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Chang C, He X, Di R, Wang X, Han M, Liang C, Chu M. Thyroid transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in small tail han sheep with FecB BB genotype. Anim Biotechnol 2024; 35:2312393. [PMID: 38421365 DOI: 10.1080/10495398.2024.2312393] [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] [Indexed: 03/02/2024]
Abstract
BACKGROUND The thyroid gland is an important endocrine gland in animals that secretes thyroid hormones and acts on various organs throughout the body. lncRNAs are long non-coding RNAs that play an important role in animal reproduction; however, there is a lack of understanding of their expression patterns and potential roles in the thyroid gland of the Small Tail Han (STH) sheep. In this study, we used RNA-Seq technology to examine the transcriptome expression pattern of the thyroid from the luteal phase (LP) and follicular phase (FP) of FecB BB (MM) STH sheep. RESULTS We identified a total of 122 and 1287 differential expression lncRNAs (DELs) and differential expression mRNAs (DEGs), respectively, which were significantly differentially expressed. These DELs target genes and DEGs can be enriched in several signalling pathways related to the animal reproduction process. CONCLUSIONS The expression profiles of DELs and DEGs in thyroid glands provide a more comprehensive resource for elucidating the reproductive regulatory mechanisms of STH sheep.
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Affiliation(s)
- Cheng Chang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Xiaoyun He
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Ran Di
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xiangyu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Miaoceng Han
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Chen Liang
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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Takihira S, Yamada D, Osone T, Takao T, Sakaguchi M, Hakozaki M, Itano T, Nakata E, Fujiwara T, Kunisada T, Ozaki T, Takarada T. PRRX1-TOP2A interaction is a malignancy-promoting factor in human malignant peripheral nerve sheath tumours. Br J Cancer 2024; 130:1493-1504. [PMID: 38448751 PMCID: PMC11058259 DOI: 10.1038/s41416-024-02632-8] [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: 08/19/2023] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Paired related-homeobox 1 (PRRX1) is a transcription factor in the regulation of developmental morphogenetic processes. There is growing evidence that PRRX1 is highly expressed in certain cancers and is critically involved in human survival prognosis. However, the molecular mechanism of PRRX1 in cancer malignancy remains to be elucidated. METHODS PRRX1 expression in human Malignant peripheral nerve sheath tumours (MPNSTs) samples was detected immunohistochemically to evaluate survival prognosis. MPNST models with PRRX1 gene knockdown or overexpression were constructed in vitro and the phenotype of MPNST cells was evaluated. Bioinformatics analysis combined with co-immunoprecipitation, mass spectrometry, RNA-seq and structural prediction were used to identify proteins interacting with PRRX1. RESULTS High expression of PRRX1 was associated with a poor prognosis for MPNST. PRRX1 knockdown suppressed the tumorigenic potential. PRRX1 overexpressed in MPNSTs directly interacts with topoisomerase 2 A (TOP2A) to cooperatively promote epithelial-mesenchymal transition and increase expression of tumour malignancy-related gene sets including mTORC1, KRAS and SRC signalling pathways. Etoposide, a TOP2A inhibitor used in the treatment of MPNST, may exhibit one of its anticancer effects by inhibiting the PRRX1-TOP2A interaction. CONCLUSION Targeting the PRRX1-TOP2A interaction in malignant tumours with high PRRX1 expression might provide a novel tumour-selective therapeutic strategy.
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Affiliation(s)
- Shota Takihira
- Department of Regenerative Science, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
- Department of Orthopedic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Daisuke Yamada
- Department of Regenerative Science, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Tatsunori Osone
- Department of Regenerative Science, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Tomoka Takao
- Department of Regenerative Science, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Masakiyo Sakaguchi
- Department of Cell Biology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Michiyuki Hakozaki
- Department of Orthopedic Surgery, Fukushima Medical University School of Medicine, Fukushima, 960-1295, Japan
| | - Takuto Itano
- Department of Orthopedic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Eiji Nakata
- Department of Orthopedic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Tomohiro Fujiwara
- Department of Orthopedic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Toshiyuki Kunisada
- Department of Orthopedic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Toshifumi Ozaki
- Department of Orthopedic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Takeshi Takarada
- Department of Regenerative Science, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan.
