1
|
Chen Y, Fan Z, Luo Z, Kang X, Wan R, Li F, Lin W, Han Z, Qi B, Lin J, Sun Y, Huang J, Xu Y, Chen S. Impacts of Nutlin-3a and exercise on murine double minute 2-enriched glioma treatment. Neural Regen Res 2025; 20:1135-1152. [PMID: 38989952 PMCID: PMC11438351 DOI: 10.4103/nrr.nrr-d-23-00875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 12/21/2023] [Indexed: 07/12/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202504000-00029/figure1/v/2024-07-06T104127Z/r/image-tiff Recent research has demonstrated the impact of physical activity on the prognosis of glioma patients, with evidence suggesting exercise may reduce mortality risks and aid neural regeneration. The role of the small ubiquitin-like modifier (SUMO) protein, especially post-exercise, in cancer progression, is gaining attention, as are the potential anti-cancer effects of SUMOylation. We used machine learning to create the exercise and SUMO-related gene signature (ESLRS). This signature shows how physical activity might help improve the outlook for low-grade glioma and other cancers. We demonstrated the prognostic and immunotherapeutic significance of ESLRS markers, specifically highlighting how murine double minute 2 (MDM2), a component of the ESLRS, can be targeted by nutlin-3. This underscores the intricate relationship between natural compounds such as nutlin-3 and immune regulation. Using comprehensive CRISPR screening, we validated the effects of specific ESLRS genes on low-grade glioma progression. We also revealed insights into the effectiveness of Nutlin-3a as a potent MDM2 inhibitor through molecular docking and dynamic simulation. Nutlin-3a inhibited glioma cell proliferation and activated the p53 pathway. Its efficacy decreased with MDM2 overexpression, and this was reversed by Nutlin-3a or exercise. Experiments using a low-grade glioma mouse model highlighted the effect of physical activity on oxidative stress and molecular pathway regulation. Notably, both physical exercise and Nutlin-3a administration improved physical function in mice bearing tumors derived from MDM2-overexpressing cells. These results suggest the potential for Nutlin-3a, an MDM2 inhibitor, with physical exercise as a therapeutic approach for glioma management. Our research also supports the use of natural products for therapy and sheds light on the interaction of exercise, natural products, and immune regulation in cancer treatment.
Collapse
Affiliation(s)
- Yisheng Chen
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhongcheng Fan
- Department of Orthopedic Surgery, Hainan Province Clinical Medical Center, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou, Hainan Province, China
| | - Zhiwen Luo
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Xueran Kang
- Department of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Renwen Wan
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Fangqi Li
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Weiwei Lin
- Department of Neurosurgery, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Zhihua Han
- Department of Orthopedics, Shanghai General Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, China
| | - Beijie Qi
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinrong Lin
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yaying Sun
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiebin Huang
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yuzhen Xu
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Shiyi Chen
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
2
|
Liu Y, Qi L, Ye B, Wang A, Lu J, Qu L, Luo P, Wang L, Jiang A. MOICS, a novel classier deciphering immune heterogeneity and aid precise management of clear cell renal cell carcinoma at multiomics level. Cancer Biol Ther 2024; 25:2345977. [PMID: 38659199 PMCID: PMC11057626 DOI: 10.1080/15384047.2024.2345977] [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: 02/19/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
Recent studies have indicated that the tumor immune microenvironment plays a pivotal role in the initiation and progression of clear cell renal cell carcinoma (ccRCC). However, the characteristics and heterogeneity of tumor immunity in ccRCC, particularly at the multiomics level, remain poorly understood. We analyzed immune multiomics datasets to perform a consensus cluster analysis and validate the clustering results across multiple internal and external ccRCC datasets; and identified two distinctive immune phenotypes of ccRCC, which we named multiomics immune-based cancer subtype 1 (MOICS1) and subtype 2 (MOICS2). The former, MOICS1, is characterized by an immune-hot phenotype with poor clinical outcomes, marked by significant proliferation of CD4+ and CD8+ T cells, fibroblasts, and high levels of immune inhibitory signatures; the latter, MOICS2, exhibits an immune-cold phenotype with favorable clinical characteristics, characterized by robust immune activity and high infiltration of endothelial cells and immune stimulatory signatures. Besides, a significant negative correlation between immune infiltration and angiogenesis were identified. We further explored the mechanisms underlying these differences, revealing that negatively regulated endopeptidase activity, activated cornification, and neutrophil degranulation may promote an immune-deficient phenotype, whereas enhanced monocyte recruitment could ameliorate this deficiency. Additionally, significant differences were observed in the genomic landscapes between the subtypes: MOICS1 exhibited mutations in TTN, BAP1, SETD2, MTOR, MUC16, CSMD3, and AKAP9, while MOICS2 was characterized by notable alterations in the TGF-β pathway. Overall, our work demonstrates that multi-immune omics remodeling analysis enhances the understanding of the immune heterogeneity in ccRCC and supports precise patient management.
Collapse
Affiliation(s)
- Ying Liu
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Lin Qi
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, Hunan, China
| | - Bicheng Ye
- School of Clinical Medicine, Medical College of Yangzhou Polytechnic College, Yangzhou, China
| | - Anbang Wang
- Department of Urology, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Juan Lu
- Vocational Education Center, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Le Qu
- Department of Urology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| |
Collapse
|
3
|
Wu X, Chen M, Liu K, Wu Y, Feng Y, Fu S, Xu H, Zhao Y, Lin F, Lin L, Ye S, Lin J, Xiao T, Li W, Lou M, Lv H, Qiu Y, Yu R, Chen W, Li M, Feng X, Luo Z, Guo L, Ke H, Zhao L. Molecular classification of geriatric breast cancer displays distinct senescent subgroups of prognostic significance. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102309. [PMID: 39296329 PMCID: PMC11408383 DOI: 10.1016/j.omtn.2024.102309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/12/2024] [Indexed: 09/21/2024]
Abstract
Breast cancer in the elderly presents distinct biological characteristics and clinical treatment responses compared with cancer in younger patients. Comprehensive Geriatric Assessment is recommended for evaluating treatment efficacy in elderly cancer patients based on physiological classification. However, research on molecular classification in older cancer patients remains insufficient. In this study, we identified two subgroups with distinct senescent clusters among geriatric breast cancer patients through multi-omics analysis. Using various machine learning algorithms, we developed a comprehensive scoring model called "Sene_Signature," which more accurately distinguished elderly breast cancer patients compared with existing methods and better predicted their prognosis. The Sene_Signature was correlated with tumor immune cell infiltration, as supported by single-cell transcriptomics, RNA sequencing, and pathological data. Furthermore, we observed increased drug responsiveness in patients with a high Sene_Signature to treatments targeting the epidermal growth factor receptor and cell-cycle pathways. We also established a user-friendly web platform to assist investigators in assessing Sene_Signature scores and predicting treatment responses for elderly breast cancer patients. In conclusion, we developed a novel model for evaluating prognosis and therapeutic responses, providing a potential molecular classification that assists in the pre-treatment assessment of geriatric breast cancer.
Collapse
Affiliation(s)
- Xia Wu
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
- Ningbo Clinical Pathology Diagnosis Center, Ningbo, Zhejiang 315021, China
| | - Mengxin Chen
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Kang Liu
- Ganzhou People's Hospital, Ganzhou 341000, China
| | - Yixin Wu
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Yun Feng
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Shiting Fu
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Huaimeng Xu
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Yongqi Zhao
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Feilong Lin
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Liang Lin
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Shihui Ye
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Junqiang Lin
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Taiping Xiao
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Wenhao Li
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Meng Lou
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Hongyu Lv
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Ye Qiu
- Huankui Academy, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Ruifan Yu
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Wenyan Chen
- Department of Medical Oncology, Nanchang People's Hospital, Nanchang 330008, China
| | - Mengyuan Li
- Department of Gynaecology and Obstetrics, Chongqing General Hospital, Chongqing 401147, China
| | - Xu Feng
- Xianlin High School, Weinan 714000, China
| | | | - Lu Guo
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310000, China
| | - Hao Ke
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China
- School of Life Science, Nanchang University, Nanchang 330031, China
| | - Limin Zhao
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| |
Collapse
|
4
|
Yue D, Wang R, Zhao Y, Wu B, Li S, Zeng W, Wan S, Liu L, Dai Y, Shi Y, Xu R, Yang Z, Wang X, Zou Y. Investigating the molecular mechanisms between type 1 diabetes and mild cognitive impairment using bioinformatics analysis, with a focus on immune response. Int Immunopharmacol 2024; 142:113256. [PMID: 39340997 DOI: 10.1016/j.intimp.2024.113256] [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: 03/23/2024] [Revised: 09/17/2024] [Accepted: 09/23/2024] [Indexed: 09/30/2024]
Abstract
The immune system is involved in the development and progression of several diseases. Type 1 diabetes mellitus (T1DM), an autoimmune disorder, influences the progression of several other conditions; however, the link between T1DM and mild cognitive impairment (MCI) remains unclear. This study investigated the underlying immune response mechanisms that contribute to the development and progression of T1DM and MCI. Microarray datasets for MCI (GSE63060) and T1DM (GSE30208) were retrieved from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified using the limma package. To explore the functional implications of these DEGs, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were conducted using ClusterProfiler. Protein-protein interaction networks for the DEGs were constructed using the STRING database and visualized using Cytoscape. The Molecular Complex Detection algorithm was used to analyze DEGs. Immune cell infiltration in patients with T1DM and MCI was analyzed using the xCell method. Gene set enrichment analysis was used to gain in-depth insights into the functional characteristics of T1DM and MCI. Immune-related genes were obtained from the GeneCards and ImmPort databases. Machine learning algorithms were used to identify potential hub genes associated with immunity for T1DM and MCI diagnosis, and the diagnostic value was assessed using the receiver operating characteristic curve. The identified genes were validated using quantitative polymerase chain reaction. In the T1DM and MCI datasets, 610 DEGs showed consistent trends, of which 232 and 378 were upregulated and downregulated, respectively. Immune response analysis revealed significant changes in the immune cells associated with MCI and T1DM. Using immune-related genes, DEGs, and machine learning techniques, we identified CD3D in the MCI and T1DM groups. We observed a gradual decline in the cognitive function of mice with T1DM as the disease progressed. CD3D expression increased with increasing disease severity; CD3D primarily affected CD4+ T cells. This study revealed a complex interaction between T1DM and MCI, providing novel insights into the intricate relationship between immune dysregulation and cognitive impairment and expanding our understanding of these two interconnected disorders. These findings will facilitate the development of therapeutic interventions and identification of potential therapeutic targets.
