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Albihlal WS, Chan WY, van Werven FJ. Budding yeast as an ideal model for elucidating the role of N 6-methyladenosine in regulating gene expression. Yeast 2024; 41:148-157. [PMID: 38238962 DOI: 10.1002/yea.3925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 02/24/2024] Open
Abstract
N6-methyladenosine (m6A) is a highly abundant and evolutionarily conserved messenger RNA (mRNA) modification. This modification is installed on RRACH motifs on mRNAs by a hetero-multimeric holoenzyme known as m6A methyltransferase complex (MTC). The m6A mark is then recognised by a group of conserved proteins known as the YTH domain family proteins which guide the mRNA for subsequent downstream processes that determine its fate. In yeast, m6A is installed on thousands of mRNAs during early meiosis by a conserved MTC and the m6A-modified mRNAs are read by the YTH domain-containing protein Mrb1/Pho92. In this review, we aim to delve into the recent advances in our understanding of the regulation and roles of m6A in yeast meiosis. We will discuss the potential functions of m6A in mRNA translation and decay, unravelling their significance in regulating gene expression. We propose that yeast serves as an exceptional model organism for the study of fundamental molecular mechanisms related to the function and regulation of m6A-modified mRNAs. The insights gained from yeast research not only expand our knowledge of mRNA modifications and their molecular roles but also offer valuable insights into the broader landscape of eukaryotic posttranscriptional regulation of gene expression.
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Affiliation(s)
- Waleed S Albihlal
- The Francis Crick Institute, Cell Fate and Gene Regulation Laboratory, London, UK
| | - Wei Yee Chan
- The Francis Crick Institute, Cell Fate and Gene Regulation Laboratory, London, UK
| | - Folkert J van Werven
- The Francis Crick Institute, Cell Fate and Gene Regulation Laboratory, London, UK
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2
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Febrimarsa, Gornik SG, Barreira SN, Salinas‐Saavedra M, Schnitzler CE, Baxevanis AD, Frank U. Randomly incorporated genomic N6-methyldeoxyadenosine delays zygotic transcription initiation in a cnidarian. EMBO J 2023; 42:e112934. [PMID: 37708295 PMCID: PMC10390872 DOI: 10.15252/embj.2022112934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 09/16/2023] Open
Abstract
N6-methyldeoxyadenosine (6mA) is a chemical alteration of DNA, observed across all realms of life. Although the functions of 6mA are well understood in bacteria and protists, its roles in animal genomes have been controversial. We show that 6mA randomly accumulates in early embryos of the cnidarian Hydractinia symbiolongicarpus, with a peak at the 16-cell stage followed by clearance to background levels two cell cycles later, at the 64-cell stage-the embryonic stage at which zygotic genome activation occurs in this animal. Knocking down Alkbh1, a putative initiator of animal 6mA clearance, resulted in higher levels of 6mA at the 64-cell stage and a delay in the initiation of zygotic transcription. Our data are consistent with 6mA originating from recycled nucleotides of degraded m6A-marked maternal RNA postfertilization. Therefore, while 6mA does not function as an epigenetic mark in Hydractinia, its random incorporation into the early embryonic genome inhibits transcription. In turn, Alkbh1 functions as a genomic 6mA "cleaner," facilitating timely zygotic genome activation. Given the random nature of genomic 6mA accumulation and its ability to interfere with gene expression, defects in 6mA clearance may represent a hitherto unknown cause of various pathologies.
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Affiliation(s)
- Febrimarsa
- Centre for Chromosome Biology, School of Biological and Chemical SciencesUniversity of GalwayGalwayRepublic of Ireland
| | - Sebastian G Gornik
- Centre for Chromosome Biology, School of Biological and Chemical SciencesUniversity of GalwayGalwayRepublic of Ireland
- Present address:
Centre for Organismal StudiesHeidelberg UniversityHeidelbergGermany
| | - Sofia N Barreira
- Computational and Statistical Genomics Branch, Division of Intramural ResearchNational Human Genome Research Institute, National Institutes of HealthBethesdaMDUSA
| | - Miguel Salinas‐Saavedra
- Centre for Chromosome Biology, School of Biological and Chemical SciencesUniversity of GalwayGalwayRepublic of Ireland
| | - Christine E Schnitzler
- Whitney Laboratory for Marine BioscienceUniversity of FloridaSt. AugustineFLUSA
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, Division of Intramural ResearchNational Human Genome Research Institute, National Institutes of HealthBethesdaMDUSA
| | - Uri Frank
- Centre for Chromosome Biology, School of Biological and Chemical SciencesUniversity of GalwayGalwayRepublic of Ireland
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CRISPR-Cas9-Mediated Mutation of Methyltransferase METTL4 Results in Embryonic Defects in Silkworm Bombyx mori. Int J Mol Sci 2023; 24:ijms24043468. [PMID: 36834878 PMCID: PMC9965800 DOI: 10.3390/ijms24043468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
DNA N6-methyladenine (6mA) has recently been found to play regulatory roles in gene expression that links to various biological processes in eukaryotic species. The functional identification of 6mA methyltransferase will be important for understanding the underlying molecular mechanism of epigenetic 6mA methylation. It has been reported that the methyltransferase METTL4 can catalyze the methylation of 6mA; however, the function of METTL4 remains largely unknown. In this study, we aim to investigate the role of the Bombyx mori homolog METTL4 (BmMETTL4) in silkworm, a lepidopteran model insect. By using CRISPR-Cas9 system, we somatically mutated BmMETTL4 in silkworm individuates and found that disruption of BmMETTL4 caused the developmental defect of late silkworm embryo and subsequent lethality. We performed RNA-Seq and identified that there were 3192 differentially expressed genes in BmMETTL4 mutant including 1743 up-regulated and 1449 down-regulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that genes involved in molecular structure, chitin binding, and serine hydrolase activity were significantly affected by BmMETTL4 mutation. We further found that the expression of cuticular protein genes and collagens were clearly decreased while collagenases were highly increased, which had great contributions to the abnormal embryo and decreased hatchability of silkworm. Taken together, these results demonstrated a critical role of 6mA methyltransferase BmMETTL4 in regulating embryonic development of silkworm.
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Sendinc E, Shi Y. RNA m6A methylation across the transcriptome. Mol Cell 2023; 83:428-441. [PMID: 36736310 DOI: 10.1016/j.molcel.2023.01.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 02/05/2023]
Abstract
Since the early days of foundational studies of nucleic acids, many chemical moieties have been discovered to decorate RNA and DNA in diverse organisms. In mammalian cells, one of these chemical modifications, N6-methyl adenosine (m6A), is unique in a way that it is highly abundant not only on RNA polymerase II (RNAPII) transcribed, protein-coding transcripts but also on non-coding RNAs, such as ribosomal RNAs and snRNAs, mediated by distinct, evolutionarily conserved enzymes. Here, we review RNA m6A modification in the light of the recent appreciation of nuclear roles for m6A in regulating chromatin states and gene expression, as well as the recent discoveries of the evolutionarily conserved methyltransferases, which catalyze methylation of adenosine on diverse sets of RNAs. Considering that the substrates of these enzymes are involved in many important biological processes, this modification warrants further research to understand the molecular mechanisms and functions of m6A in health and disease.