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Zhou H, Wang YX, Wu M, Lan X, Xiang D, Cai R, Ma Q, Miao J, Fang X, Wang J, Luo D, He Z, Cui Y, Liang P, Wang Y, Bian XW. FANCD2 deficiency sensitizes SHH medulloblastoma to radiotherapy via ferroptosis. J Pathol 2024; 262:427-440. [PMID: 38229567 DOI: 10.1002/path.6245] [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: 07/27/2023] [Revised: 10/26/2023] [Accepted: 11/24/2023] [Indexed: 01/18/2024]
Abstract
Radiotherapy is one of the standard therapeutic regimens for medulloblastoma (MB). Tumor cells utilize DNA damage repair (DDR) mechanisms to survive and develop resistance during radiotherapy. It has been found that targeting DDR sensitizes tumor cells to radiotherapy in several types of cancer, but whether and how DDR pathways are involved in the MB radiotherapy response remain to be determined. Single-cell RNA sequencing was carried out on 38 MB tissues, followed by expression enrichment assays. Fanconi anemia group D2 gene (FANCD2) expression was evaluated in MB samples and public MB databases. The function of FANCD2 in MB cells was examined using cell counting assays (CCK-8), clone formation, lactate dehydrogenase activity, and in mouse orthotopic models. The FANCD2-related signaling pathway was investigated using assays of peroxidation, a malondialdehyde assay, a reduced glutathione assay, and using FerroOrange to assess intracellular iron ions (Fe2+ ). Here, we report that FANCD2 was highly expressed in the malignant sonic hedgehog (SHH) MB subtype (SHH-MB). FANCD2 played an oncogenic role and predicted worse prognosis in SHH-MB patients. Moreover, FANCD2 knockdown markedly suppressed viability, mobility, and growth of SHH-MB cells and sensitized SHH-MB cells to irradiation. Mechanistically, FANCD2 deficiency led to an accumulation of Fe2+ due to increased divalent metal transporter 1 expression and impaired glutathione peroxidase 4 activity, which further activated ferroptosis and reduced proliferation of SHH-MB cells. Using an orthotopic mouse model, we observed that radiotherapy combined with silencing FANCD2 significantly inhibited the growth of SHH-MB cell-derived tumors in vivo. Our study revealed FANCD2 as a potential therapeutic target in SHH-MB and silencing FANCD2 could sensitize SHH-MB cells to radiotherapy via inducing ferroptosis. © 2024 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Hong Zhou
- School of Medicine, Chongqing University, Chongqing, PR China
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
| | - Yan-Xia Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
| | - Min Wu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, PR China
| | - Xi Lan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
| | - Dongfang Xiang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
| | - Ruili Cai
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
| | - Qinghua Ma
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
| | - Jingya Miao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
| | - Xuanyu Fang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
| | - Junjie Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
| | - Dan Luo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
| | - Zhicheng He
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
| | - Youhong Cui
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
| | - Ping Liang
- Department of Neurosurgery, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Yan Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
- Jinfeng Laboratory, Institute of Advanced Pathology, Chongqing, PR China
| | - Xiu-Wu Bian
- School of Medicine, Chongqing University, Chongqing, PR China
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Chongqing, PR China
- Jinfeng Laboratory, Institute of Advanced Pathology, Chongqing, PR China
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Li O, Li X, He J. Knockdown of TOP2A suppresses IL-17 signaling pathway and alleviates the progression of ulcerative colitis. Immun Inflamm Dis 2024; 12:e1207. [PMID: 38661103 PMCID: PMC11044219 DOI: 10.1002/iid3.1207] [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: 10/11/2023] [Revised: 02/05/2024] [Accepted: 02/15/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Ulcerative colitis (UC) is a chronic inflammatory disease of the colonic mucosa, with a gradually increasing incidence. Therefore, it is necessary to actively seek targets for the treatment of UC. METHODS Common differentially expressed genes (DEGs) were screened