Collapse
Affiliation(s)
- Dongxu Yue
- Department of Pathology and Pathophysiology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, PR China
| | - Runze Wang
- Department of Pathology and Pathophysiology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, PR China
| | - Yanli Zhao
- Department of Pathology and Pathophysiology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, PR China
| | - Bangxu Wu
- Department of Pathology and Pathophysiology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, PR China
| | - Shude Li
- Department of Biochemistry and Molecular Biology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, PR China
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, PR China
| | - Shanshan Wan
- Department of Radiology, The Second Affiliated Hospital of Kunming Medical University, Kunming, PR China
| | - Lifang Liu
- Department of Pathology and Pathophysiology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, PR China
| | - Yating Dai
- Department of Pathology and Pathophysiology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, PR China
| | - Yuling Shi
- Department of Pathology and Pathophysiology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, PR China
| | - Ruobing Xu
- Department of Pathology and Pathophysiology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, PR China
| | - Zhihong Yang
- Department of Pathology and Pathophysiology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, PR China.
| | - Xie Wang
- Department of Pathology and Pathophysiology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, PR China.
| | - Yingying Zou
- Department of Pathology and Pathophysiology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, PR China.
| |
Collapse
|
5
|
Ding R, Lu J, Huang X, Deng M, Wei H, Jiang G, Zhu H, Yuan H. The effect of immunotherapy PD-1 blockade on acute bone cancer pain: Insights from transcriptomic and microbiomic profiling. Int Immunopharmacol 2024; 142:113100. [PMID: 39244901 DOI: 10.1016/j.intimp.2024.113100] [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: 05/20/2024] [Revised: 08/08/2024] [Accepted: 09/03/2024] [Indexed: 09/10/2024]
Abstract
INTRODUCTION The skeletal system ranks as the third most common site for cancer metastasis, often leading to pain with nociceptive and neuropathic features. Programmed cell death protein 1 (PD-1)-targeting therapeutic antibodies offer effective cancer treatment but can cause treatment-related acute pain. Understanding the mechanisms of this pain and identifying potential interventions is still a challenge. METHODS A murine model of bone cancer pain was established using Lewis lung carcinoma (LLC) cells, followed by intravenous administration of nivolumab, a human anti-PD-1 monoclonal antibody. Pain thresholds were measured, and micro-CT images of the skeletal system were obtained. High-throughput sequencing of the spinal cord/colon transcriptome during the acute phase of bone cancer pain and gut microbiota analysis at the end of the treatment were performed. Immunofluorescence staining and western blot experiments assessed spinal cord microglia activation and acute pain-associated molecules. RESULTS PD-1 inhibition with nivolumab protected against bone degradation initiated by LLC cell administration but consistently induced acute pain during nivolumab treatment. Spinal cord and colon transcriptomics revealed an immunopathological pattern during tumor progression and the acute pain phase, with notable changes in interleukin and S100 gene families. Gut microbiota analysis post-immunotherapy showed a decline in beneficial bacteria associated with short-chain fatty acid (SCFA) production. Activation of spinal cord microglia and enhanced glycolytic metabolism were confirmed as key factors in inducing acute pain following immunotherapy. CONCLUSIONS This study reveals that nivolumab induces acute pain by activating microglia and enhancing glycolytic metabolism in the treatment of bone cancer and uncovers connections between transcriptomic changes, gut microbiota, and acute pain following immune checkpoint blockade (ICB) treatment. It offers novel insights into the relationship between immune checkpoint blockade therapies and pain management.
Collapse
Affiliation(s)
- Ruifeng Ding
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Jinfang Lu
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Xingshuai Huang
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Mengqiu Deng
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Huawei Wei
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Guowei Jiang
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Hongwei Zhu
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Hongbin Yuan
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China.
| |
Collapse
|
6
|
Hu XM, Zheng S, Zhang Q, Wan X, Li J, Mao R, Yang R, Xiong K. PANoptosis signaling enables broad immune response in psoriasis: From pathogenesis to new therapeutic strategies. Comput Struct Biotechnol J 2024; 23:64-76. [PMID: 38125299 PMCID: PMC10730955 DOI: 10.1016/j.csbj.2023.11.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
Background Accumulating evidence suggests that regulated cell death, such as pyroptosis, apoptosis, and necroptosis, is deeply involved in the pathogenesis of psoriasis. As a newly recognized form of systematic cell death, PANoptosis is involved in a variety of inflammatory disorders through amplifying inflammatory and immune cascades, but its role in psoriasis remains elusive. Objectives To reveal the role of PANoptosis in psoriasis for a potential therapeutic strategy. Methods Multitranscriptomic analysis and experimental validation were used to identify PANoptosis signaling in psoriasis. RNA-seq and scRNA-seq analyses were performed to establish a PANoptosis-mediated immune response in psoriasis, which revealed hub genes through WGCNA and predicted disulfiram as a potential drug. The effect and mechanism of disulfiram were verified in imiquimod (IMQ)-induced psoriasis. Results Here, we found a highlighted PANoptosis signature in psoriasis patients through multitranscriptomic analysis and experimental validation. Based on this, two distinct PANoptosis patterns (non/high) were identified, which were the options for clinical classification. The high-PANoptosis-related group had a higher response rate to immune cell infiltration (such as M1 macrophages and keratinocytes). Subsequently, WGCNA showed the hub genes (e.g., S100A12, CYCS, NOD2, STAT1, HSPA4, AIM2, MAPK7), which were significantly associated with clinical phenotype, PANoptosis signature, and identified immune response in psoriasis. Finally, we explored disulfiram (DSF) as a candidate drug for psoriasis through network pharmacology, which ameliorated IMQ-mediated psoriatic symptoms through antipyroptosis-mediated inflammation and enhanced apoptotic progression. By analyzing the specific ligand-receptor interaction pairs within and between cell lineages, we speculated that DSF might exert its effects by targeting keratinocytes directly or targeting M1 macrophages to downregulate the proliferation of keratinocytes. Conclusions PANoptosis with its mediated immune cell infiltration provides a roadmap for research on the pathogenesis and therapeutic strategies of psoriasis.
Collapse
Affiliation(s)
- Xi-min Hu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Shengyuan Zheng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Qi Zhang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Xinxing Wan
- Department of Endocrinology, Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Rui Mao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ronghua Yang
- Department of Burn and Plastic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou 510000, China
| | - Kun Xiong
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
- Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Emergency and Trauma, Ministry of Education, College of Emergency and Trauma, Hainan Medical University, Haikou 571199, China
| |
Collapse
|
7
|
Yan Q, Zhao Z, Liu D, Li J, Pan S, Duan J, Liu Z. Novel immune cross-talk between inflammatory bowel disease and IgA nephropathy. Ren Fail 2024; 46:2337288. [PMID: 38628140 PMCID: PMC11025414 DOI: 10.1080/0886022x.2024.2337288] [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: 09/15/2023] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
The mechanisms underlying the complex correlation between immunoglobulin A nephropathy (IgAN) and inflammatory bowel disease (IBD) remain unclear. This study aimed to identify the optimal cross-talk genes, potential pathways, and mutual immune-infiltrating microenvironments between IBD and IgAN to elucidate the linkage between patients with IBD and IgAN. The IgAN and IBD datasets were obtained from the Gene Expression Omnibus (GEO). Three algorithms, CIBERSORTx, ssGSEA, and xCell, were used to evaluate the similarities in the infiltrating microenvironment between the two diseases. Weighted gene co-expression network analysis (WGCNA) was implemented in the IBD dataset to identify the major immune infiltration modules, and the Boruta algorithm, RFE algorithm, and LASSO regression were applied to filter the cross-talk genes. Next, multiple machine learning models were applied to confirm the optimal cross-talk genes. Finally, the relevant findings were validated using histology and immunohistochemistry analysis of IBD mice. Immune infiltration analysis showed no significant differences between IBD and IgAN samples in most immune cells. The three algorithms identified 10 diagnostic genes, MAPK3, NFKB1, FDX1, EPHX2, SYNPO, KDF1, METTL7A, RIDA, HSDL2, and RIPK2; FDX1 and NFKB1 were enhanced in the kidney of IBD mice. Kyoto Encyclopedia of Genes and Genomes analysis showed 15 mutual pathways between the two diseases, with lipid metabolism playing a vital role in the cross-talk. Our findings offer insights into the shared immune mechanisms of IgAN and IBD. These common pathways, diagnostic cross-talk genes, and cell-mediated abnormal immunity may inform further experimental studies.
