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Xu Y, Wang Y, Zhang D, Zhang H, Wang Y, Wang W, Hu X. An autophagy-associated diagnostic signature based on peripheral blood for antibody-mediated rejection in renal transplantation. Transpl Immunol 2024; 84:102021. [PMID: 38452984 DOI: 10.1016/j.trim.2024.102021] [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: 10/04/2023] [Revised: 03/03/2024] [Accepted: 03/03/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Antibody-mediated rejection (ABMR) emerged as a major cause of graft loss in renal transplantation. Needle biopsy is the gold standard for diagnosis of ABMR in renal allografts. Thus, noninvasive diagnosis methods of ABMR with high accuracy are urgently needed to prevent unnecessary biopsies. METHODS We collected peripheral blood transcriptome data from two independent renal transplantation cohorts with patients with ABMR, stable well-functioning transplants (STA), and T-cell mediated rejection (TCMR). Differentially expressed genes (DEGs) were identified by comparing the ABMR group with the STA group. In addition, functional enrichment analysis and gene set enrichment analysis were performed to seek new key underlying mechanisms in ABMR. Subsequently, we utilized a Boruta algorithm and least absolute shrinkage and selection operator logistic algorithm to establish a diagnostic model which was then evaluated and validated in an independent cohort. RESULTS According to functional enrichment analysis, autophagy was found to be the primary upregulated biological process in ABMR. Based on algorithms, three autophagy-associated genes, ubiquitin specific peptidase 33 (USP33), Ras homolog mTORC1 binding (RHEB), and ABL proto-oncogene 2 (ABL2), were selected to establish the diagnostic model in the training cohort. This autophagy-related gene model possessed good diagnostic value in distinguishing ABMR from STA blood samples in the training cohort (AUC = 0.907) and in the validation cohort (AUC = 0.972). In addition, this model also showed good discernibility in distinguishing ABMR from TCMR in the training and validation cohorts (AUCs = 0.908 and 0.833). CONCLUSION We identified and validated an autophagy-associated diagnostic model with high accuracy for renal transplant patients with ABMR. Our study provided a new potential test for the non-invasive diagnosis of ABMR in clinical practice and highlighted the importance of autophagy in ABMR.
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Affiliation(s)
- Yue Xu
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; Institute of Urology, Capital Medical University, Beijing 100020, China
| | - Yuxuan Wang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; Institute of Urology, Capital Medical University, Beijing 100020, China
| | - Di Zhang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; Institute of Urology, Capital Medical University, Beijing 100020, China
| | - Hao Zhang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; Institute of Urology, Capital Medical University, Beijing 100020, China
| | - Yicun Wang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; Institute of Urology, Capital Medical University, Beijing 100020, China
| | - Wei Wang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; Institute of Urology, Capital Medical University, Beijing 100020, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; Institute of Urology, Capital Medical University, Beijing 100020, China.
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Hayashi Y, Kimura S, Yano E, Yoshimoto S, Saeki A, Yasukochi A, Hatakeyama Y, Moriyama M, Nakamura S, Jimi E, Kawakubo-Yasukochi T. Id4 modulates salivary gland homeostasis and its expression is downregulated in IgG4-related disease via miR-486-5p. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119404. [PMID: 36535369 DOI: 10.1016/j.bbamcr.2022.119404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/09/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022]
Abstract
Salivary glands are physiologically orchestrated by the coordinated balance between cell differentiation, proliferation, apoptosis, and interactions between epithelial, mesenchymal endothelial, and neuronal cells, and they are frequent sites of manifestations of Sjögren's syndrome (SS) or IgG4-related disease (IgG4-RD). However, little is known about salivary gland homeostasis and its involvement in those diseases. Inhibitor of DNA binding/differentiation 4 (Id4) is an Id protein involved in the transcriptional control of many biological events, including differentiation. Studies of Id4-deficient mice revealed that Id4-deficient submandibular glands were smaller and exhibited accelerated differentiation, compared with those from wild-type littermates. In addition, dry mouth symptoms and Th17 expansion in splenocytes were also observed in the absence of Id4. Furthermore, Id4 levels in the salivary glands of patients with IgG4-RD, but not SS, were significantly decreased compared with those of healthy controls. miRNA-mRNA integrated analysis demonstrated that miR-486-5p was upregulated in IgG4-RD patients and that it might regulate Id4 in the lesion sites. Together, these results provide evidence for the inhibitory role of Id4 in salivary differentiation, and a critical association between Id4 downregulation and IgG4-RD.
