1
|
Damarov IS, Korbolina EE, Rykova EY, Merkulova TI. Multi-Omics Analysis Revealed the rSNPs Potentially Involved in T2DM Pathogenic Mechanism and Metformin Response. Int J Mol Sci 2024; 25:9297. [PMID: 39273245 PMCID: PMC11394919 DOI: 10.3390/ijms25179297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/14/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
The goal of our study was to identify and assess the functionally significant SNPs with potentially important roles in the development of type 2 diabetes mellitus (T2DM) and/or their effect on individual response to antihyperglycemic medication with metformin. We applied a bioinformatics approach to identify the regulatory SNPs (rSNPs) associated with allele-asymmetric binding and expression events in our paired ChIP-seq and RNA-seq data for peripheral blood mononuclear cells (PBMCs) of nine healthy individuals. The rSNP outcomes were analyzed using public data from the GWAS (Genome-Wide Association Studies) and Genotype-Tissue Expression (GTEx). The differentially expressed genes (DEGs) between healthy and T2DM individuals (GSE221521), including metformin responders and non-responders (GSE153315), were searched for in GEO RNA-seq data. The DEGs harboring rSNPs were analyzed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We identified 14,796 rSNPs in the promoters of 5132 genes of human PBMCs. We found 4280 rSNPs to associate with both phenotypic traits (GWAS) and expression quantitative trait loci (eQTLs) from GTEx. Between T2DM patients and controls, 3810 rSNPs were detected in the promoters of 1284 DEGs. Based on the protein-protein interaction (PPI) network, we identified 31 upregulated hub genes, including the genes involved in inflammation, obesity, and insulin resistance. The top-ranked 10 enriched KEGG pathways for these hubs included insulin, AMPK, and FoxO signaling pathways. Between metformin responders and non-responders, 367 rSNPs were found in the promoters of 131 DEGs. Genes encoding transcription factors and transcription regulators were the most widely represented group and many were shown to be involved in the T2DM pathogenesis. We have formed a list of human rSNPs that add functional interpretation to the T2DM-association signals identified in GWAS. The results suggest candidate causal regulatory variants for T2DM, with strong enrichment in the pathways related to glucose metabolism, inflammation, and the effects of metformin.
Collapse
Affiliation(s)
- Igor S Damarov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elena E Korbolina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elena Y Rykova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Engineering Problems of Ecology, Novosibirsk State Technical University, 630087 Novosibirsk, Russia
| | - Tatiana I Merkulova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| |
Collapse
|
2
|
He X, Hu J, Yan C, Liu X, Zhao Y, Yang P, Wang J, Li S, Zhang W, Dong G, Zhang W, Jing H. High trophinin-associated protein expression predicts good survival in acute myeloid leukemia with normal cytogenetics. Cancer Biomark 2023; 36:221-230. [PMID: 36938721 DOI: 10.3233/cbm-210042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
BACKGROUND Nearly half of adult acute myeloid leukemia (AML) patients were classified into cytogenetic normal acute myeloid leukemia (CN-AML). The expression level of Trophinin associated protein (TROAP) was proven to be associated with the prognosis of several cancers, but it is still unclear in the prognosis of patients with CN-AML. METHODS We integrated CN-AML patients samples from 4 datasets to analyze the relationship between TROAP expression and the survival of CN-AML. In addition, we investigated 92 AML patients of The Cancer Genome Atlas (TCGA) database to analyze the relationship between TROAP expression and the survival of AML patients received chemotherapy. We investigated the relationship between the expression of TROAP and drug sensitivity in AML cell lines. RESULTS CN-AML patients with high TROAP expression were related to good event-free survival (EFS) and overall survival (OS). In AML patients received chemotherapy, high TROAP expression was associated with good survival prognosis. Additionally, the expression of TROAP gene in leukemia stem cells (LSC) + group was lower. Among multiple drugs, the lower the expression of TROAP, the lower the IC50. CONCLUSION TROAP could serve as an independent predictor of CN-AML patients and could act as a potential biomarker for the prognosis of CN-AML. TROAP expression levels were closely correlated with the drug sensitivity of multiple drugs.
