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Moreno-Corona NC, de León-Bautista MP, León-Juárez M, Hernández-Flores A, Barragán-Gálvez JC, López-Ortega O. Rab GTPases, Active Members in Antigen-Presenting Cells, and T Lymphocytes. Traffic 2024; 25:e12950. [PMID: 38923715 DOI: 10.1111/tra.12950] [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: 01/07/2024] [Revised: 04/25/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Processes such as cell migration, phagocytosis, endocytosis, and exocytosis refer to the intense exchange of information between the internal and external environment in the cells, known as vesicular trafficking. In eukaryotic cells, these essential cellular crosstalks are controlled by Rab GTPases proteins through diverse adaptor proteins like SNAREs complex, coat proteins, phospholipids, kinases, phosphatases, molecular motors, actin, or tubulin cytoskeleton, among others, all necessary for appropriate mobilization of vesicles and distribution of molecules. Considering these molecular events, Rab GTPases are critical components in specific biological processes of immune cells, and many reports refer primarily to macrophages; therefore, in this review, we address specific functions in immune cells, concretely in the mechanism by which the GTPase contributes in dendritic cells (DCs) and, T/B lymphocytes.
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Affiliation(s)
| | - Mercedes Piedad de León-Bautista
- Escuela de Medicina, Universidad Vasco de Quiroga, Morelia, Mexico
- Human Health, Laboratorio de Enfermedades Infecciosas y Genómica (INEX LAB), Morelia, Mexico
| | - Moises León-Juárez
- Laboratorio de Virología Perinatal y Diseño Molecular de Antígenos y Biomarcadores, Departamento de Inmunobioquimica, Instituto Nacional de Perinatología, Ciudad de México, Mexico
| | | | - Juan Carlos Barragán-Gálvez
- División de Ciencias Naturales y Exactas, Departamento de Farmacia, Universidad de Guanajuato, Guanajuato, Mexico
| | - Orestes López-Ortega
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institute Necker Enfants Malades, Paris, France
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2
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Wang Z, Pan F, Zhang G. Expression and prognostic role of sphingosine 1-phosphate receptor 4 (S1PR4) as a biomarker of skin cutaneous melanoma. Heliyon 2024; 10:e27505. [PMID: 38468937 PMCID: PMC10926139 DOI: 10.1016/j.heliyon.2024.e27505] [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: 06/11/2023] [Revised: 12/23/2023] [Accepted: 02/29/2024] [Indexed: 03/13/2024] Open
Abstract
Background Skin cutaneous melanoma (SKCM) is one of the most lethal skin malignancies worldwide. Sphingosine 1-phosphate (S1P) regulates tumor cells through S1P receptors (S1PRs). Unlike S1PR1/2/3/5, whose anti-apoptotic effects have been widely studied, the regulatory effect of S1PR4 on tumors has not been studied extensively. In this study, we aimed to investigate the correlation between S1PR4 expression and survival, clinical manifestations, tumor microenvironment, and immune infiltration in patients with SKCM. Results Low S1PR4 expression was associated with poor prognosis in patients with SKCM. Patients in the high-expression group had significantly longer disease survival and progression-free survival than those in the low-expression group. Conclusion High S1PR4 expression was highly associated with better prognosis and milder clinical manifestations; thus, S1PR4 may be used as a prognostic marker to help physicians monitor patients with SKCM.
