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Bax C, Aghdasi C, Fiorentino D. Novel therapeutic targets in dermatomyositis. J Dermatol 2024; 51:920-926. [PMID: 38433369 DOI: 10.1111/1346-8138.17170] [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: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 03/05/2024]
Abstract
Dermatomyositis (DM) is a systemic autoimmune disease with variable clinical presentations, including inflammation in the skin, muscle, lungs, and/or joints. Current therapeutic strategies in DM typically include broad immunosuppression; however, the currently used modalities are not universally effective and are associated with various side effects, including risk of infection. There is currently a highly unmet need for more effective and well-tolerated therapies. Recent years have witnessed increased interest in pharmaceutical development of new therapeutic strategies for DM. This review aims to summarize the landscape of therapies that are currently being tested or planned in patients with DM. These therapies have a wide variety of immunological targets, including T cells, B cells, inflammatory signaling pathways, type I interferons, autoantibodies, and other targets.
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Affiliation(s)
- Christina Bax
- Department of Dermatology, Stanford University School of Medicine, Redwood City, California, USA
| | - Carmel Aghdasi
- Department of Dermatology, Stanford University School of Medicine, Redwood City, California, USA
| | - David Fiorentino
- Department of Dermatology, Stanford University School of Medicine, Redwood City, California, USA
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2
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Talotta R. Sequence Alignment between TRIM33 Gene and Human Noncoding RNAs: A Potential Explanation for Paraneoplastic Dermatomyositis. J Pers Med 2024; 14:628. [PMID: 38929849 PMCID: PMC11204533 DOI: 10.3390/jpm14060628] [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: 05/25/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND This computational analysis investigated sequence complementarities between the TRIM33 gene and human noncoding (nc)RNAs and characterized their interactions in the context of paraneoplastic dermatomyositis. METHODS TRIM33 FASTA sequence (NCBI Reference Sequence: NC_000001.11) was used for BLASTN analysis against Human GRCh38 in the Ensembl.org database. Retrieved ncRNAs showing hits to TRIM33 were searched in the GeneCards.org database and further analyzed through RNAInter, QmRLFS-finder, Spliceator, and NcPath enrichment analysis. RESULTS A total of 100 hits were found, involving the lncRNAs NNT-AS1, MKLN1-AS, LINC01206, and PAXBP1-AS1, whose dysregulation has been reported in either cancer or dermatomyositis. Additionally, the lncRNAs NNT-AS1 and PAXBP1-AS1 may interact with microRNA-142-3p, reducing its expression and increasing that of TRIM33. Sequence complementarity affected only TRIM33 intron 1, possibly resulting in alternatively spliced isoforms of TIF1γ with increased immunogenicity. The results also revealed nucleotide alignment between TRIM33 and the gene regulatory elements of 28 ncRNA genes involved in immune pathways. CONCLUSIONS This pivotal study demonstrates sequence complementarity between TRIM33 and human ncRNAs dysregulated in cancer and dermatomyositis. This scenario may lead to the overproduction of more immunogenic TIF1γ variants in tumors and the stimulation of autoimmunity. Further experimental analyses using targeted methods such as Western blot or Chip-Seq are required to confirm these data.