Collapse
Affiliation(s)
- Xue He
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Pathology, Capital Medical University, Beijing, China.,Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jing Hu
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China.,Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Changjian Yan
- The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China.,Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiaoni Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Yali Zhao
- General Practice Medicine, The First People's Hospital of Huzhou, Huzhou, Zhejiang, China
| | - Ping Yang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China
| | - Jing Wang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China
| | - Shaoxiang Li
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Pathology, Capital Medical University, Beijing, China
| | - Wei Zhang
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Pathology, Capital Medical University, Beijing, China
| | - Gehong Dong
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Pathology, Capital Medical University, Beijing, China
| | - Weilong Zhang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China
| | - Hongmei Jing
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China
| |
Collapse
|
3
|
Dong X, Zhang D, Zhang J, Chen X, Zhang Y, Zhang Y, Zhou X, Chen T, Zhou H. Immune prognostic risk score model in acute myeloid leukemia with normal karyotype. Oncol Lett 2020; 20:380. [PMID: 33154778 DOI: 10.3892/ol.2020.12243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/08/2020] [Indexed: 01/14/2023] Open
Abstract
Acute myeloid leukemia with normal karyotype (NK-AML) is a group of diseases with high heterogeneity and immunological processes are significantly associated with its initiation and development. The implication of the immunogenomic landscape in the prognosis of patients with NK-AML has remained largely elusive. In the present study, the expression profiles of immune-related genes (IRGs) were examined and their association with overall survival (OS) was determined in 60 patients with NK-AML from The Cancer Genome Atlas dataset and 104 patients from the Gene Expression Omnibus (GEO) dataset no. GSE71014. Univariate Cox regression analysis was used to identify 42 and 203 IRGs in the two respective cohorts, which were significantly associated with OS in NK-AML. A risk model was constructed based on the regression coefficient and expression values of nine survival-associated IRGs shared between the two datasets [zinc finger CCCH-type containing, antiviral 1 like; transferrin receptor; suppressor of cytokine signaling 1; ELAV like RNA binding protein 1; roundabout guidance receptor 3; unc-93 homolog B1, Toll-like receptor signaling regulator; protein tyrosine phosphatase non-receptor type 6; interleukin 2 receptor subunit alpha (IL2RA) and IL3RA]. Using this risk model, patients with NK-AML may be divided into high- and low-risk groups in prognostic predictions. The area under the receiver operating characteristic curve for predicting OS was 0.793. The prognostic role of this risk model was successfully verified in another independent cohort (GEO dataset no. GSE71014). The prognostic risk score was positively associated with age and fms related receptor tyrosine kinase 3 mutation and correlated with infiltration by T regulatory cells. In conclusion, the results of the present study provided an IRG score model for prognostic stratification of adult patients with NK-AML, as well as further insight into the implication of IRGs in NK-AML that may lead to the development of novel immunotherapy approaches for this disease.
Collapse
Affiliation(s)
- Xiaomin Dong
- Department of Hematology, The Affiliated Beijing Luhe Hospital of Capital Medical University, Beijing 101149, P.R. China
| | - Danyang Zhang
- Department of Hematology, The Affiliated Beijing Luhe Hospital of Capital Medical University, Beijing 101149, P.R. China
| | - Juan Zhang
- Department of Hematology, The Affiliated Beijing Luhe Hospital of Capital Medical University, Beijing 101149, P.R. China
| | - Xiaolei Chen
- Department of Hematology, The Affiliated Beijing Luhe Hospital of Capital Medical University, Beijing 101149, P.R. China
| | - Yue Zhang
- Department of Hematology, The Affiliated Beijing Luhe Hospital of Capital Medical University, Beijing 101149, P.R. China
| | - Yong Zhang
- Department of Hematology, The Affiliated Beijing Luhe Hospital of Capital Medical University, Beijing 101149, P.R. China
| | - Xiaohuan Zhou
- Department of Hematology, The Affiliated Beijing Luhe Hospital of Capital Medical University, Beijing 101149, P.R. China
| | - Tingting Chen
- Department of Hematology, The Affiliated Beijing Luhe Hospital of Capital Medical University, Beijing 101149, P.R. China
| | - Hebing Zhou
- Department of Hematology, The Affiliated Beijing Luhe Hospital of Capital Medical University, Beijing 101149, P.R. China
| |
Collapse
|
4
|
