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Ye J, Wei B, Zhou G, Xu Y, He Y, Hu X, Chen X, Zhang G, Liu H. Multi-dimensional characterization of apoptosis in the tumor microenvironment and therapeutic relevance in melanoma. Cell Oncol (Dordr) 2024; 47:1333-1353. [PMID: 38502270 PMCID: PMC11322377 DOI: 10.1007/s13402-024-00930-0] [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] [Accepted: 02/23/2024] [Indexed: 03/21/2024] Open
Abstract
PURPOSE Melanoma is widely utilized as a prominent model for the development of immunotherapy, thought an inadequate immune response can occur. Moreover, the development of apoptosis-related therapies and combinations with other therapeutic strategies is impeded by the limited understanding of apoptosis's role within diverse tumor immune microenvironments (TMEs). METHODS Here, we constructed an apoptosis-related tumor microenvironment signature (ATM) and employ multi-dimensional analysis to understand the roles of apoptosis in tumor microenvironment. We further assessed the clinical applications of ATM in nine independent cohorts, and anticipated the impact of ATM on cellular drug response in cultured cells. RESULTS Our ATM model exhibits robust performance in survival prediction in multiple melanoma cohorts. Different ATM groups exhibited distinct molecular signatures and biological processes. The low ATM group exhibited significant enrichment in B cell activation-related pathways. What's more, plasma cells showed the lowest ATM score, highlighting their role as pivotal contributors in the ATM model. Mechanistically, the analysis of the interplay between plasma cells and other immune cells elucidated their crucial role in orchestrating an effective anti-tumor immune response. Significantly, the ATM signature exhibited associations with therapeutic efficacy of immune checkpoint blockade and the drug sensitivity of various agents, including FDA-approved and clinically utilized drugs targeting the VEGF signaling pathway. Finally, ATM was associated with tertiary lymphoid structures (TLS), exhibiting stronger patient stratification ability compared to classical "hot tumors". CONCLUSION Our findings indicate that ATM is a prognostic factor and is associated with the immune response and drug sensitivity in melanoma.
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Affiliation(s)
- Jing Ye
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, 410008, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, 410008, China
- Xiangya Clinical Research Center for Cancer Immunotherapy, Changsha, Hunan, 410008, China
| | - Benliang Wei
- Big Data Institute, Central South University, Changsha, Hunan, 410008, China
| | - Guowei Zhou
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, 410008, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, 410008, China
- Xiangya Clinical Research Center for Cancer Immunotherapy, Changsha, Hunan, 410008, China
| | - Yantao Xu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, 410008, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, 410008, China
- Xiangya Clinical Research Center for Cancer Immunotherapy, Changsha, Hunan, 410008, China
| | - Yi He
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, 410008, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, 410008, China
- Xiangya Clinical Research Center for Cancer Immunotherapy, Changsha, Hunan, 410008, China
| | - Xiheng Hu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China.
- Furong Laboratory, Changsha, Hunan, China.
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China.
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, 410008, China.
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, 410008, China.
- Xiangya Clinical Research Center for Cancer Immunotherapy, Changsha, Hunan, 410008, China.
- Furong Laboratory, Changsha, Hunan, China.
| | - Guanxiong Zhang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, 410008, China.
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, 410008, China.
- Xiangya Clinical Research Center for Cancer Immunotherapy, Changsha, Hunan, 410008, China.
| | - Hong Liu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, 410008, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, 410008, China.
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, 410008, China.
- Xiangya Clinical Research Center for Cancer Immunotherapy, Changsha, Hunan, 410008, China.
- Big Data Institute, Central South University, Changsha, Hunan, 410008, China.
