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Chen S, Zhang W, Li X, Cao Z, Liu C. DNA polymerase beta connects tumorigenicity with the circadian clock in liver cancer through the epigenetic demethylation of Per1. Cell Death Dis 2024; 15:78. [PMID: 38245510 PMCID: PMC10799862 DOI: 10.1038/s41419-024-06462-7] [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: 09/12/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/22/2024]
Abstract
The circadian-controlled DNA repair exhibits a strong diurnal rhythm. Disruption in circadian clock and DNA repair is closely linked with hepatocellular carcinoma (HCC) progression, but the mechanism remains unknown. Here, we show that polymerase beta (POLB), a critical enzyme in the DNA base excision repair pathway, is rhythmically expressed at the translational level in mouse livers. Hepatic POLB dysfunction dampens clock homeostasis, whereas retards HCC progression, by mediating the methylation of the 4th CpG island on the 5'UTR of clock gene Per1. Clinically, POLB is overexpressed in human HCC samples and positively associated with poor prognosis. Furthermore, the hepatic rhythmicity of POLB protein expression is orchestrated by Calreticulin (CALR). Our findings provide important insights into the molecular mechanism underlying the synergy between clock and food signals on the POLB-driven BER system and reveal new clock-dependent carcinogenetic effects of POLB. Therefore, chronobiological modulation of POLB may help to promote precise interventions for HCC.
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Affiliation(s)
- Siyu Chen
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Wenxiang Zhang
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Xiao Li
- Department of Pathology, First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Zhengyu Cao
- Jiangsu Provincial Key Laboratory for TCM Evaluation and Translational Development, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Chang Liu
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China.
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, 401135, China.
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Velazquez-Arcelay K, Colbran LL, McArthur E, Brand CM, Rinker DC, Siemann JK, McMahon DG, Capra JA. Archaic Introgression Shaped Human Circadian Traits. Genome Biol Evol 2023; 15:evad203. [PMID: 38095367 PMCID: PMC10719892 DOI: 10.1093/gbe/evad203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultraviolet radiation and increased variation in seasonal dynamics. However, whether these groups differed substantially in circadian biology and whether archaic introgression adaptively contributed to human chronotypes remain unknown. Here, we traced the evolution of chronotype based on genomes from archaic hominins and present-day humans. First, we inferred differences in circadian gene sequences, splicing, and regulation between archaic hominins and modern humans. We identified 28 circadian genes containing variants with potential to alter splicing in archaics (e.g., CLOCK, PER2, RORB, and RORC) and 16 circadian genes likely divergently regulated between present-day humans and archaic hominins, including RORA. These differences suggest the potential for introgression to modify circadian gene expression. Testing this hypothesis, we found that introgressed variants are enriched among expression quantitative trait loci for circadian genes. Supporting the functional relevance of these regulatory effects, we found that many introgressed alleles have associations with chronotype. Strikingly, the strongest introgressed effects on chronotype increase morningness, consistent with adaptations to high latitude in other species. Finally, we identified several circadian loci with evidence of adaptive introgression or latitudinal clines in allele frequency. These findings identify differences in circadian gene regulation between modern humans and archaic hominins and support the contribution of introgression via coordinated effects on variation in human chronotype.