Lv BB, Ma RR, Chen X, Zhang GH, Song L, Wang SX, Wang YW, Liu HT, Gao P. E2F1-activated SPIN1 promotes tumor growth via a MDM2-p21-E2F1 feedback loop in gastric cancer. Mol Oncol 2020; 14:2629-2645. [PMID: 32767629 PMCID: PMC7530787 DOI: 10.1002/1878-0261.12778] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 06/30/2020] [Accepted: 08/03/2020] [Indexed: 01/07/2023] Open
Abstract
Gastric cancer (GC) is one of the most common cancers around the world. Searching for specific gene expression changes during the development of GC could help identify potential therapy targets. We previously showed that the histone code reader SPIN1 may act as an oncogene in breast cancer. At present, the biological function and regulation of SPIN1 in GC remain unclear. Here, we demonstrate that SPIN1 is upregulated in GC tissues, compared with nontumorous gastric tissues. Increased expression of SPIN1 is closely associated with poor prognosis for patients with GC. Increased SPIN1 expression enhances GC cell proliferation, migration, and invasion and promotes cell cycle progression. Mechanically, SPIN1 sustains GC cell proliferation via activation of the MDM2-p21-E2F1 signaling pathway by binding to H3K4me3 of the MDM2 promoter region. Interestingly, E2F1 could directly bind to the SPIN1 promoter and activate its transcription, thus forming a positive feedback loop. Our data suggest that SPIN1 plays an important role in the development of GC and could be used as a promising prognostic biomarker and therapeutic target for GC.
Collapse
Affiliation(s)
- Bei-Bei Lv
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Pathology, Qilu Hospital, Shandong University, Jinan, China
| | - Ran-Ran Ma
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Pathology, Qilu Hospital, Shandong University, Jinan, China
| | - Xu Chen
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Pathology, Qilu Hospital, Shandong University, Jinan, China
| | - Guo-Hao Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lin Song
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Pathology, Qilu Hospital, Shandong University, Jinan, China
| | - Su-Xia Wang
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Pathology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Ya-Wen Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Hai-Ting Liu
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Pathology, Qilu Hospital, Shandong University, Jinan, China
| | - Peng Gao
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Pathology, Qilu Hospital, Shandong University, Jinan, China
| |
Collapse
|
5
|
Al-Hamed MH, Alzaidan H, Hussein M, Albaik L, Qari A, Sayer JA, Imtiaz F. Novel pathogenic MAPKBP1 variant in a family with nephronophthisis. Clin Kidney J 2020; 14:728-730. [PMID: 33623699 PMCID: PMC7886576 DOI: 10.1093/ckj/sfaa090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 04/28/2020] [Indexed: 11/23/2022] Open
Affiliation(s)
- Mohamed H Al-Hamed
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Hamad Alzaidan
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Maged Hussein
- Nephrology Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Lina Albaik
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Alya Qari
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle, UK.,National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle upon Tyne, UK
| | - Faiqa Imtiaz
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| |
Collapse
|
6
|
Comprehensive transcriptional changes in the liver of Kanglang white minnow ( Anabarilius g rahami) in response to the infection of parasite Ichthyophthirius m ultifiliis. Animals (Basel) 2020; 10:ani10040681. [PMID: 32295151 PMCID: PMC7222788 DOI: 10.3390/ani10040681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/04/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Kanglang white minnow (KWM, Anabarilius grahami), is a typical “3E” (Endangered, Endemic and Economic) fish species in Yunnan-Guizhou Plateau. As one of the traditional “Four Famous Fishes” in Yunnan province, it has become the major local aquaculture species with increasing demand after the success of artificial breeding. However, this economically important fish is highly susceptible to the infection of a parasite ciliate, Ichthyophthirius multifiliis (Ich), during the practical procedure of artificial breeding. To examine the host immune responses to Ich, we divided the experimental fishes into three groups (including control, early-infected stage, and late-infected stage) for transcriptome sequencing to analyze the differentially expressed genes (DEGs) and immune response mechanisms. Abstract The notorious parasite Ichthyophthirius multifiliis (Ich) has been recorded worldwide in fish species and causes white spot disease, posing major threats and resulting in severe losses to international fish production. Extensively effective strategies for treating Ich are not available yet, and genetic mechanisms of hosts in response to the parasite are still largely unknown. In this study, we