Collapse
Affiliation(s)
- Qianqian Yan
- Department of Integrated Traditional and Western Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, P. R. China
| | - Zihao Zhao
- Department of Integrated Traditional and Western Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, P. R. China
| | - Dongwei Liu
- Department of Integrated Traditional and Western Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, P. R. China
| | - Jia Li
- Department of Integrated Traditional and Western Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, P. R. China
| | - Shaokang Pan
- Department of Integrated Traditional and Western Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, P. R. China
| | - Jiayu Duan
- Department of Integrated Traditional and Western Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, P. R. China
| | - Zhangsuo Liu
- Department of Integrated Traditional and Western Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, P. R. China
| |
Collapse
|
8
|
Cheng X, Meng X, Chen R, Song Z, Li S, Wei S, Lv H, Zhang S, Tang H, Jiang Y, Zhang R. The molecular subtypes of autoimmune diseases. Comput Struct Biotechnol J 2024; 23:1348-1363. [PMID: 38596313 PMCID: PMC11001648 DOI: 10.1016/j.csbj.2024.03.026] [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: 11/12/2023] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024] Open
Abstract
Autoimmune diseases (ADs) are characterized by their complexity and a wide range of clinical differences. Despite patients presenting with similar symptoms and disease patterns, their reactions to treatments may vary. The current approach of personalized medicine, which relies on molecular data, is seen as an effective method to address the variability in these diseases. This review examined the pathologic classification of ADs, such as multiple sclerosis and lupus nephritis, over time. Acknowledging the limitations inherent in pathologic classification, the focus shifted to molecular classification to achieve a deeper insight into disease heterogeneity. The study outlined the established methods and findings from the molecular classification of ADs, categorizing systemic lupus erythematosus (SLE) into four subtypes, inflammatory bowel disease (IBD) into two, rheumatoid arthritis (RA) into three, and multiple sclerosis (MS) into a single subtype. It was observed that the high inflammation subtype of IBD, the RA inflammation subtype, and the MS "inflammation & EGF" subtype share similarities. These subtypes all display a consistent pattern of inflammation that is primarily driven by the activation of the JAK-STAT pathway, with the effective drugs being those that target this signaling pathway. Additionally, by identifying markers that are uniquely associated with the various subtypes within the same disease, the study was able to describe the differences between subtypes in detail. The findings are expected to contribute to the development of personalized treatment plans for patients and establish a strong basis for tailored approaches to treating autoimmune diseases.
Collapse
Affiliation(s)
| | | | | | - Zerun Song
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuai Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Siyu Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongchao Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuhao Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hao Tang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| |
Collapse
|
9
|
Li X, Zhang G, Wang M, Lu C, Zhang G, Chen Z, Ji Y. Comparison of stromal vascular fraction cell composition between Coleman fat and extracellular matrix/stromal vascular fraction gel. Adipocyte 2024; 13:2360037. [PMID: 38829527 PMCID: PMC11152101 DOI: 10.1080/21623945.2024.2360037] [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: 02/01/2024] [Accepted: 05/21/2024] [Indexed: 06/05/2024] Open
Abstract
As a mechanically condensed product of Coleman fat, extracellular matrix/stromal vascular fraction gel (ECM/SVF-gel) eliminates adipocytes, concentrates SVF cells, and improves fat graft retention. This study aims to compare SVF cell composition between Coleman fat and ECM/SVF-gel. Matched Coleman fat and ECM/SVF-gel of 28 healthy women were subjected to RNA-seq, followed by functional enrichment and cell-type-specific enrichment analyses, and deconvolution of SVF cell subsets, reconstructing SVF cell composition in the transcriptome level. ECM/SVF-gels had 9 upregulated and 73 downregulated differentially expressed genes (DEGs). Downregulated DEGs were mainly associated with inflammatory and immune responses, and enriched in fat macrophages. M2 macrophages, resting CD4+ memory T cells, M1 macrophages, resting mast cells, and M0 macrophages ranked in the top five most prevalent immune cells in the two groups. The proportions of the principal non-immune cells (e.g., adipose-derived stem cells, pericytes, preadipocytes, microvascular endothelial cells) had no statistical differences between the two groups. Our findings reveal ECM/SVF-gels share the same dominant immune cells beneficial to fat graft survival with Coleman fat, but exhibiting obvious losses of immune cells (especially macrophages), while non-immune cells necessary for adipose regeneration might have no significant loss in ECM/SVF-gels and their biological effects could be markedly enhanced by the ECM/SVF-gel's condensed nature.
Collapse
Affiliation(s)
- Xiaoyun Li
- Department of Pathology, Shantou University Medical College, Shantou, China
| | - Guohong Zhang
- Department of Pathology, Shantou University Medical College, Shantou, China
| | - Mengmeng Wang
- Medical Cosmetic Center, the First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Changhao Lu
- Department of Pathology, Shantou University Medical College, Shantou, China
| | - Guangping Zhang
- Department of Pathology, Shantou University Medical College, Shantou, China
| | - Zhehui Chen
- Medical Cosmetic Center, the First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Yingchang Ji
- Medical Cosmetic Center, the First Affiliated Hospital of Shantou University Medical College, Shantou, China
| |
Collapse
|
10
|
Ma S, Pan X, Gan J, Guo X, He J, Hu H, Wang Y, Ning S, Zhi H. DNA methylation heterogeneity attributable to a complex tumor immune microenvironment prompts prognostic risk in glioma. Epigenetics 2024; 19:2318506. [PMID: 38439715 PMCID: PMC10936651 DOI: 10.1080/15592294.2024.2318506] [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: 07/26/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024] Open
Abstract
Gliomas are malignant tumours of the human nervous system with different World Health Organization (WHO) classifications, glioblastoma (GBM) with higher grade and are more malignant than lower-grade glioma (LGG). To dissect how the DNA methylation heterogeneity in gliomas is influenced by the complex cellular composition of the tumour immune microenvironment, we first compared the DNA methylation profiles of purified human immune cells and bulk glioma tissue, stratifying three tumour immune microenvironmental subtypes for GBM and LGG samples from The Cancer Genome Atlas (TCGA). We found that more intermediate methylation sites were enriched in glioma tumour tissues, and used the Proportion of sites with Intermediate Methylation (PIM) to compare intertumoral DNA methylation heterogeneity. A larger PIM score reflected stronger DNA methylation heterogeneity. Enhanced DNA methylation heterogeneity was associated with stronger immune cell infiltration, better survival rates, and slower tumour progression in glioma patients. We then created a Cell-type-associated DNA Methylation Heterogeneity Contribution (CMHC) score to explore the impact of different immune cell types on heterogeneous CpG site (CpGct) in glioma tissues. We identified eight prognosis-related CpGct to construct a risk score: the Cell-type-associated DNA Methylation Heterogeneity Risk (CMHR) score. CMHR was positively correlated with cytotoxic T-lymphocyte infiltration (CTL), and showed better predictive performance for IDH status (AUC = 0.96) and glioma histological phenotype (AUC = 0.81). Furthermore, DNA methylation alterations of eight CpGct might be related to drug treatments of gliomas. In conclusion, we indicated that DNA methylation heterogeneity is associated with a complex tumour immune microenvironment, glioma phenotype, and patient's prognosis.
Collapse
Affiliation(s)
- Shuangyue Ma
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Xu Pan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Gan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiaxin Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiaheng He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haoyu Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yuncong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| |
Collapse
|
11
|
Chida K, Oshi M, Roy AM, Sato T, Takabe MP, Yan L, Endo I, Hakamada K, Takabe K. Enhanced cancer cell proliferation and aggressive phenotype counterbalance in breast cancer with high BRCA1 gene expression. Breast Cancer Res Treat 2024; 208:321-331. [PMID: 38972017 DOI: 10.1007/s10549-024-07421-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 06/27/2024] [Indexed: 07/08/2024]
Abstract
PURPOSE While comprehensive research exists on the mutation of the DNA repair gene BRCA1, limited information is available regarding the clinical significance of BRCA1 gene expression. Given that cancer cell proliferation is aggrevated by DNA repair, we hypothesized that high BRCA1 gene expression breast cancer (BC) might be linked with aggressive tumor biology and poor clinical outcomes. METHODS The cohorts: The Cancer Genome Atlas (TCGA, n = 1069), METABRIC (n = 1903), and SCAN-B (n = 3273) were utilzed to obtain data of 6245 BC patients. RESULTS BC patients without BRCA1 mutation exhibited higher BRCA1 expression, which was associated with DNA repair functionality. However, no such correlation was observed with BRCA2 expression. The association of high BRCA1 expression with cancer cell proliferation was evidenced by significant enrichment of cell proliferation-related gene sets, higher histological grade, and proliferation score. Furthermore, increased levels of homologous recombination deficiency, intratumoral heterogeneity, and altered fractions were associated with high BRCA1 expression. Moreover, BC with high BRCA1 expression exhibited reduced infiltration of dendritic cells and CD8 T-cells, while showing increased infiltration of Th1 cells. Surprisingly, BRCA1 expression was not associated with the survival of BC irrespective of the subtypes. Conversely, BC with low BRCA1 expression enriched cancer aggravating pathway gene sets, such as Cancer Stem Cell-related signaling (NOTCH and HEDGEHOG), Angiogenesis, Epithelial-Mesenchymal Transition, Inflammatory Response, and TGF-beta signaling. CONCLUSION Despite being linked to heightened proliferation of cancer cells and unassertive phenotype, BRCA1 expression did not show any association with survival in BC.
Collapse
Affiliation(s)
- Kohei Chida
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
- Department of Gastroenterological Surgery, Hirosaki University Graduate School of Medicine, Hirosaki, 036-8562, Japan
| | - Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan
| | - Arya Mariam Roy
- Department of Hematology and Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Takumi Sato
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
- Department of Medical Science, The University of Tokyo, Tokyo, 113-8654, Japan
| | - Maya Penelope Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan
| | - Kenichi Hakamada
- Department of Gastroenterological Surgery, Hirosaki University Graduate School of Medicine, Hirosaki, 036-8562, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA.
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan.
- Department of Surgery, School of Medicine and Biomedical Sciences, University at Buffalo Jacobs, The State University of New York, Buffalo, NY, 14263, USA.
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, 160-8402, Japan.
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan.
- Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima, 960-1295, Japan.