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Affiliation(s)
- Erdem Sendinc
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yang Shi
- Ludwig Institute for Cancer Research, University of Oxford, Roosevelt Dr, Headington, Oxford OX3 7DQ, UK.
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5
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Regulation of Gene Expression by m6Am RNA Modification. Int J Mol Sci 2023; 24:ijms24032277. [PMID: 36768600 PMCID: PMC9916840 DOI: 10.3390/ijms24032277] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/17/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023] Open
Abstract
The field of RNA modification, also referred to as "epitranscriptomics," is gaining more and more interest from the scientific community. More than 160 chemical modifications have been identified in RNA molecules, but the functional significance of most of them still needs to be clarified. In this review, we discuss the role of N6,2'-O-dimethyladenosine (m6Am) in gene expression regulation. m6Am is present in the first transcribed nucleotide close to the cap in many mRNAs and snRNAs in mammals and as internal modification in the snRNA U2. The writer and eraser proteins for these modifications have been recently identified and their deletions have been utilized to understand their contributions in gene expression regulation. While the role of U2 snRNA-m6Am in splicing regulation has been reported by different independent studies, conflicting data were found for the role of cap-associated m6Am in mRNA stability and translation. However, despite the open debate on the role of m6Am in mRNA expression, the modulation of regulators produced promising results in cancer cells. We believe that the investigation on m6Am will continue to yield relevant results in the future.
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Ju J, Liu Y, Liang H, Yang B. The role of pyroptosis in endothelial dysfunction induced by diseases. Front Immunol 2023. [DOI: 10.3389/fimmu.2023.1093985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Most organs in the body rely on blood flow, and vesicular damage is the leading cause of injury in multiple organs. The endothelium, as the barriers of vessels, play a critical role in ensuring vascular homeostasis and angiogenesis. The rapid development of risk factors in endothelial injuries has been seen in the past decade, such as smoking, infectious, and diabetes mellites. Pyroptotic endothelium is an inflammatory mode of governed endothelial cell death that depend on the metabolic disorder and severe infectious such as atherosclerosis, and sepsis-related acute lung injury, respectively. Pyroptotic endothelial cells need GSDMD cleaved into N- and C-terminal by caspase1, and the cytokines are released by a pore constructed by the N-terminal of GSDMD in the membrane of ECs, finally resulting in severe inflammation and pyroptotic cell death. This review will focus on the patho-physiological and pharmacological pathways of pyroptotic endothelial metabolism in diseases. Overall, this review indicates that pyroptosis is a significant risk factor in diseases and a potential drug target in related diseases.
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Ju J, Liu Y, Liang H, Yang B. The role of pyroptosis in endothelial dysfunction induced by diseases. Front Immunol 2023; 13:1093985. [PMID: 36776394 PMCID: PMC9910335 DOI: 10.3389/fimmu.2022.1093985] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023] Open
Abstract
Most organs in the body rely on blood flow, and vesicular damage is the leading cause of injury in multiple organs. The endothelium, as the barriers of vessels, play a critical role in ensuring vascular homeostasis and angiogenesis. The rapid development of risk factors in endothelial injuries has been seen in the past decade, such as smoking, infectious, and diabetes mellites. Pyroptotic endothelium is an inflammatory mode of governed endothelial cell death that depend on the metabolic disorder and severe infectious such as atherosclerosis, and sepsis-related acute lung injury, respectively. Pyroptotic endothelial cells need GSDMD cleaved into N- and C-terminal by caspase1, and the cytokines are released by a pore constructed by the N-terminal of GSDMD in the membrane of ECs, finally resulting in severe inflammation and pyroptotic cell death. This review will focus on the patho-physiological and pharmacological pathways of pyroptotic endothelial metabolism in diseases. Overall, this review indicates that pyroptosis is a significant risk factor in diseases and a potential drug target in related diseases.
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Affiliation(s)
- Jin Ju
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Yanyan Liu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, China
| | - Haihai Liang
- Key Laboratory of Cardiovascular Research, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Ministry of Education, Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang, China,Research Unit of Noninfectious Chronic Diseases in Frigid Zone (2019RU070), Chinese Academy of Medical Sciences, Harbin, Heilongjiang, China
| | - Baofeng Yang
- Key Laboratory of Cardiovascular Research, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Ministry of Education, Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang, China,Research Unit of Noninfectious Chronic Diseases in Frigid Zone (2019RU070), Chinese Academy of Medical Sciences, Harbin, Heilongjiang, China,*Correspondence: Baofeng Yang,
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Zhang Z, Chen P, Yun J. Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer. Front Genet 2023; 14:1156095. [PMID: 37124622 PMCID: PMC10131083 DOI: 10.3389/fgene.2023.1156095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/31/2023] [Indexed: 05/02/2023] Open
Abstract
Background: Bladder cancer (BCa) is the leading reason for death among genitourinary malignancies. RNA modifications in tumors closely link to the immune microenvironment. Our study aimed to propose a promising model associated with the "writer" enzymes of five primary RNA adenosine modifications (including m6A, m6Am, m1A, APA, and A-to-I editing), thus characterizing the clinical outcome, immune landscape and therapeutic efficacy of BCa. Methods: Unsupervised clustering was employed to categorize BCa into different RNA modification patterns based on gene expression profiles of 34 RNA modification "writers". The RNA modification "writers" score (RMS) signature composed of RNA phenotype-associated differentially expressed genes (DEGs) was established using the least absolute shrinkage and selection operator (LASSO), which was evaluated in meta-GEO (including eight independent GEO datasets) training cohort and the TCGA-BLCA validation cohort. The hub genes in the RMS model were determined via weighted gene co-expression network analysis (WGCNA) and were further validated using human specimen. The potential applicability of the RMS model in predicting the therapeutic responsiveness was assessed through the Genomics of Drug Sensitivity in Cancer database and multiple immunotherapy datasets. Results: Two distinct RNA modification patterns were determined among 1,410 BCa samples from a meta-GEO cohort, showing radically varying clinical outcomes and biological characteristics. The RMS model comprising 14 RNA modification phenotype-associated prognostic DEGs positively correlated with the unsatisfactory outcome of BCa patients in meta-GEO training cohort (HR = 3.00, 95% CI = 2.19-4.12) and TCGA-BLCA validation cohort (HR = 1.53, 95% CI = 1.13-2.09). The infiltration of immunosuppressive cells and the activation of EMT, angiogenesis, IL-6/JAK/STAT3 signaling were markedly enriched in RMS-high group. A nomogram exhibited high prognostic prediction accuracy, with a concordance index of 0.785. The therapeutic effect of chemotherapeutic agents and antibody-drug conjugates was significantly different between RMS-low and -high groups. The combination of the RMS model and conventional characteristics (TMB, TNB and PD-L1) achieved an optimal AUC value of 0.828 in differentiating responders from non-responders to immunotherapy. Conclusion: We conferred the first landscape of five forms of RNA modifications in BCa and emphasized the excellent power of an RNA modifications-related model in evaluating BCa prognosis and immune landscape.