selected Kanglang white minnow (KWM, Anabarilius grahami) to examine its liver transcriptional changes after Ich infection, as white spot disease is one bottleneck problem in exploring this economically important species. We divided the experimental fishes into three groups (control, early-infected, and late-infected) to examine differentially expressed genes (DEGs). A total of 831 DEGs were identified and classified into 128 significantly enriched GO (Gene Ontology) terms and 71 significantly enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Most of these terms or pathways were functionally enriched in immunity, inflammatory response, and apoptosis, such as nucleotide-binding oligomerization domain-like (NOD-like) receptor signaling, tumor necrosis factor (TNF) signaling, interleukin-17 (IL-17) signaling, and apoptosis pathways. We also identified 178 putative antimicrobial peptides (AMPs) and AMP precursors based on our previously reported genome assembly of KWM, and revealed that the expressional patterns varied according to different types. In summary, our work reported the first comprehensive transcriptional changes in KWM in response to the exogenous infection of Ich, which would lay a solid foundation for in-depth studies on disease defense or resistant strains selection in this valuable fish.
Collapse
|
7
|
Song Y, Zhang W, He X, Liu X, Yang P, Wang J, Hu K, Liu W, Zhang X, Jing H, Yuan X. High NCALD expression predicts poor prognosis of cytogenetic normal acute myeloid leukemia. J Transl Med 2019; 17:166. [PMID: 31109331 PMCID: PMC6528257 DOI: 10.1186/s12967-019-1904-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/03/2019] [Indexed: 12/22/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is a heterogeneous disease in terms of genetic basis, clinical, biological and prognostic, and is a malignant clonal disease of leukemia stem cells (LSCs). Nearly half of adult AML patients exhibit a cytogenetic normal acute myeloid leukemia (CN-AML). The expression level of NCALD gene was associated with the prognosis of ovarian cancer and non-small cell lung cancer (NSCLC). The expression level of NCALD gene is still unclear in the prognosis of patients with AML. Method We integrated 5 independent datasets totally 665 AML patients (497 CN-AML patients) to analyzed relation between NCALD gene expression and the clinical FAB classification, gene mutation, therapy, prognosis of CN-AML. We analyzed the NCALD gene expression with the prognosis and LSC of 165 AML patients from The Cancer Genome Atlas (TCGA) dataset and 78 AML patients from GEO dataset. Results High NCALD-expressing CN-AML patients were associated with poor event-free survival (EFS) and overall survival (OS) compared to low NCALD expression (EFS, P < 0.0001, OS, P < 0.0001). In AML patients of allogeneic hematopoietic stem cell transplantation (allo-HSCT), high NCALD expression was associated with poor survival prognosis in EFS and OS (EFS, P < 0.0051, OS, P = 0.028). Post-chemotherapy in AML patients, high NCALD expression led a worse prognosis in EFS and OS (EFS, P = 0.011; OS, P = 0.0056). In multivariate analysis, high NCALD expression was an independent prognostic factor that predicts shorter EFS and OS (EFS, P = 3.84E−05, OS, P = 8.53E−05) of CN-AML. Conclusion Our results indicate that high expression of NCALD gene is a poor prognostic factor for CN-AML. NCALD can be considered as independent predictors of CN-AML patients and can be used as a biomarker for the prognosis of CN-AML. Electronic supplementary material The online version of this article (10.1186/s12967-019-1904-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ying Song
- The First Clinical College of Gannan Medical University, Ganzhou, 341000, China
| | - Weilong Zhang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, No. 49 North Garden Road, Haidian District, Beijing, 100191, People's Republic of China
| | - Xue He
- Department of Pathology, Beijing Tiantan Hospital Affiliated With Capital Medical University, No. 6 Tiantan Xili, Beijing, 100050, China
| | - Xiaoni Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Gannan Medical University, No. 23 Qingnian Road, Zhanggong District, Ganzhou, 341000, China
| | - Ping Yang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, No. 49 North Garden Road, Haidian District, Beijing, 100191, People's Republic of China
| | - Jing Wang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, No. 49 North Garden Road, Haidian District, Beijing, 100191, People's Republic of China
| | - Kai Hu
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, No. 49 North Garden Road, Haidian District, Beijing, 100191, People's Republic of China
| | - Weiyou Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Gannan Medical University, No. 23 Qingnian Road, Zhanggong District, Ganzhou, 341000, China
| | - Xiuru Zhang
- Department of Pathology, Beijing Tiantan Hospital Affiliated With Capital Medical University, No. 6 Tiantan Xili, Beijing, 100050, China.
