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Liang Q, Fu C, Liu Y, Liu W, Guo W. Association of plasma microRNA-16-5p and abdominal aortic calcification in maintenance hemodialysis patients. Ren Fail 2024; 46:2368091. [PMID: 39049724 PMCID: PMC11275526 DOI: 10.1080/0886022x.2024.2368091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 05/30/2024] [Accepted: 06/10/2024] [Indexed: 07/27/2024] Open
Abstract
Recent studies have shown that microRNA-16-5p (miR-16-5p) plays a crucial role in the pathological mechanism of vascular calcification. Nevertheless, the expression profile of miR-16-5p in maintenance hemodialysis (MHD) patients who are predisposed to vascular calcification remains unknown. This study aims to investigate the potential associations between calcification risk and serum miR-16-5p expression among MHD patients. This cross-sectional study involved 132 MHD patients from the Dialysis Center of Beijing Friendship Hospital between 1 January 2019 and 31 December 2020. The degree of calcification in MHD patients was assessed using the Abdominal aortic calcification (AAC) score, and miR-16-5p expression was quantified using quantitative real-time polymerase chain reaction (qRT-PCR) with the 2-ΔΔCT method. Statistical analyses, including spearman correlation, linear regression and logistic regression analysis were used to explore the associations between laboratory parameters and AAC score. Calcifications were observed in 79(59.80%) patients. The linear regression showed a one-quartile decrease in miR-16-5p expression led to a significant increase in the AAC score by 5.336 (95% CI: 2.670-10.662, p = 0.000). Multivariate logistic regression analyses revealed that decreased miR-16-5p expression, reduced serum urea nitrogen, elevated white blood cell count, and longer dialysis vintage were significantly associated with an increased incidence of vascular calcification. The Area Under the Curve (AUC) of the Receiver Operating Characteristic (ROC) of the miR-16-5p-based logistic regression model was 0.842 (95% CI: 0.771-0.913, p = 0.000). There was an independent association between miR-16-5p expression and calcification degree. Lower miR-16-5p expression levels seem to be a potential risk factor of vascular calcification in MHD patients.
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Affiliation(s)
- Qiaojing Liang
- Department of Nephrology, Faculty of Kidney Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Chen Fu
- Department of Nephrology, Beijing Jishuitan Hospital, Capital Medical University, Beijing, China
| | - Yingjie Liu
- Department of Nephrology, Faculty of Kidney Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Wenhu Liu
- Department of Nephrology, Faculty of Kidney Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Weikang Guo
- Department of Nephrology, Faculty of Kidney Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China
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Hou Y, Chen Y, Zhang Y, Li M, Chen J. Prognostic role of chemokine-related genes in acute myeloid leukemia. PeerJ 2024; 12:e17862. [PMID: 39135956 PMCID: PMC11318587 DOI: 10.7717/peerj.17862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/14/2024] [Indexed: 08/15/2024] Open
Abstract
Background Chemotactic cytokines play a crucial role in the development of acute myeloid leukemia (AML). Thus, investigating the mechanisms of chemotactic cytokine-related genes (CCRGs) in AML is of paramount importance. Methods Using the TCGA-AML, GSE114868, and GSE12417 datasets, differential expression analysis identified differentially expressed CCRGs (DE-CCRGs). These genes were screened by overlapping differentially expressed genes (DEGs) between AML and control groups with CCRGs. Subsequently, functional enrichment analysis and the construction of a protein-protein interaction (PPI) network were conducted to explore the functions of the DE-CCRGs. Univariate Cox regression, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses identified relevant prognostic genes and developed a prognostic model. Survival analysis of the prognostic gene was performed, followed by functional similarity analysis, immune analysis, enrichment analysis, and drug prediction analysis. Results Differential expression analysis revealed 6,743 DEGs, of which 29 DE-CCRGs were selected for this study. Functional enrichment analysis indicated that DE-CCRGs were primarily involved in chemotactic cytokine-related functions and pathways. Six prognostic genes (CXCR3, CXCR2, CXCR6, CCL20, CCL4, and CCR2) were identified and incorporated into the risk model. The model's performance was validated using the GSE12417 dataset. Survival analysis showed significant differences in AML overall survival (OS) between prognostic gene high and low expression groups, indicating that prognostic gene might be significantly associated with patient survival. Additionally, nine different immune cells were identified between the two risk groups. Correlation analysis revealed that CCR2 had the most significant positive correlation with monocytes and the most significant negative correlation with resting mast cells. The tumor immune dysfunction and exclusion score was lower in the high-risk group. Conclusion CXCR3, CXCR2, CXCR6, CCL20, CCL4, and CCR2 were identified as prognostic genes correlated to AML and the tumor immune microenvironment. These findings offerred novel insights into the prevention and treatment of AML.