- Department of Breast Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
| |
Collapse
|
12
|
Mitra S, Farswan A, Piccinelli P, Sydow S, Hesla A, Tsagkozis P, Vult von Steyern F, Almqvist M, Eriksson M, Magnusson L, Nilsson J, Pillay N, Mertens F. Transcriptomic profiles of myxofibrosarcoma and undifferentiated pleomorphic sarcoma correlate with clinical and genomic features. J Pathol 2024; 264:293-304. [PMID: 39258383 DOI: 10.1002/path.6347] [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: 04/02/2024] [Revised: 07/01/2024] [Accepted: 08/06/2024] [Indexed: 09/12/2024]
Abstract
Myxofibrosarcoma (MFS) and undifferentiated pleomorphic sarcoma (UPS) are two common and aggressive subtypes of soft tissue sarcoma. The aim of this study was to assess potential transcriptomic differences between MFS and UPS tumours and to evaluate the extent to which differences in gene expression profiles were associated with genomic and clinical features. The study included 162 patients with tumours diagnosed as MFS (N = 62) or UPS (N = 100). The patients had been diagnosed and treated at two Swedish sarcoma centres during a 30-year period. For gene expression profiling and gene fusion detection all tumours were analysed using RNA-sequencing and could be compared with data on clinical outcome (N = 155), global copy number profiles (N = 145), and gene mutations (N = 128). Gene expression profiling revealed three transcriptomic clusters (TCs) without any clear separation of MFS and UPS. One TC was associated with longer metastasis-free survival. These tumours had lower tumour mutation burden (TMB), were enriched for a copy number signature representative of focal LOH and chromosomal instability on a diploid background, and were relatively immune-depleted. MFS and UPS showed extensive genomic overlap, with whole genome doubling occurring more frequently among the latter. The results support the idea that MFS and UPS tumours have largely overlapping genomic and transcriptomic features, with UPS tumours showing more aggressive behaviour and more complex genomes. Independently of the tumour type, clinically relevant subgroups were revealed by gene expression analysis, and the finding of multiple genomic subgroups strongly suggest the existence of subgroups of relevance to treatment stratification. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Shamik Mitra
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | | | - Paul Piccinelli
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Saskia Sydow
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Asle Hesla
- Department of Orthopedics, Karolinska University Hospital, Stockholm, Sweden
| | | | | | - Martin Almqvist
- Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Mikael Eriksson
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Linda Magnusson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Nischalan Pillay
- University College London Cancer Institute, London, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, Lund, Sweden
| |
Collapse
|
13
|
Qin F, Bian Z, Jiang L, Cao Y, Tang J, Ming L, Qin Y, Huang Z, Yin Y. A novel high-risk model identified by epithelial-mesenchymal transition predicts prognosis and radioresistance in rectal cancer. Mol Carcinog 2024; 63:2119-2132. [PMID: 39056517 DOI: 10.1002/mc.23797] [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: 05/09/2024] [Revised: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024]
Abstract
Many studies have shown that tumor cells that survive radiotherapy are more likely to metastasize, but the underlying mechanism remains unclear. Here we aimed to identify epithelial-mesenchymal transition (EMT)-related key genes, which associated with prognosis and radiosensitivity in rectal cancer. First, we obtained differentially expressed genes by analyzing the RNA expression profiles of rectal cancer retrieved from The Cancer Genome Atlas database, EMT-related genes, and radiotherapy-related databases, respectively. Then, Lasso and Cox regression analyses were used to establish an EMT-related prognosis model (EMTPM) based on the identified independent protective factor Fibulin5 (FBLN5) and independent risk gene EHMT2. The high-EMTPM group exhibited significantly poorer prognosis. Then, we evaluated the signature in an external clinical validation cohort. Through in vivo experiments, we further demonstrated that EMTPM effectively distinguishes radioresistant from radiosensitive patients with rectal cancer. Moreover, individuals in the high-EMTPM group showed increased expression of immune checkpoints compared to their counterparts. Finally, pan-cancer analysis of the EMTPM model also indicated its potential for predicting the prognosis of lung squamous cell carcinoma and breast cancer patients undergoing radiotherapy. In summary, we established a novel predictive model for rectal cancer prognosis and radioresistance based on FBLN5 and EHMT2 expressions, and suggested that immune microenvironment may be involved in the process of radioresistance. This predictive model could be used to select management strategies for rectal cancer.
Collapse
Affiliation(s)
- Feiyu Qin
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Zehua Bian
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Lingzhen Jiang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yulin Cao
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Junhui Tang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Liang Ming
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yan Qin
- Department of Pathology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yuan Yin
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| |
Collapse
|
14
|
Wang J, Xu Q, Yu J, Xu A, Yu L, Chen Z, Cao Y, Yuan R, Yu Z. SCGB1A1 as a novel biomarker and promising therapeutic target for the management of HNSCC. Oncol Lett 2024; 28:527. [PMID: 39268163 PMCID: PMC11391500 DOI: 10.3892/ol.2024.14660] [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: 02/22/2024] [Accepted: 07/18/2024] [Indexed: 09/15/2024] Open
Abstract
Head and neck cancer (HNC) is the sixth most common type of cancer worldwide, and head and neck squamous cell carcinoma (HNSCC) accounts for 90% of HNC cases. Furthermore, HNSCC accounts for 400,000 cancer-associated deaths worldwide each year. However, at present there is an absence of a versatile biomarker that can be used for diagnosis, prognosis evaluation and as a therapeutic target for HNSCC. In the present study, bioinformatics analysis was used to assess the relationship between hub genes and the clinical features of patients with HNSCC. The findings from the bioinformatics analysis were then verified using clinical samples and in vitro experiments. A total of 51 overlapping genes were identified from the intersection of differentially expressed genes and co-expressed genes. The top 10 hub genes were obtained from a protein-protein interaction network of overlapping genes. Among the hub genes, only secretoglobin family 1A member 1 (SCGB1A1) was significantly associated with both overall and disease-free survival. Specifically, upregulated SCGB1A1 expression levels were associated with prolonged overall and disease-free survival. Moreover, the SCGB1A1 expression levels were negatively correlated with drug sensitivity. Notably, it was demonstrated that SCGB1A1 was involved in tumor immunoreaction by affecting the infiltration of cells and checkpoint regulation of immune cells. Additionally, it was shown that SCGB1A1 regulated multiple key cancer-related signaling pathways, including extracellular matrix receptor interaction, transforming growth factor-β and tumor metabolism signaling pathways. Based on the results of the present study, SCGB1A1 may serve as a novel biomarker for predicting the diagnosis, prognosis and therapeutic effectiveness of certain drugs in patients with HNSCC. Moreover, SCGB1A1 may serve as a potential therapeutic target for the management of HNSCC.
Collapse
Affiliation(s)
- Jing Wang
- Center of Oral Medicine, Qingdao Municipal Hospital, Qingdao, Shandong 266000, P.R. China
- R&D, Shandong Yinfeng Life Science Research Institute, Jinan, Shandong 250000, P.R. China
| | - Qianqian Xu
- Qingdao Cancer Institute, School of Basic Medicine, Qingdao Medical College, Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Jiangbo Yu
- Center of Oral Medicine, Qingdao Municipal Hospital, Qingdao, Shandong 266000, P.R. China
| | - Aotian Xu
- R&D, Qingdao Sino-cell Biomedicine Co., Ltd., Qingdao, Shandong 266000, P.R. China
| | - Lizheng Yu
- Department of Vascular Surgery, Qingdao Medical College, Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Zhenggang Chen
- Center of Oral Medicine, Qingdao Municipal Hospital, Qingdao, Shandong 266000, P.R. China
| | - Yang Cao
- Center of Oral Medicine, Qingdao Municipal Hospital, Qingdao, Shandong 266000, P.R. China
| | - Rongtao Yuan
- Center of Oral Medicine, Qingdao Municipal Hospital, Qingdao, Shandong 266000, P.R. China
| | - Zhongjie Yu
- R&D, Qingdao Sino-cell Biomedicine Co., Ltd., Qingdao, Shandong 266000, P.R. China
| |
Collapse
|
15
|
Xu L, Wu Q, Zhao K, Li X, Yao W. Prognostic prediction signature and molecular subtype for liver cancer: A CTC/CTM‑related gene prediction model and independent external validation. Oncol Lett 2024; 28:531. [PMID: 39290961 PMCID: PMC11406422 DOI: 10.3892/ol.2024.14664] [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: 03/26/2024] [Accepted: 07/31/2024] [Indexed: 09/19/2024] Open
Abstract
Liver cancer is the second leading cause of tumor-related death worldwide, and a serious threat to lives and health. Circulating tumor cells (CTCs) facilitate the progression of various cancers, including liver cancer. The relationship between CTC/circulating tumor microemboli-related genes (CRGs) and the prognosis of liver cancer is unclear. The aim of the present study was to identify CTC/circulating tumour microemboli-related genes (CRGs) in hepatocellular carcinoma and to investigate their clinical significance. Transcriptomic data from The Cancer Genome Atlas (International Cancer Genome Consortium (ICGC) and GSE117623 databases were combined, and differentially expressed CRGs were identified. These were subsequently analyzed via least absolute shrinkage and selection operator and multivariate Cox analyses, and a five-gene risk signature was constructed. The signature was validated in the ICGC and GSE14520 dataset with survival analysis and receiver operating characteristic curve analysis. Immunocyte infiltration, tumor mutation burden (TMB), tumor immune dysfunction and exclusion (TIDE), and the somatic mutation rate were also compared between high- and low-risk groups, based on the median predictive index, to further evaluate the immunotherapeutic value of the model. Molecular subtypes of liver cancer were characterized by the non-negative matrix factorization method and potential therapeutic compounds were evaluated for different subtypes. Nomograms were utilized to predict the prognosis of patients, and the signature was compared with previous literature models. Additionally, the biological function of one of the CRGs, tumor protein p53 inducible protein 3 (TP53I3), in liver cancer was further explored through in vitro experiments. Analysis of the prognostic characteristics of the five CRGs led to the identification of two liver cancer subtypes. Patients in the low-risk group had a longer survival compared with those in the high-risk group, and patients in the latter group were associated with a higher TMB, immunocyte infiltration and somatic mutation rate, and lower TIDE scores. The prognostic profile was validated in the ICGC and GSE14520 datasets and exhibited a good predictive performance. In vitro analysis showed that the knockdown of TP53I3 suppressed liver cancer cell proliferation. In summary, CRGs were used to develop a new prognostic signature to predict the prognosis of patients with liver cancer. This signature may be used to assess the prognosis of patients and may provide new insights for clinical management strategies. In addition, TP53I3 is potentially a therapeutic target for liver cancer.