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Affiliation(s)
- Ziying Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Peng Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jingping Yun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- *Correspondence: Jingping Yun,
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Zhang C, Dai D, Zhang W, Yang W, Guo Y, Wei Q. Role of m6A RNA methylation in the development of hepatitis B virus-associated hepatocellular carcinoma. J Gastroenterol Hepatol 2022; 37:2039-2050. [PMID: 36066844 DOI: 10.1111/jgh.15999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/10/2022] [Accepted: 09/03/2022] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) is the most common liver malignancy that can be developed from hepatitis B and cirrhosis. Many pathophysiological alterations, including hepatitis B virus (HBV) DNA integration, oxidative stress, cytokine release, telomerase homeostasis, mitochondrial damage, epigenetic modification, and tumor microenvironment, are involved in the biological process from hepatitis B to cirrhosis and HCC. N6-methyladenosine (m6A), as an epitranscriptomic modification of RNAs, can regulate the stability, splicing, degradation, transcription, and translation of downstream target RNAs in HBV and liver cancer cells. m6A regulators (writers, erasers, and readers) play an important role in the pathogenesis of HBV-associated HCC by regulating cell proliferation, apoptosis, migration, autophagy, differentiation, inflammation, angiogenesis, and tumor microenvironment. This review summarizes the current progress of m6A methylation in the molecular mechanisms, biological functions, and potential clinical implications of HBV-associated HCC.
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Affiliation(s)
- Cheng Zhang
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China.,Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Dongjun Dai
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wangjian Zhang
- School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenjun Yang
- Department of Pathology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Yinglu Guo
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qichun Wei
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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Structural insights into molecular mechanism for N 6-adenosine methylation by MT-A70 family methyltransferase METTL4. Nat Commun 2022; 13:5636. [PMID: 36163360 PMCID: PMC9512776 DOI: 10.1038/s41467-022-33277-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/12/2022] [Indexed: 11/08/2022] Open
Abstract
METTL4 belongs to a subclade of MT-A70 family members of methyltransferase (MTase) proteins shown to mediate N6-adenosine methylation for both RNA and DNA in diverse eukaryotes. Here, we report that Arabidopsis METTL4 functions as U2 snRNA MTase for N6-2'-O-dimethyladenosine (m6Am) in vivo that regulates flowering time, and specifically catalyzes N6-methylation of 2'-O-methyladenosine (Am) within a single-stranded RNA in vitro. The apo structures of full-length Arabidopsis METTL4 bound to S-adenosyl-L-methionine (SAM) and the complex structure with an Am-containing RNA substrate, combined with mutagenesis and in vitro enzymatic assays, uncover a preformed L-shaped, positively-charged cavity surrounded by four loops for substrate binding and a catalytic center composed of conserved residues for specific Am nucleotide recognition and N6-methylation activity. Structural comparison of METTL4 with the mRNA m6A enzyme METTL3/METTL14 heterodimer and modeling analysis suggest a catalytic mechanism for N6-adenosine methylation by METTL4, which may be shared among MT-A70 family members.
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Luan M, Zhao M, Wang H, Xu R, Cai J. Role of 5-methylcytosine in determining the prognosis, tumor microenvironment, and applicability of precision medicine in patients with hepatocellular carcinoma. Front Genet 2022; 13:984033. [PMID: 36186468 PMCID: PMC9523584 DOI: 10.3389/fgene.2022.984033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/02/2022] [Indexed: 12/09/2022] Open
Abstract
Background: 5-methylcytosine has a profound impact on the development and progression of hepatocellular carcinoma. The aim of this study was to investigate the usefulness of 5-methylcytosine in determining the prognosis, tumor microenvironment, and applicability of precision medicine in hepatocellular carcinoma. Methods: We collected data of seven hepatocellular carcinoma cohorts (The Cancer Genome Atlas, International Cancer Genome Consortium, GSE14520, GSE6764, GSE9843, GSE63898, GSE76427). An unsupervised clustering method was used to identify novel subtypes of hepatocellular carcinoma based on the expression 5-methylcytosine gene signatures. The 5-methylcytosine score was determined using the least absolute shrinkage and selection operator method based on the differential expression of genes in the identified subtypes. Subsequently, we investigated the association between 5-methylcytosine-based clusters (according to the 5-methylcytosine score) and clinical outcomes, immunophenotypes, classical molecular subtypes, and therapeutic opportunities in hepatocellular carcinoma. Finally, we examined the sensitivity of patients with high 5-methylcytosine score to drugs. Results: We identified two hepatocellular carcinoma-specific, 5-methylcytosine-based subtypes (clusters 1 and 2). Cluster 1 exhibited significantly higher 5-methylcytosine scores versus cluster 2. The 5-methylcytosine-based subtypes accurately predicted classical molecular subtypes, immunophenotypes, prognosis, and therapeutic opportunities for patients with hepatocellular carcinoma. Cluster 1 (high 5-methylcytosine score) was characterized by lower anticancer immunity and worse prognosis versus cluster 2 (low 5-methylcytosine score). Moreover, cluster 1 (high 5-methylcytosine score) exhibited low sensitivity to cancer immunotherapy, but high sensitivity to radiotherapy and targeted therapy with lenvatinib. Conclusion: The novel 5-methylcytosine-based subtypes (according to the 5-methylcytosine score) may reflect the prognosis, tumor microenvironment, and applicability of precision medicine in patients with hepatocellular carcinoma.
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Affiliation(s)
- Mingyuan Luan
- Qingdao University Medical College, Qingdao, Shandong, China
| | - Min Zhao
- Center of Laboratory Medicine, Qilu Hospital of Shandong University (Qingdao), Qingdao, Shandong, China
| | - Haiying Wang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Shandong Provincial Key Laboratory of Fishery Resources and Ecological Environment, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Rongjian Xu
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Rongjian Xu, ; Jinzhen Cai,
| | - Jinzhen Cai
- Organ Transplantation Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- *Correspondence: Rongjian Xu, ; Jinzhen Cai,
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12
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Jia X, Zhang G. Characterization of chromatin regulators in hepatocellular carcinoma to guide clinical therapy. Front Genet 2022; 13:961018. [PMID: 36092923 PMCID: PMC9452841 DOI: 10.3389/fgene.2022.961018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is notorious for its high mortality and incidence. Accumulating evidence confirms that chromatin regulators (CRs) have a significant impact on cancer. Therefore, exploring the mode of action and prognostic value of CRs is imminent for the treatment of hepatocellular carcinoma. Method: Transcriptome and clinical data for this study have been downloaded from TCGA (https://portal.gdc.cancer.gov/) and ICGC (https://dcc.icgc.org/). Univariate analysis was used to screen CRs with prognostic value, and our prognostic risk score signature was developed using least absolute shrinkage along with selection operator (lasso) Cox regression analysis. The CRs-based prognostic model was constructed in the TCGA dataset, and low-risk HCC patients had a better prognosis, which was finally validated in the ICGC dataset. We used the receiver operating characteristic curve to identify the accuracy of the prediction model and establish a line chart to prove the clinical effectiveness of the model. We also discussed the differences in drug sensitivity via CellMiner database, tumor immune microenvironment via ssGSEA algorithm, and clinical characteristics among different risk groups. Results: A prognostic model consisting of seven CRs was constructed and verified in HCC patients. Furthermore, we found that this risk score prognostic signature could independently predict the prognosis of HCC patients. Functional enrichment analysis revealed that CRs are mainly associated with cancer-related signaling pathways and metabolic pathways. In addition, immune cell abundance correlates with risk score levels Conclusion: In brief, we systematically explored the mode of action of CRs in HCC patients and established a reliable prognostic prediction model.
