251
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Liu H, Xu H, Lan X, Cao X, Pan C. The InDel variants of sheep IGF2BP1 gene are associated with growth traits. Anim Biotechnol 2021; 34:134-142. [PMID: 34255980 DOI: 10.1080/10495398.2021.1942029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) plays positive roles in the growth, proliferation of cells and early embryos development by binding mRNA targets. Recently, it had been shown that some polymorphic loci within IGF2BP1 gene were associated with growth traits in animals, especially in goats. Therefore, it has been hypothesized that some variants within IGF2BP1 gene may be also involved in growth traits of sheep. Nine insertion/deletion (InDel) mutations within IGF2BP1 were identified and three loci were polymorphic. Meanwhile, the association analyses between three InDels and growth traits were carried out in 745 sheep. The results showed that all InDels included 5 bp InDel in downstream region, 9 bp InDel in intron 4 and 15 bp InDel in intron 2 within IGF2BP1 were significantly associated with growth traits (p<.05). Furthermore, at 5 and 9 bp InDel loci, the individuals of heterozygous genotype (ID) had superior growing performance especially at body weight (BW). In all, three InDels were crucial variants correlated with growth traits and could be applied in marker-assisted selection (MAS) in sheep.
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Affiliation(s)
- Hongfei Liu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, P. R. China.,College of Animal Science and Technology, Northwest A&F University, Yangling, P. R. China
| | - Hongwei Xu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, P. R. China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, P. R. China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, P. R. China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, P. R. China
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252
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The biological function of IGF2BPs and their role in tumorigenesis. Invest New Drugs 2021; 39:1682-1693. [PMID: 34251559 DOI: 10.1007/s10637-021-01148-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/30/2021] [Indexed: 01/09/2023]
Abstract
The insulin-like growth factor-2 mRNA-binding proteins (IGF2BPs) pertain to a highly conservative RNA-binding family that works as a post-transcriptional fine-tuner for target transcripts. Emerging evidence suggests that IGF2BPs regulate RNA processing and metabolism, including stability, translation, and localization, and are involved in various cellular functions and pathophysiologies. In this review, we summarize the roles and molecular mechanisms of IGF2BPs in cancer development and progression. We mainly discuss the functional relevance of IGF2BPs in embryo development, neurogenesis, metabolism, RNA processing, and tumorigenesis. Understanding IGF2BPs role in tumor progression will provide new insight into cancer pathophysiology.
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253
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Zheng J, Guo J, Cao B, Zhou Y, Tong J. Identification and validation of lncRNAs involved in m6A regulation for patients with ovarian cancer. Cancer Cell Int 2021; 21:363. [PMID: 34238292 PMCID: PMC8268297 DOI: 10.1186/s12935-021-02076-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
Background Both N6-methyladenosine (m6A) modification and lncRNAs play an important role in the carcinogenesis and cancer inhibition of ovarian cancer (OC). However, lncRNAs involved in m6A regulation (LI-m6As) have never been reported in OC. Herein, we aimed to identify and validate a signature based on LI-m6A for OC. Methods RNA sequencing profiles with corresponding clinical information associated with OC and 23 m6A regulators were extracted from TCGA. The Pearson correlation coefficient (PCC) between lncRNAs and 23 m6A regulators (|PCC|> 0.4 and p < 0.01) was calculated to identify LI-m6As. The LI-m6As with significant prognostic value were screened based on univariate Cox regression analysis to construct a risk model by LASSO Cox regression. Gene Set Enrichment Analysis (GSEA) was implemented to survey the biological functions of the risk groups. Several clinicopathological characteristics were utilized to evaluate their ability to predict prognosis, and a nomogram was constructed to evaluate the accuracy of survival prediction. Besides, immune microenvironment, checkpoint, and drug sensitivity in the two risk groups were compared using comprehensive algorithms. Finally, real-time qPCR analysis and cell counting kit-8 assays were performed on an alternative lncRNA, CACNA1G-AS1. Results The training cohort involving 258 OC patients and the validation cohort involving 111 OC patients were downloaded from TCGA. According to the PCC between the m6A regulators and lncRNAs, 129 LI-m6As were obtained to perform univariate Cox regression analysis and then 10 significant prognostic LI-m6As were identified. A prognostic signature containing four LI-m6As (AC010894.3, ACAP2-IT1, CACNA1G-AS1, and UBA6-AS1) was constructed according to the LASSO Cox regression analysis of the 10 LI-m6As. The prognostic signature was validated to show completely opposite prognostic value in the two risk groups and adverse overall survival (OS) in several clinicopathological characteristics. GSEA indicated that differentially expressed genes in disparate risk groups were enriched in several tumor-related pathways. At the same time, we found significant differences in some immune cells and chemotherapeutic agents between the two groups. An alternative lncRNA, CACNA1G-AS1, was proven to be upregulated in 30 OC specimens and 3 OC cell lines relative to control. Furthermore, knockdown of CACNA1G‐AS1 was proven to restrain the multiplication capacity of OC cells. Conclusions Based on the four LI-m6As (AC010894.3, ACAP2-IT1, CACNA1G-AS1, and UBA6-AS1), the risk model we identified can independently predict the OS and therapeutic value of OC. CACNA1G‐AS1 was preliminarily proved to be a malignant lncRNA. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02076-7.
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Affiliation(s)
- Jianfeng Zheng
- Department of Obstetrics and Gynecology, Affiliated Hangzhou Hospital, Nanjing Medical University, Hangzhou, 310008, Zhejiang Province, China.,Department of Obstetrics and Gynecology, Hangzhou Women's Hospital, Hangzhou, 310008, Zhejiang Province, China
| | - Jialu Guo
- Department of Obstetrics and Gynecology, Hangzhou Women's Hospital, Hangzhou, 310008, Zhejiang Province, China.,Department of Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310006, Zhejiang Province, China
| | - Benben Cao
- Department of Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310006, Zhejiang Province, China
| | - Ying Zhou
- Department of Obstetrics and Gynecology, Affiliated Hangzhou Hospital, Nanjing Medical University, Hangzhou, 310008, Zhejiang Province, China.,Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310008, Zhejiang Province, China
| | - Jinyi Tong
- Department of Obstetrics and Gynecology, Affiliated Hangzhou Hospital, Nanjing Medical University, Hangzhou, 310008, Zhejiang Province, China. .,Department of Obstetrics and Gynecology, Hangzhou Women's Hospital, Hangzhou, 310008, Zhejiang Province, China.
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254
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Laine VN, Verschuuren M, van Oers K, Espín S, Sánchez-Virosta P, Eeva T, Ruuskanen S. Does Arsenic Contamination Affect DNA Methylation Patterns in a Wild Bird Population? An Experimental Approach. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8947-8954. [PMID: 34110128 DOI: 10.1101/2020.12.08.415745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Pollutants, such as toxic metals, negatively influence organismal health and performance, even leading to population collapses. Studies in model organisms have shown that epigenetic marks, such as DNA methylation, can be modulated by various environmental factors, including pollutants, influencing gene expression, and various organismal traits. Yet experimental data on the effects of pollution on DNA methylation from wild animal populations are largely lacking. We here experimentally investigated for the first time the effects of early-life exposure to environmentally relevant levels of a key pollutant, arsenic (As), on genome-wide DNA methylation in a wild bird population. We experimentally exposed nestlings of great tits (Parus major) to arsenic during their postnatal developmental period (3 to 14 days post-hatching) and compared their erythrocyte DNA methylation levels to those of respective controls. In contrast to predictions, we found no overall hypomethylation in the arsenic group. We found evidence for loci to be differentially methylated between the treatment groups, but for five CpG sites only. Three of the sites were located in gene bodies of zinc finger and BTB domain containing 47 (ZBTB47), HIVEP zinc finger 3 (HIVEP3), and insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1). Further studies are needed to evaluate whether epigenetic dysregulation is a commonly observed phenomenon in polluted populations and what are the consequences for organism functioning and for population dynamics.
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Affiliation(s)
- Veronika N Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen 6708 PB, The Netherlands
| | - Mark Verschuuren
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen 6708 PB, The Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen 6708 PB, The Netherlands
| | - Silvia Espín
- Area of Toxicology, Department of Socio-Sanitary Sciences, University of Murcia, Murcia 30003, Spain
- Department of Biology, University of Turku, Turku 20500, Finland
| | - Pablo Sánchez-Virosta
- Area of Toxicology, Department of Socio-Sanitary Sciences, University of Murcia, Murcia 30003, Spain
- Department of Biology, University of Turku, Turku 20500, Finland
| | - Tapio Eeva
- Department of Biology, University of Turku, Turku 20500, Finland
| | - Suvi Ruuskanen
- Department of Biology, University of Turku, Turku 20500, Finland
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
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255
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Laine V, Verschuuren M, van Oers K, Espín S, Sánchez-Virosta P, Eeva T, Ruuskanen S. Does Arsenic Contamination Affect DNA Methylation Patterns in a Wild Bird Population? An Experimental Approach. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8947-8954. [PMID: 34110128 PMCID: PMC8277128 DOI: 10.1021/acs.est.0c08621] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Pollutants, such as toxic metals, negatively influence organismal health and performance, even leading to population collapses. Studies in model organisms have shown that epigenetic marks, such as DNA methylation, can be modulated by various environmental factors, including pollutants, influencing gene expression, and various organismal traits. Yet experimental data on the effects of pollution on DNA methylation from wild animal populations are largely lacking. We here experimentally investigated for the first time the effects of early-life exposure to environmentally relevant levels of a key pollutant, arsenic (As), on genome-wide DNA methylation in a wild bird population. We experimentally exposed nestlings of great tits (Parus major) to arsenic during their postnatal developmental period (3 to 14 days post-hatching) and compared their erythrocyte DNA methylation levels to those of respective controls. In contrast to predictions, we found no overall hypomethylation in the arsenic group. We found evidence for loci to be differentially methylated between the treatment groups, but for five CpG sites only. Three of the sites were located in gene bodies of zinc finger and BTB domain containing 47 (ZBTB47), HIVEP zinc finger 3 (HIVEP3), and insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1). Further studies are needed to evaluate whether epigenetic dysregulation is a commonly observed phenomenon in polluted populations and what are the consequences for organism functioning and for population dynamics.
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Affiliation(s)
- Veronika
N. Laine
- Department
of Animal Ecology, Netherlands Institute
of Ecology (NIOO-KNAW), Wageningen 6708 PB, The Netherlands
| | - Mark Verschuuren
- Department
of Animal Ecology, Netherlands Institute
of Ecology (NIOO-KNAW), Wageningen 6708 PB, The Netherlands
| | - Kees van Oers
- Department
of Animal Ecology, Netherlands Institute
of Ecology (NIOO-KNAW), Wageningen 6708 PB, The Netherlands
| | - Silvia Espín
- Area
of Toxicology, Department of Socio-Sanitary Sciences, University of Murcia, Murcia 30003, Spain
- Department
of Biology, University of Turku, Turku 20500, Finland
| | - Pablo Sánchez-Virosta
- Area
of Toxicology, Department of Socio-Sanitary Sciences, University of Murcia, Murcia 30003, Spain
- Department
of Biology, University of Turku, Turku 20500, Finland
| | - Tapio Eeva
- Department
of Biology, University of Turku, Turku 20500, Finland
| | - Suvi Ruuskanen
- Department
of Biology, University of Turku, Turku 20500, Finland
- Department
of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
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256
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Insulin-Like Growth Factor 2 mRNA-Binding Protein 1 (IGF2BP1) Is a Prognostic Biomarker and Associated with Chemotherapy Responsiveness in Colorectal Cancer. Int J Mol Sci 2021; 22:ijms22136940. [PMID: 34203267 PMCID: PMC8267666 DOI: 10.3390/ijms22136940] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/12/2021] [Accepted: 06/24/2021] [Indexed: 12/18/2022] Open
Abstract
Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) is an RNA-binding protein and serves as a post-transcriptional fine-tuner regulating the expression of mRNA targets. However, the clinicopathological roles of IGF2BP1 in colorectal cancer (CRC) remains limited. Thus, we aimed to elucidate the clinical significance and biomarker potentials of IGF2BP1 in CRC. A total of 266 specimens from two sets of CRC patients were collected. IGF2BP1 expression was studied by immunohistochemical (IHC) staining. The Kaplan-Meier survival plot and a log-rank test were used for survival analysis. The Cox proportional hazards model was applied to determine the survival impact of IGF2BP1. Public datasets sets from The Cancer Genome Atlas (TCGA) and Human Cancer Metastasis Database (HCMDB), receiver operating characteristic (ROC) plotter, and two CRC cell lines, HCT-116 and DLD-1, were used for validating our findings. We showed that IGF2BP1 was overexpressed in tumor specimens compared to 13 paired normal parts by examining the immunoreactivity of IGF2BP1 (p = 0.045). The increased expression of IGF2BP1 in primary tumor parts was observed regardless of metastatic status (p < 0.001) in HCMDB analysis. IGF2BP1 expression was significantly associated with young age (59.6% vs. 46.7%, p-value = 0.043) and advanced stage (61.3% vs. 40.0%, p-value = 0.001). After controlling for confounding factors, IGF2BP1 remained an independent prognostic factor (HR = 1.705, p-value = 0.005). TCGA datasets analysis indicated that high IGF2BP1 expression showed a lower 5-year survival rate (58% vs. 65%) in CRC patients. The increased expression of IGF2BP1 in chemotherapy non-responder rectal cancer patients was observed using a ROC plotter. Overexpression of IGF2BP1 promoted the colony-forming capacity and 5-fluorouracil and etoposide resistance in CRC cells. Here, IGF2BP1 was an independent poor prognostic marker in CRC patients and contributed to aggressive phenotypes in CRC cell lines.