| | - Hongmei Jing
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, No. 49 North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.
| | - Xiaoliang Yuan
- Department of Respiratory Medicine, The First Affiliated Hospital of Gannan Medical University, No. 23 Qingnian Road, Zhanggong District, Ganzhou, 341000, China.
| |
Collapse
|
8
|
Transcriptome-wide analysis of alternative mRNA splicing signature in the diagnosis and prognosis of stomach adenocarcinoma. Oncol Rep 2018; 40:2014-2022. [PMID: 30106437 PMCID: PMC6111597 DOI: 10.3892/or.2018.6623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 07/17/2018] [Indexed: 12/12/2022] Open
Abstract
Alternative mRNA splicing (AS) contributes greatly to expanding the diversity and function of the proteome. Increasing evidence has suggested that dysregulation of mRNA splicing may be associated with various types of cancer. In the present study, RNA sequencing data were used to investigate alterations to the global mRNA splicing landscape of cellular genes from 452 stomach adenocarcinoma (STAD) tissues available in The Cancer Genome Atlas. Seven types of AS events, including the profiles of exon skipping events, were analyzed using SpliceSeq software. A total of 60,754 AS events in 10,611 genes were detected, more than half of which were exon skipping events. The AS events were compared between 415 STAD tissues and 37 normal tissues, and 3,895 differentially spliced cancer-specific events were identified. In addition, the association of the AS events with the overall survival of 373 STAD patients was analyzed. Multivariate Cox regression analysis revealed that prognosis prediction models based on the AS events with clinical parameters had an excellent performance in predicting the survival of STAD patients. This study provides a comprehensive portrait of global changes in mRNA splicing signatures that occur in gastric cancer. These results allowed the identification of a core set of AS in gastric cancer and indicated that AS events may serve as prognostic indicators.
Collapse
|
9
|
High expression of RUNX1 is associated with poorer outcomes in cytogenetically normal acute myeloid leukemia. Oncotarget 2017; 7:15828-39. [PMID: 26910834 PMCID: PMC4941280 DOI: 10.18632/oncotarget.7489] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/24/2016] [Indexed: 12/13/2022] Open
Abstract
Depending on its expression level, RUNX1 can act as a tumor promoter or suppressor in hematological malignancies. The clinical impact of RUNX1 expression in cytogenetically normal acute myeloid leukemia (CN-AML) remained unknown, however. We evaluated the prognostic significance of RUNX1 expression using several public microarray datasets. In the testing group (n = 157), high RUNX1 expression (RUNX1high) was associated with poorer overall survival (OS; P = 0.0025) and event-free survival (EFS; P = 0.0025) than low RUNX1 expression (RUNX1low). In addition, the prognostic significance of RUNX1 was confirmed using European Leukemia Net (ELN) genetic categories and multivariable analysis, which was further validated using a second independent CN-AML cohort (n = 162, OS; P = 0.03953). To better understand the mechanisms of RUNX1, we investigated genome-wide gene/microRNAs expression signatures and cell signaling pathways associated with RUNX1 expression status. Several known oncogenes/oncogenic microRNAs and cell signaling pathways were all up-regulated, while some anti-oncogenes and molecules of immune activation were down-regulated in RUNX1high CN-AML patients. These findings suggest RUNX1high is a prognostic biomarker of unfavorable outcome in CN-AML, which is supported by the distinctive gene/microRNA signatures and cell signaling pathways.