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Lu B, Zhang Y, Wang J, Yang D, Liu M, Ma L, Yi W, Liang Y, Xu Y, Fan H, Liu W, Tang J, Zeng S, Cai L, Zhang L, Nie J, Zhang F, Gu X, Rosa Duque JS, Lu G, Zhang Y. PD1 +CD4 + T cells promote receptor editing and suppress autoreactivity of CD19 +CD21 low B cells within the lower respiratory airways in adenovirus pneumonia. Mucosal Immunol 2024:S1933-0219(24)00071-0. [PMID: 39038753 DOI: 10.1016/j.mucimm.2024.07.005] [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: 02/15/2024] [Revised: 06/07/2024] [Accepted: 07/18/2024] [Indexed: 07/24/2024]
Abstract
Human adenovirus (HAdV) pneumonia poses a major health burden for young children, however, factors that contribute to disease severity remain elusive. We analyzed immune cells from bronchoalveolar lavage (BAL) of children with HAdV pneumonia and found that CD19+CD21low B cells were significantly enriched in the BAL and were associated with increased autoantibody concentrations and disease severity. Myeloid cells, PD-1+CD4+ T helper cells and CD21low B cells formed tertiary lymphoid structures within the respiratory tracts. Myeloid cells promoted autoantibody production by expressing high amounts of B cell activating factor (BAFF). In contrast, PD-1+CD4+ T helper cells induced production of IgG1 and IgG3 antibodies but suppressed autoreactive IgGs by initiating B cell receptor editing. In summary, this study reveals cellular components involved in protective versus autoreactive immune pathways in the respiratory tract, and these findings provide potential therapeutic targets for severe HAdV lower respiratory tract infections.
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Affiliation(s)
- Bingtai Lu
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China; Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, China
| | - Yanfang Zhang
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Jun Wang
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Diyuan Yang
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Ming Liu
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Liuheyi Ma
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Weijing Yi
- Zybio Inc., Chongqing Municipality, 400039, China
| | - Yufeng Liang
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Yingyi Xu
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Huifeng Fan
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Wei Liu
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Jue Tang
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Sengqiang Zeng
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Li Cai
- Department of Hospital Infection Control, Guangdong Provincial Hospital of Traditional Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, China
| | - Li Zhang
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Junli Nie
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Fen Zhang
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Xiaoqiong Gu
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Jaime S Rosa Duque
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China; Department of Paediatric and Adolescent Medicine, the University of Hong Kong, Hong Kong, China.
| | - Gen Lu
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China.
| | - Yuxia Zhang
- Department of Respiratory Medicine, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong 510623, China; The Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
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Feng Z, Wu Z, Zhang Y. Integration of bioinformatics and machine learning approaches for the validation of pyrimidine metabolism-related genes and their implications in immunotherapy for osteoporosis. BMC Musculoskelet Disord 2024; 25:402. [PMID: 38778304 PMCID: PMC11110368 DOI: 10.1186/s12891-024-07512-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Osteoporosis (OP), the "silent epidemic" of our century, poses a significant challenge to public health, predominantly affecting postmenopausal women and the elderly. It evolves from mild symptoms to pronounced severity, stabilizing eventually. Unique among OP's characteristics is the altered metabolic profile of affected cells, particularly in pyrimidine metabolism (PyM), a crucial pathway for nucleotide turnover and pyrimidine decomposition. While metabolic adaptation is acknowledged as a therapeutic target in various diseases, the specific role of PyM genes (PyMGs) in OP's molecular response remains to be clarified. METHODS In pursuit of elucidating and authenticating PyMGs relevant to OP, we embarked on a comprehensive bioinformatics exploration. This entailed the integration of Weighted Gene Co-expression Network Analysis (WGCNA) with a curated list of 37 candidate PyMGs, followed by the examination of their biological functions and pathways via Gene Set Variation Analysis (GSVA). The Least Absolute Shrinkage and Selection Operator (LASSO) technique was harnessed to identify crucial hub genes. We evaluated the diagnostic prowess of five PyMGs in OP detection and explored their correlation with OP's clinical traits, further validating their expression profiles through independent datasets (GSE2208, GSE7158, GSE56815, and GSE35956). RESULTS Our analytical rigor unveiled five PyMGs-IGKC, TMEM187, RPS11, IGLL3P, and GOLGA8N-with significant ties to OP. A deeper dive into their biological functions highlighted their roles in estrogen response modulation, cytosolic calcium ion concentration regulation, and GABAergic synaptic transmission. Remarkably, these PyMGs emerged as potent diagnostic biomarkers for OP, distinguishing affected individuals with substantial accuracy. CONCLUSIONS This investigation brings to light five PyMGs intricately associated with OP, heralding new avenues for biomarker discovery and providing insights into its pathophysiological underpinnings. These findings not only deepen our comprehension of OP's complexity but also herald the advent of more refined diagnostic and therapeutic modalities.
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Affiliation(s)
- Zichen Feng
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zixuan Wu
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510006, China
| | - Yongchen Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, China.
