2023] Open
Abstract
The circadian clock refers to the intrinsic biological rhythms of physiological functions and behaviours. It synergises with the solar cycle and has profound effects on normal metabolism and organismal fitness. Recent studies have suggested that the circadian clock exerts great influence on the differentiation of stem cells. Here, we focus on the close relationship between the circadian clock and mesenchymal stem cell fate decisions in the skeletal system. The underlying mechanisms include hormone signals and the activation and repression of different transcription factors under circadian regulation. Additionally, the clock interacts with epigenetic modifiers and non-coding RNAs and is even involved in chromatin remodelling. Although the specificity and safety of circadian therapy need to be further studied, the circadian regulation of stem cells can be regarded as a promising candidate for health improvement and disease prevention.
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Affiliation(s)
- Wenzhen Gao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Rong Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Meilin Ye
- Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, School and Hospital of Stomatology, Shandong University, Jinan, 250012, China
| | - Lanxin Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Jiawen Zheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yuqing Yang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Xiaoyu Wei
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Qing Zhao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
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D’Agostino Y, Frigato E, Noviello TM, Toni M, Frabetti F, Cigliano L, Ceccarelli M, Sordino P, Cerulo L, Bertolucci C, D’Aniello S. Loss of circadian rhythmicity in bdnf knockout zebrafish larvae. iScience 2022; 25:104054. [PMID: 35345456 PMCID: PMC8957028 DOI: 10.1016/j.isci.2022.104054] [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: 07/04/2021] [Revised: 01/14/2022] [Accepted: 03/08/2022] [Indexed: 12/13/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) plays a pivotal role in neuronal growth and differentiation, neuronal plasticity, learning, and memory. Using CRISPR/Cas9 technology, we generated a vital Bdnf null mutant line in zebrafish and carried out its molecular and behavioral characterization. Although no defects are evident on a morphological inspection, 66% of coding genes and 37% of microRNAs turned out to be differentially expressed in bdnf−/− compared with wild type sibling embryos. We deeply investigated the circadian clock pathway and confirmed changes in the rhythmic expression of clock (arntl1a, clock1a and clock2) and clock-controlled (aanat2) genes. The modulatory role of Bdnf on the zebrafish circadian clock was then validated by behavioral tests highlighting the absence of circadian activity rhythms in bdnf−/− larvae. The circadian behavior was partially rescued by pharmacological treatment. The bdnf−/− zebrafish line presented here is the first valuable and stable vertebrate model for the study of BDNF-related neurodevelopmental diseases Generation of a viable bdnf KO line in zebrafish Bdnf deficiency affects locomotor activity and thigmotaxis in larvae Differential RNA-seq analysis shows changes in expression of circadian clock genes Bdnf mutant fails in the generation of the behavioral circadian rhythmicity
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The Expression and Function of Circadian Rhythm Genes in Hepatocellular Carcinoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:4044606. [PMID: 34697563 PMCID: PMC8541861 DOI: 10.1155/2021/4044606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 09/07/2021] [Accepted: 09/25/2021] [Indexed: 12/25/2022]
Abstract
Hepatocellular carcinoma (HCC) is among the most common and lethal form of cancer worldwide. However, its diagnosis and treatment are still dissatisfactory, due to limitations in the understanding of its pathogenic mechanism. Therefore, it is important to elucidate the molecular mechanisms and identify novel therapeutic targets for HCC. Circadian rhythm-related genes control a variety of biological processes. These genes play pivotal roles in the initiation and progression of HCC and are potential diagnostic markers and therapeutic targets. This review gives an update on the research progress of circadian rhythms, their effects on the initiation, progression, and prognosis of HCC, in a bid to provide new insights for the research and treatment of HCC.
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Circadian Clock and Liver Cancer. Cancers (Basel) 2021; 13:cancers13143631. [PMID: 34298842 PMCID: PMC8306099 DOI: 10.3390/cancers13143631] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/06/2021] [Accepted: 07/15/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary The circadian coordination of metabolism is tightly regulated, and its alteration can trigger several diseases, including liver steatohepatitis and cancer. Many factors (such as diet and jet lag) shape both the liver molecular clock and the circadian transcription/translation of genes related to different metabolic pathways. Here, we summarize our current knowledge about the molecular mechanisms that control this circadian regulation of liver metabolism. Abstract Circadian clocks control several homeostatic processes in mammals through internal molecular mechanisms. Chronic perturbation of circadian rhythms is associated with metabolic diseases and increased cancer risk, including liver cancer. The hepatic physiology follows a daily rhythm, driven by clock genes that control the expression of several proteins involved in distinct metabolic pathways. Alteration of the liver clock results in metabolic disorders, such as non-alcoholic fatty liver diseases (NAFLD) and impaired glucose metabolism, that can trigger the activation of oncogenic pathways, inducing spontaneous hepatocarcinoma (HCC). In this review, we provide an overview of the role of the liver clock in the metabolic and oncogenic changes that lead to HCC and discuss new potentially useful targets for prevention and management of HCC.
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