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Affiliation(s)
- Xiangen Jia
- North China University of Science and Technology Affiliated Hospital, Tangshan, China
- North China University of Science and Technology, Tangshan, China
| | - Guozhi Zhang
- North China University of Science and Technology Affiliated Hospital, Tangshan, China
- North China University of Science and Technology, Tangshan, China
- *Correspondence: Guozhi Zhang,
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13
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Li Z, Li Y, Shen L, Shen L, Li N. Molecular characterization, clinical relevance and immune feature of m7G regulator genes across 33 cancer types. Front Genet 2022; 13:981567. [PMID: 36092891 PMCID: PMC9453236 DOI: 10.3389/fgene.2022.981567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Over 170 RNA modifications have been identified after transcriptions, involving in regulation of RNA splicing, processing, translation and decay. Growing evidence has unmasked the crucial role of N6-methyladenosine (m6A) in cancer development and progression, while, as a relative newly found RNA modification, N7-methylguanosine (m7G) is also certified to participate in tumorigenesis via different catalytic machinery from that of m6A. However, system analysis on m7G RNA modification-related regulator genes is lack. In this study, we first investigated the genetic alteration of m7G related regulator genes in 33 cancers, and found mRNA expression levels of most regulator genes were positively correlated with copy number variation (CNV) and negatively correlated with methylation in most cancers. We built a m7G RNA modification model based on the enrichment of the regulator gene scores to evaluate the m7G modification levels in 33 cancers, and investigated the connections of m7G scores to clinical outcomes. Furthermore, we paid close attention to the role of m7G in immunology due to the widely used immune checkpoint blockade therapy. Our results showed the higher m7G scores related to immunosuppression of tumor cells. Further confirmation with phase 3 clinical data with application of anti-PDL1/PDL indicated the impact of m7G modification level on immunotherapy effect. Relevance of m7G regulator genes and drug sensitivity was also evaluated to provide a better treatment choice when treating cancers. In summary, our study uncovered the profile of m7G RNA modification through various cancers, and figured out the connection of m7G modification levels with therapeutical outcomes, providing potential better options of cancer treatment.
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Affiliation(s)
- Zhanzhan Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Yanyan Li
- Department of Nursing, Xiangya Hospital, Central South University, Changsha, China
| | - Lin Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Liangfang Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Na Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Na Li,
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Luo L, Zhen Y, Peng D, Wei C, Zhang X, Liu X, Han L, Zhang Z. The role of N6-methyladenosine-modified non-coding RNAs in the pathological process of human cancer. Cell Death Discov 2022; 8:325. [PMID: 35851061 PMCID: PMC9293946 DOI: 10.1038/s41420-022-01113-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 12/13/2022] Open
Abstract
Non-coding RNAs (ncRNAs) account for the majority of the widespread transcripts of mammalian genomes. They rarely encode proteins and peptides, but their regulatory role is crucial in numerous physiological and pathological processes. The m6A (N6-methyladenosine) modification is one of the most common internal RNA modifications in eukaryotes and is associated with all aspects of RNA metabolism. Accumulating researches have indicated a close association between m6A modification and ncRNAs, and suggested m6A-modified ncRNAs played a crucial role in tumor progression. The correlation between m6A modification and ncRNAs offers a novel perspective for investigating the potential mechanisms of cancer pathological processes, which suggests that both m6A modification and ncRNAs are critical prognostic markers and therapeutic targets in numerous malignancies. In the present report, we summarized the interaction between m6A modification and ncRNA, emphasizing how their interaction regulates pathological processes in cancer.
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Affiliation(s)
- Lin Luo
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 480082, China.,Academy of medical sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Yingwei Zhen
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 480082, China
| | - Dazhao Peng
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Cheng Wei
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Xiaoyang Zhang
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Xianzhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 480082, China.
| | - Lei Han
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China.
| | - Zhenyu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 480082, China.
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Ren Z, Tang B, Xing J, Liu C, Cai X, Hendy A, Kamran M, Liu H, Zheng L, Huang J, Chen XL. MTA1-mediated RNA m 6 A modification regulates autophagy and is required for infection of the rice blast fungus. THE NEW PHYTOLOGIST 2022; 235:247-262. [PMID: 35338654 DOI: 10.1111/nph.18117] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
In eukaryotes, N6 -methyladenosine (m6 A) is abundant on mRNA, and plays key roles in the regulation of RNA function. However, the roles and regulatory mechanisms of m6 A in phytopathogenic fungi are still largely unknown. Combined with biochemical analysis, MeRIP-seq and RNA-seq methods, as well as biological analysis, we showed that Magnaporthe oryzae MTA1 gene is an orthologue of human METTL4, which is involved in m6 A modification and plays a critical role in autophagy for fungal infection. The Δmta1 mutant showed reduced virulence due to blockage of appressorial penetration and invasive growth. Moreover, the autophagy process was severely disordered in the mutant. MeRIP-seq identified 659 hypomethylated m6 A peaks covering 595 mRNAs in Δmta1 appressoria, 114 m6 A peaks was negatively related to mRNA abundance, including several ATG gene transcripts. Typically, the mRNA abundance of MoATG8 was also increased in the single m6 A site mutant ∆atg8/MoATG8A982C , leading to an autophagy disorder. Our findings reveal the functional importance of the m6 A methylation in infection of M. oryzae and provide novel insight into the regulatory mechanisms of plant pathogenic fungi.
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Affiliation(s)
- Zhiyong Ren
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bozeng Tang
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, UK
| | - Junjie Xing
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Caiyun Liu
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuan Cai
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ahmed Hendy
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Muhammad Kamran
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Liu
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lu Zheng
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junbing Huang
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiao-Lin Chen
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
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16
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Su X, Zheng G, Gui Z, Yang X, Zhang L, Pan F. A Systematic Analysis Reveals the Prognostic and Immunological Role of Reptin/RUVBL2 in Human Tumors. Front Genet 2022; 13:911223. [PMID: 35754815 PMCID: PMC9213802 DOI: 10.3389/fgene.2022.911223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/16/2022] [Indexed: 12/03/2022] Open
Abstract
Reptin/RUVBL2 is involved in the remodeling of chromatin, DNA damage repair, and regulation of the cell cycle, all of which help to play essential roles in cancer. However, relevant pan-cancer analysis of Reptin is lacking. This study first investigated the potential oncogenic roles of Reptin and revealed a relationship between Reptin with clinicopathological characteristics and immune infiltration based on big data. Here, we showed that Reptin is overexpressed in many cancers. A significant association exists between the expression of Reptin and the prognosis of cancer cases. Reptin had a meaningful interaction with the immune infiltration of CD4+ Th1 cells and immune modulator genes in multiple cancer types. And negative correlation exists between Reptin and cancer-associated fibroblasts in BRCA, PRAD, TGCT, and THYM. A significant negative association exists between Reptin and regulatory T cells in TGCT and THCA. Moreover, Reptin is significantly associated with genomic heterogeneity, DNA mismatch repair genes, methyltransferase, and RNA modification genes in specific cancer types. Spliceosome, Hippo signaling pathway, DNA replication pathway, and acetyltransferase activity-associated functions were observed in the effect of Reptin on the tumor. This systematic analysis highlights Reptin as a vital cancer regulator among numerous genes and proved its potential prognosticator value and therapeutic target role for specific tumor types.