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257
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Zhong S, Lin Z, Chen H, Mao L, Feng J, Zhou S. The m 6A-related gene signature for predicting the prognosis of breast cancer. PeerJ 2021; 9:e11561. [PMID: 34141492 PMCID: PMC8183431 DOI: 10.7717/peerj.11561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/13/2021] [Indexed: 11/20/2022] Open
Abstract
N6-methyladenosine (m6A) modification has been shown to participate in tumorigenesis and metastasis of human cancers. The present study aimed to investigate the roles of m6A RNA methylation regulators in breast cancer. We used LASSO regression to identify m6A-related gene signature predicting breast cancer survival with the datasets downloaded from Gene Expression Omnibus and The Cancer Genome Atlas (TCGA). RNA-Seq data of 3409 breast cancer patients from GSE96058 and 1097 from TCGA were used in present study. A 10 m6A-related gene signature associated with prognosis was identified from 22 m6A RNA methylation regulators. The signature divided patients into low- and high-risk group. High-risk patients had a worse prognosis than the low-risk group. Further analyses indicated that IGF2BP1 may be a key m6A RNA methylation regulator in breast cancer. Survival analysis showed that IGF2BP1 is an independent prognostic factor of breast cancer, and higher expression level of IGF2BP1 is associated with shorter overall survival of breast cancer patients. In conclusion, we identified a 10 m6A-related gene signature associated with overall survival of breast cancer. IGF2BP1 may be a key m6A RNA methylation regulator in breast cancer.
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Affiliation(s)
- Shanliang Zhong
- Center of Clinical Laboratory Science, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Zhenzhong Lin
- Department of Pathology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Huanwen Chen
- Xinglin laboratory, The First Affiliated Hospital of Xiamen University, Nanjing, China
| | - Ling Mao
- Department of Thyroid Breast Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Jifeng Feng
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Siying Zhou
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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258
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Feng G, Zhao J, Lei J, Wang L, Wang S, Zhang T, Lu H. Identification of Igf2bp1 gene family and effect on chicken myoblast proliferation. JOURNAL OF APPLIED ANIMAL RESEARCH 2021. [DOI: 10.1080/09712119.2021.1932916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Guang Feng
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Jiarong Zhao
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Jingjing Lei
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Ling Wang
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Shanshan Wang
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Tao Zhang
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Hongzhao Lu
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, People’s Republic of China
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259
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Korn SM, Ulshöfer CJ, Schneider T, Schlundt A. Structures and target RNA preferences of the RNA-binding protein family of IGF2BPs: An overview. Structure 2021; 29:787-803. [PMID: 34022128 DOI: 10.1016/j.str.2021.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/12/2021] [Accepted: 04/30/2021] [Indexed: 02/08/2023]
Abstract
Insulin-like growth factor 2 mRNA-binding proteins (IMPs, IGF2BPs) act in mRNA transport and translational control but are oncofetal tumor marker proteins. The IMP protein family represents a number of bona fide multi-domain RNA-binding proteins with up to six RNA-binding domains, resulting in a high complexity of possible modes of interactions with target mRNAs. Their exact mechanism in stability control of oncogenic mRNAs is only partially understood. Our and other laboratories' recent work has significantly pushed the understanding of IMP protein specificities both toward RNA engagement and between each other from NMR and crystal structures serving the basis for systematic biochemical and functional investigations. We here summarize the known structural and biochemical information about IMP RNA-binding domains and their RNA preferences. The article also touches on the respective roles of RNA secondary and protein tertiary structures for specific RNA-protein complexes, including the limited knowledge about IMPs' protein-protein interactions, which are often RNA mediated.
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Affiliation(s)
- Sophie Marianne Korn
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Corinna Jessica Ulshöfer
- Institute of Biochemistry, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Tim Schneider
- Institute of Biochemistry, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.
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260
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Haftorn KL, Lee Y, Denault WRP, Page CM, Nustad HE, Lyle R, Gjessing HK, Malmberg A, Magnus MC, Næss Ø, Czamara D, Räikkönen K, Lahti J, Magnus P, Håberg SE, Jugessur A, Bohlin J. An EPIC predictor of gestational age and its application to newborns conceived by assisted reproductive technologies. Clin Epigenetics 2021; 13:82. [PMID: 33875015 PMCID: PMC8056641 DOI: 10.1186/s13148-021-01055-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/11/2021] [Indexed: 01/11/2023] Open
Abstract
Background Gestational age is a useful proxy for assessing developmental maturity, but correct estimation of gestational age is difficult using clinical measures. DNA methylation at birth has proven to be an accurate predictor of gestational age. Previous predictors of epigenetic gestational age were based on DNA methylation data from the Illumina HumanMethylation 27 K or 450 K array, which have subsequently been replaced by the Illumina MethylationEPIC 850 K array (EPIC). Our aims here were to build an epigenetic gestational age clock specific for the EPIC array and to evaluate its precision and accuracy using the embryo transfer date of newborns from the largest EPIC-derived dataset to date on assisted reproductive technologies (ART). Methods We built an epigenetic gestational age clock using Lasso regression trained on 755 randomly selected non-ART newborns from the Norwegian Study of Assisted Reproductive Technologies (START)—a substudy of the Norwegian Mother, Father, and Child Cohort Study (MoBa). For the ART-conceived newborns, the START dataset had detailed information on the embryo transfer date and the specific ART procedure used for conception. The predicted gestational age was compared to clinically estimated gestational age in 200 non-ART and 838 ART newborns using MM-type robust regression. The performance of the clock was compared to previously published gestational age clocks in an independent replication sample of 148 newborns from the Prediction and Prevention of Preeclampsia and Intrauterine Growth Restrictions (PREDO) study—a prospective pregnancy cohort of Finnish women. Results Our new epigenetic gestational age clock showed higher precision and accuracy in predicting gestational age than previous gestational age clocks (R2 = 0.724, median absolute deviation (MAD) = 3.14 days). Restricting the analysis to CpGs shared between 450 K and EPIC did not reduce the precision of the clock. Furthermore, validating the clock on ART newborns with known embryo transfer date confirmed that DNA methylation is an accurate predictor of gestational age (R2 = 0.767, MAD = 3.7 days). Conclusions We present the first EPIC-based predictor of gestational age and demonstrate its robustness and precision in ART and non-ART newborns. As more datasets are being generated on the EPIC platform, this clock will be valuable in studies using gestational age to assess neonatal development. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01055-z.
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Affiliation(s)
- Kristine L Haftorn
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway. .,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway. .,Institute of Health and Society, University of Oslo, Oslo, Norway.
| | - Yunsung Lee
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - William R P Denault
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Mathematics, University of Oslo, Oslo, Norway
| | - Haakon E Nustad
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Deepinsight, Karl Johans Gate 8, Oslo, Norway
| | - Robert Lyle
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Anni Malmberg
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Bristol Medical School, Population Health Sciences, Bristol, UK
| | - Øyvind Næss
- Institute of Health and Society, University of Oslo, Oslo, Norway.,Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Jon Bohlin
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Division for Infection Control and Environmental Health, Department of Infectious Disease Epidemiology and Modelling, Norwegian Institute of Public Health, Oslo, Norway
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261
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Xie F, Huang C, Liu F, Zhang H, Xiao X, Sun J, Zhang X, Jiang G. CircPTPRA blocks the recognition of RNA N 6-methyladenosine through interacting with IGF2BP1 to suppress bladder cancer progression. Mol Cancer 2021; 20:68. [PMID: 33853613 PMCID: PMC8045402 DOI: 10.1186/s12943-021-01359-x] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 04/06/2021] [Indexed: 12/20/2022] Open
Abstract
Background Circular RNAs (circRNAs) have been found to have significant impacts on bladder cancer (BC) progression through various mechanisms. In this study, we aimed to identify novel circRNAs that regulate the function of IGF2BP1, a key m6A reader, and explore the regulatory mechanisms and clinical significances in BC. Methods Firstly, the clinical role of IGF2BP1 in BC was studied. Then, RNA immunoprecipitation sequencing (RIP-seq) analysis was performed to identify the circRNAs interacted with IGF2BP1 in BC cells. The overall biological roles of IGF2BP1 and the candidate circPTPRA were investigated in both BC cell lines and animal xenograft studies. Subsequently, we evaluated the regulation effects of circPTPRA on IGF2BP1 and screened out its target genes through RNA sequencing. Finally, we explored the underlying molecular mechanisms that circPTPRA might act as a blocker in recognition of m6A. Results We demonstrated that IGF2BP1 was predominantly binded with circPTPRA in the cytoplasm in BC cells. Ectopic expression of circPTPRA abolished the promotion of cell proliferation, migration and invasion of BC cells induced by IGF2BP1. Importantly, circPTPRA downregulated IGF2BP1-regulation of MYC and FSCN1 expression via interacting with IGF2BP1. Moreover, the recognition of m6A-modified RNAs mediated by IGF2BP1 was partly disturbed by circPTPRA through its interaction with KH domains of IGF2BP1. Conclusions This study identifies exonic circular circPTPRA as a new tumor suppressor that inhibits cancer progression through endogenous blocking the recognition of IGF2BP1 to m6A-modified RNAs, indicating that circPTPRA may serve as an exploitable therapeutic target for patients with BC. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01359-x.
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Affiliation(s)
- Fei Xie
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, 266013, China
| | - Chao Huang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Feng Liu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hui Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xingyuan Xiao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jiayin Sun
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Guosong Jiang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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262
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Wang J, Yuan X, Ding N. IGF2BP2 knockdown inhibits LPS-induced pyroptosis in BEAS-2B cells by targeting caspase 4, a crucial molecule of the non-canonical pyroptosis pathway. Exp Ther Med 2021; 21:593. [PMID: 33884031 PMCID: PMC8056110 DOI: 10.3892/etm.2021.10025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/01/2021] [Indexed: 12/29/2022] Open
Abstract
Insulin-like growth factor 2 (IGF2) mRNA-binding protein 2 (IGF2BP2) is a secreted protein that can bind to IGF2 and has been reported to promote inflammation. The data from the ENCORI database have predicted that IGF2BP2 can bind caspase 4, which mediates pyroptosis and promotes airway inflammation and lipopolysaccharide (LPS)-induced lung injury. The present study investigated whether IGF2BP2 can regulate LPS-induced lung cell inflammation by targeting caspase 4. Therefore, the non-tumorigenic lung epithelial cell line Beas-2B was transfected with short hairpin RNA (shRNA)-IGF2BP2 and stimulated with LPS. A number of parameters, including cell viability, production of interleukin (IL)-1β and IL-18, activation of gasdermin D (GSDMD) and the expression levels of IGF2BP2, caspase 4 and cleaved-caspase 1, were subsequently assessed using CCK-8, ELISA kits, western blotting and immunofluorescence staining, respectively. RNA pull-down assay was used to probe the possible interaction between IGF2BP2 and caspase 4 RNA. LPS treatment was found to inhibit cell viability, trigger IL-1β and IL-18 production and increase IGF2BP2 expression in a concentration-dependent manner. Compared with cells transfected with shRNA-negative control, cells that were transfected with shRNA-IGF2BP2 exhibited enhanced cell viability, reduced IL-1β and IL-18 concentrations, decreased GSDMD activation in addition to reduced expression levels of caspase 4 and cleaved-caspase 1 following stimulation with 1 µg/ml LPS. Concomitantly, the effects of IGF2BP2 silencing on caspase 4 expression were higher compared with those noted on caspase 1. In addition, binding of IGF2BP2 to caspase 4 RNA was also observed. To conclude, data from the present study suggest that IGF2BP2 knockdown inhibited LPS-induced Beas-2B cell inflammation by targeting caspase 4, thereby inhibiting the non-canonical pyroptosis pathway.
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Affiliation(s)
- Jing Wang
- Department of Emergency Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Xiaoli Yuan
- Department of Emergency Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Ning Ding
- Department of Emergency Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
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263
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Tuo H, Yao B, He B, Yu S, Li D, Li W, Jin L. Silence of Insulin-Like Growth Factor 2 mRNA-Binding Protein 1 Prevents Vascular Smooth Muscle Cells Proliferation via Nuclear Factor of Activated T Cells Isoform-3/Ca 2+/Calmodulin Pathway. J BIOMATER TISS ENG 2021. [DOI: 10.1166/jbt.2021.2747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Increased proliferation of vascular smooth muscle cells (VSMCs) contributes to the pathogenesis of atherosclerosis (AS), and the insulin like growth factor 2 (IGF2) is involved in AS through effects on VSMCs growth and migration. The IGF2 mRNA-binding protein 1(IGF2BP1) is a secreted
protein that can bind to IGF2 and regulate its localization, however, whether IGF2BP1 could regulate VSMCs proliferation remains to be elucidated. This study aimed to investigate the role of IGF2BP1 in VSMCs proliferation and uncover the potential mechanism. Primary human aortic VSMCs that
transfected with or without shRNA-IGF2BP1 were stimulated by platelet-derived growth factor-BB (PDGF-BB), and then cell proliferation, intracellular Ca2+ level, cell apoptosis and the expression of IGF2BP1, calmodulin (CaM) and cell cycle-related proteins were detected. RNA pull
down assay was used to determine the interaction between IGF2BP1 and nuclear factor of activated T cells isoform-3 (NFATc3). We found that PDGF-BB promoted cell proliferation and enhanced IGF2BP1 protein expression in a concentration-dependent manner. The 10 μg/L PDGF-BB significantly increased
intracellular Ca2+ level, NFATc3, CaM and calcineurin A protein expression, TUNEL-positive cells, and the expression of cell cycle-related proteins cyclin D1/E1/B1. However, knockdown of IGF2BP1 significantly blunted all these effects induced by PDGF-BB. In addition, IGF2BP1 could
bind to NFATc3 RNA. Collectively, knockdown of IGF2BP1 could inhibit PDGFBB- induced VSMCs proliferation via targeting NFATc3/Ca2+/calmodulin pathway and disturbing the effect of NFATc3/ on cell cycle.