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Affiliation(s)
- Zi Wang
- Beijing University of Chinese Medicine, Beijing, China
- Department of Dermatology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Fei Pan
- Beijing University of Chinese Medicine, Beijing, China
- Department of Dermatology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Guangzhong Zhang
- Department of Dermatology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
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3
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Shen J, Ying L, Wu J, Fang Y, Zhou W, Qi C, Gu L, Mou S, Yan Y, Tian M, Ni Z, Che X. Integrative ATAC-seq and RNA-seq analysis associated with diabetic nephropathy and identification of novel targets for treatment by dapagliflozin. Cell Biochem Funct 2024; 42:e3943. [PMID: 38379015 DOI: 10.1002/cbf.3943] [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: 07/22/2023] [Revised: 12/01/2023] [Accepted: 01/12/2024] [Indexed: 02/22/2024]
Abstract
Dapagliflozin (DAPA) are clinically effective in improving diabetic nephropathy (DN). However, whether and how chromatin accessibility changed by DN responds to DAPA treatment is unclear. Therefore, we performed ATAC-seq, RNA-seq, and weighted gene correlation network analysis to identify the chromatin accessibility, the messenger RNA (mRNA) expression, and the correlation between clinical phenotypes and mRNA expression using kidney from three mouse groups: db/m mice (Controls), db/db mice (case group), and those treated with DAPA (treatment group). RNA-Seq and ATAC-seq conjoint analysis revealed many overlapping pathways and networks suggesting that the transcriptional changes of DN and DAPA intervention largely occured dependently on chromatin remodeling. Specifically, the results showed that some key signal transduction pathways, such as immune dysfunction, glucolipid metabolism, oxidative stress and xenobiotic and endobiotic metabolism, were repeatedly enriched in the analysis of the RNA-seq data alone, as well as combined analysis with ATAC-seq data. Furthermore, we identified some candidate genes (UDP glucuronosyltransferase 1 family, Dock2, Tbc1d10c, etc.) and transcriptional regulators (KLF6 and GFI1) that might be associated with DN and DAPA restoration. These reversed genes and regulators confirmed that pathways related to immune response and metabolism pathways were critically involved in DN progression.
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Affiliation(s)
- Jianxiao Shen
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liang Ying
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiajia Wu
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Fang
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenyan Zhou
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaojun Qi
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Leyi Gu
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shan Mou
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuru Yan
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Tian
- Department of Burn, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaohui Ni
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiajing Che
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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4
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Villagomez FR, Lang J, Webb P, Neville M, Woodruff ER, Bitler BG. Claudin-4 modulates autophagy via SLC1A5/LAT1 as a tolerance mechanism for genomic instability in ovarian cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576263. [PMID: 38293054 PMCID: PMC10827183 DOI: 10.1101/2024.01.18.576263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Genome instability is key for tumor heterogeneity and derives from defects in cell division and DNA damage repair. Tumors show tolerance for this characteristic, but its accumulation is regulated somehow to avoid catastrophic chromosomal alterations and cell death. Claudin-4 is upregulated and closely associated with genome instability and worse patient outcome in ovarian cancer. This protein is commonly described as a junctional protein participating in processes such as cell proliferation and DNA repair. However, its biological association with genomic instability is still poorly-understood. Here, we used CRISPRi and a claudin mimic peptide (CMP) to modulate the cladudin-4 expression and its function, respectively in in-vitro (high-grade serous carcinoma cells) and in-vivo (patient-derived xenograft in a humanized-mice model) systems. We found that claudin-4 promotes a protective cellular-mechanism that links cell-cell junctions to genome integrity. Disruption of this axis leads to irregular cellular connections and cell cycle that results in chromosomal alterations, a phenomenon associated with a novel functional link between claudin-4 and SLC1A5/LAT1 in regulating autophagy. Consequently, claudin-4's disruption increased autophagy and associated with engulfment of cytoplasm-localized DNA. Furthermore, the claudin-4/SLC1A5/LAT1 biological axis correlates with decrease ovarian cancer patient survival and targeting claudin-4 in-vivo with CMP resulted in increased niraparib (PARPi) efficacy, correlating with increased tumoral infiltration of T CD8+ lymphocytes. Our results show that the upregulation of claudin-4 enables a mechanism that promotes tolerance to genomic instability and immune evasion in ovarian cancer; thus, suggesting the potential of claudin-4 as a translational target for enhancing ovarian cancer treatment.