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Affiliation(s)
- Yanfei Hou
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Yu Chen
- Department of Hematology, The Second Affiliated Hospital of Wannan Medical College, Wuhu, Anhui Province, China
| | - Yaofang Zhang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Mengyao Li
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Jianfang Chen
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
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Abulimiti M, Jia ZY, Wu Y, Yu J, Gong YH, Guan N, Xiong DQ, Ding N, Uddin N, Wang J. Exploring and clinical validation of prognostic significance and therapeutic implications of copper homeostasis-related gene dysregulation in acute myeloid leukemia. Ann Hematol 2024; 103:2797-2826. [PMID: 38879648 DOI: 10.1007/s00277-024-05841-6] [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: 05/09/2024] [Accepted: 06/08/2024] [Indexed: 07/28/2024]
Abstract
The patterns and biological functions of copper homeostasis-related genes (CHRGs) in acute myeloid leukemia (AML) remain unclear. We explored the patterns and biological functions of CHRGs in AML. Using independent cohorts, including TCGA-GTEx, GSE114868, GSE37642, and clinical samples, we identified 826 common differentially expressed genes. Specifically, 12 cuproptosis-related genes (e.g., ATP7A, ATP7B) were upregulated, while 17 cuproplasia-associated genes (e.g., ATOX1, ATP7A) were downregulated in AML. We used LASSO-Cox, Kaplan-Meier, and Nomogram analyses to establish prognostic risk models, effectively stratifying patients with AML into high- and low-risk groups. Subgroup analysis revealed that high-risk patients exhibited poorer overall survival and involvement in fatty acid metabolism, apoptosis, and glycolysis. Immune infiltration analysis indicated differences in immune cell composition, with notable increases in B cells, cytotoxic T cells, and memory T cells in the low-risk group, and increased monocytes and neutrophils in the high-risk group. Single-cell sequencing analysis corroborated the expression characteristics of critical CHRGs, such as MAPK1 and ATOX1, associated with the function of T, B, and NK cells. Drug sensitivity analysis suggested potential therapeutic agents targeting copper homeostasis, including Bicalutamide and Sorafenib. PCR validation confirmed the differential expression of 4 cuproptosis-related genes (LIPT1, SLC31A1, GCSH, and PDHA1) and 9 cuproplasia-associated genes (ATOX1, CCS, CP, MAPK1, SOD1, COA6, PDK1, DBH, and PDE3B) in AML cell line. Importantly, these genes serve as potential biomarkers for patient stratification and treatment. In conclusion, we shed light on the expression patterns and biological functions of CHRGs in AML. The developed risk models provided prognostic implications for patient survival, offering valuable information on the regulatory characteristics of CHRGs and potential avenues for personalized treatment in AML.
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Affiliation(s)
| | - Zheng-Yi Jia
- School of Pharmacy, Xinjiang Medical University, Urumqi, 830011, China
| | - Yun Wu
- Department of General Medicine, The First Affiliated Hospital of the Xinjiang Medical University, Urumqi, 830011, China
| | - Jing Yu
- Department of Teaching and Research, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Yue-Hong Gong
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, 830011, China
| | - Na Guan
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Dai-Qin Xiong
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, 830011, China
| | - Nan Ding
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, 830011, China
| | - Nazim Uddin
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Jie Wang
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China.
- Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, 830011, China.
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Keshavarz A, Navidinia AA, Kuhestani Dehaghi BH, Amiri V, Mohammadi MH, Allahbakhshian Farsani M. Identification of Prognostic Genes in Acute Myeloid Leukemia Microenvironment: A Bioinformatic and Experimental Analysis. Mol Biotechnol 2024:10.1007/s12033-024-01128-3. [PMID: 38714601 DOI: 10.1007/s12033-024-01128-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 02/27/2024] [Indexed: 05/10/2024]
Abstract
Acute myeloid leukemia (AML) is a lethal hematologic malignancy with a variable prognosis that is highly dependent on the bone marrow microenvironment. Consequently, a better understanding of the AML microenvironment is crucial for early diagnosis, risk stratification, and personalized therapy. In recent years, the role of bioinformatics as a powerful tool in clarifying the complexities of cancer has become more prominent. Gene expression profile and clinical data of 173 AML patients were downloaded from the TCGA database, and the xCell algorithm was applied to calculate the microenvironment score (MS). Then, the correlation of MS with FAB classification, and CALGB cytogenetic risk category was investigated. Differentially expressed genes (DEGs) were identified, and the correlation analysis of DEGs with patient survival was done using univariate cox. The prognostic value of candidate prognostic DEGs was confirmed based on the GEO database. In the last step, real-time PCR was used to compare the expression of the top three prognostic genes between patients and the control group. During TCGA data analysis, 716 DEGs were identified, and survival analysis results showed that 152 DEGs had survival-related changes. In addition, the prognostic value of 31 candidate prognostic genes was confirmed by GEO data analysis. Finally, the expression analysis of FLVCR2, SMO, and CREB5 genes, the most related genes to patients' survival, was significantly different between patients and control groups. In summary, we identified key microenvironment-related genes that influence the survival of AML patients and may serve as prognostic and therapeutic targets.