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Affiliation(s)
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Evonne McArthur
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Colin M Brand
- Department of Epidemiology and Biostatistics, University of California, SanFrancisco, California, USA
- Bakar Computational Health Sciences Institute, University of California, SanFrancisco, California, USA
| | - David C Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Justin K Siemann
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Douglas G McMahon
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - John A Capra
- Department of Epidemiology and Biostatistics, University of California, SanFrancisco, California, USA
- Bakar Computational Health Sciences Institute, University of California, SanFrancisco, California, USA
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Velazquez-Arcelay K, Colbran LL, McArthur E, Brand C, Rinker D, Siemann J, McMahon D, Capra JA. Archaic Introgression Shaped Human Circadian Traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.527061. [PMID: 36778254 PMCID: PMC9915721 DOI: 10.1101/2023.02.03.527061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Introduction When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultra-violet radiation and increased variation in seasonal dynamics. However, whether these groups differed substantially in circadian biology, and whether archaic introgression adaptively contributed to human chronotypes remains unknown. Results Here we traced the evolution of chronotype based on genomes from archaic hominins and present-day humans. First, we inferred differences in circadian gene sequences, splicing, and regulation between archaic hominins and modern humans. We identified 28 circadian genes containing variants with potential to alter splicing in archaics (e.g., CLOCK, PER2, RORB, RORC), and 16 circadian genes likely divergently regulated between present-day humans and archaic hominins, including RORA. These differences suggest the potential for introgression to modify circadian gene expression. Testing this hypothesis, we found that introgressed variants are enriched among eQTLs for circadian genes. Supporting the functional relevance of these regulatory effects, we found that many introgressed alleles have associations with chronotype. Strikingly, the strongest introgressed effects on chronotype increase morningness, consistent with adaptations to high latitude in other species. Finally, we identified several circadian loci with evidence of adaptive introgression or latitudinal clines in allele frequency. Conclusions These findings identify differences in circadian gene regulation between modern humans and archaic hominins and support the contribution of introgression via coordinated effects on variation in human chronotype.
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Affiliation(s)
| | - Laura L. Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania
| | | | - Colin Brand
- Department of Epidemiology and Biostatistics, University of California, San Francisco
- Bakar Computational Health Sciences Institute, University of California, San Francisco
| | - David Rinker
- Department of Biological Sciences, Vanderbilt University
| | - Justin Siemann
- Department of Biological Sciences, Vanderbilt University
| | | | - John A. Capra
- Department of Epidemiology and Biostatistics, University of California, San Francisco
- Bakar Computational Health Sciences Institute, University of California, San Francisco
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Barber LE, VoPham T, White LF, Roy HK, Palmer JR, Bertrand KA. Circadian Disruption and Colorectal Cancer Incidence in Black Women. Cancer Epidemiol Biomarkers Prev 2023; 32:927-935. [PMID: 36409509 PMCID: PMC10199956 DOI: 10.1158/1055-9965.epi-22-0808] [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: 07/21/2022] [Revised: 10/11/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Animal and experimental studies suggest circadian disruption increases colorectal cancer risk, but evidence in humans is limited. We examined night shift work, chronotype, and residential position within a time zone, proxies for circadian disruption, in relation to colorectal cancer risk. METHODS Participants in the Black Women's Health Study, a prospective cohort of 59,000 Black American women established in 1995, reported history of night shift work and chronotype on follow-up questionnaires. Residential position within a time zone was estimated using participant addresses at each questionnaire cycle. Number of colorectal cancer cases and follow-up duration varied by analysis depending on timing of exposure assessment, ranging from 204 over the 2005 to 2018 night shift work study period to 452 over the 1995 to 2018 residential position study period. Cox proportional hazards regression was used to estimate multivariable-adjusted HRs and 95% confidence intervals (CI). RESULTS Compared with never having worked a night shift, working a night shift for ≥10 years was associated with increased colorectal cancer risk (HR = 1.64; 95% CI, 1.01-2.66). However, shorter duration was not. The HR for evening versus morning chronotype was 0.96 (95% CI, 0.73-1.27). Westward position of residence within a time zone was not associated with colorectal cancer risk (HR per 5-degree longitude increase: 0.92; 95% CI, 0.82-1.03). CONCLUSIONS Our findings suggest a possible increased risk of colorectal cancer associated with long duration night shift work; however, results require confirmation in larger studies. IMPACT Circadian disruption from long-term night shift work may contribute to colorectal cancer development in Black women.