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Affiliation(s)
- Yoshikazu Hayashi
- OBT Research Center, Faculty of Dental Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; Division of Functional Structure, Department of Morphological Biology, Fukuoka Dental College, 2-15-1 Tamura, Sawara-ku, Fukuoka 814-0193, Japan
| | - Soi Kimura
- OBT Research Center, Faculty of Dental Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ena Yano
- OBT Research Center, Faculty of Dental Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shohei Yoshimoto
- Section of Pathology, Department of Morphological Biology, Division of Biomedical Sciences, Fukuoka Dental College, Fukuoka 814-0193, Japan; Oral Medicine Research Center, Fukuoka Dental College, Fukuoka 814-0193, Japan
| | - Ayaka Saeki
- OBT Research Center, Faculty of Dental Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Atsushi Yasukochi
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuji Hatakeyama
- Division of Functional Structure, Department of Morphological Biology, Fukuoka Dental College, 2-15-1 Tamura, Sawara-ku, Fukuoka 814-0193, Japan
| | - Masafumi Moriyama
- OBT Research Center, Faculty of Dental Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Seiji Nakamura
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Eijiro Jimi
- OBT Research Center, Faculty of Dental Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tomoyo Kawakubo-Yasukochi
- OBT Research Center, Faculty of Dental Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Taheri M, Jamali E. The emerging role non-coding RNAs in B cell-related disorders. Cancer Cell Int 2022; 22:91. [PMID: 35193592 PMCID: PMC8862212 DOI: 10.1186/s12935-022-02521-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/10/2022] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs and microRNAs have recently attained much attention regarding their role in the development of B cell lineage as well as participation in the lymphomagenesis. These transcripts have a highly cell type specific signature which endows them the potential to be used as biomarkers for clinical situations. Aberrant expression of several non-coding RNAs has been linked with B cell malignancies and immune related disorders such as rheumatoid arthritis, systemic lupus erythematous, asthma and graft-versus-host disease. Moreover, these transcripts can alter response of immune system to infectious conditions. miR-7, miR-16-1, miR-15a, miR-150, miR-146a, miR-155, miR-212 and miR-132 are among microRNAs whose role in the development of B cell-associated disorders has been investigated. Similarly, SNHG14, MALAT1, CRNDE, AL133346.1, NEAT1, SMAD5-AS1, OR3A4 and some other long non-coding RNAs participate in this process. In the current review, we describe the role of non-coding RNAs in B cell malignancies.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Erbil, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran. .,Institute of Human Genetics, Jena University Hospital, Jena, Germany.
| | - Elena Jamali
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Wu J, Zhang F, Zhang J, Sun Z, Wang W. Advances of miRNAs in kidney graft injury. Transplant Rev (Orlando) 2020; 35:100591. [PMID: 33309915 DOI: 10.1016/j.trre.2020.100591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/14/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022]
Abstract
Kidney transplantation is the preferred treatment for patients with end-stage renal disease. However, various types of kidney graft injury after transplantation are still key factors that affect the survival of the kidney graft. Therefore, exploring the underlying mechanisms involved is very important. Current diagnostic measures for kidney graft injury (including needle biopsy, blood creatinine, eGFR, etc.) have many limiting factors such as invasiveness, insufficient sensitivity and specificity, so they cannot provide timely and effective information to clinicians. As for kidney grafts that have occurred injury, the traditional treatment has a little efficacy and many side effects. Therefore, there is an urgent need for developing new biomarkers and targeted treatment for kidney graft injury. Recently, studies have found that miRNAs are involved in the regulation of the progression of kidney graft injury. At the same time, it has high stability in blood, urine, and other body fluids, so it is suggested to have the potential as a biomarker and therapeutic target for kidney graft injury. Here, we reviewed the miRNAs involved in the pathophysiology of kidney graft injury such as ischemia/reperfusion injury, acute rejection, drug-induced nephrotoxicity, chronic allograft dysfunction, BK virus infection, and the latest advances of miRNAs as biomarkers and therapeutic targets of kidney graft injury, then summarized the specific data of miRNAs expression level in kidney graft injury, which aims to provide a reference for subsequent basic research and clinical transformation.
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Affiliation(s)
- Jiyue Wu
- Institute of Urology, Beijing Chaoyang Hospital, Capital Medical Unversity, China
| | - Feilong Zhang
- Institute of Urology, Beijing Chaoyang Hospital, Capital Medical Unversity, China
| | - Jiandong Zhang
- Institute of Urology, Beijing Chaoyang Hospital, Capital Medical Unversity, China
| | - Zejia Sun
- Institute of Urology, Beijing Chaoyang Hospital, Capital Medical Unversity, China
| | - Wei Wang
- Institute of Urology, Beijing Chaoyang Hospital, Capital Medical Unversity, China.
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Transcriptomic analysis of the mechanisms of alleviating renal interstitial fibrosis using the traditional Chinese medicine Kangxianling in a rat model. Sci Rep 2020; 10:10682. [PMID: 32606425 PMCID: PMC7327068 DOI: 10.1038/s41598-020-67690-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/10/2020] [Indexed: 12/16/2022] Open
Abstract
Renal interstitial fibrosis (RIF) is currently recognized as a crucial mechanism of the pathogenesis of chronic kidney disease (CKD). Kangxianling (KXL, anti-fibrin) is a traditional Chinese medicine that has been proven to significantly reduce the levels of ECM deposition and inhibit renal fibrosis.
To characterize the mechanisms and drug targets of KXL, we established a RIF rat model and treated the rats with KXL and losartan. Histological analyses validated the establishment of the RIF model and the treatment effect of KXL. Multiple levels of transcriptomic datasets were generated using lncRNA, mRNA and microRNA sequencing of kidney tissues. Functional annotations and pathway analyses were performed to unravel the therapeutic mechanisms.
A multi-level transcriptomic regulatory network was built to illustrate the core factors in fibrosis pathogenesis and therapeutic regulation. KXL and losartan significantly reduced the progression of RIF, and a better therapeutic effect was shown with higher concentrations of KXL. According to the cluster analysis results of the RNA-seq data, the normal control (NC) and high concentration of KXL (HK) treatment groups were the closest in terms of differentially expressed genes. The WNT, TGF-β and MAPK pathways were enriched and dominated the pathogenesis and therapy of RIF. miR-15b, miR-21, and miR-6216 were upregulated and miR-107 was downregulated in the fibrosis model. These small RNAs were shown to play critical roles in the regulation of the above fibrosis-related genes and could be inhibited by KXL treatment. Finally, based on the lncRNA datasets, we constructed a mRNA-lncRNA-miRNA coexpression ceRNA network, which identified key regulatory factors in the pathogenesis of kidney fibrosis and therapeutic mechanisms of KXL. Our work revealed the potential mechanism of the Chinese medicine Kangxianling in inhibiting renal interstitial fibrosis and supported the clinical use of KXL in the treatment of kidney fibrosis.
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