from two microarray data sets related to UC. Protein-protein interaction network was constructed to find the hub genes. The UC mouse model and cell model were induced by dextran sulfate sodium (DSS). The pathological changes of colon tissue were observed by hematoxylin-eosin staining. Immunohistochemistry and immunofluorescence were performed to detect the expressions of Ki67 and Claudin-1. The performance of mice was observed by disease activity index (DAI). The effect of TOP2A on proliferation, inflammation, oxidative stress, and interleukin-17 (IL-17) signaling pathway in UC model was measured by cell counting kit-8, enzyme-linked immunosorbent assay, and western blot. RESULTS Through bioinformatics analysis, 295 common DEGs were screened, and the hub gene TOP2A was selected. In UC model, there was obvious inflammatory cell infiltration in the colon and less goblet cells, while si-TOP2A lessened it. More Ki67 positive cells and less Claudin-1 positive cells were observed in UC model mice. Furthermore, knockdown of TOP2A increased the body weight and colon length of UC mice, while the DAI was decreased. Through in vivo and in vitro experiments, knockdown of TOP2A also inhibited inflammation and IL-17 signaling pathway, and promoted proliferation in DSS-induced NCM460 cells. CONCLUSION Knockdown of TOP2A alleviated the progression of UC by suppressing inflammation and inhibited IL-17 signaling pathway.
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Affiliation(s)
- Ou Li
- Department of ProctologyZhuJiang Hospital of Southern Medical UniversityGuangzhouGuangdongChina
| | - Xuexiao Li
- Department of ProctologyZhuJiang Hospital of Southern Medical UniversityGuangzhouGuangdongChina
| | - Jianping He
- Department of ProctologyZhuJiang Hospital of Southern Medical UniversityGuangzhouGuangdongChina
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Liu Y, Yang Y, Ni F, Tai G, Yu C, Jiang X, Wang D. Research on radiotherapy related genes and prognostic target identification of rectal cancer based on multi-omics. J Transl Med 2023; 21:856. [PMID: 38012642 PMCID: PMC10680259 DOI: 10.1186/s12967-023-04753-9] [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: 07/31/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Radiosensitivity of rectal cancer is related to the radiotherapy efficacy and prognosis of patients with rectal cancer, and the genes and molecular mechanisms related to radiosensitivity of rectal cancer have not been clarified. We explored the radiosensitivity related genes of rectal cancer at a multi omics level. METHODS mRNA expression data and rectum adenocarcinoma (READ) data were obtained from the Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus Database (GEO) (GSE150082, GSE60331, GSE46862, GSE46862). Differentially expressed genes between radiotherapy sensitive group and radiotherapy insensitive group were screened. GO analysis and KEGG pathway analysis were performed for differentially expressed genes. Among the differentially expressed genes, five core genes associated with rectal cancer prognosis were selected using random survival forest analysis. For these five core genes, drug sensitivity analysis, immune cell infiltration analysis, TISIDB database immune gene correlation analysis, GSEA enrichment analysis, construction of Nomogram prediction model, transcriptional regulatory network analysis, and qRT-PCR validation was performed on human rectal adenocarcinoma tissue. RESULTS We found that 600 up-regulated genes and 553 down-regulated genes were significantly different between radiotherapy sensitive group and radiotherapy insensitive group in rectal cancer. Five key genes, TOP2A, MATR3, APOL6, JOSD1, and HOXC6, were finally screened by random survival forest analysis. These five key genes were associated with different immune cell infiltration, immune-related genes, and chemosensitivity. A comprehensive transcriptional regulatory network was constructed based on these five core genes. qRT-PCR revealed that MATR3 expression was different in rectal cancer tissues and adjacent non-cancerous tissues, while APOL6, HOXC6, JOSD1, and TOP2A expression was not different. CONCLUSION Five radiosensitivity-related genes related to the prognosis of rectal cancer: TOP2A, MATR3, APOL6, JOSD1, HOXC6, are involved in multiple processes such as immune cell infiltration, immune-related genes, chemosensitivity, signaling pathways and transcriptional regulatory networks and may be potential biomarkers for radiotherapy of rectal cancer.