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Affiliation(s)
- Lauren E. Barber
- Department of Epidemiology, Boston University School of Public Health, Boston, MA
- Slone Epidemiology Center at Boston University, Boston, MA
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA
| | - Trang VoPham
- Epidemiology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Laura F. White
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Hemant K. Roy
- Department of Medicine, Baylor College of Medicine, Houston, TX
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Martínez Báez A, Castro Romero I, Chihu Amparan L, Castañeda JR, Ayala G. The Insulin Receptor Substrate 2 Mediates the Action of Insulin on HeLa Cell Migration via the PI3K/Akt Signaling Pathway. Curr Issues Mol Biol 2023; 45:2296-2308. [PMID: 36975518 PMCID: PMC10047682 DOI: 10.3390/cimb45030148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/14/2023] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
Insulin signaling plays an important role in the development and progression of cancer since it is involved in proliferation and migration processes. It has been shown that the A isoform of the insulin receptor (IR-A) is often overexpressed, and its stimulation induces changes in the expression of the insulin receptor substrates (IRS-1 and IRS-2), which are expressed differently in the different types of cancer. We study the participation of the insulin substrates IRS-1 and IRS-2 in the insulin signaling pathway in response to insulin and their involvement in the proliferation and migration of the cervical cancer cell line. Our results showed that under basal conditions, the IR-A isoform was predominantly expressed. Stimulation of HeLa cells with 50 nM insulin led to the phosphorylation of IR-A, showing a statistically significant increase at 30 min (p ≤ 0.05). Stimulation of HeLa cells with insulin induces PI3K and AKT phosphorylation through the activation of IRS2, but not IRS1. While PI3K reached the highest level at 30 min after treatment (p ≤ 0.05), AKT had the highest levels from 15 min (p ≤ 0.05) and remained constant for 6 h. ERK1 and ERK2 expression was also observed, but only ERK2 was phosphorylated in a time-dependent manner, reaching a maximum peak 5 min after insulin stimulation. Although no effect on cell proliferation was observed, insulin stimulation of HeLa cells markedly promoted cell migration.
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Affiliation(s)
- Anabel Martínez Báez
- Infection Disease Research Center, National Institute of Public Health, Cuernavaca 62100, Mexico
| | - Ivone Castro Romero
- Subdirectorate of Training and Medical Update, Secretary of Health, Mexico City 06900, Mexico
| | - Lilia Chihu Amparan
- Infection Disease Research Center, National Institute of Public Health, Cuernavaca 62100, Mexico
| | | | - Guadalupe Ayala
- Infection Disease Research Center, National Institute of Public Health, Cuernavaca 62100, Mexico
- Correspondence:
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Chen X, Li H, Liu X, Wu Y, Feng Q. Are sleep duration, sleep apnea, and shift work associated with colorectal cancer risk? J Gastrointest Oncol 2023; 14:474-475. [PMID: 36915425 PMCID: PMC10007925 DOI: 10.21037/jgo-22-1179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/09/2023] [Indexed: 03/03/2023] Open
Affiliation(s)
- Xinyang Chen
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hancong Li
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoyin Liu
- Department of Neurosurgery, West China Medical School, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Wu
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Qingbo Feng
- Department of Liver Surgery and Liver Transplantation Centre, West China Hospital, Sichuan University, Chengdu, China
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Wang G, Wang JJ, Lin CH, Zhou Q, Wang WL, Qin T, Li X, Wang ZJ. Association of sleep duration, sleep apnea, and shift work with risk of colorectal neoplasms: a systematic review and meta-analysis. J Gastrointest Oncol 2022; 13:1805-1817. [PMID: 36092341 PMCID: PMC9459215 DOI: 10.21037/jgo-22-682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/10/2022] [Indexed: 11/06/2022] Open
Abstract
Background Although studies have reported that certain sleep characteristics, such as sleep duration and sleep apnea, are linked to the risk of colorectal cancer (CRC), this link remains contentious because of the limited evidence from individual studies. Furthermore, evidence indicated that shift work involving circadian disruption as a probable human carcinogen. This systematic review and meta-analysis aimed to examine the associations between sleep duration, sleep apnea, and shift work with the risk of colorectal neoplasms, including CRC and colorectal adenoma (CRA). Methods We conducted a comprehensive literature search in PubMed, Embase, and Web of Science databases. The inclusion criteria were determined using PICOS principles. Observational studies reporting associations of sleep duration, sleep apnea, or shift work with risk of CRC or CRA were included. We assessed the risk of bias on the basis of the Newcastle-Ottawa Scale. Results A total of 18 observational studies were included. Of these studies, nine studies reported the effect of sleep duration on risk of colorectal neoplasms, five reported the effect of sleep apnea, and six reported the effect of shift work. The relative risk (RR) for colorectal neoplasms was 1.06 [95% confidence interval (CI): 0.94, 1.20] in the short sleep duration group compared with the moderate sleep duration group. Long sleep duration was associated with an increased risk of colorectal neoplasms (RR: 1.33, 95% CI: 1.07, 1.65). The pooled results showed that sleep apnea was associated with an increased risk of colorectal neoplasms (RR: 1.75, 95% CI: 1.56, 1.97). Furthermore, results showed that the association between shift work and the risk of colorectal neoplasms was not significant (RR: 1.06, 95% CI: 0.95, 1.17). No publication bias was observed in all the analyses (all P>0.05). The sensitivity analysis showed that no individual study substantially influenced the pooled RRs for colorectal neoplasms and CRC. Conclusions Our findings suggest the significant positive association of long sleep duration and sleep apnea with risk of colorectal neoplasms and CRC. Given that sleep characteristics may be a potentially modifiable risk factor for colorectal neoplasms, further understanding of its role in carcinogenesis will provide valuable insight for cancer prevention.