Collapse
|
10
|
Wang XX, Zhang R, Li Y. Expression of the miR-148/152 Family in Acute Myeloid Leukemia and its Clinical Significance. Med Sci Monit 2017; 23:4768-4778. [PMID: 28978904 PMCID: PMC5639952 DOI: 10.12659/msm.902689] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Background MicroRNAs (miRNAs) play an important role in the development and progression of acute myeloid leukemia (AML). The miR-148/152 family has been reported to be express differently in various kinds of tumors. We investigated the expression level of the miR-148/152 family in AML patients and their clinical significance. Material/Methods Expression levels of the miR-148/152 family in 80 patients with newly diagnosed AML and 20 healthy participants were analyzed by qRT-PCR. We also evaluated the relationship between the expression levels of the miR-148/152 family and clinicopathological features of AML patients. Results Compared with healthy controls, we found a significant lower expression of downregulated miR-148/152 in AML patients (p<0.0001). The expression of miR148/152 family was associated with various AML clinicopathological risk parameters including FAB classifications, cytogenetics, and gene mutations. The number of patients with high expression levels of miR-148a/b was significantly increased in the low-risk group and significantly decreased in the high-risk group. (p=0.025, p=0.000, respectively). Patients with higher expression of miR-148b showed a higher complete remission (CR) rate (p=0.043). Importantly, higher expression of miR-148a/b was correlated with lower relapse rate (p=0.035, p=0.027, respectively) and showed a longer relapse-free survival (RFS) (p=0.0321, p=0.002, respectively). In the subgroup analysis, RFS was significantly affected by the expression of miR-148a/b in patients the high and the intermediate-risk groups (p=0.0499, p=0.0114, respectively). Conclusions The expression levels of the miR-148/152 family were lower in patients with AML compared to healthy controls, and were associated with various AML clinicopathological parameters and therapeutic effect. The miR-148/152 family may prove to be a new biomarker for AML.
Collapse
Affiliation(s)
- Xiao-Xue Wang
- Department of Hematology, The First Hospital, China Medical University, Shenyang, Liaoning, China (mainland)
| | - Rui Zhang
- Department of Hematology, The First Hospital, China Medical University, Shenyang, Liaoning, China (mainland)
| | - Yan Li
- Department of Hematology, The First Hospital, China Medical University, Shenyang, Liaoning, China (mainland)
| |
Collapse
|
11
|
Abstract
The biological activity and geographical distribution of honey bees is strongly temperature-dependent, due to their ectothermic physiology. In China, the endemic Apis cerana cerana exhibits stronger cold hardiness than Western honey bees, making the former species important pollinators of winter-flowering plants. Although studies have examined behavioral and physiological mechanisms underlying cold resistance in bees, data are scarce regarding the exact molecular mechanisms. Here, we investigated gene expression in A. c. cerana under two temperature treatments, using transcriptomic analysis to identify differentially expressed genes (DEGs) and relevant biological processes, respectively. Across the temperature treatments, 501 DEGs were identified. A gene ontology analysis showed that DEGs were enriched in pathways related to sugar and amino acid biosynthesis and metabolism, as well as calcium ion channel activity. Additionally, heat shock proteins, zinc finger proteins, and serine/threonine-protein kinases were differentially expressed between the two treatments. The results of this study provide a general digital expression profile of thermoregulation genes responding to cold hardiness in A. c. cerana. Our data should prove valuable for future research on cold tolerance mechanisms in insects, and may be beneficial in breeding efforts to improve bee hardiness.