Collapse
Affiliation(s)
- Ling Xu
- Department of Nursing, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Qiansheng Wu
- Department of Nursing, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Kai Zhao
- Department of Biliary and Pancreatic Surgery/Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Xiangyu Li
- Department of Thoracic Surgery, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Wei Yao
- Department of Oncology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| |
Collapse
|
16
|
Xiao Z, Chen H, Xu N, Chen Y, Wang S, Xu X. MATR3 promotes liver cancer progression by suppressing DHX58-mediated type I interferon response. Cancer Lett 2024; 604:217231. [PMID: 39276912 DOI: 10.1016/j.canlet.2024.217231] [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: 05/24/2024] [Revised: 08/14/2024] [Accepted: 09/04/2024] [Indexed: 09/17/2024]
Abstract
MATR3 is a nuclear matrix protein implicated in various cancers; however, its specific role in tumor progression remains unclear. The study utilized the TCGA database to reveal that MATR3 expression is upregulated in liver cancer and is correlated with poor prognosis. Functionally, MATR3 promoted liver cancer cell proliferation and metastasis. Comprehensive RNA sequencing analysis showed that MATR3 significantly affected the type I IFN signaling pathway and DHX58 is a downstream target of MATR3. Further experiments showed that MATR3 bound to DHX58 mRNA through its RRM structural domain and recruited YTHDF2, an m6A reader, leading to degradation of DHX58 mRNA and suppression of the type I IFN signaling pathway. The knockout of MATR3 in liver cancer cells triggered a natural immune response that stimulated CD8+ T cells to eliminate liver cancer cells. This study demonstrated that MATR3 downregulates type I IFN signaling in liver cancer cells through m6A modification and inhibits immune cell infiltration within tumors. These findings expand our understanding of the role of MATR3 in liver cancer.
Collapse
Affiliation(s)
- Zhaofeng Xiao
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China; Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Hangzhou, 310006, China
| | - Huan Chen
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China; Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Hangzhou, 310006, China
| | - Nan Xu
- Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yiyuan Chen
- Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Shuai Wang
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Hangzhou, 310006, China.
| | - Xiao Xu
- School of Clinical Medicine, Hangzhou Medical College, Hangzhou, 310053, China; Institute of Translational Medicine, Zhejiang University, Hangzhou, 310000, China.
| |
Collapse
|
17
|
Ruixin S, Yifan L, Yansha S, Min Z, Yiwei D, Xiaoli H, Bizhi S, Hua J, Zonghai L. Dual targeting chimeric antigen receptor cells enhance antitumour activity by overcoming T cell exhaustion in pancreatic cancer. Br J Pharmacol 2024; 181:4628-4646. [PMID: 39129178 DOI: 10.1111/bph.16505] [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: 12/14/2023] [Revised: 05/15/2024] [Accepted: 05/29/2024] [Indexed: 08/13/2024] Open
Abstract
BACKGROUND AND PURPOSE Although our previous data indicated that claudin 18 isoform 2 (CLDN18.2)-targeted chimeric antigen receptor (CAR) T cells displayed remarkable clinical efficacy in CLDN18.2-positive gastric cancer, their efficacy is limited in pancreatic ductal adenocarcinoma (PDAC). The tumour microenvironment (TME) is one of the main obstacles to the efficacy of CAR-T and remodelling the TME may be a possible way to overcome this obstacle. The TME of PDAC is characterized by abundant cancer-related fibroblasts (CAFs), which hinder the infiltration and function of CLDN18.2-targeted CAR-T cells. The expression of fibroblast activation protein alpha (FAP) is an important feature of active CAFs, providing potential targets for eliminating CAFs. EXPERIMENTAL APPROACH In this study, we generated 10 FAP/CLDN 18.2 dual-targeted CAR-T cells and evaluated their anti-tumour ability in vitro and in vivo. KEY RESULTS Compared with conventional CAR-T cells, some dual-targeted CAR-T cells showed improved therapeutic effects in mouse pancreatic cancers. Further, dual-targeted CAR-T cells with better anti-tumour effect could suppress the recruitment of myeloid-derived suppressor cells (MDSCs) to improve the immunosuppressive TME, which contributes to the survival of CD8+ T cells. Moreover, dual-targeted CAR-T cells reduced the exhaustion of T cells in transforming TGF-β dependent manner. CONCLUSION AND IMPLICATIONS The dual-targeted CAR-T cells obtained enhancement of T effector function, inhibition of T cell exhaustion, and improvement of tumour microenvironment. Our findings provide a theoretical rationale for dual-targeted FAP/CLDN 18.2 CAR-T cells therapy in PDAC.
Collapse
Affiliation(s)
- Sun Ruixin
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Liu Yifan
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Sun Yansha
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhou Min
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Dong Yiwei
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hu Xiaoli
- CARsgen Therapeutics, Shanghai, China
| | - Shi Bizhi
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- CARsgen Therapeutics, Shanghai, China
| | - Jiang Hua
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- CARsgen Therapeutics, Shanghai, China
| | - Li Zonghai
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- CARsgen Therapeutics, Shanghai, China
| |
Collapse
|
18
|
Zhou K, Zhang M, Zhai D, Wang Z, Liu T, Xie Y, Shi Y, Shi H, Chen Q, Li X, Xu J, Cai Z, Zhang Y, Shao N, Lin Y. Genomic and transcriptomic profiling of inflammatory breast cancer reveals distinct molecular characteristics to non-inflammatory breast cancers. Breast Cancer Res Treat 2024; 208:441-459. [PMID: 39030466 DOI: 10.1007/s10549-024-07437-0] [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] [Received: 02/23/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
PURPOSE Inflammatory breast cancer (IBC), a rare and highly aggressive form of breast cancer, accounts for 10% of breast cancer-related deaths. Previous omics studies of IBC have focused solely on one of genomics or transcriptomics and did not discover common differences that could distinguish IBC from non-IBC. METHODS Seventeen IBC patients and five non-IBC patients as well as additional thirty-three Asian breast cancer samples from TCGA-BRCA were included for the study. We performed whole-exon sequencing (WES) to investigate different somatic genomic alterations, copy number variants, and large structural variants between IBC and non-IBC. Bulk RNA sequencing (RNA-seq) was performed to examine the differentially expressed genes, pathway enrichment, and gene fusions. WES and RNA-seq data were further investigated in combination to discover genes that were dysregulated in both genomics and transcriptomics. RESULTS Copy number variation analysis identified 10 cytobands that showed higher frequency in IBC. Structural variation analysis showed more frequent deletions in IBC. Pathway enrichment and immune infiltration analysis indicated increased immune activation in IBC samples. Gene fusions including CTSC-RAB38 were found to be more common in IBC. We demonstrated more commonly dysregulated RAS pathway in IBC according to both WES and RNA-seq. Inhibitors targeting RAS signaling and its downstream pathways were predicted to possess promising effects in IBC treatment. CONCLUSION We discovered differences unique in Asian women that could potentially explain IBC etiology and presented RAS signaling pathway as a potential therapeutic target in IBC treatment.
Collapse
Affiliation(s)
- Kaiwen Zhou
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Mengmeng Zhang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Duanyang Zhai
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zilin Wang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ting Liu
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yubin Xie
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yawei Shi
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Huijuan Shi
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qianjun Chen
- Department of Breast Oncology, Traditional Chinese Medicine Hospital of Guangdong Province, Guangzhou, Guangdong, China
| | - Xiaoping Li
- Department of Breast Oncology, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Juan Xu
- Department of Breast Oncology, Maternal and Child Health Care Hospital of Guangdong Province, Guangzhou, China
| | - Zhenhai Cai
- Department of Breast Oncology, Jieyang People's Hospital, Jieyang, Guangdong, China
| | - Yunjian Zhang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Nan Shao
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Ying Lin
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
| |
Collapse
|
19
|
Zhang Y, Wu D, Yu T, Liu Y, Zhao C, Xue R. Prognostic value of TMTC1 in pan-cancer analysis. Heliyon 2024; 10:e38308. [PMID: 39397950 PMCID: PMC11471174 DOI: 10.1016/j.heliyon.2024.e38308] [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: 11/24/2023] [Revised: 09/20/2024] [Accepted: 09/22/2024] [Indexed: 10/15/2024] Open
Abstract
Background Transmembrane and tetratricopeptide repeat containing 1 (TMTC1) is a recently discovered enzyme involved in the O-mannosylation of cadherins and protocadherins. It has been implicated in various types of cancer, but the overall prognostic significance of TMTC1 in pan-cancer and its potential as an immunotherapeutic target remain unclear. Methods We applied various bioinformatics methods to investigate the potential oncogenic roles of TMTC1 using public databases. This analysis involved examining the expression, prognosis, genetic alterations, immune infiltration, immunotherapy response, drug sensitivity, and regulatory mechanisms of the TMTC1 gene in diverse cancer types. Results In this study, we observed that TMTC1 expression is reduced in 19 types of cancer (ACC, BLCA, BRCA, CESC, COAD, ESCA, GBM, KICH, KIRC, KIRP, LAML, LUAD, LUSC, PRAD, READ, STAD, THCA, UCEC, and UCS) compared to normal tissues. Conversely, TMTC1 expression is elevated in OV and PAAD relative to normal tissues. Moreover, our analysis revealed that high expression of TMTC1 was associated with worse overall survival (OS) outcomes in patients with ACC, BLCA, COAD, GBM, KIRP, OV, STAD, and UCEC, but better OS outcomes in patients with CESC, KIRC, LUSC, and PAAD. Notably, patients with TMTC1 mutations or deep deletions demonstrated longer OS, while those with TMTC1 amplification showed shorter OS. There was a significant correlation between the expression level of TMTC1 and the infiltration of cancer-associated fibroblasts (CAFs) and endothelial cells. Using data from six real-world immunotherapy cohorts of BLCA, SKCM and RCC, we discovered that high TMTC1 expression was associated with better OS or progression-free survival (PFS). Lastly, through TMTC1-related gene enrichment analysis, some biological processes and pathways were found to be significantly enriched, such as vascular endothelial growth factor receptor signaling pathway and ECM-receptor interaction. Conclusions Our study demonstrates the prognostic significance of TMTC1 in pan-cancer and highlights its potential as an immunotherapeutic target.