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Omotesho QA, Escamilla A, Pérez-Ruiz E, Frecha CA, Rueda-Domínguez A, Barragán I. Epigenetic targets to enhance antitumor immune response through the induction of tertiary lymphoid structures. Front Immunol 2024; 15:1348156. [PMID: 38333212 PMCID: PMC10851080 DOI: 10.3389/fimmu.2024.1348156] [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: 12/01/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024] Open
Abstract
Tertiary lymphoid structures (TLS) are ectopic lymphoid aggregates found in sites of chronic inflammation such as tumors and autoimmune diseases. The discovery that TLS formation at tumor sites correlated with good patient prognosis has triggered extensive research into various techniques to induce their formation at the tumor microenvironment (TME). One strategy is the exogenous induction of specific cytokines and chemokine expression in murine models. However, applying such systemic chemokine expression can result in significant toxicity and damage to healthy tissues. Also, the TLS formed from exogenous chemokine induction is heterogeneous and different from the ones associated with favorable prognosis. Therefore, there is a need to optimize additional approaches like immune cell engineering with lentiviral transduction to improve the TLS formation in vivo. Similarly, the genetic and epigenetic regulation of the different phases of TLS neogenesis are still unknown. Understanding these molecular regulations could help identify novel targets to induce tissue-specific TLS in the TME. This review offers a unique insight into the molecular checkpoints of the different stages and mechanisms involved in TLS formation. This review also highlights potential epigenetic targets to induce TLS neogenesis. The review further explores epigenetic therapies (epi-therapy) and ongoing clinical trials using epi-therapy in cancers. In addition, it builds upon the current knowledge of tools to generate TLS and TLS phenotyping biomarkers with predictive and prognostic clinical potential.
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Affiliation(s)
- Quadri Ajibola Omotesho
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy and Epigenetics), Regional and Clinical University Hospitals, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Malaga, Spain
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Alejandro Escamilla
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy and Epigenetics), Regional and Clinical University Hospitals, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Malaga, Spain
- Department of Human Physiology, Human Histology, Pathological Anatomy and Physical Sport Education, University of Malaga, Malaga, Spain
| | - Elisabeth Pérez-Ruiz
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy and Epigenetics), Regional and Clinical University Hospitals, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Malaga, Spain
| | - Cecilia A. Frecha
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Civil Hospital, Malaga, Spain
| | - Antonio Rueda-Domínguez
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy and Epigenetics), Regional and Clinical University Hospitals, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Malaga, Spain
| | - Isabel Barragán
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy and Epigenetics), Regional and Clinical University Hospitals, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Malaga, Spain
- Group of Pharmacoepigenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
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Wang L, Deng C, Wu Z, Zhu K, Yang Z. Bioinformatics and machine learning were used to validate glutamine metabolism-related genes and immunotherapy in osteoporosis patients. J Orthop Surg Res 2023; 18:685. [PMID: 37710308 PMCID: PMC10503203 DOI: 10.1186/s13018-023-04152-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND Osteoporosis (OP), often referred to as the "silent disease of the twenty-first century," poses a significant public health concern due to its severity, chronic nature, and progressive course, predominantly affecting postmenopausal women and elderly individuals. The pathogenesis and progression of this disease have been associated with dysregulation in tumor metabolic pathways. Notably, the metabolic utilization of glutamine has emerged as a critical player in cancer biology. While metabolic reprogramming has been extensively studied in various malignancies and linked to clinical outcomes, its comprehensive investigation within the context of OP remains lacking. METHODS This study aimed to identify and validate potential glutamine metabolism genes (GlnMgs) associated with OP through comprehensive bioinformatics analysis. The identification of GlnMgs was achieved by integrating the weighted gene co-expression network analysis and a set of 28 candidate GlnMgs. Subsequently, the putative biological functions and pathways associated with GlnMgs were elucidated using gene set variation analysis. The LASSO method was employed to identify key hub genes, and the diagnostic efficacy of five selected GlnMgs in OP detection was assessed. Additionally, the relationship between hub GlnMgs and clinical characteristics was investigated. Finally, the expression levels of the five GlnMgs were validated using independent datasets (GSE2208, GSE7158, GSE56815, and GSE35956). RESULTS Five GlnMgs, namely IGKC, TMEM187, RPS11, IGLL3P, and GOLGA8N, were identified in this study. To gain insights into their biological functions, particular emphasis was placed on synaptic transmission GABAergic, inward rectifier potassium channel activity, and the cytoplasmic side of the lysosomal membrane. Furthermore, the diagnostic potential of these five GlnMgs in distinguishing individuals with OP yielded promising results, indicating their efficacy as discriminative markers for OP. CONCLUSIONS This study discovered five GlnMgs that are linked to OP. They shed light on potential new biomarkers for OP and tracking its progression.