Collapse
|
12
|
Shi JL, Fu L, Ang Q, Wang GJ, Zhu J, Wang WD. Overexpression of ATP1B1 predicts an adverse prognosis in cytogenetically normal acute myeloid leukemia. Oncotarget 2016; 7:2585-95. [PMID: 26506237 PMCID: PMC4823057 DOI: 10.18632/oncotarget.6226] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 10/09/2015] [Indexed: 11/25/2022] Open
Abstract
ATP1B1 encodes the Na,K-ATPase β subunit, a key regulator of the Na+ and K+ electrochemical gradients across the plasma membrane and an essential regulator of cellular activity. We used several microarray datasets to test the prognostic efficacy of ATP1B1 expression in cytogenetically normal acute myeloid leukemia (CN-AML). Within the primary cohort (n = 157), high ATP1B1 expression (ATP1B1high) was associated with shorter overall survival (OS) and event-free survival (EFS) (P = 0.0068, P = 0.0039, respectively). Similar results were also obtained in the European Leukemia Net (ELN) Intermediate-I genetic category (OS: P = 0.0035, EFS: P = 0.0007). Multivariable analyses confirmed ATP1B1high is an independent predictor of shorter OS (P = 0.042) and EFS (P = 0.035). Analysis of another CN-AML cohort confirmed that ATP1B1high is associated with shorter OS (P = 0.0046, n = 162). In addition, up-regulation of oncogenes/onco-microRNAs such as MYCN, CCND2, CDK6, KIT and miR-155, among others, was associated with ATP1B1high, which may be indicative of ATP1B1's leukemogenicity. Our results may improve risk stratification and indicate new therapeutic targets for CN-AML.
Collapse
Affiliation(s)
- Jin-long Shi
- Medical Engineering Support Center, Chinese PLA General Hospital, Beijing, China
| | - Lin Fu
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing, China
| | - Qing Ang
- Medical Engineering Support Center, Chinese PLA General Hospital, Beijing, China
| | - Guo-jing Wang
- Medical Engineering Support Center, Chinese PLA General Hospital, Beijing, China
| | - Jun Zhu
- Medical Engineering Support Center, Chinese PLA General Hospital, Beijing, China
| | - Wei-dong Wang
- Medical Engineering Support Center, Chinese PLA General Hospital, Beijing, China
| |
Collapse
|
13
|
Shi J, Fu H, Jia Z, He K, Fu L, Wang W. High Expression of CPT1A Predicts Adverse Outcomes: A Potential Therapeutic Target for Acute Myeloid Leukemia. EBioMedicine 2016; 14:55-64. [PMID: 27916548 PMCID: PMC5161445 DOI: 10.1016/j.ebiom.2016.11.025] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/13/2016] [Accepted: 11/21/2016] [Indexed: 02/07/2023] Open
Abstract
Carnitine palmitoyl transferase 1A (CPT1A) protein catalyzes the rate-limiting step of Fatty-acid oxidation (FAO) pathway, which can promote cell proliferation and suppress apoptosis. Targeting CPT1A has shown remarkable anti-leukemia activity. But, its prognostic value remains unclear in Acute Myeloid Leukemia (AML). In two independent cohorts of cytogenetically normal AML (CN-AML) patients, compared to low expression of CPT1A (CPT1Alow), high expression of CPT1A (CPT1Ahigh) was significantly associated with adverse outcomes, which was also shown in European Leukemia Network (ELN) Intermediate-I category. Multivariable analyses adjusting for known factors confirmed CPT1Ahigh as a high risk factor. Significant associations between CPT1Ahigh and adverse outcomes were further validated whether for all AML patients (OS: P = 0.008; EFS: P = 0.002, n = 334, no M3) or for National Comprehensive Cancer Network (NCCN) Intermediate-Risk subgroup (OS: P = 0.021, EFS: P = 0.024, n = 173). Multiple omics analysis revealed aberrant alterations of genomics and epigenetics were significantly associated with CPT1A expression, including up- and down-regulation of oncogenes and tumor suppressor, activation and inhibition of leukemic (AML, CML) and immune activation pathways, hypermethylation enrichments on CpG island and gene promoter regions. Combined with the previously reported anti-leukemia activity of CPT1A's inhibitor, our results proved CPT1A as a potential prognosticator and therapeutic target for AML. High expression of CPT1A is an adverse prognostic biomarker in AML. Aberrant alterations of genomic and epigenomic patterns are significantly associated with CPT1A expression.
Identification of prognostic biomarkers is essential for therapeutic choice of AML. This study represents direct evidences that high expression of CPT1A is significantly associated with poor outcomes and abnormal genomic and epigenomic patterns in AML patients. CPT1A is an important catalyzer for fatty-acid oxidation pathway, which may provide alternative carbon source for leukemia proliferation. Findings of this study may indicate the significance of fat metabolism in leukemogenesis.