Collapse
Affiliation(s)
- Ying Zhang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Labouratory of Embryo Original Diseases, 200030, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Dan Wu
- Department of Obstrics and Gynecology, The First People's Hospital of Jiande, Hangzhou, China
| | - Tiantian Yu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Labouratory of Embryo Original Diseases, 200030, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Yao Liu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Labouratory of Embryo Original Diseases, 200030, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Chunbo Zhao
- Department of Obstrics and Gynecology, The First People's Hospital of Jiande, Hangzhou, China
| | - Ruihong Xue
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Labouratory of Embryo Original Diseases, 200030, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
| |
Collapse
|
20
|
Xu H, Leng J, Liu F, Chen T, Qu J, Yang Y, Ning C, Ke X, Xiao B, Zhang Y, Sun L. Tumor microbiota of renal cell carcinoma affects clinical prognosis by influencing the tumor immune microenvironment. Heliyon 2024; 10:e38310. [PMID: 39397906 PMCID: PMC11470785 DOI: 10.1016/j.heliyon.2024.e38310] [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: 11/20/2023] [Revised: 09/05/2024] [Accepted: 09/22/2024] [Indexed: 10/15/2024] Open
Abstract
Despite reported influences of the intratumoral microbiome on cancer progression, its role in this subtype remains unclear. This study aimed to characterize the microbial landscape and signatures of kidney renal clear cell carcinoma using RNA-Seq data from The Cancer Genome Atlas. Following microbial decontamination, differential microbial analysis was conducted between tumorous and adjacent non-tumorous samples. Compared to non-tumorous samples, tumorous microbiota exhibited reduced α and β diversity and distinct phylum-level communities. Differential microbial analysis between patients exhibiting long and short overall survival revealed ten significant differential microbial genera, with six genera correlating with a positive prognosis (Plasmodium, Babesia, Toxoplasma, Cytobacillus, Alicyclobacillus, Verrucomicrobium) and four with a negative prognosis (Colletotrichum, Leuconostoc, Gluconobacter, and Parabacteroides). Employing Cox regression analysis and support vector machines, a prognosis-related microbiome risk signature was developed, achieving an AUC of 0.809. Based on this risk signature, two microbiome-based subtypes were found to be significantly associated with distinct clinical prognoses and immune microenvironments. These findings were corroborated by significant correlations between prognostic-relevant microorganisms and 30 immune-related differentially expressed genes. Specifically, microbial genera associated with a negative prognosis were linked to a pro-tumor acute inflammatory immune response, whereas genera related to a positive prognosis were associated with an anti-tumor adaptive immune response. In conclusion, microbiome-based subtyping revealed correlations between tumor microbiome, clinical prognosis, and tumor microenvironment, indicating intratumoral microbiota as a promising prognostic biomarker for kidney renal clear cell carcinoma.
Collapse
Affiliation(s)
- Hengyi Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, China
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Jingze Leng
- School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Fengshuo Liu
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Tianxiang Chen
- School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Jiangming Qu
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Yufan Yang
- School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Chun Ning
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Xindi Ke
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Bin Xiao
- Department of Spine Surgery, Beijing Jishuitan Hospital, Affiliated Hospital of Capital Medicine University, 100035, Beijing, China
| | - Yanbin Zhang
- Department of Spine Surgery, Beijing Jishuitan Hospital, Affiliated Hospital of Capital Medicine University, 100035, Beijing, China
| | - Lejia Sun
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, China
| |
Collapse
|
21
|
He Q, Zhang Y, Li W, Chen S, Xiong J, Zhao R, Yuan K, Hu Q, Liu S, Gao G, Bedford MT, Tang DG, Xu B, Zou C, Zhang D. Inhibition of PRMT5 moderately suppresses prostate cancer growth in vivo but enhances its response to immunotherapy. Cancer Lett 2024; 602:217214. [PMID: 39218291 DOI: 10.1016/j.canlet.2024.217214] [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: 05/07/2024] [Revised: 08/11/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
Protein arginine methylation is a common post-translational modification (PTM) catalyzed by nine protein arginine methyltransferases (PRMTs). As the major symmetric arginine methyltransferase that methylates both histone and non-histone substrates, PRMT5 plays key roles in a number of biological processes critical for development and tumorigenesis. PRMT5 overexpression has been reported in multiple cancer types including prostate cancer (PCa), but the exact biological and mechanistic understanding of PRMT5 in aggressive PCa remains ill-defined. Here, we show that PRMT5 is upregulated in PCa, correlates with worse patient survival, promotes corrupted RNA splicing, and functionally cooperates with an array of pro-tumorigenic pathways to enhance oncogenesis. PRMT5 inhibition via either genetic knockdown or pharmacological inhibition reduces stemness with paralleled differentiation and arrests cell cycle progression without causing appreciable apoptosis. Strikingly, the severity of antitumor effect of PRMT5 inhibition correlates with disease aggressiveness, with AR+ PCa being less affected. Molecular characterization pinpoints MYC, but not (or at least to a lesser degree) AR, as the main partner of PRMT5 to form a positive feedback loop to exacerbate malignancy in both AR+ and AR- PCa cells. Inspired by the surprising finding that PRMT5 negatively correlates with tumor immune infiltration and transcriptionally suppresses an immune-gene program, we further show that although PRMT5 inhibitor (PRMT5i) EPZ015666 or anti-PD-1 immunotherapy alone exhibits limited antitumor effects, combination of PRMT5i with anti-PD-1 displays superior efficacy in inhibiting castration-resistant PCa (CRPC) in vivo. Finally, to expand the potential use of PRMT5i through a synthetic lethality concept, we also perform a global CRISPR/Cas9 knockout screen to unravel that many clinical-grade drugs of known oncogenic pathways can be repurposed to target CRPC when used in combination with PRMT5i at low doses. Collectively, our findings establish a rationale to exploit PRMT5i in combination with immunotherapy or other targeted therapies to treat aggressive PCa.
Collapse
Affiliation(s)
- Qinju He
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Yuanzhen Zhang
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Wenchao Li
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China
| | - Saisai Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China
| | - Jiangling Xiong
- Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Ruizhe Zhao
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA; Current Address: Department of Urology, First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410000, China
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, 14263, New York, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, 14263, New York, USA
| | - Guozhen Gao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dean G Tang
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China.
| | - Cheng Zou
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China; Shenzhen Research Institute, Hunan University, Shenzhen, 518000, China.
| | - Dingxiao Zhang
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China; Shenzhen Research Institute, Hunan University, Shenzhen, 518000, China.
| |
Collapse
|
22
|
Xu S, Wan M, Ye C, Chen R, Li Q, Zhang X, Ruan J. Machine learning based on biological context facilitates the identification of microvascular invasion in intrahepatic cholangiocarcinoma. Carcinogenesis 2024; 45:721-734. [PMID: 39086220 DOI: 10.1093/carcin/bgae052] [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: 05/27/2024] [Accepted: 07/31/2024] [Indexed: 08/02/2024] Open
Abstract
Intrahepatic cholangiocarcinoma is a rare disease associated with a poor prognosis, primarily due to early recurrence and metastasis. An important feature of this condition is microvascular invasion (MVI). However, current predictive models based on imaging have limited efficacy in this regard. This study employed a random forest model to construct a predictive model for MVI identification and uncover its biological basis. Single-cell transcriptome sequencing, whole exome sequencing, and proteome sequencing were performed. The area under the curve of the prediction model in the validation set was 0.93. Further analysis indicated that MVI-associated tumor cells exhibited functional changes related to epithelial-mesenchymal transition and lipid metabolism due to alterations in the nuclear factor-kappa B and mitogen-activated protein kinase signaling pathways. Tumor cells were also differentially enriched for the interleukin-17 signaling pathway. There was less infiltration of SLC30A1+ CD8+ T cells expressing cytotoxic genes in MVI-associated intrahepatic cholangiocarcinoma, whereas there was more infiltration of myeloid cells with attenuated expression of the major histocompatibility complex II pathway. Additionally, MVI-associated intercellular communication was closely related to the SPP1-CD44 and ANXA1-FPR1 pathways. These findings resulted in a brilliant predictive model and fresh insights into MVI.