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5
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Zhang Y, Jin Y, Wang H, He L, Zhang Y, Liu Q, Xin Y, Li X. Identification of Genes Associated with Decreasing Abundance of Monocytes in Long-Term Peritoneal Dialysis Patients. Int J Gen Med 2023; 16:5017-5030. [PMID: 37942472 PMCID: PMC10629397 DOI: 10.2147/ijgm.s435041] [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: 08/23/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023] Open
Abstract
Purpose Chronic kidney disease (CKD) will become an end-stage renal disease (ESRD) at stage 5. Peritoneal dialysis (PD) is required for renal replacement therapy. This study aims to identify monocytes-related genes in peritoneal cells from long-term PD (LPD) patients and short-term PD (SPD) patients. Methods Bulk RNA-seq data (GSE125498 dataset) and ScRNA-seq data (GSE130888) were downloaded to identify differentially expressed genes, monocytes-related genes, and monocytes marker genes in LPD patients. Immune infiltration was analyzed in the GSE125498 dataset. Core genes associated with monocytes changes were screened out, followed by functional analysis and expression validation using RT-PCR. Results Monocytes are the most abundant immune cell in PD. The number of monocytes was remarkably decreased in LPD compared with SPD. A total of 16 up-regulated core genes negatively correlated with the abundance of monocytes were obtained in LPD. The expression of 16 core genes was lower in monocyte clusters than that in other cell clusters. In addition, LCK, CD3G, CD3E, CD3D, and LAT were involved in the signaling pathways of Th1 and Th2 cell differentiation, T cell receptor signaling pathway, and Th17 cell differentiation. CD2 was involved in hematopoietic cell lineage signaling pathway. Conclusion Identification of monocytes related-genes and related signaling pathways could be helpful in understanding the molecular mechanism of monocytes changes during PD.
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Affiliation(s)
- Yinghui Zhang
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Yanhua Jin
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Huan Wang
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Long He
- Organ Transplant Center, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Yanning Zhang
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Qi Liu
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Yu Xin
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Xueyu Li
- Nursing Department, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
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6
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Gu Y, Lin X, Dong Y, Wood G, Seidah NG, Werstuck G, Major P, Bonert M, Kapoor A, Tang D. PCSK9 facilitates melanoma pathogenesis via a network regulating tumor immunity. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2023; 42:2. [PMID: 36588164 PMCID: PMC9806914 DOI: 10.1186/s13046-022-02584-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/26/2022] [Indexed: 01/03/2023]
Abstract
BACKGROUND PCSK9 regulates cholesterol homeostasis and promotes tumorigenesis. However, the relevance of these two actions and the mechanisms underlying PCSK9's oncogenic roles in melanoma and other cancers remain unclear. METHODS PCSK9's association with melanoma was analysed using the TCGA dataset. Empty vector (EV), PCSK9, gain-of-function (D374Y), and loss-of-function (Q152H) PCSK9 mutant were stably-expressed in murine melanoma B16 cells and studied for impact on B16 cell-derived oncogenesis in vitro and in vivo using syngeneic C57BL/6 and Pcsk9-/- mice. Intratumoral accumulation of cholesterol was determined. RNA-seq was performed on individual tumor types. Differentially-expressed genes (DEGs) were derived from the comparisons of B16 PCSK9, B16 D374Y, or B16 Q152H tumors to B16 EV allografts and analysed for pathway alterations. RESULTS PCSK9 expression and its network negatively correlated with the survival probability of patients with melanoma. PCSK9 promoted B16 cell proliferation, migration, and growth in soft agar in vitro, formation of tumors in C57BL/6 mice in vivo, and accumulation of intratumoral cholesterol in a manner reflecting its regulation of the low-density lipoprotein receptor (LDLR): Q152H, EV, PCSK9, and D374Y. Tumor-associated T cells, CD8 + T cells, and NK cells were significantly increased in D374Y tumors along with upregulations of multiple immune checkpoints, IFNγ, and 143 genes associated with T cell dysfunction. Overlap of 36 genes between the D374Y DEGs and the PCSK9 DEGs predicted poor prognosis of melanoma and resistance to immune checkpoint blockade (ICB) therapy. CYTH4, DENND1C, AOAH, TBC1D10C, EPSTI1, GIMAP7, and FASL (FAS ligand) were novel predictors of ICB therapy and displayed high level of correlations with multiple immune checkpoints in melanoma and across 30 human cancers. We observed FAS ligand being among the most robust biomarkers of ICB treatment and constructed two novel and effective multigene panels predicting response to ICB therapy. The profiles of allografts produced by B16 EV, PCSK9, D374Y, and Q152H remained comparable in C57BL/6 and Pcsk9-/- mice. CONCLUSIONS Tumor-derived PCSK9 plays a critical role in melanoma pathogenesis. PCSK9's oncogenic actions are associated with intratumoral cholesterol accumulation. PCSK9 systemically affects the immune system, contributing to melanoma immune evasion. Novel biomarkers derived from the PCSK9-network effectively predicted ICB therapy responses.