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Affiliation(s)
- Rossella Talotta
- Rheumatology Unit, Department of Clinical and Experimental Medicine, University Hospital "Gaetano Martino", 98124 Messina, Italy
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Feng W, Ma XN, Wu Q, Zhong XQ, Chen SL, Lin CS, Xu Q. Serum 25-hydroxyvitamin D levels and dermatomyositis: A 2-sample mendelian randomization study. Int J Rheum Dis 2024; 27:e15204. [PMID: 38831528 DOI: 10.1111/1756-185x.15204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/15/2024] [Accepted: 05/13/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Previous studies have reported low serum 25-hydroxyvitamin D [25(OH)D] levels in dermatomyositis (DM) patients, but the exact causal relationship between them remains elusive. Our aim is to confirm the causal relationship between 25(OH)D and DM risk through a Mendelian randomization study. METHODS Retrieve genome-wide association study (GWAS) data on 25(OH)D (n = 441 291) and DM (n cases = 201, n controls = 172 834) from the GWAS database (https://gwas.mrcieu.ac.uk/). Select single-nucleotide polymorphisms (SNPs) strongly correlated with 25(OH)D as instrumental variables (IVs). The primary analytical approach involves the use of the inverse-variance weighted method (IVW), supplemented by MR-Egger regression and weighted median methods to enhance the reliability of the results. Heterogeneity and sensitivity analyses were conducted using Cochran's Q and leave-one-out approaches, respectively. RESULTS The IVW analysis confirmed a positive causal relationship between genetic variation in 25(OH)D levels and DM (OR = 2.36, 95% CI = 1.01-5.52, p = .048). Although not statistically significant (all p > .05), the other methods also suggested a protective effect of 25(OH)D on DM. Based on MR-Egger intercepts and Cochran's Q analysis, the selected SNPs showed no horizontal pleiotropy and heterogeneity. Sensitivity analysis demonstrated the robustness of the results against individual SNPs. CONCLUSION We provide the first evidence of a causal relationship between 25(OH)D levels and DM. Our findings support the importance of measuring serum 25(OH)D levels and considering vitamin D supplementation in clinical practice for patients with DM.
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Affiliation(s)
- Wei Feng
- State Key Laboratory of Traditional Chinese Medicine Syndrome, The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiao-Na Ma
- State Key Laboratory of Traditional Chinese Medicine Syndrome, The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qi Wu
- State Key Laboratory of Traditional Chinese Medicine Syndrome, The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiao-Qin Zhong
- State Key Laboratory of Traditional Chinese Medicine Syndrome, The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shu-Lin Chen
- State Key Laboratory of Traditional Chinese Medicine Syndrome, The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chang-Song Lin
- State Key Laboratory of Traditional Chinese Medicine Syndrome, The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou, China
- Department of Rheumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiang Xu
- State Key Laboratory of Traditional Chinese Medicine Syndrome, The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou, China
- Department of Rheumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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Cai W, Chen M. Envoplakin Inhibits Macrophage Polarization by Altering the Inflammatory Tumor Microenvironment of Melanoma Through the RAS / ERK Signaling Pathway. J Inflamm Res 2024; 17:1687-1706. [PMID: 38504693 PMCID: PMC10950027 DOI: 10.2147/jir.s447934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/29/2024] [Indexed: 03/21/2024] Open
Abstract
Purpose Tumor growth induces the tumor margin to become a transition zone rich in immune cells. EVPL is a potential prognostic biomarker for melanoma. Melanoma is difficult to cure because of its high metastasis, so it is urgent to find effective genes to inhibit tumor progression and regulate tumor microenvironment. Methods Firstly, differentially expressed genes (DEGs) among normal skin, nevus and melanoma samples in GSE3189 were screened. Bioinformatics was used to further explore the hub genes and enriched pathways closely related to the inflammatory response of DEGs in melanoma. We selected EVPL, which is associated with the Ras/Raf signaling pathway, for in vitro study. CCK-8, colony formation, wound healing, Transwell and flow cytometry assays were respectively used to evaluate the proliferation, migration, invasion, and apoptosis of cancer cells. Enzyme-linked immunosorbent assay was conducted for the monitoring of changes in the tumor microenvironment. To evaluate the effect of EVPL on macrophage recruitment, we established a co-culture system in a Transwell chamber. The polarization of macrophages was examined after treatment of cells with RAS/ERK signaling inhibitors SCH772984 and sh-EVPL. Additionally, changes in the expression of pathway proteins were measured by Western blot. Results Among the screened hub genes, EVPL was associated with the Ras/Raf pathway, a key signaling pathway in melanoma, and may be involved in regulating the inflammatory microenvironment of melanoma. Oe-EVPL was proved to suppress melanoma cell malignant progression. By inhibiting EVPL expression, the inhibitory effects on melanoma progression induced by the addition of SCH772984 were reversed. Furthermore, EVPL was found to inhibit the expression of chemokines, the recruitment of macrophages, and the polarization of macrophages through the Ras/Raf/ERK signaling pathway. Conclusion EVPL can inhibit the progression of melanoma through the RAS/ERK signaling pathway, change the inflammatory tumor microenvironment of melanoma, and inhibit the recruitment of macrophages.