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Affiliation(s)
- Lei Wang
- Shandong University of Traditional Chinese Medicine, Jinan, China
- Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chaosheng Deng
- The Third People Hospital of Longgang District, Shenzhen, Guangdong Province, China
| | - Zixuan Wu
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Kaidong Zhu
- Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China.
| | - Zhenguo Yang
- Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China.
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Strasser MK, Gibbs DL, Gascard P, Bons J, Hickey JW, Schürch CM, Tan Y, Black S, Chu P, Ozkan A, Basisty N, Sangwan V, Rose J, Shah S, Camilleri-Broet S, Fiset PO, Bertos N, Berube J, Djambazian H, Li R, Oikonomopoulos S, Fels-Elliott DR, Vernovsky S, Shimshoni E, Collyar D, Russell A, Ragoussis I, Stachler M, Goldenring JR, McDonald S, Ingber DE, Schilling B, Nolan GP, Tlsty TD, Huang S, Ferri LE. Concerted epithelial and stromal changes during progression of Barrett's Esophagus to invasive adenocarcinoma exposed by multi-scale, multi-omics analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544265. [PMID: 37333362 PMCID: PMC10274886 DOI: 10.1101/2023.06.08.544265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Esophageal adenocarcinoma arises from Barrett's esophagus, a precancerous metaplastic replacement of squamous by columnar epithelium in response to chronic inflammation. Multi-omics profiling, integrating single-cell transcriptomics, extracellular matrix proteomics, tissue-mechanics and spatial proteomics of 64 samples from 12 patients' paths of progression from squamous epithelium through metaplasia, dysplasia to adenocarcinoma, revealed shared and patient-specific progression characteristics. The classic metaplastic replacement of epithelial cells was paralleled by metaplastic changes in stromal cells, ECM and tissue stiffness. Strikingly, this change in tissue state at metaplasia was already accompanied by appearance of fibroblasts with characteristics of carcinoma-associated fibroblasts and of an NK cell-associated immunosuppressive microenvironment. Thus, Barrett's esophagus progresses as a coordinated multi-component system, supporting treatment paradigms that go beyond targeting cancerous cells to incorporating stromal reprogramming.
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Association of Circular RNA and Long Non-Coding RNA Dysregulation with the Clinical Response to Immune Checkpoint Blockade in Cutaneous Metastatic Melanoma. Biomedicines 2022; 10:biomedicines10102419. [DOI: 10.3390/biomedicines10102419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/02/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
Cutaneous melanoma (CM) is the most lethal form of skin cancer if it becomes metastatic, where treatment options and survival chances decrease dramatically. Immunotherapy treatments based on the immunologic checkpoint inhibitors programmed death cell protein 1 (PD-1) and cytotoxic T-lymphocyte antigen 4 (CTLA-4) constituted a main breakthrough in the treatment of metastatic CM, particularly for the achievement of long-term benefits. Even though it is a very promising therapy, resistance to primary immune checkpoint blockade (ICB) arises in about 70% of CM patients treated with a CTLA-4 inhibitor, and 40–65% of CM patients administered with a PD-1-targeting treatment. Some long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) are implicated in triggering pro- and anti-tumorigenic responses to various cancer treatments. The relationship between lncRNAs, circRNAs and ICB immunotherapy has not been explored in cutaneous metastatic melanoma (CMM). The aim of this pilot study is to evaluate the potential role of circRNA and lncRNA expression as pre-treatment predictors of the clinical response to immunotherapy in CMM patients. RNA-seq from 12 formalin-fixed paraffin-embedded (FFPE) samples from the metastatic biopsies of CMM patients treated with nivolumab was used to identify response-associated transcripts. Our findings indicate that specific lncRNAs and circRNAs, probably acting as competitive endogenous RNAs (ceRNAs), are involved in the regulatory networks of the immune response against metastatic melanoma that these patients have under treatment with nivolumab. Moreover, we established a risk score that yields predictions of the overall survival (OS) and progression-free survival (PFS) of CMM patients with high accuracy. This proof-of-principle work provides a possible insight into the function of ceRNAs, contributing to efforts to decipher the complex molecular mechanisms of ICB cancer treatment response.
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