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Affiliation(s)
- Yan Gu
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
| | - Xiaozeng Lin
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
| | - Ying Dong
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
| | - Geoffrey Wood
- grid.34429.380000 0004 1936 8198Department of Pathology, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Nabil G. Seidah
- grid.511547.30000 0001 2106 1695Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute, University of Montreal, Montreal, QC H2W 1R7 Canada
| | - Geoff Werstuck
- grid.25073.330000 0004 1936 8227Department of Medicine, McMaster University, Hamilton, ON L8S 4K1 Canada
| | - Pierre Major
- grid.25073.330000 0004 1936 8227Department of Oncology, McMaster University, Hamilton, ON L8S 4K1 Canada
| | - Michael Bonert
- grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4K1 Canada
| | - Anil Kapoor
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
| | - Damu Tang
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
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Wang Q, Zhao Y, Wang F, Tan G. A novel immune signature predicts immunotherapy responsiveness and reveals the landscape of the tumor immune microenvironment in head and neck squamous cell carcinoma. Front Genet 2022; 13:1051051. [DOI: 10.3389/fgene.2022.1051051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Immune-checkpoint blockade (ICB) has been routinely implemented to treat head and neck squamous cell carcinoma (HNSCC) patients. However, only a few patients benefit from immune checkpoint inhibitor (ICI) therapies.Methods: In this study, we used a combined cohort (including the GSE41613, GSE65858, TCGA, and CELL cohorts) to identify hub genes significantly associated with ICB and activated CD8+ T-cell gene signatures. We performed single‐sample gene set enrichment analysis (ssGSEA) to quantify the expression of hub genes; we then constructed a novel immune signature named “the IMS” that can predict immunotherapy responsiveness, prognosis, immune infiltration, and clinical characteristics. Data from the GSE102349 external cohort and the pembrolizumab cohort obtained from a clinical trial were used to validate the efficiency of the IMS. In addition, we revealed potential mechanisms of the antitumor response by analyzing the HNSCC single-cell database. Finally, we used the LASSO algorithm to build an IMS-related risk model.Results: The high IMS group was associated with significant immune activation, better prognosis, and increased immunotherapy responsiveness; thus, the IMS potentially represents a candidate biomarker for ICB. Moreover, a tumor microenvironment with a higher IMS underwent remarkable metabolic reprogramming characterized by enrichment in the glycolysis/gluconeogenesis, oxidative phosphorylation, and citrate cycle (TCA cycle) pathways. We also revealed key information on cellular crosstalk between the IMS and other immune lineages, which may mechanistically explain immune escape. In addition, we constructed and validated a risk prediction model (CD2, TBC1D10C, and CD3E) that could stratify HNSCC patients based on survival and response to ICB treatment.Conclusion: IMS is a signature closely correlated with the tumor immune microenvironment. The findings of this study contribute to the understanding of the immune landscape in HNSCC patients. IMS may aid in the clinical management of HNSCC patients through the identification of effective immunotherapies for specific patients.