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Affiliation(s)
- Hu Tuo
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan 430060, RP China
| | - Baozhen Yao
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan 430060, RP China
| | - Bing He
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan 430060, RP China
| | - Shiqian Yu
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan 430060, RP China
| | - Danni Li
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan 430060, RP China
| | - Wenjing Li
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan 430060, RP China
| | - Lin Jin
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan 430060, RP China
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264
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Glaß M, Misiak D, Bley N, Müller S, Hagemann S, Busch B, Rausch A, Hüttelmaier S. IGF2BP1, a Conserved Regulator of RNA Turnover in Cancer. Front Mol Biosci 2021; 8:632219. [PMID: 33829040 PMCID: PMC8019740 DOI: 10.3389/fmolb.2021.632219] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 02/02/2021] [Indexed: 12/13/2022] Open
Abstract
The oncofetal IGF2 mRNA-binding protein 1 (IGF2BP1) promotes tumor progression in a variety of solid tumors and its expression is associated with adverse prognosis. The main role proposed for IGF2BP1 in cancer cells is the stabilization of mRNAs encoding pro-oncogenic factors. Several IGF2BP1-RNA association studies, however, revealed a plethora of putative IGF2BP1-RNA targets. Thus, at present the main conserved target RNAs and pathways controlled by IGF2BP1 in cancer remain elusive. In this study, we present a set of genes and cancer hallmark pathways showing a conserved pattern of deregulation in dependence of IGF2BP1 expression in cancer cell lines. By the integrative analysis of these findings with publicly available cancer transcriptome and IGF2BP1-RNA association data, we compiled a set of prime candidate target mRNAs. These analyses confirm a pivotal role of IGF2BP1 in controlling cancer cell cycle progression and reveal novel cancer hallmark pathways influenced by IGF2BP1. For three novel target mRNAs identified by these studies, namely AURKA, HDLBP and YWHAZ, we confirm IGF2BP1 mRNA stabilization. In sum our findings confirm and expand previous findings on the pivotal role of IGF2BP1 in promoting oncogenic gene expression by stabilizing target mRNAs in a mainly 3'UTR, m6A-, miRNA-, and potentially AU-rich element dependent manner.
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Affiliation(s)
- Markus Glaß
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Danny Misiak
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Nadine Bley
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Simon Müller
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Sven Hagemann
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Bianca Busch
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Alexander Rausch
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
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265
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Characterization and Comparative Transcriptomic Analysis of Skeletal Muscle in Pekin Duck at Different Growth Stages Using RNA-Seq. Animals (Basel) 2021; 11:ani11030834. [PMID: 33809502 PMCID: PMC8000258 DOI: 10.3390/ani11030834] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 01/13/2023] Open
Abstract
Simple Summary Skeletal muscle is an important tissue and its development is strictly regulated by genes. In this study, in order to understand the muscle-related gene expression in Pekin duck, RNA-seq was performed to analyze and compare skeletal muscle at different growth stages. Alternative splicing, single nucleotide polymorphisms and insertion–deletions were detected, and 299 novel genes were discovered. MYL4, IGF2BP1, CSRP3, SPP1, KLHL31, LAMB2, LAMA2, ITGB1 and OPN played crucial roles in skeletal muscle development. Oxidative phosphorylation, ECM-receptor interaction, focal adhesion, carbon metabolism, and biosynthesis of amino acids participated in the regulation of skeletal muscle development in Pekin duck. This study provides an important reference for revealing the developmental mechanisms of pectoral and leg muscles in duck. Abstract Skeletal muscle, accounting for approximately 50% of body weight, is the largest and most important tissue. In this study, the gene expression profiles and pathways in skeletal muscle of Pekin duck were investigated and compared at embryonic day 17, 21, and 27 and postnatally at 6 months of age. An average of 49,555,936 reads in each sample was obtained from the transcriptome libraries. Over 70.0% of alternative splicing (AS) in each sample was mainly alternative 5′ first exon (transcription start site)—the first exon splicing (TSS) and alternative 3′ last exon (transcription terminal site)—the last exon splicing (TTS), indicating that TSS and TTS were the most common AS event in Pekin ducks, and these AS events were closely related to the regulation of muscle development at different growth stages. The results provided a valuable genomic resource for selective breeding and functional studies of genes. A total of 299 novel genes with ≥2 exons were obtained. There were 294 to 2806 differentially expressed genes (DEGs) in each pairwise comparison of Pekin duck. Notably, 90 DEGs in breast muscle and 9 DEGs in leg muscle were co-expressed at all developmental points. DEGs were validated by qPCR analysis, which confirmed the tendency of the expression. DEGs related to muscle development were involved in biological processes such as “endodermal cell differentiation”, “muscle cell cellular homeostasis”, “skeletal muscle tissue growth” and “skeletal muscle cell differentiation”, and were involved in pathways such as oxidative phosphorylation, ECM-receptor (extracellular matrix receptor) interaction, focal adhesion, carbon metabolism, and biosynthesis of amino acids. Some DEGs, including MYL4, IGF2BP1, CSRP3, SPP1 and KLHL31, as well as LAMB2, LAMA2, ITGB1 and OPN, played crucial roles in muscle growth and development. This study provides valuable information about the expression profile of mRNAs and pathways from duck skeletal muscle at different growth stages, and further functional study of these mRNAs and pathways could provide new ideas for studying the molecular networks of growth and development in duck skeletal muscle.
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266
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Biegel JM, Dhamdhere M, Gao S, Gowda CP, Kawasawa YI, Spiegelman VS. Inhibition of the mRNA-Binding Protein IGF2BP1 Suppresses Proliferation and Sensitizes Neuroblastoma Cells to Chemotherapeutic Agents. Front Oncol 2021; 11:608816. [PMID: 33796454 PMCID: PMC8008117 DOI: 10.3389/fonc.2021.608816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/02/2021] [Indexed: 12/13/2022] Open
Abstract
Gain at chromosome 17q21 in neuroblastoma is associated with a poor prognosis, independent of MYCN amplification status. Several potential proto-oncogenes have been identified in this region, one of them-insulin-like growth-factor-2 mRNA binding protein (IGF2BP1)-is expressed at high levels in stage 4 tumors, and associated with overall lower patient survival. Here, we demonstrate that down-regulation of IGF2BP1 activity, either by transcript silencing or chemical inhibition, suppresses neuroblastoma cell growth. Furthermore, the combination of IGF2BP1 inhibition along with commonly used chemotherapeutics that broadly affect DNA synthesis, or cyclin-dependent kinase (CDK) inhibitors that disrupt signal transduction, have a synergistic effect on the suppression of neuroblastoma cell proliferation.
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Affiliation(s)
- Jason M. Biegel
- Division of Hematology and Oncology, Pediatric Department, Penn State College of Medicine, Hershey, PA, United States
| | - Mayura Dhamdhere
- Division of Hematology and Oncology, Pediatric Department, Penn State College of Medicine, Hershey, PA, United States
| | - Shuang Gao
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, United States
| | - Chethana P. Gowda
- Division of Hematology and Oncology, Pediatric Department, Penn State College of Medicine, Hershey, PA, United States
| | - Yuka Imamura Kawasawa
- Departments of Pharmacology and Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, United States
| | - Vladimir S. Spiegelman
- Division of Hematology and Oncology, Pediatric Department, Penn State College of Medicine, Hershey, PA, United States
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267
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Novel Regulators of the IGF System in Cancer. Biomolecules 2021; 11:biom11020273. [PMID: 33673232 PMCID: PMC7918569 DOI: 10.3390/biom11020273] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023] Open
Abstract
The insulin-like growth factor (IGF) system is a dynamic network of proteins, which includes cognate ligands, membrane receptors, ligand binding proteins and functional downstream effectors. It plays a critical role in regulating several important physiological processes including cell growth, metabolism and differentiation. Importantly, alterations in expression levels or activation of components of the IGF network are implicated in many pathological conditions including diabetes, obesity and cancer initiation and progression. In this review we will initially cover some general aspects of IGF action and regulation in cancer and then focus in particular on the role of transcriptional regulators and novel interacting proteins, which functionally contribute in fine tuning IGF1R signaling in several cancer models. A deeper understanding of the biological relevance of this network of IGF1R modulators might provide novel therapeutic opportunities to block this system in neoplasia.
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268
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Qiu L, Zheng L, Gan C, Deng W, Sun Y, Wang T. circBICD2 targets miR-149-5p/IGF2BP1 axis to regulate oral squamous cell carcinoma progression. J Oral Pathol Med 2021; 50:668-680. [PMID: 33382158 DOI: 10.1111/jop.13156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/25/2020] [Accepted: 12/28/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND Circular RNAs (circRNAs) are related to oral squamous cell carcinoma (OSCC) progression. circRNA bicaudal D cargo adaptor 2 (circBICD2) has been reported to be abnormally expressed in OSCC. However, the function and mechanism of this circRNA in OSCC progression remain largely unknown. METHODS circBICD2, microRNA-149-5p (miR-149-5p), and insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) abundances were examined via quantitative reverse transcription polymerase chain reaction or Western blot. The function of circBICD2 was investigated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), colony formation, flow cytometry, wound healing, transwell, specific kits, Western blot, and xenograft analyses. Dual-luciferase reporter analysis and RNA immunoprecipitation were carried out to analyze the binding interaction. RESULTS circBICD2 expression was enhanced in OSCC tissues and cells. circBICD2 silence suppressed OSCC cell proliferation, migration, invasion, and glutaminolysis and facilitated apoptosis. miR-149-5p was targeted via circBICD2 and decreased in OSCC tissues and cells. miR-149-5p knockdown attenuated silence of circBICD2 on the influence of OSCC cell proliferation, apoptosis, migration, invasion, and glutaminolysis. IGF2BP1 was targeted via miR-149-5p, and circBICD2 could regulate IGF2BP1 via miR-149-5p. IGF2BP1 interference constrained OSCC cell proliferation, migration, invasion, and glutaminolysis and promoted apoptosis. circBICD2 silence reduced OSCC cell growth in xenograft model. CONCLUSION circBICD2 knockdown repressed OSCC cell proliferation, migration, invasion, and glutaminolysis and increased apoptosis via modulating miR-149-5p/IGF2BP1 axis, which might act as a potential target for OSCC treatment.
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Affiliation(s)
- Lehong Qiu
- Department of Stomatology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Linlin Zheng
- Department of Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University Haikou, Hainan, China
| | - Chengwen Gan
- Department of Stomatology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Wei Deng
- Department of Stomatology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Ying Sun
- Department of Stomatology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Tao Wang
- Department of Stomatology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
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269
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Wu H, Dong H, Fu Y, Tang Y, Dai M, Chen Y, Wang G, Wu Y. Expressions of m6A RNA methylation regulators and their clinical predictive value in cervical squamous cell carcinoma and endometrial adenocarcinoma. Clin Exp Pharmacol Physiol 2021; 48:270-278. [PMID: 33006785 DOI: 10.1111/1440-1681.13412] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 09/11/2020] [Accepted: 09/27/2020] [Indexed: 01/22/2023]
Abstract
The mortality caused by cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) ranks second among female malignant tumour deaths, but their diagnostic and therapeutic targets are still limited. N6-methyladenosine (m6A) is the most common and extensive modification in mRNA molecules, and its methylation regulators participate in regulating the occurrence and development of many tumours. However, whether m6A RNA methylation regulators can be used as independent prognostic indicators of CESC remains unknown. This study unveiled differential expression of 20 m6A RNA methylation regulators between normal and CESC tumour samples, which RNA sequence data and clinical information were obtained from TCGA database. As a result, five m6A RNA methylation regulators (FTO, HNRNPA2B1, RBM15, IGF2BP1, IGF2BP3) were identified to be significantly linked to CESC tumour status. After Lasso cox regression analysis, six m6A RNA methylation regulators (YTHDC2, YTHDC1, ALKBH5, ZC3H13, RBMX, YTHDF1) were chosen to construct a risk signature. CESC patients were then classified as high-risk and low-risk group based on the median risk score. The overall survival (OS) of the CESC patients in high-risk group was significantly lower than that in low-risk group, and the area under curve (AUC) is 0.718. Moreover, the risk model can be an independent prognosis factors for CESC patients and can predict OS of CESC patients with different clinical factors. In conclusion, m6A RNA methylation regulators are closely correlated with CESC clinical characteristics and the selected six m6A RNA methylation regulators may be useful for CESC patients personalized treatment.