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Affiliation(s)
- Xiaoru Su
- Department of Clinical Laboratory, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Gaoming Zheng
- Department of Clinical Laboratory, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Zhifang Gui
- Department of Clinical Laboratory, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Xiao Yang
- Department of Clinical Laboratory, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Lahong Zhang
- Department of Clinical Laboratory, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Feng Pan
- Department of Clinical Laboratory, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
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17
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Yang G, Shan D, Zhao R, Li G. Metabolism-Associated DNA Methylation Signature Stratifies Lower-Grade Glioma Patients and Predicts Response to Immunotherapy. Front Cell Dev Biol 2022; 10:902298. [PMID: 35784470 PMCID: PMC9240391 DOI: 10.3389/fcell.2022.902298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/23/2022] [Indexed: 11/24/2022] Open
Abstract
Metabolism and DNA methylation (DNAm) are closely linked. The value of the metabolism-DNAm interplay in stratifying glioma patients has not been explored. In the present study, we aimed to stratify lower-grade glioma (LGG) patients based on the DNAm associated with metabolic reprogramming. Four data sets of LGGs from three databases (TCGA/CGGA/GEO) were used in this study. By screening the Kendall’s correlation of DNAm with 87 metabolic processes from KEGG, we identified 391 CpGs with a strong correlation with metabolism. Based on these metabolism-associated CpGs, we performed consensus clustering and identified three distinct subgroups of LGGs. These three subgroups were characterized by distinct molecular features and clinical outcomes. We also constructed a subgroup-related, quantifiable CpG signature with strong prognostic power to stratify LGGs. It also serves as a potential biomarker to predict the response to immunotherapy. Overall, our findings provide new perspectives for the stratification of LGGs and for understanding the mechanisms driving malignancy.
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Affiliation(s)
- Guozheng Yang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
| | - Dezhi Shan
- Department of Neurosurgery, Beijing Hospital, Chinese Academy of Medical Sciences, Graduate School of Peking Union Medical College, Beijing, China
| | - Rongrong Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
- *Correspondence: Gang Li,
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18
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Liu S, Zhang Y, Qiu L, Zhang S, Meng Y, Huang C, Chen Z, Zhang B, Han J. Uncovering N4-Acetylcytidine-Related mRNA Modification Pattern and Landscape of Stemness and Immunity in Hepatocellular Carcinoma. Front Cell Dev Biol 2022; 10:861000. [PMID: 35493106 PMCID: PMC9046676 DOI: 10.3389/fcell.2022.861000] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/04/2022] [Indexed: 12/25/2022] Open
Abstract
N4-acetylcytidine (ac4C) is an ancient and conserved RNA modification. Previously, ac4C mRNA modification has been reported promoting proliferation and metastasis of tumor cells. However, it remains unclear whether and how ac4C-related mRNA modification patterns influencing the prognosis of hepatocellular carcinoma (HCC) patients. Hereby, we constructed an ac4Cscore model and classified patients into two groups and investigated the potential intrinsic and extrinsic characteristics of tumor. The ac4Cscore model, including COL15A1, G6PD and TP53I3, represented ac4C-related mRNA modification patterns in HCC. According to ac4Cscore, patients were stratified to high and low groups with distinct prognosis. Patients subject to high group was related to advanced tumor stage, higher TP53 mutation rate, higher tumor stemness, more activated pathways in DNA-repair system, lower stromal score, higher immune score and higher infiltrating of T cells regulatory. While patients attributed to low group were correlated with abundance of T cells CD4 memory, less aggressive immune subtype and durable therapy benefit. We also found ac4Cscore as a novel marker to predict patients’ prognosis with anti-PD1 immunotherapy and/or mTOR inhibitor treatment. Our study for the first time showed the association between ac4C-related mRNA modification patterns and tumor intrinsic and extrinsic characteristics, thus influencing the prognosis of patients.
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Affiliation(s)
- Sicheng Liu
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yaguang Zhang
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Lei Qiu
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Su Zhang
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Meng
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Canhua Huang
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Zhixin Chen
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- Department of Gastrointestinal Surgery, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Bo Zhang
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- Department of Gastrointestinal Surgery, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Junhong Han
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Junhong Han,
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19
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Lin G, Feng Q, Zhan F, Yang F, Niu Y, Li G. Generation and Analysis of Pyroptosis-Based and Immune-Based Signatures for Kidney Renal Clear Cell Carcinoma Patients, and Cell Experiment. Front Genet 2022; 13:809794. [PMID: 35281845 PMCID: PMC8908022 DOI: 10.3389/fgene.2022.809794] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/31/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Pyroptosis is a programmed cell death caused by inflammasomes, which is closely related to immune responses and tumor progression. The present study aimed to construct dual prognostic indices based on pyroptosis-associated and immune-associated genes and to investigate the impact of the biological signatures of these genes on Kidney Renal Clear Cell Carcinoma (KIRC). Materials and Methods: All the KIRC samples from the Cancer Genome Atlas (TCGA) were randomly and equally divided into the training and testing datasets. Cox and Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis were used to screen crucial pyroptosis-associated genes (PAGs), and a pyroptosis-associated genes prognostic index (PAGsPI) was constructed. Immune-associated genes (IAGs) related to PAGs were identified, and then screened through Cox and LASSO regression analyses, and an immune-associated genes prognostic index (IAGsPI) was developed. These two prognostic indices were verified by using the testing and the Gene Expression Omnibus (GEO) datasets and an independent cohort. The patients’ response to immunotherapy was analyzed. A nomogram was constructed and calibrated. qRT-PCR was used to detect the expression of PAGs and IAGs in the tumor tissues and normal tissues. Functional experiment was carried out. Results: 86 PAGs and 1,774 differentially expressed genes (DEGs) were obtained. After intersecting PAGs with DEGs, 22 differentially expressed PAGs (DEPAGs) were included in Cox and LASSO regression analyses, identifying 5 crucial PAGs. The PAGsPI was generated. Patients in the high-PAGsPI group had a poor prognosis. 82 differentially expressed IAGs (DEIAGs) were highly correlated with DEPAGs. 7 key IAGs were screened out, and an IAGsPI was generated. Patients in the high-IAGsPI group had a poor prognosis. PAGsPI and IAGsPI were verified to be robust and reliable. The results revealed patients in low-PAGsPI group and high-IAGsPI group may be more sensitive to immunotherapy. The calibrated nomogram was proved to be reliable. An independent cohort study also proved that PAGsPI and IAGsPI performed well in prognosis prediction. We found that the expression of AIM2 may affect proliferation of KIRC cells. Conclusion: PAGsPI and IAGsPI could be regarded as potential biomarkers for predicting the prognosis of patients with KIRC.