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Affiliation(s)
- Weilin Cai
- Medical School of Chinese PLA, Beijing, People’s Republic of China
- Senior Department of Burns and Plastic Surgery, the Fourth Medical Center of PLA General Hospital, Beijing, People’s Republic of China
| | - Minliang Chen
- Senior Department of Burns and Plastic Surgery, the Fourth Medical Center of PLA General Hospital, Beijing, People’s Republic of China
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Rutkowska-Zapała M, Grabowska-Gurgul A, Lenart M, Szaflarska A, Kluczewska A, Mach-Tomalska M, Baj-Krzyworzeka M, Siedlar M. Gene Signature of Regulatory T Cells Isolated from Children with Selective IgA Deficiency and Common Variable Immunodeficiency. Cells 2024; 13:417. [PMID: 38474381 DOI: 10.3390/cells13050417] [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: 12/29/2023] [Revised: 02/09/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Selective IgA deficiency (SIgAD) is the most common form and common variable immunodeficiency (CVID) is the most symptomatic form of predominant antibody deficiency. Despite differences in the clinical picture, a similar genetic background is suggested. A common feature of both disorders is the occurrence of autoimmune conditions. Regulatory T cells (Tregs) are the major immune cell type that maintains autoimmune tolerance. As the different types of abnormalities of Treg cells have been associated with autoimmune disorders in primary immunodeficiency (PID) patients, in our study we aimed to analyze the gene expression profiles of Treg cells in CVID and SIgAD patients compared to age-matched healthy controls. The transcriptome-wide gene profiling was performed by microarray technology. As a result, we analyzed and visualized gene expression patterns of isolated population of Treg cells. We showed the differences at the gene level between patients with and without autoimmunizations. Our findings suggest that the gene signatures of Treg cells isolated from SIgAD and CVID patients differ from age-matched healthy controls and from each other, presenting transcriptional profiles enriched in innate immune or Th response, respectively. The occurrence of autoimmunity in both types of PID is associated with down-regulation of class I IFNs signaling pathways. In summary, our findings improve our understanding of Treg dysfunctions in patients with common PIDs and associated autoimmunity.
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Affiliation(s)
- Magdalena Rutkowska-Zapała
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Agnieszka Grabowska-Gurgul
- Department of Medical Genetics, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Marzena Lenart
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Anna Szaflarska
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Anna Kluczewska
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Monika Mach-Tomalska
- Department of Clinical Immunology, University Children's Hospital, Wielicka 265, 30-663 Krakow, Poland
| | - Monika Baj-Krzyworzeka
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Maciej Siedlar
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
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Pettorossi F, Gasparotto M, Ghirardello A, Franco C, Ceolotto G, Giannella A, Iaccarino L, Zanatta E, Doria A, Gatto M. MicroRNAs in idiopathic inflammatory myopathies: state-of-the-art and future perspectives. Curr Opin Rheumatol 2023; 35:374-382. [PMID: 37582051 DOI: 10.1097/bor.0000000000000960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
PURPOSE OF REVIEW Idiopathic inflammatory myopathies (IIMs) are a group of rare autoimmune disorders characterized by muscle weakness and inflammation. MicroRNAs (miRNAs) are the main class of small noncoding RNAs regulating a wide range of physiological and pathological processes and play a role in mediating autoimmunity and inflammation. In this review, we summarize the latest knowledge on the role of miRNAs in systemic autoimmune diseases with particular focus on IIMs. RECENT FINDINGS Study on miRNA expression in IIMs is helping in understanding the pathogenetic basis of the disease at a tissue and systemic level. Several miRNAs, even with a muscle-specific expression (myomiRs), have been shown to be involved in immune and nonimmune mechanisms of myofiber damage. MiRNAs modulate and orchestrate the local inflammatory infiltrate and could be used as potential biomarkers as they correlate with disease activity and response to therapy. SUMMARY IIMs comprise different clinical phenotypes and still little is known about the molecular signature of each subset. Further research about miRNA profiling will provide additional insights in the disease characterization with an expected impact on the therapeutic strategies.