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García-Hidalgo MC, Peláez R, González J, Santisteve S, Benítez ID, Molinero M, Perez-Pons M, Belmonte T, Torres G, Moncusí-Moix A, Gort-Paniello C, Aguilà M, Seck F, Carmona P, Caballero J, Barberà C, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Lorente-Balanza JÁ, Menéndez R, Motos A, Peñuelas O, Riera J, Bermejo-Martin JF, Torres A, Barbé F, de Gonzalo-Calvo D, Larráyoz IM. Genome-wide transcriptional profiling of pulmonary functional sequelae in ARDS- secondary to SARS-CoV-2 infection. Biomed Pharmacother 2022; 154:113617. [PMID: 36058144 PMCID: PMC9424524 DOI: 10.1016/j.biopha.2022.113617] [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: 07/13/2022] [Revised: 08/18/2022] [Accepted: 08/27/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Up to 80% of patients surviving acute respiratory distress syndrome (ARDS) secondary to SARS-CoV-2 infection present persistent anomalies in pulmonary function after hospital discharge. There is a limited understanding of the mechanistic pathways linked to post-acute pulmonary sequelae. AIM To identify the molecular underpinnings associated with severe lung diffusion involvement in survivors of SARS-CoV-2-induced ARDS. METHODS Survivors attended to a complete pulmonary evaluation 3 months after hospital discharge. RNA sequencing (RNA-seq) was performed using Illumina technology in whole-blood samples from 50 patients with moderate to severe diffusion impairment (DLCO<60%) and age- and sex-matched individuals with mild-normal lung function (DLCO≥60%). A transcriptomic signature for optimal classification was constructed using random forest. Transcriptomic data were analyzed for biological pathway enrichment, cellular deconvolution, cell/tissue-specific gene expression and candidate drugs. RESULTS RNA-seq identified 1357 differentially expressed transcripts. A model composed of 14 mRNAs allowed the optimal discrimination of survivors with severe diffusion impairment (AUC=0.979). Hallmarks of lung sequelae involved cell death signaling, cytoskeleton reorganization, cell growth and differentiation and the immune response. Resting natural killer (NK) cells were the most important immune cell subtype for the prediction of severe diffusion impairment. Components of the signature correlated with neutrophil, lymphocyte and monocyte counts. A variable expression profile of the transcripts was observed in lung cell subtypes and bodily tissues. One upregulated gene, TUBB4A, constitutes a target for FDA-approved drugs. CONCLUSIONS This work defines the transcriptional programme associated with post-acute pulmonary sequelae and provides novel insights for targeted interventions and biomarker development.
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Affiliation(s)
- María C. García-Hidalgo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Rafael Peláez
- Biomarkers and Molecular Signaling Group, Neurodegenerative Diseases Area Center for Biomedical Research of La Rioja, CIBIR, Logroño, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Sally Santisteve
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Iván D. Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Manel Perez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Thalía Belmonte
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Maria Aguilà
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Faty Seck
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Paola Carmona
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Jesús Caballero
- Grup de Recerca Medicina Intensiva, Intensive Care Department Hospital Universitari Arnau de Vilanova, Lleida, Spain
| | - Carme Barberà
- Intensive Care Department, University Hospital Santa María, IRBLleida, Lleida, Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Hospital Universitari Sagrat Cor, Barcelona, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Servei de Pneumologia, Hospital Clinic; Universitat de Barcelona; IDIBAPS, Barcelona, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Intensive Care Department, Vall d’Hebron Hospital Universitari. SODIR Research Group, Vall d’Hebron Institut de Recerca (VHIR), Spain
| | | | - Jose Ángel Lorente-Balanza
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Hospital Universitario de Getafe, Madrid, Spain
| | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Servei de Pneumologia, Hospital Clinic; Universitat de Barcelona; IDIBAPS, Barcelona, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Hospital Universitario de Getafe, Madrid, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Intensive Care Department, Vall d’Hebron Hospital Universitari. SODIR Research Group, Vall d’Hebron Institut de Recerca (VHIR), Spain
| | - Jesús F. Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Pneumology Department, Clinic Institute of Thorax (ICT), Hospital Clinic of Barcelona, Insitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), ICREA, University of Barcelona (UB), Barcelona, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Correspondence to: Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Avda. Alcalde Rovira Roure 80, Lleida 25198, Spain
| | - Ignacio M. Larráyoz
- Biomarkers and Molecular Signaling Group, Neurodegenerative Diseases Area Center for Biomedical Research of La Rioja, CIBIR, Logroño, Spain,GRUPAC, Department of Nursing, University of La Rioja, Logroño, Spain,Correspondence to: Biomarkers and Molecular Signaling Group, Neurodegenerative Diseases Area, Center for Biomedical Research of La Rioja, CIBIR. C. Piqueras, 98, Logroño 26006, Spain
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ATMP-classified, scalable, autologous cell spray for the treatment of skin wounds and assessment of its effects on wound healing clinically and on molecular level. Burns 2022:S0305-4179(22)00240-6. [DOI: 10.1016/j.burns.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022]
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