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Affiliation(s)
- Hongyuan Wu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Heling Dong
- School of Physical Education, Jinan University, Guangzhou, China
| | - You Fu
- Department of Health Management, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yu Tang
- Department of Health Management, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Meng Dai
- Department of Health Management, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanya Chen
- Department of Obstetrics and Gynecology, Affiliated Dongguan People's Hospital, Southern Medical University, Dongguan, China
| | - Gang Wang
- Department of Radiology, Affiliated Dongguan People's Hospital, Southern Medical University, Dongguan, China
| | - Yifen Wu
- Department of Oncology, Affiliated Dongguan People's Hospital, Southern Medical University, Dongguan, China
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270
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Elcheva IA, Spiegelman VS. Targeting RNA-binding proteins in acute and chronic leukemia. Leukemia 2021; 35:360-376. [PMID: 33149266 PMCID: PMC7868134 DOI: 10.1038/s41375-020-01066-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 01/01/2023]
Abstract
RNA-binding proteins (RBPs) play a crucial role in cellular physiology by regulating RNA processing, translation, and turnover. In neoplasms, RBP support of cancer-relevant expression of alternatively spliced, modified, and stabilized mRNA transcripts is essential to self-renewal, proliferation, and adaptation to stress. In this review, we assess the impact of key families of RBPs in leukemogenesis, review progress in targeting those proteins with small molecules, and discuss how multilevel composition of posttranscriptional regulation of gene expression could be used for potential therapies in acute and chronic leukemia.
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Affiliation(s)
- Irina A Elcheva
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Vladimir S Spiegelman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
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271
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Zhu P, He F, Hou Y, Tu G, Li Q, Jin T, Zeng H, Qin Y, Wan X, Qiao Y, Qiu Y, Teng Y, Liu M. A novel hypoxic long noncoding RNA KB-1980E6.3 maintains breast cancer stem cell stemness via interacting with IGF2BP1 to facilitate c-Myc mRNA stability. Oncogene 2021; 40:1609-1627. [PMID: 33469161 PMCID: PMC7932928 DOI: 10.1038/s41388-020-01638-9] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/13/2020] [Accepted: 12/18/2020] [Indexed: 01/13/2023]
Abstract
The hostile hypoxic microenvironment takes primary responsibility for the rapid expansion of breast cancer tumors. However, the underlying mechanism is not fully understood. Here, using RNA sequencing (RNA-seq) analysis, we identified a hypoxia-induced long noncoding RNA (lncRNA) KB-1980E6.3, which is aberrantly upregulated in clinical breast cancer tissues and closely correlated with poor prognosis of breast cancer patients. The enhanced lncRNA KB-1980E6.3 facilitates breast cancer stem cells (BCSCs) self-renewal and tumorigenesis under hypoxic microenvironment both in vitro and in vivo. Mechanistically, lncRNA KB-1980E6.3 recruited insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) to form a lncRNA KB-1980E6.3/IGF2BP1/c-Myc signaling axis that retained the stability of c-Myc mRNA through increasing binding of IGF2BP1 with m6A-modified c-Myc coding region instability determinant (CRD) mRNA. In conclusion, we confirm that lncRNA KB-1980E6.3 maintains the stemness of BCSCs through lncRNA KB-1980E6.3/IGF2BP1/c-Myc axis and suggest that disrupting this axis might provide a new therapeutic target for refractory hypoxic tumors.
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Affiliation(s)
- Pengpeng Zhu
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Fang He
- Department of pharmacy, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Yixuan Hou
- Experimental Teaching Center of Basic Medicine Science, Chongqing Medical University, Chongqing, 400016, China
| | - Gang Tu
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Qiao Li
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Ting Jin
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Huan Zeng
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Yilu Qin
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Xueying Wan
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Yina Qiao
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Yuxiang Qiu
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Yong Teng
- Department of Oral Biology and Dx Sciences, Dental College of Georgia; Georgia Cancer Center, Augusta University, Augusta, GA, 30907, USA
| | - Manran Liu
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China.
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Transcriptome-wide high-throughput mapping of protein-RNA occupancy profiles using POP-seq. Sci Rep 2021; 11:1175. [PMID: 33441968 PMCID: PMC7806670 DOI: 10.1038/s41598-020-80846-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/28/2020] [Indexed: 11/13/2022] Open
Abstract
Interaction between proteins and RNA is critical for post-transcriptional regulatory processes. Existing high throughput methods based on crosslinking of the protein–RNA complexes and poly-A pull down are reported to contribute to biases and are not readily amenable for identifying interaction sites on non poly-A RNAs. We present Protein Occupancy Profile-Sequencing (POP-seq), a phase separation based method in three versions, one of which does not require crosslinking, thus providing unbiased protein occupancy profiles on whole cell transcriptome without the requirement of poly-A pulldown. Our study demonstrates that ~ 68% of the total POP-seq peaks exhibited an overlap with publicly available protein–RNA interaction profiles of 97 RNA binding proteins (RBPs) in K562 cells. We show that POP-seq variants consistently capture protein–RNA interaction sites across a broad range of genes including on transcripts encoding for transcription factors (TFs), RNA-Binding Proteins (RBPs) and long non-coding RNAs (lncRNAs). POP-seq identified peaks exhibited a significant enrichment (p value < 2.2e−16) for GWAS SNPs, phenotypic, clinically relevant germline as well as somatic variants reported in cancer genomes, suggesting the prevalence of uncharacterized genomic variation in protein occupied sites on RNA. We demonstrate that the abundance of POP-seq peaks increases with an increase in expression of lncRNAs, suggesting that highly expressed lncRNA are likely to act as sponges for RBPs, contributing to the rewiring of protein–RNA interaction network in cancer cells. Overall, our data supports POP-seq as a robust and cost-effective method that could be applied to primary tissues for mapping global protein occupancies.
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273
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Yan Y, Huang P, Mao K, He C, Xu Q, Zhang M, Liu H, Zhou Z, Zhou Q, Zhou Q, Ou B, Liu Q, Lin J, Chen R, Wang J, Zhang J, Xiao Z. Anti-oncogene PTPN13 inactivation by hepatitis B virus X protein counteracts IGF2BP1 to promote hepatocellular carcinoma progression. Oncogene 2021; 40:28-45. [PMID: 33051595 PMCID: PMC7790756 DOI: 10.1038/s41388-020-01498-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 09/02/2020] [Accepted: 09/30/2020] [Indexed: 02/05/2023]
Abstract
Hepatitis B x protein (HBx) affects cellular protein expression and participates in the tumorigenesis and progression of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). Metabolic reprogramming contributed to the HCC development, but its role in HBV-related HCC remains largely unclear. Tyrosine-protein phosphatase nonreceptor type 13 (PTPN13) is a significant regulator in tumor development, however, its specific role in hepatocarcinogenesis remains to be explored. Here, we found that decreased PTPN13 expression was associated with HBV/HBx. Patients with low PTPN13 expression showed a poor prognosis. Functional assays revealed that PTPN13 inhibited proliferation and tumorigenesis in vitro and in vivo. Further mechanistic studies indicated that HBx inhibited PTPN13 expression by upregulating the expression of DNMT3A and interacting with DNMT3A. Furthermore, we found that DNMT3A bound to the PTPN13 promoter (-343 to -313 bp) in an epigenetically controlled manner associated with elevated DNA methylation and then inhibited PTPN13 transcription. In addition, we identified IGF2BP1 as a novel PTPN13-interacting gene and demonstrated that PTPN13 influences c-Myc expression by directly and competitively binding to IGF2BP1 to decrease the intracellular concentration of functional IGF2BP1. Overexpressing PTPN13 promoted c-Myc mRNA degradation independent of the protein tyrosine phosphatase (PTP) activity of PTPN13. Importantly, we discovered that the PTPN13-IGF2BP1-c-Myc axis was important for cancer cell growth through promoting metabolic reprogramming. We verified the significant negative correlations between PTPN13 expression and c-Myc, PSPH, and SLC7A1 expression in clinical HCC tissue samples. In summary, our findings demonstrate that PTPN13 is a novel regulator of HBV-related hepatocarcinogenesis and may play an important role in HCC. PTPN13 may serve as a prognostic marker and therapeutic target in HBV-related HCC patients.
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Affiliation(s)
- Yongcong Yan
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
| | - Pinbo Huang
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China.
| | - Kai Mao
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
| | - Chuanchao He
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
| | - Qiaodong Xu
- Department of Biliary-Pancreatic Minimally Invasive Surgery, The First Affiliated Hospital of Shantou University Medical College, 515041, Shantou, China
| | - Mengyu Zhang
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
| | - Haohan Liu
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
| | - Zhenyu Zhou
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
| | - Qiming Zhou
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
| | - Qianlei Zhou
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
| | - Bing Ou
- Department of Ultrasound, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
| | - Qinghua Liu
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
| | - Jianhong Lin
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
| | - Ruibin Chen
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
| | - Jie Wang
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
| | - Jianlong Zhang
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
| | - Zhiyu Xiao
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China.
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Mysona DP, Tran L, Bai S, dos Santos B, Ghamande S, Chan J, She JX. Tumor-intrinsic and -extrinsic (immune) gene signatures robustly predict overall survival and treatment response in high grade serous ovarian cancer patients. Am J Cancer Res 2021; 11:181-199. [PMID: 33520368 PMCID: PMC7840710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 09/14/2020] [Indexed: 06/12/2023] Open
Abstract
In the present study, we developed a transcriptomic signature capable of predicting prognosis and response to primary therapy in high grade serous ovarian cancer (HGSOC). Proportional hazard analysis was performed on individual genes in the TCGA RNAseq data set containing 229 HGSOC patients. Ridge regression analysis was performed to select genes and develop multigenic models. Survival analysis identified 120 genes whose expression levels were associated with overall survival (OS) (HR = 1.49-2.46 or HR = 0.48-0.63). Ridge regression modeling selected 38 of the 120 genes for development of the final Ridge regression models. The consensus model based on plurality voting by 68 individual Ridge regression models classified 102 (45%) as low, 23 (10%) as moderate and 104 patients (45%) as high risk. The median OS was 31 months (HR = 7.63, 95% CI = 4.85-12.0, P < 1.0-10) and 77 months (HR = ref) in the high and low risk groups, respectively. The gene signature had two components: intrinsic (proliferation, metastasis, autophagy) and extrinsic (immune evasion). Moderate/high risk patients had more partial and non-responses to primary therapy than low risk patients (odds ratio = 4.54, P < 0.001). We concluded that the overall survival and response to primary therapy in ovarian cancer is best assessed using a combination of gene signatures. A combination of genes which combines both tumor intrinsic and extrinsic functions has the best prediction. Validation studies are warranted in the future.
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Affiliation(s)
- David P Mysona
- University of North CarolinaChapel Hill, NC 27517, USA
- Jinfiniti Precision Medicine, Inc.Augusta, GA 30907, USA
| | - Lynn Tran
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta UniversityAugusta, GA 30912, USA
| | - Shan Bai
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta UniversityAugusta, GA 30912, USA
| | | | - Sharad Ghamande
- Department of OBGYN, Medical College of Georgia at Augusta UniversityAugusta, GA 30912, USA
| | - John Chan
- Palo Alto Medical Foundation Research InstitutePalo Alto, CA 94301, USA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta UniversityAugusta, GA 30912, USA
- Department of OBGYN, Medical College of Georgia at Augusta UniversityAugusta, GA 30912, USA
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275
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Lambrianidou A, Sereti E, Soupsana K, Komini C, Dimas K, Trangas T. mTORC2 deploys the mRNA binding protein IGF2BP1 to regulate c-MYC expression and promote cell survival. Cell Signal 2021; 80:109912. [PMID: 33388443 DOI: 10.1016/j.cellsig.2020.109912] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 11/15/2022]
Abstract
mTORC2 promotes cell survival by phosphorylating AKT and enhancing its activity. Inactivation of mTORC2 reduces viability through down-regulation of E2F1 caused by up-regulation of c-MYC. An additional target of mTORC2 is IGF2BP1, an oncofetal RNA binding protein expressed de novo in a wide array of malignancies. IGF2BP1 enhances c-MYC expression by protecting the coding region instability sequence (CRD) of its mRNA from endonucleolytic cleavage. Here we show that repression of mTORC2 signalling and prevention of Ser181 phosphorylation of IGF2BP1 enhanced translation and destabilization of the endogenous c-myc mRNA as well as the mRNA of reporter transcripts carrying the CRD sequence in frame. The consequent increase in c-MYC protein was accompanied by the emergence of an apoptotic c-MYC overexpressing population. On the other hand, preventing phosphorylation of IGF2BP1 on Tyr396 by Src kinase caused the accumulation of translationally silent transcripts through sequestration by IGF2BP1 into cytoplasmic granules. The apoptotic effect of mTORC2 signalling deprivation was augmented when preceded by inhibition of IGF2BP1 phosphorylation by the Src kinase in concert with further increase of c-MYC levels because of enhanced translation of the previously stored mRNA only in the presence of IGF2BP1. Furthermore, the combined administration of mTORC2 and Src inhibitors exhibited synergism in delaying xenograft growth in female NOD.CB17-Prkdcscid/J mice. The above in vitro and in vivo findings may be applied for the induction of targeted apoptosis of cells expressing de novo the oncofetal protein IGF2BP1, a feature of aggressive malignancies resulting in a more focused anticancer therapeutic approach.
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Affiliation(s)
- Andromachi Lambrianidou
- Biochemistry Laboratory, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Evangelia Sereti
- Department of Pharmacology, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Katerina Soupsana
- Laboratory of Biological Chemistry, University of Ioannina, Faculty of Medicine, Ioannina, Greece
| | - Chrysoula Komini
- Biochemistry Laboratory, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Konstantinos Dimas
- Department of Pharmacology, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Theoni Trangas
- Biochemistry Laboratory, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece.