Collapse
Affiliation(s)
- Shuaishuai Xu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, 25 Taiping Road, Luzhou 646000, Sichuan Province, China
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, 79 Qingchun Road, Hangzhou 310000, Zhejiang Province, China
| | - Mingyu Wan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, 79 Qingchun Road, Hangzhou 310000, Zhejiang Province, China
| | - Chanqi Ye
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, 79 Qingchun Road, Hangzhou 310000, Zhejiang Province, China
| | - Ruyin Chen
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, 79 Qingchun Road, Hangzhou 310000, Zhejiang Province, China
| | - Qiong Li
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, 79 Qingchun Road, Hangzhou 310000, Zhejiang Province, China
| | - Xiaochen Zhang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, 79 Qingchun Road, Hangzhou 310000, Zhejiang Province, China
| | - Jian Ruan
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, 25 Taiping Road, Luzhou 646000, Sichuan Province, China
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, 79 Qingchun Road, Hangzhou 310000, Zhejiang Province, China
| |
Collapse
|
23
|
Mao C, Chen Y, Xing D, Zhang T, Lin Y, Long C, Yu J, Luo Y, Ming T, Xie W, Han Z, Mei D, Xiang D, Lu M, Shen X, Xue X. Resting natural killer cells promote the progress of colon cancer liver metastasis by elevating tumor-derived stem cell factor. eLife 2024; 13:RP97201. [PMID: 39387546 PMCID: PMC11466454 DOI: 10.7554/elife.97201] [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] [Indexed: 10/14/2024] Open
Abstract
The abundance and biological contribution of natural killer (NK) cells in cancer are controversial. Here, we aim to uncover clinical relevance and cellular roles of NK cells in colon cancer liver metastasis (CCLM). Here, we integrated single-cell RNA-sequencing, spatial transcriptomics (ST), and bulk RNA-sequencing datasets to investigate NK cells' biological properties and functions in the microenvironment of primary and liver metastatic tumors. Results were validated through an in vitro co-culture experiment based on bioinformatics analysis. Useing single-cell RNA-sequencing and ST, we mapped the immune cellular landscape of colon cancer and well-matched liver metastatic cancer. We discovered that GZMK+ resting NK cells increased significantly in tumor tissues and were enriched in the tumor regions of both diseases. After combining bulk RNA and clinical data, we observed that these NK cell subsets contributed to a worse prognosis. Meanwhile, KIR2DL4+ activated NK cells exhibited the opposite position and relevance. Pseudotime cell trajectory analysis revealed the evolution of activated to resting NK cells. In vitro experiments further confirmed that tumor-cell-co-cultured NK cells exhibited a decidual-like status, as evidenced by remarkable increasing CD9 expression. Functional experiments finally revealed that NK cells exhibited tumor-activating characteristics by promoting the dissociation of SCF (stem cell factor) on the tumor cells membrane depending on cell-to-cell interaction, as the supernatant of the co-culture system enhanced tumor progression. In summary, our findings revealed resting NK cells exhibited a clinical relevance with CCLM, which may be exploited for novel strategies to improve therapeutic outcomes for patients with CCLM.
Collapse
Affiliation(s)
- Chenchen Mao
- Department of General Surgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical UniversityWenzhouChina
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical UniversityWenzhouChina
| | - Yanyu Chen
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical UniversityWenzhouChina
- Department of Pediatric Thoracic Surgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Dong Xing
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical UniversityWenzhouChina
| | - Teming Zhang
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical UniversityWenzhouChina
| | - Yangxuan Lin
- Department of Thoracic Surgery, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Cong Long
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical UniversityWenzhouChina
| | - Jiaye Yu
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical UniversityWenzhouChina
| | - Yunhui Luo
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical UniversityWenzhouChina
| | - Tao Ming
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical UniversityWenzhouChina
| | - Wangkai Xie
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical UniversityWenzhouChina
| | - Zheng Han
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical UniversityWenzhouChina
| | - Dianfeng Mei
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical UniversityWenzhouChina
| | - Dan Xiang
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical UniversityWenzhouChina
| | - Mingdong Lu
- Department of General Surgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Xian Shen
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Xiangyang Xue
- Department of General Surgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical UniversityWenzhouChina
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical UniversityWenzhouChina
| |
Collapse
|
24
|
Huang J, Shi Z, Huang Z, Lai S. Identification and Verification of Potential Markers Related to Myocardial Fibrosis by Bioinformatics Analysis. Biochem Genet 2024:10.1007/s10528-024-10937-9. [PMID: 39387979 DOI: 10.1007/s10528-024-10937-9] [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: 10/07/2023] [Accepted: 10/01/2024] [Indexed: 10/15/2024]
Abstract
Mounting evidence indicates that myocardial fibrosis (MF) is frequently intertwined with immune and metabolic disorders. This comprehensive review aims to delve deeply into the crucial role of immune-related signature genes in the pathogenesis and progression of MF. This exploration holds significant importance as understanding the underlying mechanisms of MF is essential for developing effective diagnostic and therapeutic strategies. The dataset GSE9735 about myocardial fibrosis and non-fibrosis was downloaded from GEO database. Differentially expressed genes (DEGs) were identified by 'limma' package in R software. Then, the biological function of DEG was determined by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. XCell was used to estimate the composition pattern of matrix and immune cells. Protein-protein interaction (PPI) network was constructed based on STRING analysis software, and Hub genes were screened and functional modules were analyzed. The correlation between hub genes and immune cell subtypes was analyzed. Hub genes with |correlation coefficient|> 0.45 and p-value < 0.05 were used as characteristic biomarkers. Finally, the logistic regression model is used to verify the three markers in the training set and verification set (GSE97358 and GSE225336). A total of 635 DEGs were identified. Functional enrichment analysis shows that inflammation and immune response, extracellular matrix and structural remodeling play an important role in the pathological mechanism of MF. Immune cell infiltration analysis showed that immune cells (Plasma cells, Eosinophils, Chondrocytes and Th2 cells) significantly changed in MF pathological conditions. In PPI network analysis, IL1β, TTN, PTPRC, IGF1, ALDH1A1, CYP26A1, ALDH1A3, MYH11, CSF1R and CD80 were identified as hub genes, among which IL1β, CYP26A1 and GNG2 were regarded as immune-related characteristic markers. The AUC scores of the three biomarkers are all above 0.65, which proves that they have a good discrimination effect in MF. In this study, three immune-related genes were identified as diagnostic biomarkers of MF, which provided a new perspective for exploring the molecular mechanism of MF. This study takes a comprehensive approach to understanding the intricate relationship between myocardial fibrosis and immune metabolism. By identifying key immune-related biomarkers, this study not only reveals the molecular basis of myocardial fibrosis but also paves the way for the development of novel diagnostic tools and therapeutic strategies. These findings are critical for improving patient prognosis and may have broader implications for studying and treating other cardiovascular diseases associated with immune dysregulation.
Collapse
Affiliation(s)
- Jiazhuo Huang
- Department of Cardiology, The First People's Hospital of Zhaoqing City, No.9 Donggang East Road, Zhaoqing, 526040, Guangdong, China
| | - Zhentao Shi
- Department of Cardiology, The First People's Hospital of Zhaoqing City, No.9 Donggang East Road, Zhaoqing, 526040, Guangdong, China
| | - Zhifeng Huang
- Department of Cardiology, The First People's Hospital of Zhaoqing City, No.9 Donggang East Road, Zhaoqing, 526040, Guangdong, China
| | - Shaobin Lai
- Department of Cardiology, The First People's Hospital of Zhaoqing City, No.9 Donggang East Road, Zhaoqing, 526040, Guangdong, China.
| |
Collapse
|
25
|
Egeland EV, Seip K, Skourti E, Øy GF, Pettersen SJ, Pandya AD, Dahle MA, Haugen MH, Kristian A, Nakken S, Engebraaten O, Mælandsmo GM, Prasmickaite L. The SRC-family serves as a therapeutic target in triple negative breast cancer with acquired resistance to chemotherapy. Br J Cancer 2024:10.1038/s41416-024-02875-5. [PMID: 39390250 DOI: 10.1038/s41416-024-02875-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 09/26/2024] [Accepted: 10/02/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Resistance to chemotherapy, combined with heterogeneity among resistant tumors, represents a significant challenge in the clinical management of triple negative breast cancer (TNBC). By dissecting molecular pathways associated with treatment resistance, we sought to define patient sub-groups and actionable targets for next-line treatment. METHODS Bulk RNA sequencing and reverse phase protein array profiling were performed on isogenic patient-derived xenografts (PDX) representing paclitaxel-sensitive and -resistant tumors. Pathways identified as upregulated in the resistant model were further explored as targets in PDX explants. Their clinical relevance was assessed in two distinct patient cohorts (NeoAva and MET500). RESULTS Increased activity in signaling pathways involving SRC-family kinases (SFKs)- and MAPK/ERK was found in treatment resistant PDX, with targeted inhibitors being significantly more potent in resistant tumors. Up-regulation of SFKs- and MAPK/ERK-pathways was also detected in a sub-group of chemoresistant patients after neoadjuvant treatment. Furthermore, High SFK expression (of either SRC, FYN and/or YES1) was detected in metastatic lesions of TNBC patients with fast progressing disease (median disease-free interval 27 vs 105 months). CONCLUSIONS Upregulation of SFK-signaling is found in a subset of chemoresistant tumors and is persistent in metastatic lesions. Based on pre-clinical results, these patients may respond favorably to treatment targeting SFKs.