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Affiliation(s)
- Ali Keshavarz
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran
| | - Amir Abbas Navidinia
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran
| | - Bentol Hoda Kuhestani Dehaghi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran
| | - Vahid Amiri
- Department of Laboratory Sciences, School of Paramedicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Hossein Mohammadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran
- HSCT Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Allahbakhshian Farsani
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran.
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Cao C, Wang T, Luo Y, Zhang Y, Dai YY, Shen Y. Comprehensive analysis of cuproptosis-associated LncRNAs predictive value and related CeRNA network in acute myeloid leukemia. Heliyon 2023; 9:e22532. [PMID: 38058427 PMCID: PMC10696213 DOI: 10.1016/j.heliyon.2023.e22532] [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: 05/29/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/08/2023] Open
Abstract
Background Acute myeloid leukemia (AML) is characterized by a high recurrence and mortality rate. Cuproptosis is involved in cell death regulation in in a variety of solid tumors. Long non-coding RNAs that regulate cuproptosis genes in the pathogenesis of acute leukemia have yet to be explored. Methods First, cuproptosis genes with distinct expression levels were discovered by contrasting AML with normal samples from the TCGA and GTEx cohorts. Pearson correlation and univariate Cox-regression analysis were performed to identify cuproptosis-associated lncRNAs with significant prognostic values. Then the least absolute shrinkage and selection operator (LASSO) Cox regression was utilized to establish a multi-gene signature to predict AML prognosis. Next, Kaplan-Meier estimator, receiver operating characteristic curve, and a nomogram were performed to evaluate the predictive capacity of the risk signature. Functional enrichment analyses were employed to assess their function. Moreover, qRT-PCR testing of lncRNA expression in AML samples was conducted. The competing endogenous RNA (ceRNA) network was constructed to find the target genes. Results A risk model based on the signature of three cuproptosis-associated lncRNAs was developed. The results showed that the model possessed excellent prognostic potential. The nomogram raised the accuracy in predicting AML survival. In addition, functional enrichment analyses demonstrated an enrichment of inflammatory and immune-related pathways. Moreover, correlations between the risk signature and clinicopathological variables, tumor mutational burden, RNA stemness score, immune profile, and drug sensitivity were observed. Furthermore, we discovered that TRAF3IP2-AS1 may function as a ceRNA to regulate cuproptosis and ferroptosis gene expression. Conclusion The risk signature established in this study could serve as a reliable biosignature for AML prognosis. And the findings presented here may facilitate research on cuproptosis in AML.
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Affiliation(s)
- Chun Cao
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Teng Wang
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yun Luo
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yin Zhang
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yue-yu Dai
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yan Shen
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Korbecki J, Kupnicka P, Barczak K, Bosiacki M, Ziętek P, Chlubek D, Baranowska-Bosiacka I. The Role of CXCR1, CXCR2, CXCR3, CXCR5, and CXCR6 Ligands in Molecular Cancer Processes and Clinical Aspects of Acute Myeloid Leukemia (AML). Cancers (Basel) 2023; 15:4555. [PMID: 37760523 PMCID: PMC10526350 DOI: 10.3390/cancers15184555] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/09/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Acute myeloid leukemia (AML) is a type of leukemia known for its unfavorable prognoses, prompting research efforts to discover new therapeutic targets. One area of investigation involves examining extracellular factors, particularly CXC chemokines. While CXCL12 (SDF-1) and its receptor CXCR4 have been extensively studied, research on other CXC chemokine axes in AML is less developed. This study aims to bridge that gap by providing an overview of the significance of CXC chemokines other than CXCL12 (CXCR1, CXCR2, CXCR3, CXCR5, and CXCR6 ligands and CXCL14 and CXCL17) in AML's oncogenic processes. We explore the roles of all CXC chemokines other than CXCL12, in particular CXCL1 (Gro-α), CXCL8 (IL-8), CXCL10 (IP-10), and CXCL11 (I-TAC) in AML tumor processes, including their impact on AML cell proliferation, bone marrow angiogenesis, interaction with non-leukemic cells like MSCs and osteoblasts, and their clinical relevance. We delve into how they influence prognosis, association with extramedullary AML, induction of chemoresistance, effects on bone marrow microvessel density, and their connection to French-American-British (FAB) classification and FLT3 gene mutations.