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276
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Chong W, Shang L, Liu J, Fang Z, Du F, Wu H, Liu Y, Wang Z, Chen Y, Jia S, Chen L, Li L, Chen H. m 6A regulator-based methylation modification patterns characterized by distinct tumor microenvironment immune profiles in colon cancer. Am J Cancer Res 2021; 11:2201-2217. [PMID: 33500720 PMCID: PMC7797678 DOI: 10.7150/thno.52717] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/21/2020] [Indexed: 12/28/2022] Open
Abstract
Recent studies have highlighted the biological significance of RNA N6-methyladenosine (m6A) modification in tumorigenicity and progression. However, it remains unclear whether m6A modifications also have potential roles in immune regulation and tumor microenvironment (TME) formation. Methods: In this study, we curated 23 m6A regulators and performed consensus molecular subtyping with NMF algorithm to determine m6A modification patterns and the m6A-related gene signature in colon cancer (CC). The ssGSEA and CIBERSORT algorithms were employed to quantify the relative infiltration levels of various immune cell subsets. An PCA algorithm based m6Sig scoring scheme was used to evaluate the m6A modification patterns of individual tumors with an immune response. Results: Three distinct m6A modification patterns were identified among 1307 CC samples, which were also associated with different clinical outcomes and biological pathways. The TME characterization revealed that the identified m6A patterns were highly consistent with three known immune profiles: immune-inflamed, immune-excluded, and immune-desert, respectively. Based on the m6Sig score, which was extracted from the m6A-related signature genes, CC patients can be divided into high and low score subgroups. Patients with lower m6Sig score was characterized by prolonged survival time and enhanced immune infiltration. Further analysis indicated that lower m6Sig score also correlated with greater tumor mutation loads, PD-L1 expression, and higher mutation rates in SMGs (e.g., PIK3CA and SMAD4). In addition, patients with lower m6Sig scores showed a better immune responses and durable clinical benefits in three independent immunotherapy cohorts. Conclusions: This study highlights that m6A modification is significantly associated with TME diversity and complexity. Quantitatively evaluating the m6A modification patterns of individual tumors will strengthen our understanding of TME characteristics and promote more effective immunotherapy strategies.
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277
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Zhang L, Wan Y, Zhang Z, Jiang Y, Gu Z, Ma X, Nie S, Yang J, Lang J, Cheng W, Zhu L. IGF2BP1 overexpression stabilizes PEG10 mRNA in an m6A-dependent manner and promotes endometrial cancer progression. Theranostics 2021; 11:1100-1114. [PMID: 33391523 PMCID: PMC7738899 DOI: 10.7150/thno.49345] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/16/2020] [Indexed: 01/18/2023] Open
Abstract
Rationale: N6-methyladenosine (m6A) mRNA methylation is the most abundant chemical posttranscriptional modification in mRNA and is involved in the regulation of a number of biological processes. Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) has recently been reported as having the capacity to recognize m6A sites in mRNA and plays a role in regulating mRNA metabolization. However, it is unclear which genes IGF2BP1 targets to identify m6A sites and what are their respective functions in endometrial cancer (EC). Methods: Quantitative PCR, western blot and immunohistochemistry were used to measure IGF2BP1 expression in EC cell lines and tissues. Xenograft experiments were performed to examine the in vivo role of IGF2BP1 in EC cell growth. RNA-binding protein immunoprecipitation sequencing, methylated RNA-binding protein immunoprecipitation sequencing and RNA-sequencing were also conducted to identify potential IGF2BP1 targets involved in EC regulation. Co-immunoprecipitation and mass spectrometry were used to identify IGF2BP1-interacting proteins. Results: IGF2BP1 expression increased in EC, and high expression of this protein correlated with poor prognosis. IGF2BP1 overexpression/knockdown can promote (and inhibit) cell proliferation and regulate the tumor cell cycle and cancer progression, both in vivo and in vitro. Mechanistically, IGF2BP1 can recognize m6A sites in the 3' untranslated region (3'UTR) of Paternally Expressed Gene 10 (PEG10) mRNA and recruits polyadenylate-binding protein 1 (PABPC1) to enhance PEG10 mRNA stability, which consequently promotes PEG10 protein expression. Additionally, it would appear that a large number of PEG10 proteins bind p16 and p18 gene promoter sequences, thereby repressing expression and accelerating the cell cycle. Conclusion: This investigation found that IGF2BP1 has a crucial role in the m6A-dependent regulatory mechanism for endometrial cancer. This study provides new insights into our understanding of disease progression and provides another potential route for understanding biological functions.
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Affiliation(s)
- Lin Zhang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100010, China
| | - Yicong Wan
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu 210029, China
| | - Zihan Zhang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100010, China
| | - Yi Jiang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu 210029, China
| | - Zhiyue Gu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100010, China
| | - Xiaoling Ma
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu 210029, China
| | - Sipei Nie
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu 210029, China
| | - Jing Yang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu 210029, China
| | - Jinghe Lang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100010, China
| | - Wenjun Cheng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu 210029, China
| | - Lan Zhu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100010, China
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278
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Blocking the IGF2BP1-promoted glucose metabolism of colon cancer cells via direct de-stabilizing mRNA of the LDHA enhances anticancer effects. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 23:835-846. [PMID: 33614233 PMCID: PMC7868688 DOI: 10.1016/j.omtn.2020.12.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/19/2020] [Indexed: 01/01/2023]
Abstract
Colorectal cancer (CRC) is a commonly diagnosed cancer with poor prognosis and high mortality rate. Hyperthermia (HT) is an adjunctive therapy to enhance the antitumor effects of traditional chemo- or radio- therapy. Here, we report that a cluster of essential regulator genes and speed-limit enzymes of glucose metabolism were significantly elevated under HT from a glucose metabolism PCR array analysis. Under low glucose supply or glucose metabolism inhibition, CRC cells displayed increased sensitivity to HT treatments. By transcript sequencing from the established HT resistant (HTR) colon cancer cell line LoVo HTR, we observed that IGF2BP1, an RNA-binding protein, was significantly upregulated in HTR cells compared with parental cells. Furthermore, LDHA mRNA was identified as an IGF2BP1 direct target. An RNA immunoprecipitation assay and RNA pull-down assay consistently illustrated IGF2BP1 specifically bonds to the 3′ UTR of LDHA mRNA, leading to enhanced stability of LDHA mRNA. Finally, we demonstrated that inhibiting the IGF2BP1-promoted glycolysis sensitized colon cancer cells to HT treatment via both in vitro and in vivo experiments. Our findings suggest that targeting the IGF2BP1-LDHA-glycolysis pathway might be a promising therapeutic approach to enhance the anti-cancer effects of HT treatment.
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279
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Okholm TLH, Sathe S, Park SS, Kamstrup AB, Rasmussen AM, Shankar A, Chua ZM, Fristrup N, Nielsen MM, Vang S, Dyrskjøt L, Aigner S, Damgaard CK, Yeo GW, Pedersen JS. Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression. Genome Med 2020; 12:112. [PMID: 33287884 PMCID: PMC7722315 DOI: 10.1186/s13073-020-00812-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 11/12/2020] [Indexed: 12/25/2022] Open
Abstract
Background Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions in different biological contexts. Methods We conduct an extensive screen of circRNA-RBP interactions in the ENCODE cell lines HepG2 and K562. We profile circRNAs in deep-sequenced total RNA samples and analyze circRNA-RBP interactions using a large set of eCLIP data with binding sites of 150 RBPs. We validate interactions for select circRNAs and RBPs by performing RNA immunoprecipitation and functionally characterize our most interesting candidates by conducting knockdown studies followed by RNA-Seq. Results We generate a comprehensive catalog of circRNA-RBP interactions in HepG2 and K562 cells. We show that KHSRP binding sites are enriched in flanking introns of circRNAs and that KHSRP depletion affects circRNA biogenesis. We identify circRNAs that are highly covered by RBP binding sites and experimentally validate individual circRNA-RBP interactions. We show that circCDYL, a highly expressed circRNA with clinical and functional implications in bladder cancer, is almost completely covered with GRWD1 binding sites in HepG2 cells, and that circCDYL depletion counteracts the effect of GRWD1 depletion. Furthermore, we confirm interactions between circCDYL and RBPs in bladder cancer cells and demonstrate that circCDYL depletion affects hallmarks of cancer and perturbs the expression of key cancer genes, e.g., TP53. Finally, we show that elevated levels of circCDYL are associated with overall survival of bladder cancer patients. Conclusions Our study demonstrates transcriptome-wide and cell-type-specific circRNA-RBP interactions that could play important regulatory roles in tumorigenesis.
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Affiliation(s)
- Trine Line Hauge Okholm
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark. .,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark.
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California San Diego, CA, 92093, La Jolla, USA
| | - Samuel S Park
- Department of Cellular and Molecular Medicine, University of California San Diego, CA, 92093, La Jolla, USA
| | | | - Asta Mannstaedt Rasmussen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Archana Shankar
- Department of Cellular and Molecular Medicine, University of California San Diego, CA, 92093, La Jolla, USA
| | - Zong Ming Chua
- Department of Cellular and Molecular Medicine, University of California San Diego, CA, 92093, La Jolla, USA
| | - Niels Fristrup
- Department of Oncology, Aarhus University Hospital, 8200, Aarhus N, Denmark
| | - Morten Muhlig Nielsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Søren Vang
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, CA, 92093, La Jolla, USA
| | | | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, CA, 92093, La Jolla, USA
| | - Jakob Skou Pedersen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark. .,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark. .,Bioinformatics Research Center (BiRC), Aarhus University, 8000, Aarhus C, Denmark.
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280
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Identification of Two Novel Circular RNAs Deriving from BCL2L12 and Investigation of Their Potential Value as a Molecular Signature in Colorectal Cancer. Int J Mol Sci 2020; 21:ijms21228867. [PMID: 33238574 PMCID: PMC7709015 DOI: 10.3390/ijms21228867] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/06/2020] [Accepted: 11/15/2020] [Indexed: 02/07/2023] Open
Abstract
The utility of circular RNAs (circRNAs) as molecular biomarkers has recently emerged. However, only a handful of them have already been studied in colorectal cancer (CRC). The purpose of this study was to identify new circRNAs deriving from BCL2L12, a member of the BCL2 apoptosis-related family, and investigate their potential as biomarkers in CRC. Total RNA extracts from CRC cell lines and tissue samples were reversely transcribed. By combining PCR with divergent primers and nested PCR followed by Sanger sequencing, we were able to discover two BCL2L12 circRNAs. Subsequently, bioinformatical tools were used to predict the interactions of these circRNAs with microRNAs (miRNAs) and RNA-binding proteins (RBPs). Following a PCR-based pre-amplification, real-time qPCR was carried out for the quantification of each circRNA in CRC samples and cell lines. Biostatistical analysis was used to assess their potential prognostic value in CRC. Both novel BCL2L12 circRNAs likely interact with particular miRNAs and RBPs. Interestingly, circ-BCL2L12-2 expression is inversely associated with TNM stage, while circ-BCL2L12-1 overexpression is associated with shorter overall survival in CRC, particularly among TNM stage II patients. Overall, we identified two novel BCL2L12 circRNAs, one of which can further stratify TNM stage II patients into two subgroups with substantially distinct prognosis.
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Zhai S, Xu Z, Xie J, Zhang J, Wang X, Peng C, Li H, Chen H, Shen B, Deng X. Epigenetic silencing of LncRNA LINC00261 promotes c-myc-mediated aerobic glycolysis by regulating miR-222-3p/HIPK2/ERK axis and sequestering IGF2BP1. Oncogene 2020; 40:277-291. [PMID: 33122827 PMCID: PMC7808938 DOI: 10.1038/s41388-020-01525-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/01/2020] [Accepted: 10/13/2020] [Indexed: 12/19/2022]
Abstract
Long noncoding RNAs have been identified as key regulators in the progression of various cancers. LINC00261 has been reported as a tumor suppressor in multiple cancers. However, its function and underlying mechanisms in pancreatic cancer remain largely unclear. Quantitative real-time PCR was performed to detect RNA expression. In situ hybridization was used to discover the subcellular location. The direct binding of LINC00261 to miR-222-3p was verified using a dual-luciferase reporter assay and RNA immunoprecipitation. LINC00261-binding proteins were detected using an RNA pulldown assay. LINC00261 was downregulated in pancreatic cancer tissues and cell lines. Its reduced expression was correlated with advanced pathological stage and poor prognosis. Forced expression of LINC00261 suppressed pancreatic cancer glycolysis and proliferation and induced cell cycle arrest and apoptosis. Mechanistically, downregulation of LINC00261 was caused by hypermethylation of the CpG island in the promoter region and EZH2-mediated histone H3 lysine 27 trimethylation. Moreover, LINC00261 exerted its biological function by binding to miR-222-3p to activate the HIPK2/ERK/c-myc pathway. In addition, LINC00261 could also reduce c-myc expression by sequestering IGF2BP1. Our study suggests that LINC00261 functions as a tumor suppressor in pancreatic cancer and identifies novel epigenetic and posttranscriptional regulatory mechanisms of LINC00261, which contribute to the targeted therapy of pancreatic cancer.
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Affiliation(s)
- Shuyu Zhai
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Zhiwei Xu
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Junjie Xie
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jun Zhang
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xinjing Wang
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Chenghong Peng
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Hongwei Li
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Hao Chen
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China. .,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China. .,State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China.
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China. .,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China. .,State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China.
| | - Xiaxing Deng
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China. .,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China. .,State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China.