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Affiliation(s)
- Yi Liu
- Department of Radiotherapy, Affiliated Tumor Hospital of Nantong University, Nantong Tumor Hospital, Nantong, Jiangsu, China
| | - Yanguang Yang
- Department of Radiotherapy, Affiliated Tumor Hospital of Nantong University, Nantong Tumor Hospital, Nantong, Jiangsu, China
| | - Feng Ni
- Department of Radiotherapy, Affiliated Tumor Hospital of Nantong University, Nantong Tumor Hospital, Nantong, Jiangsu, China
| | - Guomei Tai
- Department of Radiotherapy, Affiliated Tumor Hospital of Nantong University, Nantong Tumor Hospital, Nantong, Jiangsu, China
| | - Cenming Yu
- Department of Radiotherapy, Affiliated Tumor Hospital of Nantong University, Nantong Tumor Hospital, Nantong, Jiangsu, China
| | - Xiaohui Jiang
- Department of Gastrointestinal Surgery, Affiliated Tumor Hospital of Nantong University, Nantong Tumor Hospital, Nantong, Jiangsu, China.
| | - Ding Wang
- Department of Gastrointestinal Surgery, Affiliated Tumor Hospital of Nantong University, Nantong Tumor Hospital, Nantong, Jiangsu, China.
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Alhattab DM, Isaioglou I, Alshehri S, Khan ZN, Susapto HH, Li Y, Marghani Y, Alghuneim AA, Díaz-Rúa R, Abdelrahman S, Al-Bihani S, Ahmed F, Felimban RI, Alkhatabi H, Alserihi R, Abedalthagafi M, AlFadel A, Awidi A, Chaudhary AG, Merzaban J, Hauser CAE. Fabrication of a three-dimensional bone marrow niche-like acute myeloid Leukemia disease model by an automated and controlled process using a robotic multicellular bioprinting system. Biomater Res 2023; 27:111. [PMID: 37932837 PMCID: PMC10626721 DOI: 10.1186/s40824-023-00457-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/29/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is a hematological malignancy that remains a therapeutic challenge due to the high incidence of disease relapse. To better understand resistance mechanisms and identify novel therapies, robust preclinical models mimicking the bone marrow (BM) microenvironment are needed. This study aimed to achieve an automated fabrication process of a three-dimensional (3D) AML disease model that recapitulates the 3D spatial structure of the BM microenvironment and applies to drug screening and investigational studies. METHODS To build this model, we investigated a unique class of tetramer peptides with an innate ability to self-assemble into stable hydrogel. An automated robotic bioprinting process was established to fabricate a 3D BM (niche-like) multicellular AML disease model comprised of leukemia cells and the BM's stromal and endothelial cellular fractions. In addition, monoculture and dual-culture models were also fabricated. Leukemia cell compatibility, functionalities (in vitro and in vivo), and drug assessment studies using our model were performed. In addition, RNAseq and gene expression analysis using TaqMan arrays were also performed on 3D cultured stromal cells and primary leukemia cells. RESULTS The selected peptide hydrogel formed a highly porous network of nanofibers with mechanical properties similar to the BM extracellular matrix. The robotic bioprinter and the novel quadruple coaxial nozzle enabled the automated fabrication of a 3D BM niche-like AML disease model with controlled deposition of multiple cell types into the model. This model supported the viability and growth of primary leukemic, endothelial, and stromal cells and recapitulated cell-cell and cell-ECM interactions. In addition, AML cells in our model possessed quiescent characteristics with improved chemoresistance attributes, resembling more the native conditions as indicated by our in vivo results. Moreover, the whole transcriptome data demonstrated the effect of 3D culture on enhancing BM niche cell characteristics. We identified molecular pathways upregulated in AML cells in our 3D model that might contribute to AML drug resistance and disease relapse. CONCLUSIONS Our results demonstrate the importance of developing 3D biomimicry models that closely recapitulate the in vivo conditions to gain deeper insights into drug resistance mechanisms and novel therapy development. These models can also improve personalized medicine by testing patient-specific treatments.