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Affiliation(s)
- Jan Korbecki
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland; (J.K.); (P.K.); (M.B.); (D.C.)
- Department of Anatomy and Histology, Collegium Medicum, University of Zielona Góra, Zyty 28, 65-046 Zielona Góra, Poland
| | - Patrycja Kupnicka
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland; (J.K.); (P.K.); (M.B.); (D.C.)
| | - Katarzyna Barczak
- Department of Conservative Dentistry and Endodontics, Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland;
| | - Mateusz Bosiacki
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland; (J.K.); (P.K.); (M.B.); (D.C.)
| | - Paweł Ziętek
- Department of Orthopaedics, Traumatology and Orthopaedic Oncology, Pomeranian Medical University, Unii Lubelskiej 1, 71-252 Szczecin, Poland;
| | - Dariusz Chlubek
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland; (J.K.); (P.K.); (M.B.); (D.C.)
| | - Irena Baranowska-Bosiacka
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland; (J.K.); (P.K.); (M.B.); (D.C.)
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Li Q, Hujiaaihemaiti M, Wang J, Uddin MN, Li MY, Aierken A, Wu Y. Identifying key transcription factors and miRNAs coregulatory networks associated with immune infiltrations and drug interactions in idiopathic pulmonary arterial hypertension. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:4153-4177. [PMID: 36899621 DOI: 10.3934/mbe.2023194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
BACKGROUND The deregulated genetic factors are critically associated with idiopathic pulmonary arterial hypertension (IPAH) development and progression. However, the identification of hub-transcription factors (TFs) and miRNA-hub-TFs co-regulatory network-mediated pathogenesis in IPAH remains lacking. METHODS We used GSE48149, GSE113439, GSE117261, GSE33463, and GSE67597 for identifying key genes and miRNAs in IPAH. We used a series of bioinformatics approaches, including R packages, protein-protein interaction (PPI) network, and gene set enrichment analysis (GSEA) to identify the hub-TFs and miRNA-hub-TFs co-regulatory networks in IPAH. Also, we employed a molecular docking approach to evaluate the potential protein-drug interactions. RESULTS We found that 14 TFs encoding genes, including ZNF83, STAT1, NFE2L3, and SMARCA2 are upregulated, and 47 TFs encoding genes, including NCOR2, FOXA2, NFE2, and IRF5 are downregulated in IPAH relative to the control. Then, we identified the differentially expressed 22 hub-TFs encoding genes, including four upregulated (STAT1, OPTN, STAT4, and SMARCA2) and 18 downregulated (such as NCOR2, IRF5, IRF2, MAFB, MAFG, and MAF) TFs encoding genes in IPAH. The deregulated hub-TFs regulate the immune system, cellular transcriptional signaling, and cell cycle regulatory pathways. Moreover, the identified differentially expressed miRNAs (DEmiRs) are involved in the co-regulatory network with hub-TFs. The six hub-TFs encoding genes, including STAT1, MAF, CEBPB, MAFB, NCOR2, and MAFG are consistently differentially expressed in the peripheral blood mononuclear cells of IPAH patients, and these hub-TFs showed significant diagnostic efficacy in distinguishing IPAH cases from the healthy individuals. Moreover, we revealed that the co-regulatory hub-TFs encoding genes are correlated with the infiltrations of various immune signatures, including CD4 regulatory T cells, immature B cells, macrophages, MDSCs, monocytes, Tfh cells, and Th1 cells. Finally, we discovered that the protein product of STAT1 and NCOR2 interacts with several drugs with appropriate binding affinity. CONCLUSIONS The identification of hub-TFs and miRNA-hub-TFs co-regulatory networks may provide a new avenue into the mechanism of IPAH development and pathogenesis.
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Affiliation(s)
- Qian Li
- Department of General Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
| | - Minawaer Hujiaaihemaiti
- Department of General Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
| | - Jie Wang
- Department of Pharmacy, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
| | - Md Nazim Uddin
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka 1205, Bangladesh
| | - Ming-Yuan Li
- Department of General Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
| | - Alidan Aierken
- Department of General Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
| | - Yun Wu
- Department of General Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
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