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282
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Gao W, Cheng L, He S, Li W, Zhou C, Zhou B, Liu J, Xu J, Yu X, Zhu H. Multiomics integrative analysis for gene signatures and prognostic values of m 6A regulators in pancreatic adenocarcinoma: a retrospective study in The Cancer Genome Atlas project. Aging (Albany NY) 2020; 12:20587-20610. [PMID: 33082301 PMCID: PMC7655159 DOI: 10.18632/aging.103942] [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: 02/27/2020] [Accepted: 08/03/2020] [Indexed: 12/15/2022]
Abstract
N6-methyladenosine(m6A) is the most abundant post-transcriptional RNA modification in eukaryotes. However, little is known about its role in pancreatic adenocarcinoma (PAAD). The aim of our study was to identify gene signatures and prognostic values of m6A regulators in PAAD. Patients from 3 different datasets with complete genomic and transcriptomic sequencing data were enrolled. Survival analysis for different gene alterations was performed using log-rank tests and Cox regression model. The association between alteration of m6A regulators and clinicopathological characteristics was examined using chi-square test. Results showed a high frequency of copy number alterations (CNAs) of m6A regulatory genes in PAAD patients, but somatic mutations were rarely happened. CNAs and mutations of m6A regulatory genes was associated with patient's gender, pathologic stage and resected tumor size. Patients with "gain of function" for m6A "reader" genes combined with copy number loss of "writers" or "erasers" had worse overall survival (OS) compared with other patterns. Moreover, copy number gain of m6A "reader" gene insulin growth factor 2 binding protein 2 (IGF2BP2) was an independent risk factor for OS (HR = 2.392, 95%CI: 1.392-4.112, p<0.001) and disease-free survival (DFS) (HR = 2.400, 95%CI: 1.236-4.659, p=0.010). Gene Set Enrichment Analysis (GSEA) indicated that IGF2BP2 was correlated with multiple biological processes associated with cancer, of which the most significant processes were relevant to cancer cell cycle, cell immortalization and tumor immunity. To sum up, a significant relationship was found between m6A genomic alterations and worse clinical outcomes. These innovative findings are expected to guide further research on the mechanism of m6A in PAAD.
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Affiliation(s)
- Wenzhe Gao
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan Province, China
| | - Liuyang Cheng
- Medical College of Xiangya, Central South University, Changsha 410013, Hunan Province, China
| | - Shuhan He
- Medical College of Xiangya, Central South University, Changsha 410013, Hunan Province, China
| | - Wei Li
- Medical College of Xiangya, Central South University, Changsha 410013, Hunan Province, China
| | - Chengyu Zhou
- Medical College of Xiangya, Central South University, Changsha 410013, Hunan Province, China
| | - Bixia Zhou
- Medical College of Xiangya, Central South University, Changsha 410013, Hunan Province, China
| | - Jiamiao Liu
- Medical College of Xiangya, Central South University, Changsha 410013, Hunan Province, China
| | - Jiahao Xu
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan Province, China
| | - Xiao Yu
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan Province, China
| | - Hongwei Zhu
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan Province, China
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283
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Xu Z, Peng B, Cai Y, Wu G, Huang J, Gao M, Guo G, Zeng S, Gong Z, Yan Y. N6-methyladenosine RNA modification in cancer therapeutic resistance: Current status and perspectives. Biochem Pharmacol 2020; 182:114258. [PMID: 33017575 DOI: 10.1016/j.bcp.2020.114258] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 02/05/2023]
Abstract
Several strategies, including chemotherapy and radiotherapy, have improved therapeutic outcomes among cancer patients in clinical practice. However, due to their heterogeneity, cancer cells frequently display primary or acquired therapeutic resistance, thereby resulting in treatment failure. The mechanisms underlying cancer therapeutic resistance are complex and varied. Among them, N6-methyladenosine (m6A) RNA modification has gained increasing attention as a potential determinant of therapy resistance within various cancers. In this review, we primarily describe evidence for the effect of the m6A epitranscriptome on RNA homeostasis modulation, which has been shown to alter multiple cellular pathways in cancer research and treatment. Additionally, we discuss the profiles and biological implications of m6A RNA methylation, which is undergoing intensive investigation for its effect on the control of therapeutic resistance.
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Affiliation(s)
- Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Geting Wu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
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284
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Fan L, Lin Y, Lei H, Shu G, He L, Yan Z, Rihan H, Yin G. A newly defined risk signature, consisting of three m 6A RNA methylation regulators, predicts the prognosis of ovarian cancer. Aging (Albany NY) 2020; 12:18453-18475. [PMID: 32950970 PMCID: PMC7585096 DOI: 10.18632/aging.103811] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 07/20/2020] [Indexed: 01/24/2023]
Abstract
N6-methyladenosine (m6A) RNA methylation, involved in cancer initiation and progression, is dynamically regulated by the m6A RNA methylation regulators. However, the expression of m6A RNA methylation regulators in ovarian cancer and their correlation with prognosis remain elusive. Here, we demonstrated that the 18 central m6A RNA methylation regulators were expressed differently between ovarian cancer (OC) and normal tissues. By applying consensus clustering, all ovarian cancer patient cases can be divided into three subgroups (cluster1/2/3) based on overall expression levels of all 18 m6A RNA methylation regulators. We systematically analyzed the prognostic value of transcription levels of 18 m6A RNA methylation regulators in ovarian cancer and found that insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1), vir like m6A methyltransferase associated (VIRMA), and zinc finger CCCH-type containing 13 (ZC3H13) yield the highest scores for predicting the prognosis of ovarian cancer. Accordingly, we derived a risk signature consisting of transcription levels of these three selected m6A RNA methylation regulators as an independent prognostic marker for OC and validated our findings with data derived from a different ovarian cancer cohort. Moreover, by the Gene Set Enrichment Analysis (GSEA), we demonstrated that the three selected regulators were all correlated with pathways in cancer and WNT signaling pathways. In conclusion, m6A RNA methylation regulators are vital participants in ovarian cancer pathology; and IGF2BP1, VIRMA, and ZC3H13 mRNA levels are valuable factors for prognosis prediction and treatment strategy development.
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Affiliation(s)
- Lili Fan
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
| | - Ying Lin
- Department of Immunology, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
| | - Han Lei
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
| | - Guang Shu
- School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
| | - Liuer He
- School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
| | - Zhipeng Yan
- Hunan Cancer Hospital, the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan Province, China
| | - Hai Rihan
- School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
| | - Gang Yin
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
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285
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Zhang J, Luo W, Chi X, Zhang L, Ren Q, Wang H, Zhang W. IGF2BP1 silencing inhibits proliferation and induces apoptosis of high glucose-induced non-small cell lung cancer cells by regulating Netrin-1. Arch Biochem Biophys 2020; 693:108581. [PMID: 32926844 DOI: 10.1016/j.abb.2020.108581] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/28/2020] [Accepted: 09/07/2020] [Indexed: 11/30/2022]
Abstract
Non-small cell lung cancer (NSCLC) accompanied by diabetes is an important risk factor affecting the prognosis of patients with NSCLC in clinical practice. However, the effect of high glucose (HG) in the pathogenesis of NSCLC remains elusive. It has been found that the RNA-binding protein Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) plays important roles in various diseases, including NSCLC and diabetes. The aim of this study was to explore the role of IGF2BP1 in HG-treated NSCLC cells, and further investigate its underlying molecular mechanism. Results showed that IGF2BP1 was highly expressed in HG-treated NSCLC cells. Knockdown of IGF2BP1 inhibited cancer cell proliferation, migration and invasion, as well as induced cell cycle arrest and apoptosis. Besides, IGF2BP1 silencing decreased the Netrin-1 level in HG-treated NSCLC cells. Reintroduction of Netrin-1 expression rescued IGF2BP1 deficiency-induced cell proliferation reduction, migration suppression, cell cycle arrest and apoptosis. These findings suggest that IGF2BP1 silencing inhibits the occurrence of tumor events through down-regulating Netrin-1 expression, indicating that the IGF2BP1/Netrin-1 axis exerts an oncogenic role in HG-treated NSCLC cells.
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Affiliation(s)
- Jiawen Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, People's Republic of China
| | - Wen Luo
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, People's Republic of China
| | - Xiaowen Chi
- Department of Pediatrics, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, People's Republic of China
| | - Lijuan Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, People's Republic of China
| | - Qiu Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, People's Republic of China
| | - Hui Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, People's Republic of China
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, People's Republic of China.
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286
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Zhang J, Hu K, Yang YQ, Wang Y, Zheng YF, Jin Y, Li P, Cheng L. LIN28B-AS1-IGF2BP1 binding promotes hepatocellular carcinoma cell progression. Cell Death Dis 2020; 11:741. [PMID: 32917856 PMCID: PMC7486890 DOI: 10.1038/s41419-020-02967-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/21/2020] [Accepted: 08/27/2020] [Indexed: 11/09/2022]
Abstract
IGF2BP1 overexpression promotes hepatocellular carcinoma (HCC) progression. Long non-coding RNA LIN28B-AS1 directly binds to IGF2BP1. In the present study, LIN28B-AS1 and IGF2BP1 expression and their potential functions in HCC cells were tested. Genetic strategies were applied to interfere their expression, and cell survival, proliferation and apoptosis were analyzed. We show that LIN28B-AS1 is expressed in established/primary human HCC cells and HCC tissues. RNA-immunoprecipitation (RIP) and RNA pull-down results confirmed that LIN28B-AS1 directly associated with IGF2BP1 protein in HCC cells. LIN28B-AS1 silencing (by targeted siRNAs) or knockout (KO, by CRISPR-Cas9 method) depleted IGF2BP1-dependent mRNAs (IGF2, Gli1, and Myc), inhibiting HCC cell growth, proliferation, migration, and invasion. Conversely, ectopic overexpression of LIN28B-AS1 upregulated IGF2BP1-dependent mRNAs and promoted HCC cell progression in vitro. Importantly, ectopic IGF2BP1 overexpression failed to rescue LIN28B-AS1-KO HepG2 cells. LIN28B-AS1 siRNA and overexpression were ineffective in IGF2BP1-KO HepG2 cells. In vivo, LIN28B-AS1 KO-HepG2 xenograft tumors grew significantly slower than the control tumors in the nude mice. Taken together, we conclude that LIN28B-AS1 associates with IGF2BP1 to promote human HCC cell progression in vitro and in vivo.
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Affiliation(s)
- Jian Zhang
- Department of Interventional Radiology, the Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Kewei Hu
- Department of Gastroenterology, the Second Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
| | - Yong-Qiang Yang
- Department of Radiotherapy and Oncology, the Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yin Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Yu-Fan Zheng
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Yong Jin
- Department of Interventional Radiology, the Second Affiliated Hospital of Soochow University, Suzhou, China.
| | - Ping Li
- Department of Radiotherapy and Oncology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, China.
| | - Long Cheng
- Department of Interventional Radiology, the Second Affiliated Hospital of Soochow University, Suzhou, China.
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287
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Wang Y, Ren F, Song Z, Wang X, Ma X. Multiomics profile and prognostic gene signature of m6A regulators in uterine corpus endometrial carcinoma. J Cancer 2020; 11:6390-6401. [PMID: 33033522 PMCID: PMC7532517 DOI: 10.7150/jca.46386] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
Uterine corpus endometrial carcinoma (UCEC) is the most common type of gynecologic malignancy worldwide. Despite advances in the treatments of UCEC, its incidence and mortality rates are still increasing. N6-methyladenosine (m6A) is the most common form of RNA modification and has attracted increasing interest in cancer pathogenesis and progression. Thus, we aimed to identify the landscape of m6A regulators and build a prognostic gene signature in UCEC. In this study, we first analyzed copy number variations (CNVs), single nucleotide variations (SNVs) and gene expression profiles as well as matched clinical information of UCEC patients from The Cancer Genome Atlas (TCGA) database. Next, we determined that CNVs in m6A regulatory genes had a significant negative impact on patient survival. The mRNA expression levels of a total of 16 m6A regulators were significantly correlated with different CNV patterns. Using univariate Cox regression analysis, IGF2BP1, KIAA1429, IGF2BP3, YTHDF3, and IGF2BP2 were found to be closely associated with UCEC patient survival outcomes. Based on the least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression models, we built a 3-gene (IGF2BP3, KIAA1429 and IGF2BP1) signature of m6A regulators with prognostic value in UCEC that could effectively predict patient prognosis (log-rank test p-value < 0.0001). In addition, risk scores were significantly different between patients stratified by tumor stage, SNV, and CNV. Multivariate Cox regression analysis suggested that risk score might be an independent prognostic indicator for the overall survival of patients with UCEC (p-value < 0.05). Gene enrichment analysis indicated that high IGF2BP1 gene expression is associated with cytoplasmic stress granules. KIAA1429 gene expression is associated with cellular nucleic acid metabolism. The expression of the IGF2BP3 gene is associated with RNA binding processes. In conclusion, we determined that genetic alterations in m6A regulatory genes could be effective and reliable biomarkers for UCEC prognosis prediction.
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Affiliation(s)
- Yizi Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang 110004, China
| | - Fang Ren
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang 110004, China
| | - Zixuan Song
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang 110004, China
| | - Xiaoying Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang 110004, China
| | - Xiaoxin Ma
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang 110004, China
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288
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Dai N. The Diverse Functions of IMP2/IGF2BP2 in Metabolism. Trends Endocrinol Metab 2020; 31:670-679. [PMID: 32586768 DOI: 10.1016/j.tem.2020.05.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/28/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022]
Abstract
The human insulin-like growth factor 2 (IGF2) mRNA binding protein family (IMPs/IGF2BPs) is involved in a spectrum of biological processes, including development, tumorigenesis, and stemness. IMPs play a major role in post-transcriptional regulation of RNAs through the ribonucleoprotein complex (RNP). They have emerged as direct mammalian target of rapamycin (mTOR) substrates that coordinate nutrient stimulation and RNA life cycle control. IMP2 is a human type 2 diabetes (T2D) gene associated with impaired insulin secretion. Recently, using murine models, the substantial progress in understanding disease mechanisms has highlighted the significance of IMP2 in metabolism. This new knowledge may have the potential for therapeutic benefit.