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Affiliation(s)
- Dana M Alhattab
- Laboratory for Nanomedicine, Bioengineering Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- KAUST Smart Health Initiative (KSHI), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Ioannis Isaioglou
- Cell Migration and Signaling Laboratory, Bioscience Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Salwa Alshehri
- Laboratory for Nanomedicine, Bioengineering Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Department of Biochemistry, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Zainab N Khan
- Laboratory for Nanomedicine, Bioengineering Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Hepi H Susapto
- Laboratory for Nanomedicine, Bioengineering Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Yanyan Li
- Cell Migration and Signaling Laboratory, Bioscience Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yara Marghani
- Laboratory for Nanomedicine, Bioengineering Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Arwa A Alghuneim
- Cell Migration and Signaling Laboratory, Bioscience Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Rubén Díaz-Rúa
- Core Laboratories, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sherin Abdelrahman
- Laboratory for Nanomedicine, Bioengineering Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Shuroug Al-Bihani
- Core Laboratories, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Farid Ahmed
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Innovation in Personalized Medicine (CIPM), King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Raed I Felimban
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Innovation in Personalized Medicine (CIPM), King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Heba Alkhatabi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Innovation in Personalized Medicine (CIPM), King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Hematology Research Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Raed Alserihi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Innovation in Personalized Medicine (CIPM), King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Malak Abedalthagafi
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Atlanta, USA
| | - AlShaibani AlFadel
- Division of Hematology, Stem Cell Transplantation & Cellular Therapy, Oncology Center, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Abdalla Awidi
- Cell Therapy Center, The University of Jordan, Amman, Jordan
- Medical School, The University of Jordan, Amman, Jordan
- Jordan University Hospital, Amman, Jordan
| | - Adeel Gulzar Chaudhary
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Innovation in Personalized Medicine (CIPM), King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Jasmeen Merzaban
- Cell Migration and Signaling Laboratory, Bioscience Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Charlotte A E Hauser
- Laboratory for Nanomedicine, Bioengineering Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- KAUST Smart Health Initiative (KSHI), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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Sato Y, Yoshino H, Ishikawa J, Monzen S, Yamaguchi M, Kashiwakura I. Prediction of hub genes and key pathways associated with the radiation response of human hematopoietic stem/progenitor cells using integrated bioinformatics methods. Sci Rep 2023; 13:10762. [PMID: 37402866 DOI: 10.1038/s41598-023-37981-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/30/2023] [Indexed: 07/06/2023] Open
Abstract
Hematopoietic stem cells (HSCs) are indispensable for the maintenance of the entire blood program through cytokine response. However, HSCs have high radiosensitivity, which is often a problem during radiation therapy and nuclear accidents. Although our previous study has reported that the combination cytokine treatment (interleukin-3, stem cell factor, and thrombopoietin) improves the survival of human hematopoietic stem/progenitor cells (HSPCs) after radiation, the mechanism by which cytokines contribute to the survival of HSPCs is largely unclear. To address this issue, the present study characterized the effect of cytokines on the radiation-induced gene expression profile of human CD34+ HSPCs and explored the hub genes that play key pathways associated with the radiation response using a cDNA microarray, a protein-protein interaction-MCODE module analysis and Cytohubba plugin tool in Cytoscape. This study identified 2,733 differentially expressed genes (DEGs) and five hub genes (TOP2A, EZH2, HSPA8, GART, HDAC1) in response to radiation in only the presence of cytokines. Furthermore, functional enrichment analysis found that hub genes and top DEGs based on fold change were enriched in the chromosome organization and organelle organization. The present findings may help predict the radiation response and improve our understanding of this response of human HSPCs.