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Affiliation(s)
- Federico Pettorossi
- Division of Rheumatology, Department of Medicine, University of Padua, Padua
| | - Michela Gasparotto
- Division of Rheumatology, Department of Medicine, University of Padua, Padua
- Department of Medical Surgical and Health Sciences, University of Trieste, Cattinara Teaching Hospital, Trieste
| | - Anna Ghirardello
- Division of Rheumatology, Department of Medicine, University of Padua, Padua
| | - Chiara Franco
- Division of Rheumatology, Department of Medicine, University of Padua, Padua
| | | | - Alessandra Giannella
- Division of Thrombotic and Hemorrhagic Diseases, Department of Medicine, University of Padua, Padua
| | - Luca Iaccarino
- Division of Rheumatology, Department of Medicine, University of Padua, Padua
| | - Elisabetta Zanatta
- Division of Rheumatology, Department of Medicine, University of Padua, Padua
| | - Andrea Doria
- Division of Rheumatology, Department of Medicine, University of Padua, Padua
| | - Mariele Gatto
- Division of Rheumatology, Department of Medicine, University of Padua, Padua
- Unit of Rheumatology, Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
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Zhang Z, Pang J, Li Y, Zuo Y, Cui X, Xu H. Imbalance of peripheral blood Th17/Treg increases neutrophil-to-lymphocyte ratio in patients with dermatomyositis. Am J Transl Res 2023; 15:6106-6114. [PMID: 37969179 PMCID: PMC10641349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 09/06/2023] [Indexed: 11/17/2023]
Abstract
OBJECTIVE To explore and analyze the association between peripheral blood Th17/Treg balance and neutrophil-to-lymphocyte ratio (NLR) in patients with dermatomyositis (DM). METHODS Data of 83 DM patients hospitalized between January 2020 to April 2022 were collected, including 43 patients in the active phase (DM active-phase group) and 40 in the remission phase (DM remission-phase group). Additionally, data of 50 healthy subjects who underwent physical examinations and immunologic function testing in the same period were taken as a control group. We detected the percentage of Th17 and Treg cells by flow cytometry, calculated patient's NLR and laboratory test indicators, and analyzed the correlation of Th17/Treg balance with NLR and laboratory indicators. RESULTS Th17 percentage and Th7/Treg ratio in the DM active-phase group were higher than those in the DM remission-phase group (P<0.05), while Treg percentage was lower in the active-phase group than in the remission-phase group (P<0.05). The creatine kinase (CK), lactate dehydrogenase (LDH), aspartate aminotransferase (AST), alanine aminotransferase (ALT), erythrocyte deposition rate (ESR), and NLR in DM patients were significantly higher than those of the control group (P<0.05), and were associated with the disease activity of DM. The ratio of Th17/Treg was positively correlated with CK, LDH, AST, ALT, ESR, and NLR (P<0.05). NLR was positively correlated with CK, LDH, AST, ALT, and ESR (P<0.05). CONCLUSION DM patients exhibit changes in immune balance of Th17/Treg and an increase in the NLR. The Th17/Treg ratio in the patients is closely associated with the NLR, which suggests that the immune balance mechanism may interact with the inflammatory response of the body, collectively contributing to the progression of DM.