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Affiliation(s)
- Gang Wang
- Department of Gastrointestinal Surgery, the Affiliated Hospital of Guizhou Medical University, Guiyang, China.,Department of Gastrointestinal surgery, the Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, China
| | - Jian-Jiang Wang
- Department of General Surgery, People's Hospital of Yinjiang Autonomous County, Tongren, China
| | - Chao-Huang Lin
- Department of Gastrointestinal surgery, the Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, China
| | - Qing Zhou
- Department of Gastrointestinal surgery, the Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, China
| | - Wei-Long Wang
- Department of Gastrointestinal surgery, the Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, China
| | - Tao Qin
- Department of Gastrointestinal surgery, the Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, China
| | - Xin Li
- Department of General Surgery, People's Hospital of Yinjiang Autonomous County, Tongren, China
| | - Ze-Jun Wang
- Department of Gastrointestinal Surgery, the Affiliated Hospital of Guizhou Medical University, Guiyang, China.,Department of Gastrointestinal surgery, the Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, China
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Analysis of Cross-Association between mRNA Expression and RNAi Efficacy for Predictive Target Discovery in Colon Cancers. Cancers (Basel) 2020; 12:cancers12113091. [PMID: 33114107 PMCID: PMC7690798 DOI: 10.3390/cancers12113091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/20/2022] Open
Abstract
Simple Summary This study focused on finding genes for which mRNA expression was able to predict the anticancer efficacy of its RNAi treatment. Predictive target discovery is of critical importance in developing biomarker-based strategies of precision medicine. We demonstrated this carrying out cross-association analysis on collateral mRNA expression and RNAi treatment data of ~12,000 genes on a colon cell line panel. The analysis revealed several genes with significant association between mRNA expression level and the inhibitory efficacy of its RNAi treatment. The experimental validation confirm that this simple approach has general applications for studying gene association between omics data from diverse cancer lineages. Abstract The availability of large-scale, collateral mRNA expression and RNAi data from diverse cancer cell types provides useful resources for the discovery of anticancer targets for which inhibitory efficacy can be predicted from gene expression. Here, we calculated bidirectional cross-association scores (predictivity and descriptivity) for each of approximately 18,000 genes identified from mRNA and RNAi (i.e., shRNA and sgRNA) data from colon cancer cell lines. The predictivity score measures the difference in RNAi efficacy between cell lines with high vs. low expression of the target gene, while the descriptivity score measures the differential mRNA expression between groups of cell lines exhibiting high vs. low RNAi efficacy. The mRNA expression of 90 and 74 genes showed significant (p < 0.01) cross-association scores with the shRNA and sgRNA data, respectively. The genes were found to be from diverse molecular classes and have different functions. Cross-association scores for the mRNA expression of six genes (CHAF1B, HNF1B, HTATSF1, IRS2, POLR2B and SATB2) with both shRNA and sgRNA efficacy were significant. These genes were interconnected in cancer-related transcriptional networks. Additional experimental validation confirmed that siHNF1B efficacy is correlated with HNF1B mRNA expression levels in diverse colon cancer cell lines. Furthermore, KIF26A and ZIC2 gene expression, with which shRNA efficacy displayed significant scores, were found to correlate with the survival rate from colon cancer patient data. This study demonstrates that bidirectional predictivity and descriptivity calculations between mRNA and RNAi data serve as useful resources for the discovery of predictive anticancer targets.
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