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Affiliation(s)
- Yoshiaki Sato
- Department of Radiation Science, Hirosaki University Graduate School of Health Sciences, Hirosaki, Aomori, 036-8564, Japan
| | - Hironori Yoshino
- Department of Radiation Science, Hirosaki University Graduate School of Health Sciences, Hirosaki, Aomori, 036-8564, Japan
| | - Junya Ishikawa
- Department of Medical Radiologic Technology, Faculty of Health Sciences, Kyorin University, Mitaka, Tokyo, 181-8612, Japan
| | - Satoru Monzen
- Department of Radiation Science, Hirosaki University Graduate School of Health Sciences, Hirosaki, Aomori, 036-8564, Japan
| | - Masaru Yamaguchi
- Department of Radiation Science, Hirosaki University Graduate School of Health Sciences, Hirosaki, Aomori, 036-8564, Japan
| | - Ikuo Kashiwakura
- Department of Radiation Science, Hirosaki University Graduate School of Health Sciences, Hirosaki, Aomori, 036-8564, Japan.
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8
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Xu Y, Wang S, Xu B, Lin H, Zhan N, Ren J, Song W, Han R, Cheng L, Zhang M, Zhang X. AURKA, TOP2A and MELK are the key genes identified by WGCNA for the pathogenesis of lung adenocarcinoma. Oncol Lett 2023; 25:238. [PMID: 37153047 PMCID: PMC10161350 DOI: 10.3892/ol.2023.13824] [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: 09/22/2022] [Accepted: 02/23/2023] [Indexed: 05/09/2023] Open
Abstract
The comprehensive analysis of single or multiple microarray datasets is currently available in Gene Expression Omnibus (GEO) databases, with several studies having identified genes strongly associated with the development of lung adenocarcinoma (LUAD). However, the mechanisms of LUAD development remain largely unknown and has not yet been systematically studied; thus, further studies are required in this field. In the present study, weighted gene co-expression network analysis (WGCNA) was used for the evaluation of key genes with potential high risk of LUAD, and to provide more reliable evidence concerning its pathogenesis. The GSE140797 dataset from the high-throughput GEO database was downloaded and was first analyzed using the Limma package in the R language in order to determine the differentially expressed genes. The dataset was then analyzed using the WGCNA package to analyze the co-expressed genes, and the modular genes with the highest correlation with the clinical phenotype were identified. Subsequently, the pathogenic genes shared in common between the result of the two analyses were imported into the STRING database for protein-protein interaction network analysis. The hub genes were screened out using Cytoscape, and then The Cancer Genome Atlas analysis, receiver operating characteristic analysis and survival analysis were subsequently performed. Finally, the key genes were evaluated using reverse transcription-quantitative PCR and western blot analysis. Bioinformatics analysis of the GSE140797 dataset revealed eight key genes: AURKA, BUB1, CCNB1, CDK1, MELK, NUSAP1, TOP2A and PBK. Finally, the AURKA, TOP2A and MELK genes were evaluated in samples from patients with lung cancer using WGCNA and RT-qPCR, western blot analysis experiments, providing basis for further research on the mechanisms of LUAD development and targeted therapy.
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Affiliation(s)
- Yunqing Xu
- Department of Oncology, People's Hospital of Huangpi District, Wuhan, Hubei 430000, P.R. China
| | - Sen Wang
- Department of Forensic Medicine, Guangxi Medical University, Nanning, Guanxi 530021, P.R. China
- School of Basic Medicine Sciences, Guangxi Medical University, Nanning, Guanxi 530021, P.R. China
| | - Bin Xu
- Department of Oncology, People's Hospital of Huangpi District, Wuhan, Hubei 430000, P.R. China
| | - Huiqing Lin
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Na Zhan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Jiacai Ren
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Wenling Song
- Department of Oncology, People's Hospital of Huangpi District, Wuhan, Hubei 430000, P.R. China
| | - Rong Han
- Department of Oncology, People's Hospital of Huangpi District, Wuhan, Hubei 430000, P.R. China
| | - Liping Cheng
- Department of Oncology, People's Hospital of Huangpi District, Wuhan, Hubei 430000, P.R. China
| | - Man Zhang
- Department of Oncology, People's Hospital of Huangpi District, Wuhan, Hubei 430000, P.R. China
| | - Xiuyun Zhang
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
- Correspondence to: Dr Xiuyun Zhang, Department of Pathology, Renmin Hospital of Wuhan University, 238 Jiefang Road, 99 Zhangzhidong Road, Wuchang, Wuhan, Hubei 430060, P.R. China, E-mail:
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