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Affiliation(s)
- Gaoteng Lin
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Qingfu Feng
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Fangfang Zhan
- Department of Neurology, The Affiliated Hospital of Putian University, Putian, China
| | - Fan Yang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yuanjie Niu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Gang Li
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
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20
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Boulias K, Greer EL. Means, mechanisms and consequences of adenine methylation in DNA. Nat Rev Genet 2022; 23:411-428. [PMID: 35256817 PMCID: PMC9354840 DOI: 10.1038/s41576-022-00456-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2022] [Indexed: 12/29/2022]
Abstract
N6-methyl-2'-deoxyadenosine (6mA or m6dA) has been reported in the DNA of prokaryotes and eukaryotes ranging from unicellular protozoa and algae to multicellular plants and mammals. It has been proposed to modulate DNA structure and transcription, transmit information across generations and have a role in disease, among other functions. However, its existence in more recently evolved eukaryotes remains a topic of debate. Recent technological advancements have facilitated the identification and quantification of 6mA even when the modification is exceptionally rare, but each approach has limitations. Critical assessment of existing data, rigorous design of future studies and further development of methods will be required to confirm the presence and biological functions of 6mA in multicellular eukaryotes.
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21
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Gu Z, Du Y, Zhao X, Wang C. Diagnostic, Therapeutic, and Prognostic Value of the m 6A Writer Complex in Hepatocellular Carcinoma. Front Cell Dev Biol 2022; 10:822011. [PMID: 35223847 PMCID: PMC8864226 DOI: 10.3389/fcell.2022.822011] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/25/2022] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) has poor prognosis and is usually diagnosed only at an advanced stage. Identification of novel biomarkers is critical to early diagnosis and better prognosis for HCC patients. N6-methyladenosine (m6A) RNA methylation regulators play important roles in the development of many tumors. However, the m6A writer complex, a key executor of m6A methylation modification, has not been independently investigated, and its specific bioinformatics analysis has not yet been performed in HCC. In this study, we used multiple public databases to evaluate the diagnostic, therapeutic, and prognostic value of the m6A writers in HCC. The results showed that expression levels of METTL3, VIRMA and CBLL1 were significantly increased, while expression levels of METTL14 and ZC3H13 were significantly decreased in HCC, which was closely related to clinicopathological factors, such as tumor stage and prognosis. Bioinformatics further explored the possible underlying mechanisms by which the m6A writer complex are involved in activation of tumor-promoting pathways and/or inhibition of tumor-suppressing pathways, including apoptosis, cell cycle, DNA damage response and EMT. Furthermore, we showed that the m6A writer complex is correlated with immune cell infiltration and immunoregulator expression in HCC. In conclusion, the m6A writer complex may represent a promising biomarker and target that can guide targeted therapy or immunotherapy for HCC patients.
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Affiliation(s)
- Zongting Gu
- Department of Abdominal Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongxing Du
- Department of Abdominal Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xueping Zhao
- School of Life Science and Biopharmaceutical, Shenyang Pharmaceutical University, Shenyang, China
| | - Chengfeng Wang
- Department of Abdominal Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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22
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Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA. Nat Commun 2022; 13:1072. [PMID: 35228526 PMCID: PMC8885841 DOI: 10.1038/s41467-022-28471-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/21/2022] [Indexed: 01/04/2023] Open
Abstract
DNA modifications are used to regulate gene expression and defend against invading genetic elements. In eukaryotes, modifications predominantly involve C5-methylcytosine (5mC) and occasionally N6-methyladenine (6mA), while bacteria frequently use N4-methylcytosine (4mC) in addition to 5mC and 6mA. Here we report that 4mC can serve as an epigenetic mark in eukaryotes. Bdelloid rotifers, tiny freshwater invertebrates with transposon-poor genomes rich in foreign genes, lack canonical eukaryotic C5-methyltransferases for 5mC addition, but encode an amino-methyltransferase, N4CMT, captured from bacteria >60 Mya. N4CMT deposits 4mC at active transposons and certain tandem repeats, and fusion to a chromodomain shapes its “histone-read-DNA-write” architecture recognizing silent chromatin marks. Furthermore, amplification of SETDB1 H3K9me3 histone methyltransferases yields variants preferentially binding 4mC-DNA, suggesting “DNA-read-histone-write” partnership to maintain chromatin-based silencing. Our results show how non-native DNA methyl groups can reshape epigenetic systems to silence transposons and demonstrate the potential of horizontal gene transfer to drive regulatory innovation in eukaryotes. Eukaryotic DNA can be methylated as 5-methylcytosine and N6-methyladenine, but whether other forms of DNA methylation occur has been controversial. Here the authors show that a bacterial DNA methyltransferase was acquired >60 Mya in bdelloid rotifers that catalyzes N4-methylcytosine addition and is involved in suppression of transposon proliferation.
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23
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Evolutionary History of RNA Modifications at N6-Adenosine Originating from the R-M System in Eukaryotes and Prokaryotes. BIOLOGY 2022; 11:biology11020214. [PMID: 35205080 PMCID: PMC8868631 DOI: 10.3390/biology11020214] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/13/2022] [Accepted: 01/24/2022] [Indexed: 12/11/2022]
Abstract
Simple Summary The m6A is the most abundant and well-studied modification of mRNA, and plays an important role in transcription and translation. It is known to be evolutionarily conserved machinery present in the last eukaryotic common ancestor (LECA). The writers and erasers responsible for adding or removing m6A belong to specific protein families, respectively, suggesting that these members are evolutionarily related. However, only some of these mRNA m6A modification-associated proteins have been studied from an evolutionary perspective, while there has been no comprehensive and systematic analysis of the distributions and evolutionary history of N6mA-associated proteins in the three kingdoms of life. In this study, we identified orthologues of all the reported N6mA-associated proteins in 88 organisms from three kingdoms of life and comprehensively reconstructed the evolutionary history of the RNA N6mA modification machinery. The results demonstrate that RNA N6mA-MTases are derived from at least two different types of prokaryotic DNA MTases (class α and β MTases). As the m6A reader, YTH proteins may be acquired by LECA from an individual prokaryotic YTH-domain protein that evolved from the N-terminals of an R-M system endonuclease. In addition, the origin of eukaryotic ALKBH family proteins is inferred to be driven by at least two occasions of independent HTG from the bacterial ALKB family. Abstract Methylation at the N6-position of adenosine (N6mA) on mRNA (m6A) is one of the most widespread, highly selective and dynamically regulated RNA modifications and plays an important role in transcription and translation. In the present study, a comprehensive analysis of phylogenetic relationships, conserved domain sequence characteristics and protein structure comparisons were employed to explore the distribution of RNA N6mA modification (m6A, m6,6A, m6Am, m6, 6Am and m6t6A)-associated proteins (writers, readers and erasers) in three kingdoms of life and reveal the evolutionary history of these modifications. These findings further confirmed that the restriction-modification (R-M) system is the origin of DNA and RNA N6mA modifications. Among them, the existing mRNA m6A modification system derived from the last eukaryotic common ancestor (LECA) is the evolutionary product of elements from the last universal common ancestor (LUCA) or driven by horizontal gene transfer (HGT) from bacterial elements. The subsequent massive gene gains and losses contribute to the development of unique and diverse functions in distinct species. Particularly, RNA methyltransferases (MTases) as the writer responsible for adding N6mA marks on mRNA and ncRNAs may have evolved from class α and β prokaryotic “orphan” MTases originating from the R-M system. The reader, YTH proteins that specifically recognize the m6A deposit, may be acquired by LECA from an individual prokaryotic YTH-domain protein that evolved from N-terminals of an R-M system endonuclease. The eraser, which emerged from the ALKB family (ALKBH5 and FTO) in eukaryotes, may be driven by independent HTG from bacterial ALKB proteins. The evolutionary history of RNA N6mA modifications was inferred in the present study, which will deepen our understanding of these modifications in different species.