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Affiliation(s)
- Zongfang Zhang
- Department of Rheumatology, Cangzhou Central Hospital Cangzhou 061000, Hebei, China
| | - Jie Pang
- Department of Rheumatology, Cangzhou Central Hospital Cangzhou 061000, Hebei, China
| | - Yanxia Li
- Department of Rheumatology, Cangzhou Central Hospital Cangzhou 061000, Hebei, China
| | - Yanhua Zuo
- Department of Rheumatology, Cangzhou Central Hospital Cangzhou 061000, Hebei, China
| | - Xin Cui
- Department of Rheumatology, Cangzhou Central Hospital Cangzhou 061000, Hebei, China
| | - Huaheng Xu
- Department of Rheumatology, Cangzhou Central Hospital Cangzhou 061000, Hebei, China
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8
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Yang Y, GuangXuan H, GenMeng W, MengHuan L, Bo C, XueJie Y. Idiopathic inflammatory myopathy and non-coding RNA. Front Immunol 2023; 14:1227945. [PMID: 37744337 PMCID: PMC10512060 DOI: 10.3389/fimmu.2023.1227945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/11/2023] [Indexed: 09/26/2023] Open
Abstract
Idiopathic inflammatory myopathies (IIMs) are common autoimmune diseases that affect skeletal muscle quality and function. The lack of an early diagnosis and treatment can lead to irreversible muscle damage. Non-coding RNAs (ncRNAs) play an important role in inflammatory transfer, muscle regeneration, differentiation, and regulation of specific antibody levels and pain in IIMs. ncRNAs can be detected in blood and hair; therefore, ncRNAs detection has great potential for diagnosing, preventing, and treating IIMs in conjunction with other methods. However, the specific roles and mechanisms underlying the regulation of IIMs and their subtypes remain unclear. Here, we review the mechanisms by which micro RNAs and long non-coding RNA-messenger RNA networks regulate IIMs to provide a basis for ncRNAs use as diagnostic tools and therapeutic targets for IIMs.
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Affiliation(s)
- Yang Yang
- School of Kinesiology, Shanghai University of Sport, Shanghai, China
| | - Hu GuangXuan
- School of Physical Education, Liaoning Normal University, Dalian, Liaoning, China
| | - Wan GenMeng
- College of Exercise and Health, Shenyang Sport University, Shenyang, China
| | - Li MengHuan
- College of Exercise and Health, Shenyang Sport University, Shenyang, China
| | - Chang Bo
- College of Exercise and Health, Shenyang Sport University, Shenyang, China
| | - Yi XueJie
- Social Science Research Center, Shenyang Sport University, Shenyang, Liaoning, China
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Pan Y, Wang Y, Hu M, Xu S, Jiang F, Han Y, Chen F, Liu Z. Aggrephagy-related patterns in tumor microenvironment, prognosis, and immunotherapy for acute myeloid leukemia: a comprehensive single-cell RNA sequencing analysis. Front Oncol 2023; 13:1195392. [PMID: 37534253 PMCID: PMC10393257 DOI: 10.3389/fonc.2023.1195392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/12/2023] [Indexed: 08/04/2023] Open
Abstract
Acute myeloid leukemia (AML) is a complex mixed entity composed of malignant tumor cells, immune cells and stromal cells, with intra-tumor and inter-tumor heterogeneity. Single-cell RNA sequencing enables a comprehensive study of the highly complex tumor microenvironment, which is conducive to exploring the evolutionary trajectory of tumor cells. Herein, we carried out comprehensive analyses of aggrephagy-related cell clusters based on single-cell sequencing for patients with acute myeloid leukemia. A total of 11 specific cell types (T, NK, CMP, Myeloid, GMP, MEP, Promono, Plasma, HSC, B, and Erythroid cells) using t-SNE dimension reduction analysis. Several aggrephagy-related genes were highly expressed in the 11 specific cell types. Using Monocle analysis and NMF clustering analysis, six aggrephagy-related CD8+ T clusters, six aggrephagy-related NK clusters, and six aggrephagy-related Mac clusters were identified. We also evaluated the ligand-receptor links and Cell-cell communication using CellChat package and CellChatDB database. Furthermore, the transcription factors (TFs) of aggrephagy-mediated cell clusters for AML were assessed through pySCENIC package. Prognostic analysis of the aggrephagy-related cell clusters based on R package revealed the differences in prognosis of aggrephagy-mediated cell clusters. Immunotherapy of the aggrephagy-related cell clusters was investigated using TIDE algorithm and public immunotherapy cohorts. Our study revealed the significance of aggrephagy-related patterns in tumor microenvironment, prognosis, and immunotherapy for AML.