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Affiliation(s)
- Ning Dai
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA.
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289
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MNDA controls the expression of MCL-1 and BCL-2 in chronic lymphocytic leukemia cells. Exp Hematol 2020; 88:68-82.e5. [PMID: 32682001 DOI: 10.1016/j.exphem.2020.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/23/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023]
Abstract
The myeloid nuclear differentiation antigen (MNDA) is a stress-induced protein that promotes degradation of the anti-apoptotic factor MCL-1 and apoptosis in myeloid cells. MNDA is also expressed in normal lymphoid cells and in B-cell clones isolated from individuals with chronic lymphocytic leukemia (CLL), a disease characterized by abnormal apoptosis control. We found that MNDA expression levels inversely correlate with the amount of the anti-apoptotic proteins MCL-1 and BCL-2 in human CLL samples. We report that in response to chemotherapeutic agents that induce genotoxic stress, MNDA exits its typical nucleolar localization and accumulates in the nucleoplasm of CLL and lymphoid cells. Then, MNDA binds chromatin at Mcl1 and Bcl2 genes and affects the transcriptional competence of RNA polymerase II. Our data also reveal that MNDA specifically associates with Mcl1 and Bcl2 (pre-) mRNAs and favors their rapid turnover as a prompt response to genotoxic stress. We propose that this rapid dynamic tuning of RNA levels, which leads to the destabilization of Mcl1 and Bcl2 transcripts, represents a post-transcriptional mechanism of apoptosis control in CLL cells. These results provide an explanation of previous clinical data and corroborate the finding that higher MNDA expression levels in CLL are associated with a better clinical course.
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290
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Qin H, Ni H, Liu Y, Yuan Y, Xi T, Li X, Zheng L. RNA-binding proteins in tumor progression. J Hematol Oncol 2020; 13:90. [PMID: 32653017 PMCID: PMC7353687 DOI: 10.1186/s13045-020-00927-w] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/25/2020] [Indexed: 02/08/2023] Open
Abstract
RNA-binding protein (RBP) has a highly dynamic spatiotemporal regulation process and important biological functions. They are critical to maintain the transcriptome through post-transcriptionally controlling the processing and transportation of RNA, including regulating RNA splicing, polyadenylation, mRNA stability, mRNA localization, and translation. Alteration of each process will affect the RNA life cycle, produce abnormal protein phenotypes, and thus lead to the occurrence and development of tumors. Here, we summarize RBPs involved in tumor progression and the underlying molecular mechanisms whereby they are regulated and exert their effects. This analysis is an important step towards the comprehensive characterization of post-transcriptional gene regulation involved in tumor progression.
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Affiliation(s)
- Hai Qin
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Haiwei Ni
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Yichen Liu
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Yaqin Yuan
- Guizhou Medical Device Testing Center, Guiyang, 550004, Guizhou, People's Republic of China
| | - Tao Xi
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China.
| | - Xiaoman Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, People's Republic of China.
| | - Lufeng Zheng
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China.
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291
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Daniel-Moreno A, Lamsfus-Calle A, Wilber A, Chambers CB, Johnston I, Antony JS, Epting T, Handgretinger R, Mezger M. Comparative analysis of lentiviral gene transfer approaches designed to promote fetal hemoglobin production for the treatment of β-hemoglobinopathies. Blood Cells Mol Dis 2020; 84:102456. [PMID: 32498026 DOI: 10.1016/j.bcmd.2020.102456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 01/05/2023]
Abstract
β-Hemoglobinopathies are among the most common single-gene disorders and are caused by different mutations in the β-globin gene. Recent curative therapeutic approaches for these disorders utilize lentiviral vectors (LVs) to introduce a functional copy of the β-globin gene into the patient's hematopoietic stem cells. Alternatively, fetal hemoglobin (HbF) can reduce or even prevent the symptoms of disease when expressed in adults. Thus, induction of HbF by means of LVs and other molecular approaches has become an alternative treatment of β-hemoglobinopathies. Here, we performed a head-to-head comparative analysis of HbF-inducing LVs encoding for: 1) IGF2BP1, 2) miRNA-embedded shRNA (shmiR) sequences specific for the γ-globin repressor protein BCL11A, and 3) γ-globin gene. Furthermore, two novel baboon envelope proteins (BaEV)-LVs were compared to the commonly used vesicular-stomatitis-virus glycoprotein (VSV-G)-LVs. Therapeutic levels of HbF were achieved for all VSV-G-LV approaches, from a therapeutic level of 20% using γ-globin LVs to 50% for both IGF2BP1 and BCL11A-shmiR LVs. Contrarily, BaEV-LVs conferred lower HbF expression with a peak level of 13%, however, this could still ameliorate symptoms of disease. From this thorough comparative analysis of independent HbF-inducing LV strategies, we conclude that HbF-inducing VSV-G-LVs represent a promising alternative to β-globin gene addition for patients with β-hemoglobinopathies.
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Affiliation(s)
- Alberto Daniel-Moreno
- University Children's Clinic Department of Pediatrics I, Hematology and Oncology, University of Tübingen, Germany
| | - Andrés Lamsfus-Calle
- University Children's Clinic Department of Pediatrics I, Hematology and Oncology, University of Tübingen, Germany
| | - Andrew Wilber
- Department of Medical Microbiology, Immunology and Cell Biology, SIU School of Medicine, and Simmons Cancer Institute, Springfield, IL, USA
| | - Christopher B Chambers
- Department of Medical Microbiology, Immunology and Cell Biology, SIU School of Medicine, and Simmons Cancer Institute, Springfield, IL, USA
| | - Ian Johnston
- Research & Development, Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Justin S Antony
- University Children's Clinic Department of Pediatrics I, Hematology and Oncology, University of Tübingen, Germany
| | - Thomas Epting
- Clinical Chemistry and Laboratory Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Rupert Handgretinger
- University Children's Clinic Department of Pediatrics I, Hematology and Oncology, University of Tübingen, Germany
| | - Markus Mezger
- University Children's Clinic Department of Pediatrics I, Hematology and Oncology, University of Tübingen, Germany.
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292
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Wang Y, He R, Ma L. Characterization of lncRNA-Associated ceRNA Network to Reveal Potential Prognostic Biomarkers in Lung Adenocarcinoma. Front Bioeng Biotechnol 2020; 8:266. [PMID: 32426332 PMCID: PMC7212445 DOI: 10.3389/fbioe.2020.00266] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/13/2020] [Indexed: 12/22/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the most fatal malignant tumors harmful to human health. The complexity and behavior characteristics of long-non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) network in LUAD patients are still unclear. The purpose of this study was to elucidate the regulatory networks of dysregulated RNAs, view, and identify potential prognosis signatures involved in LUAD. The expression profiles of mRNAs, lncRNAs, and miRNAs were obtained from the TCGA database. In total, 2078 DEmRNAs, 257 DElncRNAs, and 101 DEmiRNAs were sorted out. A PPI network including 45 DEmRNAs was constructed. Ten hub genes in the PPI network associated with cell cycle-related pathways were identified and they played key roles in regulating cell proliferation. A total of three DEmiRNAs, seven DElncRNAs, and six DEmRNAs were enrolled in the ceRNA network. Except for certain genes without any published study reports, all the genes in the ceRNA network played an essential role in controlling tumor cell proliferation and were associated with prognosis in LUAD. Finally, based on step regression and Cox regression survival analysis, we identified four candidate biomarkers, including miR490, miR1293, LINC01740, and IGF2BP1, and established a risk model based on the four genes. Our study provided a global view and systematic dissection of the lncRNA-associated ceRNA network, and the identified four genes might be novel important prognostic factors involved in LUAD pathogenesis.
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Affiliation(s)
- Yang Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei University, Wuhan, China
| | - Ruyi He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei University, Wuhan, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei University, Wuhan, China
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293
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Sending messages in moving cells: mRNA localization and the regulation of cell migration. Essays Biochem 2020; 63:595-606. [PMID: 31324705 DOI: 10.1042/ebc20190009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022]
Abstract
Cell migration is a fundamental biological process involved in tissue formation and homeostasis. The correct polarization of motile cells is critical to ensure directed movement, and is orchestrated by many intrinsic and extrinsic factors. Of these, the subcellular distribution of mRNAs and the consequent spatial control of translation are key modulators of cell polarity. mRNA transport is dependent on cis-regulatory elements within transcripts, which are recognized by trans-acting proteins that ensure the efficient delivery of certain messages to the leading edge of migrating cells. At their destination, translation of localized mRNAs then participates in regional cellular responses underlying cell motility. In this review, we summarize the key findings that established mRNA targetting as a critical driver of cell migration and how the characterization of polarized mRNAs in motile cells has been expanded from just a few species to hundreds of transcripts. We also describe the molecular control of mRNA trafficking, subsequent mechanisms of local protein synthesis and how these ultimately regulate cell polarity during migration.
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294
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Wang Y, Zhang J, Su Y, Wang C, Zhang G, Liu X, Chen Q, Lv M, Chang Y, Peng J, Hou M, Huang X, Zhang X. miRNA-98-5p Targeting IGF2BP1 Induces Mesenchymal Stem Cell Apoptosis by Modulating PI3K/Akt and p53 in Immune Thrombocytopenia. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:764-776. [PMID: 32428701 PMCID: PMC7232042 DOI: 10.1016/j.omtn.2020.04.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/15/2020] [Accepted: 04/28/2020] [Indexed: 02/06/2023]
Abstract
Immune thrombocytopenia (ITP) is a common hematological autoimmune disease, in which defective mesenchymal stem cells (MSCs) are potentially involved. Our previous study suggested that MSCs in ITP patients displayed enhanced apoptosis. MicroRNAs (miRNAs) play important roles in ITP by affecting megakaryopoiesis, platelet production and immunoregulation, whereas the roles of miRNAs in ITP-MSCs remain unknown. In a previous study, we performed microarray analysis to obtain mRNA and miRNA profiles of ITP-MSCs. In the present study, we reanalyze the data and identify miR-98-5p as a candidate miRNA contributing to MSC deficiency in ITP. miR-98-5p acts through targeting insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), and the subsequent downregulation of insulin-like growth factor 2 (IGF-2) causes inhibition of the phosphatidylinositol 3-kinase (PI3K)/Akt pathway, which is involved in the process of MSC deficiency. Furthermore, miR-98-5p upregulates p53 by inhibiting β-transducin repeat-containing protein (β-TrCP)-dependent p53 ubiquitination. Moreover, miR-98-5p overexpression impairs the therapeutic effect of MSCs in ITP mice. All-trans retinoic acid (ATRA) protects MSCs from apoptosis by downregulating miR-98-5p, thus providing a potential therapeutic approach for ITP. Our findings demonstrate that miR-98-5p is a critical regulator of ITP-MSCs, which will help us thoroughly understand the pathogenesis of ITP.
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Affiliation(s)
- Yanan Wang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China; National Clinical Research Center for Hematologic Disease, Beijing 100044, China; Collaborative Innovation Center of Hematology, Peking University, Beijing 100044, China
| | - Jiamin Zhang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China; National Clinical Research Center for Hematologic Disease, Beijing 100044, China; Collaborative Innovation Center of Hematology, Peking University, Beijing 100044, China
| | - Yan Su
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China; National Clinical Research Center for Hematologic Disease, Beijing 100044, China; Collaborative Innovation Center of Hematology, Peking University, Beijing 100044, China
| | - Chencong Wang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China; National Clinical Research Center for Hematologic Disease, Beijing 100044, China; Collaborative Innovation Center of Hematology, Peking University, Beijing 100044, China
| | - Gaochao Zhang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China; National Clinical Research Center for Hematologic Disease, Beijing 100044, China; Collaborative Innovation Center of Hematology, Peking University, Beijing 100044, China
| | - Xiao Liu
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China; National Clinical Research Center for Hematologic Disease, Beijing 100044, China; Collaborative Innovation Center of Hematology, Peking University, Beijing 100044, China
| | - Qi Chen
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China; National Clinical Research Center for Hematologic Disease, Beijing 100044, China; Collaborative Innovation Center of Hematology, Peking University, Beijing 100044, China
| | - Meng Lv
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China; National Clinical Research Center for Hematologic Disease, Beijing 100044, China; Collaborative Innovation Center of Hematology, Peking University, Beijing 100044, China
| | - Yingjun Chang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China; National Clinical Research Center for Hematologic Disease, Beijing 100044, China; Collaborative Innovation Center of Hematology, Peking University, Beijing 100044, China
| | - Jun Peng
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - Ming Hou
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - Xiaojun Huang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China; National Clinical Research Center for Hematologic Disease, Beijing 100044, China; Collaborative Innovation Center of Hematology, Peking University, Beijing 100044, China
| | - Xiaohui Zhang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China; National Clinical Research Center for Hematologic Disease, Beijing 100044, China; Collaborative Innovation Center of Hematology, Peking University, Beijing 100044, China.