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Zhang S, Xiong Y, Zheng C, Long J, Zhou H, Zeng Z, Ouyang Y, Tang F. Crosstalk Between Four Types of RNA Modification Writers Characterizes the Tumor Immune Microenvironment Infiltration Patterns in Skin Cutaneous Melanoma. Front Cell Dev Biol 2022; 10:821678. [PMID: 35155433 PMCID: PMC8826580 DOI: 10.3389/fcell.2022.821678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
The “writers” of four types of adenosine (A)-related RNA modifications (N6-methyladenosine, N1-methyladenosine, alternative polyadenylation, as well as A-to-inosine RNA editing) are closely related to the tumorigenesis and progression of many cancer types, including skin cutaneous melanoma (SKCM). However, the potential roles of the crosstalk between these RNA modification “writers” in the tumor microenvironment (TME) remain unclear. The RNA modification patterns were identified using an unsupervised clustering method. Subsequently, based on differentially expressed genes responsible for the aforementioned RNA modification patterns, an RNA modification “writer” scoring model (W_Score) was constructed to quantify the RNA modification-associated subtypes in individual patients. Moreover, a correlation analysis for W_Score and the TME characteristics, clinical features, molecular subtypes, drug sensitivities, immune responses, and prognosis was performed. We identified three RNA modification patterns, corresponding to distinct tumor immune microenvironment characteristics and survival outcomes. Based on the W_Score score, which was extracted from the RNA modification-related signature genes, patients with SKCM were divided into high- and low-W_Score groups. The low-W_Score group was characterized by better survival outcomes and strengthened immunocyte infiltration. Further analysis showed that the low-W_Score group was positively associated with higher tumor mutation burden and PD-L1 expression. Of note, two immunotherapy cohorts demonstrated that patients with low W_Score exhibited long-term clinical benefits and an enhanced immune response. This study is the first to systematically analyze four types of A-related RNA modifications in SKCM, revealing that these “writers” essentially contribute to TME complexity and diversity. We quantitatively evaluated the RNA modification patterns in individual tumors, which could aid in developing personalized immunotherapy strategies for patients.
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Affiliation(s)
- Shichao Zhang
- Key Laboratory of Infectious Immune and Antibody Engineering in Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Yu Xiong
- Key Laboratory of Infectious Immune and Antibody Engineering in Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Chaochao Zheng
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Jinhua Long
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Houming Zhou
- Key Laboratory of Infectious Immune and Antibody Engineering in Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Zhu Zeng
- Key Laboratory of Infectious Immune and Antibody Engineering in Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
- *Correspondence: Fuzhou Tang, ; Yan Ouyang, ; Zhu Zeng,
| | - Yan Ouyang
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
- *Correspondence: Fuzhou Tang, ; Yan Ouyang, ; Zhu Zeng,
| | - Fuzhou Tang
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
- *Correspondence: Fuzhou Tang, ; Yan Ouyang, ; Zhu Zeng,
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25
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O’Brown ZK, Greer EL. N6-methyladenine: A Rare and Dynamic DNA Mark. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:177-210. [DOI: 10.1007/978-3-031-11454-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Yang Y, Chen M, Zhai Z, Dai Y, Gu H, Zhou X, Hong J. Long Non-coding RNAs Gabarapl2 and Chrnb2 Positively Regulate Inflammatory Signaling in a Mouse Model of Dry Eye. Front Med (Lausanne) 2021; 8:808940. [PMID: 34957168 PMCID: PMC8703135 DOI: 10.3389/fmed.2021.808940] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
Purpose: To elucidate the expression profile and the potential role of long non-coding ribonucleic acids (RNAs) (lncRNAs) in a dry eye disease (DED) model. Methods: A DED model was established in C57BL/6J mice with 0.2% benzalkonium chloride (BAC) twice a day for 14 days. The differentially expressed lncRNAs were detected by RNA-seq technology (Gene Expression Omnibus, GEO GSE186450) and the aberrantly expressed lncRNAs were further verified by RT-qPCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to predicate the related candidate genes and potential pathological pathways. Cells from a human corneal epithelial cell line (HCECs) were cultured under hyperosmolarity. The regulation of inflammatory factors by silencing potential targeted lncRNAs was verified in vitro in HCECs. Results: In our study, a significant increase in corneal fluorescence staining and a reduction in tear production were observed in DED mice at all follow-ups compared with the controls, and the differences were increasing over time. In total, 2,649 upregulated and 704 downregulated lncRNAs were identified in DED mice. We selected six aberrantly expressed and most abundant lncRNAs and performed RT-qPCR using the samples for RNA-seq. Chrnb2, Gabarapl2, and Usp31 were thereby confirmed as the most significantly altered lncRNAs. Pathway analysis revealed that the neuroactive ligand–receptor interaction signaling pathway was the most enriched, followed by the calcium signaling pathway and cytokine–cytokine receptor interaction. Following treatment of Gabarapl2 siRNA and Chrnb2 siRNA, tumor necrosis factor-α (TNF-α), interleukin (IL)-1β, and IL-6 were significantly downregulated in the HCECs. Conclusion: Our study suggests that Chrnb2 and Gabarapl2 may be involved in the inflammation response by regulating TNF-α, IL-1β, and IL-6 in DED. These candidate lncRNAs may be both potential biomarkers and therapeutic targets for DED.
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Affiliation(s)
- Yuhan Yang
- Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China.,Department of Ophthalmology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Minjie Chen
- Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
| | - Zimeng Zhai
- Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
| | - Yiqin Dai
- Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
| | - Hao Gu
- Department of Ophthalmology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Xujiao Zhou
- Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
| | - Jiaxu Hong
- Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China.,Department of Ophthalmology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
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27
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Figueroa F, Vega-Gibson A, Catrileo J, Gaete-Argel A, Riquelme-Barrios S, Alonso-Palomares LA, Tapia LI, Valiente-Echeverría F, Soto-Rifo R, Acevedo ML. N 6 -Methyladenosine Negatively Regulates Human Respiratory Syncytial Virus Replication. Front Cell Dev Biol 2021; 9:739445. [PMID: 34671602 PMCID: PMC8521026 DOI: 10.3389/fcell.2021.739445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification described in eukaryotic mRNA and several viral RNA including human respiratory syncytial virus (HRSV). Here, we evaluated the impact of m6A writers, erasers and readers on HRSV genomic RNA accumulation and inclusion bodies assembly during viral replication. We observed that the METTL3/METTL14 m6A writer complex plays a negative role in HRSV protein synthesis and viral titers, while m6A erasers FTO and ALKBH5 had the opposite effect. We also observed that m6A readers YTHDF1-3 bind to the viral genomic RNA inducing a decrease in its intracellular levels and thus, inhibiting viral replication. Finally, we observed that overexpression of YTHDFs proteins caused a decrease in the size of inclusion bodies (IBs), accompanied by an increase in their number. METTL3 knockdown cells showed an opposite effect indicating that the dynamics of IBs assembly and coalescence are strongly affected by m6A readers in a mechanism dependent on m6A writers. Taken together, our results demonstrated that the m6A modification negatively affects HRSV replication, possibly through a mechanism involving the assembly of inclusion bodies, the main factories of viral genomic RNA synthesis.