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Affiliation(s)
- Yan Pan
- Department of Blood Transfusion, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People’s Hospital, Quzhou, Zhejiang, China
| | - Yingjian Wang
- Department of Blood Transfusion, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Mengsi Hu
- Department of Blood Transfusion, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shoufang Xu
- Department of Blood Transfusion, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Feiyu Jiang
- Department of Blood Transfusion, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yetao Han
- Department of Blood Transfusion, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Fangjian Chen
- Department of Blood Transfusion, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People’s Hospital, Quzhou, Zhejiang, China
| | - Zhiwei Liu
- Department of Blood Transfusion, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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Huang X, Zhao C, Han Y, Li S. Establishment and validation of a prognostic signature for pancreatic ductal adenocarcinoma based on lactate metabolism-related genes. Front Mol Biosci 2023; 10:1143073. [PMID: 37363401 PMCID: PMC10288859 DOI: 10.3389/fmolb.2023.1143073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive and lethal malignancy with poor prognosis. To improve patient outcomes, it is necessary to gain a better understanding of the oncogenesis and progression of this disease. Metabolic reprogramming, particularly the regulation of lactate metabolism, is known to have a significant impact on tumor microenvironment and could provide valuable insights for the management of PDAC patients. In this study, we aimed to investigate the prognostic potential of lactate metabolism-related genes (LMRGs). Methods: Transcriptomic data of patients with PDAC along with the clinical outcomes were retrieved from The Cancer Genome Atlas database, and the expression data in normal pancreas from Genotype-Tissue Expression dataset were adopted as the normal control. By using Cox and LASSO regression models, we identified key genes that are differentially expressed in cancerous tissues and related to prognosis. To determine the prognostic value of LMRGs in PDAC, we evaluated their clinical significance and model performance using both the area under the receiver operator characteristic curve (AUC) and calibration curves. In addition, we evaluated the drug sensitivity prediction and immune infiltration by using oncoPredict algorithm, single sample gene set enrichment analysis and Tumor Immune Estimation Resource. Results: A total of 123 LMRGs were identified through differential gene screening analysis, among which 7 LMRGs were identified to comprise a LMRGs signature that independently predict overall survival of these PDAC patient. The AUC values for the LMRGs signature were 0.786, 0.820, 0.837, and 0.816 for predicting 1-, 2-, 3- and 5-year overall survival respectively. Furthermore, this prognostic signature was used to stratify patients into high-risk and low-risk groups, with the former having worse clinical outcomes. This observation was further validated through analysis of the International Cancer Genome Consortium database. In addition, lower sensitivity to gemcitabine and infiltration of immune effector cells were observed in the cancer tissue of patients in the high-risk group. Conclusion: In conclusion, our data suggests that a genomic signature comprised of these LMRGs may be a novel predictor of overall clinical outcomes and present therapeutic potential for PDAC patients.
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Affiliation(s)
- Xin Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Pancreatobiliary Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chongyu Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Pancreatobiliary Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yuanxia Han
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Pancreatobiliary Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shengping Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Pancreatobiliary Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
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11
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Li D, Cao R, Dong W, Cheng M, Pan X, Hu Z, Hao J. Identification of potential biomarkers for ankylosing spondylitis based on bioinformatics analysis. BMC Musculoskelet Disord 2023; 24:413. [PMID: 37226132 DOI: 10.1186/s12891-023-06550-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/19/2023] [Indexed: 05/26/2023] Open
Abstract
OBJECTIVE The aim of this study was to search for key genes in ankylosing spondylitis (AS) through comprehensive bioinformatics analysis, thus providing some theoretical support for future diagnosis and treatment of AS and further research. METHODS Gene expression profiles were collected from Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/ ) by searching for the term "ankylosing spondylitis". Ultimately, two microarray datasets (GSE73754 and GSE11886) were downloaded from the GEO database. A bioinformatic approach was used to screen differentially expressed genes and perform functional enrichment analysis to obtain biological functions and signalling pathways associated with the disease. Weighted correlation network analysis (WGCNA) was used to further obtain key genes. Immune infiltration analysis was performed using the CIBERSORT algorithm to conduct a correlation analysis of key genes with immune cells. The GWAS data of AS were analysed to identify the pathogenic regions of key genes in AS. Finally, potential therapeutic agents for AS were predicted using these key genes. RESULTS A total of 7 potential biomarkers were identified: DYSF, BASP1, PYGL, SPI1, C5AR1, ANPEP and SORL1. ROC curves showed good prediction for each gene. T cell, CD4 naïve cell, and neutrophil levels were significantly higher in the disease group than in the paired normal group, and key gene expression was strongly correlated with immune cells. CMap results showed that the expression profiles of ibuprofen, forskolin, bongkrek-acid, and cimaterol showed the most significant negative correlation with the expression profiles of disease perturbations, suggesting that these drugs may play a role in AS treatment. CONCLUSION The potential biomarkers of AS screened in this study are closely related to the level of immune cell infiltration and play an important role in the immune microenvironment. This may provide help in the clinical diagnosis and treatment of AS and provide new ideas for further research.