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295
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RNA-Binding Proteins as Important Regulators of Long Non-Coding RNAs in Cancer. Int J Mol Sci 2020; 21:ijms21082969. [PMID: 32340118 PMCID: PMC7215867 DOI: 10.3390/ijms21082969] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/20/2022] Open
Abstract
The majority of the genome is transcribed into pieces of non-(protein) coding RNA, among which long non-coding RNAs (lncRNAs) constitute a large group of particularly versatile molecules that govern basic cellular processes including transcription, splicing, RNA stability, and translation. The frequent deregulation of numerous lncRNAs in cancer is known to contribute to virtually all hallmarks of cancer. An important regulatory mechanism of lncRNAs is the post-transcriptional regulation mediated by RNA-binding proteins (RBPs). So far, however, only a small number of known cancer-associated lncRNAs have been found to be regulated by the interaction with RBPs like human antigen R (HuR), ARE/poly(U)-binding/degradation factor 1 (AUF1), insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), and tristetraprolin (TTP). These RBPs regulate, by various means, two aspects in particular, namely the stability and the localization of lncRNAs. Importantly, these RBPs themselves are commonly deregulated in cancer and might thus play a major role in the deregulation of cancer-related lncRNAs. There are, however, still many open questions, for example regarding the context specificity of these regulatory mechanisms that, in part, is based on the synergistic or competitive interaction between different RBPs. There is also a lack of knowledge on how RBPs facilitate the transport of lncRNAs between different cellular compartments.
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296
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Wang PF, Wang X, Liu M, Zeng Z, Lin C, Xu W, Ma W, Wang J, Xiang Q, Johnston RN, Liu H, Liu SL. The Oncogenic Functions of Insulin-like Growth Factor 2 mRNA-Binding Protein 3 in Human Carcinomas. Curr Pharm Des 2020; 26:3939-3954. [PMID: 32282295 DOI: 10.2174/1381612826666200413080936] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 04/01/2020] [Indexed: 02/07/2023]
Abstract
IGF2BP3 (also known as IMP3, KOC), a member of the insulin-like growth factor mRNA-binding protein family (IMPs), has been a research target in recent studies of promoting embryo development and exacerbating cancer. IGF2BP3 is ubiquitously expressed in early embryogenesis stages but limited in postembryonic stages, which is important in many physiological aspects such as stem cell renewal, morphological development and metabolism. A large number of studies show that IGF2BP3 interacts with many kinds of non-coding RNAs and proteins to promote cancer cell proliferation and metastasis and inhibit cancer cell apoptosis. As IGF2BP3 is highly expressed in advanced cancers and associated with poor overall survival rates of patients, it may be a potential molecular marker in cancer diagnosis for the detection of cancerous tissues and an indicator of cancer stages. Therefore, anti-IGF2BP3 drugs or monoclonal antibodies are expected as new therapeutic methods in cancer treatment. This review summarizes recent findings among IGF2BP3, RNA and proteins in cancer processes, with a focus on its cancer-promoting mechanisms and potential application as a new biomarker for cancer diagnosis and treatment.
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Affiliation(s)
- Peng-Fei Wang
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Xiaoyu Wang
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Min Liu
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Zheng Zeng
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Caiji Lin
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Wenwen Xu
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Wenqing Ma
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Jiali Wang
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Qian Xiang
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Randal N Johnston
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N1N4, Canada
| | - Huidi Liu
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Shu-Lin Liu
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
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297
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Teng H, Wei W, Li Q, Xue M, Shi X, Li X, Mao F, Sun Z. Prevalence and architecture of posttranscriptionally impaired synonymous mutations in 8,320 genomes across 22 cancer types. Nucleic Acids Res 2020; 48:1192-1205. [PMID: 31950163 PMCID: PMC7026592 DOI: 10.1093/nar/gkaa019] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
Somatic synonymous mutations are one of the most frequent genetic variants occurring in the coding region of cancer genomes, while their contributions to cancer development remain largely unknown. To assess whether synonymous mutations involved in post-transcriptional regulation contribute to the genetic etiology of cancers, we collected whole exome data from 8,320 patients across 22 cancer types. By employing our developed algorithm, PIVar, we identified a total of 22,948 posttranscriptionally impaired synonymous SNVs (pisSNVs) spanning 2,042 genes. In addition, 35 RNA binding proteins impacted by these identified pisSNVs were significantly enriched. Remarkably, we discovered markedly elevated ratio of somatic pisSNVs across all 22 cancer types, and a high pisSNV ratio was associated with worse patient survival in five cancer types. Intriguing, several well-established cancer genes, including PTEN, RB1 and PIK3CA, appeared to contribute to tumorigenesis at both protein function and posttranscriptional regulation levels, whereas some pisSNV-hosted genes, including UBR4, EP400 and INTS1, exerted their function during carcinogenesis mainly via posttranscriptional mechanisms. Moreover, we predicted three drugs associated with two pisSNVs, and numerous compounds associated with expression signature of pisSNV-hosted genes. Our study reveals the prevalence and clinical relevance of pisSNVs in cancers, and emphasizes the importance of considering posttranscriptional impaired synonymous mutations in cancer biology.
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Affiliation(s)
- Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Wenqing Wei
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinglan Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meiying Xue
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohui Shi
- Sino-Danish college, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianfeng Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Fengbiao Mao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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298
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Tang L, Chen Y, Chen H, Jiang P, Yan L, Mo D, Tang X, Yan F. DCST1-AS1 Promotes TGF-β-Induced Epithelial-Mesenchymal Transition and Enhances Chemoresistance in Triple-Negative Breast Cancer Cells via ANXA1. Front Oncol 2020; 10:280. [PMID: 32226772 PMCID: PMC7080863 DOI: 10.3389/fonc.2020.00280] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/18/2020] [Indexed: 12/27/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly metastatic breast cancer subtype, and the primary systemic treatment strategy involves conventional chemotherapy. DC-STAMP domain containing 1-antisense 1 (DCST1-AS1) is a long non-coding RNA that promotes TNBC migration and invasion. Studying the role of DCST1-AS1 in promoting epithelial–mesenchymal transition (EMT) and chemoresistance will provide a new strategy for TNBC therapy. In the present study, we found that DCST1-AS1 regulates the expression or secretion of EMT-related proteins E-cadherin, snail family zinc finger 1 (SNAI1), vimentin, matrix metallopeptidase 2 (MMP2), and matrix metallopeptidase 9 (MMP9). Interference with DCST1-AS1 impaired TGF-β-induced TNBC cell invasion and migration. DCST1-AS1 directly binds to ANXA1 in BT-549 cells and affects the expression of ANXA1. DCST1-AS1 enhances TGF-β/Smad signaling in BT-549 cells through ANXA1 to promote EMT. The combination of DCST1-AS1 and ANXA1 also contributes to enhancement of the resistance of BT-549 cells to doxorubicin and paclitaxel. In conclusion, DCST1-AS1 promotes TGF-β-induced EMT and enhances chemoresistance in TNBC cells through ANXA1, and therefore represents a potentially promising target for metastatic breast cancer therapy.
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Affiliation(s)
- Li Tang
- Department of Clinical Laboratory, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yuli Chen
- Department of Clinical Laboratory, Nanjing Qixia District Hospital, Nanjing, China
| | - Huanhuan Chen
- The Fourth Clinical Medical School, Nanjing Medical University, Nanjing, China
| | - Pan Jiang
- The Fourth Clinical Medical School, Nanjing Medical University, Nanjing, China
| | - Linping Yan
- Department of Clinical Laboratory, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Dongping Mo
- Department of Clinical Laboratory, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Xun Tang
- Department of Clinical Laboratory, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Yan
- Department of Clinical Laboratory, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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299
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Long noncoding RNA TRPM2-AS acts as a microRNA sponge of miR-612 to promote gastric cancer progression and radioresistance. Oncogenesis 2020; 9:29. [PMID: 32123162 PMCID: PMC7052141 DOI: 10.1038/s41389-020-0215-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 01/27/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as important regulators of tumorigenesis and are frequently dysregulated in cancers. Here, we identify a critical lncRNA TRPM2-AS which is aberrantly expressed in gastric cancer (GC) tissues by screening The Cancer Genome Atlas Program(TCGA) database of GC cohort, and its upregulation is clinically associated with advanced pathologic stages and poor prognosis in GC patients. Silencing TRPM2-AS inhibits the proliferation, metastasis and radioresistance of GC cell whereas ectopic expression of TRPM2-AS significantly improves the progression of GC cell in multiple experiments. Mechanistically, TRPM2-AS serves as a microRNA sponge or a competitive endogenous RNA (ceRNA) for tumor suppressive microRNA miR-612 and consequently modulates the derepression of IGF2BP1 and FOXM1. Moreover, induced upregulation of IGF2BP1 subsequently increases the expression of c-Myc and promotes GC cell progression. Meanwhile, TRPM2-AS promotes the radioreistance of GC cell through enhancing the expression of FOXM1 as well. Thus, our findings support a new regulatory axis between TRPM2-AS, miR-612, IGF2BP1, or FOXM1 which serve as crucial effectors in GC tumorigenesis and malignant development, suggesting a promising therapeutic and diagnostic direction for GC.
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Merid SK, Novoloaca A, Sharp GC, Küpers LK, Kho AT, Roy R, Gao L, Annesi-Maesano I, Jain P, Plusquin M, Kogevinas M, Allard C, Vehmeijer FO, Kazmi N, Salas LA, Rezwan FI, Zhang H, Sebert S, Czamara D, Rifas-Shiman SL, Melton PE, Lawlor DA, Pershagen G, Breton CV, Huen K, Baiz N, Gagliardi L, Nawrot TS, Corpeleijn E, Perron P, Duijts L, Nohr EA, Bustamante M, Ewart SL, Karmaus W, Zhao S, Page CM, Herceg Z, Jarvelin MR, Lahti J, Baccarelli AA, Anderson D, Kachroo P, Relton CL, Bergström A, Eskenazi B, Soomro MH, Vineis P, Snieder H, Bouchard L, Jaddoe VW, Sørensen TIA, Vrijheid M, Arshad SH, Holloway JW, Håberg SE, Magnus P, Dwyer T, Binder EB, DeMeo DL, Vonk JM, Newnham J, Tantisira KG, Kull I, Wiemels JL, Heude B, Sunyer J, Nystad W, Munthe-Kaas MC, Räikkönen K, Oken E, Huang RC, Weiss ST, Antó JM, Bousquet J, Kumar A, Söderhäll C, Almqvist C, Cardenas A, Gruzieva O, Xu CJ, Reese SE, Kere J, Brodin P, Solomon O, Wielscher M, Holland N, Ghantous A, Hivert MF, Felix JF, Koppelman GH, London SJ, Melén E. Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age. Genome Med 2020; 12:25. [PMID: 32114984 PMCID: PMC7050134 DOI: 10.1186/s13073-020-0716-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 01/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. METHODS We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: fetal brain and lung. RESULTS We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10- 7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. CONCLUSIONS We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.
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Affiliation(s)
- Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Alexei Novoloaca
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Leanne K Küpers
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alvin T Kho
- Computational Health Informatics Program, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ritu Roy
- Computational Biology And Informatics, University of California, San Francisco, San Francisco, CA, USA
- HDF Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | - Isabella Annesi-Maesano
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Pooja Jain
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK
| | - Michelle Plusquin
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
| | - Florianne O Vehmeijer
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Nabila Kazmi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, USA
| | - Faisal I Rezwan
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Genomic of Complex diseases, School of Public Health, Imperial College London, London, UK
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Sheryl L Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Phillip E Melton
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Australia
- Curtin/UWA Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Carrie V Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Nour Baiz
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Luigi Gagliardi
- Division of Neonatology and Pediatrics, Ospedale Versilia, Viareggio, AUSL Toscana Nord Ovest, Pisa, Italy
| | - Tim S Nawrot
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Department of Public Health & Primary Care, Leuven University, Leuven, Belgium
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Department of Medicine, Université de Sherbrooke, Sherbrooke, Canada
| | - Liesbeth Duijts
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ellen Aagaard Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Susan L Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Shanshan Zhao
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | | | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Marjo-Riitta Jarvelin
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Turku Institute for Advanced Studies, University of Turku, Turku, Finland
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY, USA
| | - Denise Anderson
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), University of California, Berkeley, Berkeley, CA, USA
| | - Munawar Hussain Soomro
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Luigi Bouchard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of medical biology, CIUSSS-SLSJ, Saguenay, QC, Canada
| | - Vincent W Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martine Vrijheid
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - S Hasan Arshad
- Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- The David Hide Asthma and Allergy Research Centre, Newport, Isle of Wight, UK
| | - John W Holloway
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Per Magnus
- Norwegian Institute of Public Health, Oslo, Norway
| | - Terence Dwyer
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
- Murdoch Children's Research Institute, Australia Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - John Newnham
- Faculty of Health and Medical Sciences, UWA Medical School, University of Western Australia, Perth, Australia
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Inger Kull
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children's Hospital, Södersjukhuset, 118 83, Stockholm, Sweden
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, USA
| | - Barbara Heude
- INSERM, UMR1153 Epidemiology and Biostatistics Sorbonne Paris Cité Center (CRESS), Research Team on Early life Origins of Health (EarOH), Paris Descartes University, Paris, France
| | - Jordi Sunyer
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | | | - Monica C Munthe-Kaas
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Pediatric Oncology and Hematology, Oslo University Hospital, Oslo, Norway
| | | | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Josep Maria Antó
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Jean Bousquet
- University Hospital, Montpellier, France
- Department of Dermatology, Charité, Berlin, Germany
| | - Ashish Kumar
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, The Netherlands
| | - Sarah E Reese
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Folkhälsa Research Institute, Helsinki, and Stem Cells and Metabolism Research Program, University of Helsinki Finland, Helsinki, Finland
| | - Petter Brodin
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Department of Newborn Medicine, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Olivia Solomon
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Nina Holland
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Marie-France Hivert
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, The Netherlands
| | - Stephanie J London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.
- Sachs' Children's Hospital, South General Hospital, Stockholm, Sweden.
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