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Affiliation(s)
- Fabian Figueroa
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Alonso Vega-Gibson
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Joseline Catrileo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Aracelly Gaete-Argel
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Sebastian Riquelme-Barrios
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Luis Antonio Alonso-Palomares
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Lorena I Tapia
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Department of Pediatrics and Pediatric Surgery, Hospital Roberto del Río, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Fernando Valiente-Echeverría
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Ricardo Soto-Rifo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Monica L Acevedo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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28
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Körtel N, Rücklé C, Zhou Y, Busch A, Hoch-Kraft P, Sutandy FXR, Haase J, Pradhan M, Musheev M, Ostareck D, Ostareck-Lederer A, Dieterich C, Hüttelmaier S, Niehrs C, Rausch O, Dominissini D, König J, Zarnack K. Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning. Nucleic Acids Res 2021; 49:e92. [PMID: 34157120 PMCID: PMC8450095 DOI: 10.1093/nar/gkab485] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 11/18/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic mRNAs and influences many aspects of RNA processing. miCLIP (m6A individual-nucleotide resolution UV crosslinking and immunoprecipitation) is an antibody-based approach to map m6A sites with single-nucleotide resolution. However, due to broad antibody reactivity, reliable identification of m6A sites from miCLIP data remains challenging. Here, we present miCLIP2 in combination with machine learning to significantly improve m6A detection. The optimized miCLIP2 results in high-complexity libraries from less input material. Importantly, we established a robust computational pipeline to tackle the inherent issue of false positives in antibody-based m6A detection. The analyses were calibrated with Mettl3 knockout cells to learn the characteristics of m6A deposition, including m6A sites outside of DRACH motifs. To make our results universally applicable, we trained a machine learning model, m6Aboost, based on the experimental and RNA sequence features. Importantly, m6Aboost allows prediction of genuine m6A sites in miCLIP2 data without filtering for DRACH motifs or the need for Mettl3 depletion. Using m6Aboost, we identify thousands of high-confidence m6A sites in different murine and human cell lines, which provide a rich resource for future analysis. Collectively, our combined experimental and computational methodology greatly improves m6A identification.
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Affiliation(s)
- Nadine Körtel
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | | | - You Zhou
- Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | | | - F X Reymond Sutandy
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
- Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt 60590, Germany
| | - Jacob Haase
- Institute of Molecular Medicine, Sect. Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Halle 06120, Germany
| | - Mihika Pradhan
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | | | - Dirk Ostareck
- Department of Intensive Care Medicine, University Hospital RWTH Aachen, Aachen 52074, Germany
| | - Antje Ostareck-Lederer
- Department of Intensive Care Medicine, University Hospital RWTH Aachen, Aachen 52074, Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg 69120, Germany
- German Centre for Cardiovascular Research (DZHK) - Partner Site Heidelberg/Mannheim, Heidelberg 69120, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Sect. Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Halle 06120, Germany
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Dan Dominissini
- Cancer Research Center and Wohl Institute for Translational Medicine, Chaim Sheba Medical Center, Tel HaShomer, and Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt 60438, Germany
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29
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Ge S, Hua X, Chen J, Xiao H, Zhang L, Zhou J, Liang C, Tai S. Identification of a Costimulatory Molecule-Related Signature for Predicting Prognostic Risk in Prostate Cancer. Front Genet 2021; 12:666300. [PMID: 34484286 PMCID: PMC8415313 DOI: 10.3389/fgene.2021.666300] [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: 02/10/2021] [Accepted: 07/29/2021] [Indexed: 12/26/2022] Open
Abstract
Costimulatory molecules have been proven to enhance antitumor immune responses, but their roles in prostate cancer (PCa) remain unexplored. In this study, we aimed to explore the gene expression profiles of costimulatory molecule genes in PCa and construct a prognostic signature to improve treatment decision making and clinical outcomes. Five prognosis-related costimulatory molecule genes (RELT, TNFRSF25, EDA2R, TNFSF18, and TNFSF10) were identified, and a prognostic signature was constructed based on these five genes. This signature was an independent prognostic factor according to multivariate Cox regression analysis; it could stratify PCa patients into two subgroups with different prognoses and was highly associated with clinical features. The prognostic significance of the signature was well validated in four different independent external datasets. Moreover, patients identified as high risk based on our prognostic signature exhibited a high mutation frequency, a high level of immune cell infiltration and an immunosuppressive microenvironment. Therefore, our signature could provide clinicians with prognosis predictions and help guide treatment for PCa patients.
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Affiliation(s)
- Shengdong Ge
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China.,The Institute of Urology, Anhui Medical University, Hefei, China
| | - Xiaoliang Hua
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China.,The Institute of Urology, Anhui Medical University, Hefei, China
| | - Juan Chen
- The Ministry of Education Key Laboratory of Clinical Diagnostics, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Haibing Xiao
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China.,The Institute of Urology, Anhui Medical University, Hefei, China
| | - Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China.,The Institute of Urology, Anhui Medical University, Hefei, China
| | - Jun Zhou
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China.,The Institute of Urology, Anhui Medical University, Hefei, China
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China.,The Institute of Urology, Anhui Medical University, Hefei, China
| | - Sheng Tai
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China.,The Institute of Urology, Anhui Medical University, Hefei, China
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30
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Yang A, Zhou Y, Kong Y, Wei X, Ye F, Zhang L, Zhong X, Li M, Lu S, An X, Xiao W. Identification and Validation of Immune-Related Methylation Clusters for Predicting Immune Activity and Prognosis in Breast Cancer. Front Immunol 2021; 12:704557. [PMID: 34276701 PMCID: PMC8278823 DOI: 10.3389/fimmu.2021.704557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/16/2021] [Indexed: 11/13/2022] Open
Abstract
The role of DNA methylation of breast cancer-infiltrating immune cells has not been fully explored. We conducted a cohort-based retrospective study analyzing the genome-wide immune-related DNA methylation of 1057 breast cancer patients from the TCGA cohort and GSE72308 cohort. Based on patients' overall survival (OS), a prognostic risk score system using 18 immune-related methylation genes (IRMGs) was established and further validated in an independent cohort. Kaplan-Meier analysis showed a clear separation of OS between the low- and high-risk groups. Patients in the low-risk group had a higher immune score and stromal score compared with the high-risk group. Moreover, the characteristics based on 18-IRMGs signature were related to the tumor immune microenvironment and affected the abundance of tumor-infiltrating immune cells. Consistently, the 18-IRMGs signatures showed similar influences on immune modulation and survival in another external validation cohort (GSE72308). In conclusion, the proposed 18-IRMGs signature could be a potential marker for breast cancer prognostication.
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Affiliation(s)
- Anli Yang
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Zhou
- Department of Infectious Diseases and Endemic Disease Control, Haizhu District Center for Disease Control and Prevention, Guangzhou, China
| | - Yanan Kong
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaoli Wei
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Feng Ye
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lijuan Zhang
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xian Zhong
- Department of Ultrasound, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Mingyue Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Shilin Lu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xin An
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Weikai Xiao
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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