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Affiliation(s)
- Dongxu Li
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Yuzhong, Chongqing, China
| | - Ruichao Cao
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Yuzhong, Chongqing, China
| | - Wei Dong
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Yuzhong, Chongqing, China
| | - Minghuang Cheng
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Yuzhong, Chongqing, China
| | - Xiaohan Pan
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Yuzhong, Chongqing, China
| | - Zhenming Hu
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Yuzhong, Chongqing, China
| | - Jie Hao
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China.
- Orthopedic Laboratory of Chongqing Medical University, Yuzhong, Chongqing, China.
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Pan H, Pan J, Wu J. Development and validation of a cancer-associated fibroblast-derived lncRNA signature for predicting clinical outcomes in colorectal cancer. Front Immunol 2022; 13:934221. [PMID: 35967425 PMCID: PMC9374325 DOI: 10.3389/fimmu.2022.934221] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/11/2022] [Indexed: 11/22/2022] Open
Abstract
Cancer-associated fibroblasts (CAFs) are actively involved in cancer progression through generating extracellular matrix and orchestrating the crosstalk within the tumor microenvironment (TME). This study aimed to develop and validate a CAF-derived lncRNA (long non-coding RNA) (CAFDL) signature for predicting clinical outcomes in colorectal cancer (CRC). Clinical data and transcriptomic profiles of 2,320 patients with CRC from The Cancer Genome Atlas (TCGA)-COAD and TCGA-READ datasets and 16 Gene Expression Omnibus datasets were included in this study. CAFDLs were identified using weighted gene co-expression network analysis. The CAFDL signature was constructed using the least absolute shrinkage and selection operator analysis in the TCGA-CRC training set. Multiple CRC cohorts and pan-cancer cohorts were used to validated the CAFDL signature. Patients with high CAFDL scores had significantly worse overall survival and disease-free survival than patients with low CAFDL scores in all CRC cohorts. In addition, non-responders to fluorouracil, leucovorin, and oxaliplatin (FOLFOX)/fluorouracil, leucovorin, and irinotecan (FOLFIRI) chemotherapy, chemoradiotherapy, bevacizumab, and immune checkpoint inhibitors had significantly higher CAFDL scores compared with responders. Pan-cancer analysis showed that CAFDL had prognostic predictive power in multiple cancers such as lung adenocarcinoma, breast invasive carcinoma, stomach adenocarcinoma, and thyroid carcinoma. The CAFDL signature was positively correlated with transforming growth factor-beta (TGF-β) signaling, epithelial–mesenchymal transition, and angiogenesis pathways but negatively correlated with the expression of immune checkpoints such as PDCD1, CD274, and CTLA4. The CAFDL signature reflects CAF properties from a lncRNA perspective and effectively predicts clinical outcomes in CRC and across pan-cancer. The CAFDL signature can serve as a useful tool for risk stratification and provide new insights into the underlying mechanisms of CAFs in cancer immunity.
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Affiliation(s)
- Hongda Pan
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- *Correspondence: Hongda Pan, ; Jianghong Wu,
| | - Jingxin Pan
- Department of Hematology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Jianghong Wu
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- *Correspondence: Hongda Pan, ; Jianghong Wu,
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