Collapse
Affiliation(s)
- Jinlong Shi
- Key Laboratory of Biomedical Engineering and Translational Medicine (Chinese PLA General Hospital), Ministry of Industry and Information Technology, Beijing, China; Department of Biomedical Engineering, Chinese PLA General Hospital, Beijing, China
| | - Huaping Fu
- Department of Nuclear Medicine, Chinese PLA General Hospital, Beijing, China
| | - Zhilong Jia
- Key Laboratory of Biomedical Engineering and Translational Medicine (Chinese PLA General Hospital), Ministry of Industry and Information Technology, Beijing, China
| | - Kunlun He
- Key Laboratory of Biomedical Engineering and Translational Medicine (Chinese PLA General Hospital), Ministry of Industry and Information Technology, Beijing, China
| | - Lin Fu
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.
| | - Weidong Wang
- Key Laboratory of Biomedical Engineering and Translational Medicine (Chinese PLA General Hospital), Ministry of Industry and Information Technology, Beijing, China; Department of Biomedical Engineering, Chinese PLA General Hospital, Beijing, China.
| |
Collapse
|
14
|
High expression of MAP7 predicts adverse prognosis in young patients with cytogenetically normal acute myeloid leukemia. Sci Rep 2016; 6:34546. [PMID: 27686215 PMCID: PMC5043276 DOI: 10.1038/srep34546] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 09/15/2016] [Indexed: 12/20/2022] Open
Abstract
Microtubule-associated protein 7 (MAP7) plays an important role in cancer cells. In this study, we identified the prognostic significance of MAP7 expression in cytogenetically normal acute myeloid leukemia (CN-AML) patients (aged <60 years) based on several microarray datasets. In the first group (n = 129), high MAP7 expression (MAP7high) was associated with adverse overall survival (OS; P = 0.0441) and event-free survival (EFS; P = 0.0114) compared with low MAP7 expression (MAP7low). In addition, the prognostic significance of MAP7 was confirmed by European Leukemia Net (ELN) intermediate-I genetic categories and multivariable analysis. In the second independent group of CN-AML patients (aged <60 years), MAP7high was also associated with adverse OS (n = 88, OS; P = 0.00811). To understand the inherent mechanisms of MAP7's prognosis, we investigated genome-wide gene/microRNA expression signatures associated with MAP7 expression. Several known oncogenic genes/microRNAs and anti-oncogenic genes/microRNAs were disordered in MAP7high CN-AML patients. In conclusion, MAP7high is an adverse prognostic biomarker for CN-AML, which may be attributed to the distinctive genome-wide gene/microRNA expression and related cell signaling pathways.
Collapse
|
15
|
Li L, Chen Z, Zhang L, Liu G, Hua J, Jia L, Liao M. Genome-wide targets identification of "core" pluripotency transcription factors with integrated features in human embryonic stem cells. MOLECULAR BIOSYSTEMS 2016; 12:1324-32. [PMID: 26912333 DOI: 10.1039/c6mb00006a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Embryonic stem cells (ESCs) play an important role in developmental biology which is still lacking clear molecular mechanisms. The "core" transcription factors (TFs) including OCT4, SOX2 and NANOG are essential for maintaining the stemness of ESCs. But the downstream targets of these "core" TFs are still ambiguous. Based on support vector machine (SVM) technology, this study develops a label method algorithm (LMA) for genome-wide target identification of "core" TFs in humans, which eliminates the need for negative training samples. This method integrates histone modifications and TF binding motifs as identification features. Compared with a previous mapping-convergence (M-C) algorithm, the LMA can provide more stable and reliable predictions. 4796, 3166 and 4384 target genes of OCT4, SOX2 and NANOG, respectively, were identified with the LMA model. Then verifications of the predicted targets were carried out based on their functional consistency and their connection degree in networks from a computational system biology perspective. The results showed that the targets of "core" TFs present higher gene functional similarity and closer connection distance than background levels.
Collapse
Affiliation(s)
- Leijie Li
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | | | | | | | | | | | | |
Collapse
|