Collapse
Affiliation(s)
- Eivind Valen Egeland
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
| | - Kotryna Seip
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Eleni Skourti
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Insitute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Geir Frode Øy
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Solveig J Pettersen
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Abhilash D Pandya
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Maria A Dahle
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Insitute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Mads H Haugen
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Department of Research and Innovation, Vestre Viken Hospital Trust, Drammen, Norway
| | - Alexander Kristian
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Olav Engebraaten
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Insitute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Gunhild M Mælandsmo
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Department of Medical Biology, Faculty of Health Sciences, The Arctic University of Norway-University of Tromsø, Tromsø, Norway
| | - Lina Prasmickaite
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| |
Collapse
|
26
|
Skoulidis F, Araujo HA, Do MT, Qian Y, Sun X, Cobo AG, Le JT, Montesion M, Palmer R, Jahchan N, Juan JM, Min C, Yu Y, Pan X, Arbour KC, Vokes N, Schmidt ST, Molkentine D, Owen DH, Memmott R, Patil PD, Marmarelis ME, Awad MM, Murray JC, Hellyer JA, Gainor JF, Dimou A, Bestvina CM, Shu CA, Riess JW, Blakely CM, Pecot CV, Mezquita L, Tabbó F, Scheffler M, Digumarthy S, Mooradian MJ, Sacher AG, Lau SCM, Saltos AN, Rotow J, Johnson RP, Liu C, Stewart T, Goldberg SB, Killam J, Walther Z, Schalper K, Davies KD, Woodcock MG, Anagnostou V, Marrone KA, Forde PM, Ricciuti B, Venkatraman D, Van Allen EM, Cummings AL, Goldman JW, Shaish H, Kier M, Katz S, Aggarwal C, Ni Y, Azok JT, Segal J, Ritterhouse L, Neal JW, Lacroix L, Elamin YY, Negrao MV, Le X, Lam VK, Lewis WE, Kemp HN, Carter B, Roth JA, Swisher S, Lee R, Zhou T, Poteete A, Kong Y, Takehara T, Paula AG, Parra Cuentas ER, Behrens C, Wistuba II, Zhang J, Blumenschein GR, Gay C, Byers LA, Gibbons DL, Tsao A, Lee JJ, Bivona TG, Camidge DR, Gray JE, Lieghl N, Levy B, Brahmer JR, Garassino MC, Gandara DR, Garon EB, Rizvi NA, Scagliotti GV, Wolf J, Planchard D, Besse B, Herbst RS, Wakelee HA, Pennell NA, Shaw AT, Jänne PA, Carbone DP, Hellmann MD, Rudin CM, Albacker L, Mann H, Zhu Z, Lai Z, Stewart R, Peters S, Johnson ML, Wong KK, Huang A, Winslow MM, Rosen MJ, Winters IP, Papadimitrakopoulou VA, Cascone T, Jewsbury P, Heymach JV. CTLA4 blockade abrogates KEAP1/STK11-related resistance to PD-(L)1 inhibitors. Nature 2024:10.1038/s41586-024-07943-7. [PMID: 39385035 DOI: 10.1038/s41586-024-07943-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 08/13/2024] [Indexed: 10/11/2024]
Abstract
For patients with advanced non-small-cell lung cancer (NSCLC), dual immune checkpoint blockade (ICB) with CTLA4 inhibitors and PD-1 or PD-L1 inhibitors (hereafter, PD-(L)1 inhibitors) is associated with higher rates of anti-tumour activity and immune-related toxicities, when compared with treatment with PD-(L)1 inhibitors alone. However, there are currently no validated biomarkers to identify which patients will benefit from dual ICB1,2. Here we show that patients with NSCLC who have mutations in the STK11 and/or KEAP1 tumour suppressor genes derived clinical benefit from dual ICB with the PD-L1 inhibitor durvalumab and the CTLA4 inhibitor tremelimumab, but not from durvalumab alone, when added to chemotherapy in the randomized phase III POSEIDON trial3. Unbiased genetic screens identified loss of both of these tumour suppressor genes as independent drivers of resistance to PD-(L)1 inhibition, and showed that loss of Keap1 was the strongest genomic predictor of dual ICB efficacy-a finding that was confirmed in several mouse models of Kras-driven NSCLC. In both mouse models and patients, KEAP1 and STK11 alterations were associated with an adverse tumour microenvironment, which was characterized by a preponderance of suppressive myeloid cells and the depletion of CD8+ cytotoxic T cells, but relative sparing of CD4+ effector subsets. Dual ICB potently engaged CD4+ effector cells and reprogrammed the tumour myeloid cell compartment towards inducible nitric oxide synthase (iNOS)-expressing tumoricidal phenotypes that-together with CD4+ and CD8+ T cells-contributed to anti-tumour efficacy. These data support the use of chemo-immunotherapy with dual ICB to mitigate resistance to PD-(L)1 inhibition in patients with NSCLC who have STK11 and/or KEAP1 alterations.
Collapse
Affiliation(s)
- Ferdinandos Skoulidis
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Haniel A Araujo
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Minh Truong Do
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yu Qian
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Sun
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ana Galan Cobo
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John T Le
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | | | | | - Yi Yu
- Tango Therapeutics, Boston, MA, USA
| | | | - Kathryn C Arbour
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Natalie Vokes
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephanie T Schmidt
- Department of Genomic Medicine and the Institute for Data Science in Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Molkentine
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dwight H Owen
- Division of Medical Oncology, Ohio State University-James Comprehensive Cancer Center, Columbus, OH, USA
| | - Regan Memmott
- Division of Medical Oncology, Ohio State University-James Comprehensive Cancer Center, Columbus, OH, USA
| | - Pradnya D Patil
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Melina E Marmarelis
- Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joseph C Murray
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | | | | | | | - Jonathan W Riess
- University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | | | - Chad V Pecot
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
| | - Laura Mezquita
- Department of Medical Oncology, Hospital Clinic de Barcelona, Barcelona, Spain
| | | | - Matthias Scheffler
- Department of Internal Medicine, Center for Integrated Oncology, University Hospital Cologne, Cologne, Germany
| | - Subba Digumarthy
- Department of Radiology, Massachussetts General Hospital, Boston, MA, USA
| | | | | | - Sally C M Lau
- Department of Medical Oncology, NYU Langone Perlmutter Cancer Center, New York, NY, USA
| | - Andreas N Saltos
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Julia Rotow
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rocio Perez Johnson
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Corinne Liu
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tyler Stewart
- Division of Hematology-Oncology, University of California San Diego, La Jolla, CA, USA
| | | | | | - Zenta Walther
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Kurt Schalper
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Kurtis D Davies
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Mark G Woodcock
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
| | - Valsamo Anagnostou
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kristen A Marrone
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patrick M Forde
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Deepti Venkatraman
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M Van Allen
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amy L Cummings
- David Geffen School of Medicine at the University of California, Los Angeles, CA, USA
| | - Jonathan W Goldman
- David Geffen School of Medicine at the University of California, Los Angeles, CA, USA
| | | | - Melanie Kier
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sharyn Katz
- Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Charu Aggarwal
- Division of Hematology and Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Ying Ni
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Joseph T Azok
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jeremy Segal
- Department of Pathology, University of Chicago, Chicago, USA
| | | | - Joel W Neal
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Yasir Y Elamin
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marcelo V Negrao
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiuning Le
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vincent K Lam
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Whitney E Lewis
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Haley N Kemp
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brett Carter
- Department of Thoracic Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jack A Roth
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen Swisher
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Richard Lee
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Teng Zhou
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alissa Poteete
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yifan Kong
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tomohiro Takehara
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alvaro Guimaraes Paula
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edwin R Parra Cuentas
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmen Behrens
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Zhang
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George R Blumenschein
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carl Gay
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren A Byers
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Don L Gibbons
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anne Tsao
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Jack Lee
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Trever G Bivona
- University of California San Francisco, San Francisco, CA, USA
| | | | - Jhannelle E Gray
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Natasha Lieghl
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Benjamin Levy
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Julie R Brahmer
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - David R Gandara
- University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Edward B Garon
- David Geffen School of Medicine at the University of California, Los Angeles, CA, USA
| | | | | | - Jürgen Wolf
- Department of Internal Medicine, Center for Integrated Oncology, University Hospital Cologne, Cologne, Germany
| | | | | | | | | | | | - Alice T Shaw
- Novartis Institute for Biomedical Research, Cambridge, MA, USA
| | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David P Carbone
- Division of Medical Oncology, Ohio State University-James Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | | | | | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne University, Lausanne, Switzerland
| | - Melissa L Johnson
- Sarah Cannon Research Institute, Tennessee Oncology, Nashville, TN, USA
| | - Kwok K Wong
- Division of Hematology & Medical Oncology, NYU Langone Perlmutter Cancer Center, New York, NY, USA
| | | | - Monte M Winslow
- D2G Oncology, Mountain View, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | | | | | - Tina Cascone
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - John V Heymach
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
27
|
Dai Y, Shao M, Li L, Li H, Lu T, Lyu F. Molecular characterization of PANoptosis-related genes as novel signatures for peripheral nerve injury based on time-series transcriptome sequencing. Gene 2024:148995. [PMID: 39393431 DOI: 10.1016/j.gene.2024.148995] [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: 06/25/2024] [Revised: 10/04/2024] [Accepted: 10/07/2024] [Indexed: 10/13/2024]
Abstract
Programmed cell death (PCD) pathways play pivotal roles in the development and progression of peripheral nerve injury (PNI). PANoptosis, as a novel form of PCD pathway with key features of pyroptosis, apoptosis and necroptosis, is implicated in the pathogenesis of multiple neurologic diseases. This study aimed to identify PANoptosisrelated biomarkers and characterize their molecular roles and immune landscape in PNI. PANoptosis-related genes (PRGs) were retrieved from Reactome pathway database and previous literatures. Differentially expressed PANoptosis-related genes (DEPRGs) were identified based on a time-series transcriptome sequencing dataset. DEPRGs were predicted to be enriched in inflammatory response, inflammatory complex, PCD and NOD-like receptor signaling pathway through GO, KEGG, Reactome and GSEA analysis. Hub genes, including Ripk3, Pycard and Il18, were then recognized through PPI network and multiple algorithms. The molecular regulatory mechanisms of hub genes were elucidated by transcription factor network and competing endogenous RNA network. Moreover, the immune cell landscape of hub genes was analyzed. Eventually, the expression levels of hub genes were verified through external dataset and animal model. Ripk3, Pycard and Il18 were remarkably upregulated in PNI samples, which were in consistent with the results of bioinformatic analysis. This study uncovered the molecular characterization of PANoptosis-related genes in PNI and illustrated the novel PANoptosis biomarker for PNI.
Collapse
Affiliation(s)
- Yuan Dai
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Minghao Shao
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Linli Li
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Hailong Li
- Department of Orthopedics, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200240, China
| | - Tingwei Lu
- Center of Craniofacial Orthodontics, Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 210000, China.
| | - Feizhou Lyu
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai 200040, China; Department of Orthopedics, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200240, China.
| |
Collapse
|
28
|
Qin H, Wang Q, Xu J, Zeng H, Liu J, Yu F, Yang J. Integrative analysis of anoikis-related genes prognostic signature with immunotherapy and identification of CDKN3 as a key oncogene in lung adenocarcinoma. Int Immunopharmacol 2024; 143:113282. [PMID: 39383787 DOI: 10.1016/j.intimp.2024.113282] [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: 07/27/2024] [Revised: 09/01/2024] [Accepted: 09/26/2024] [Indexed: 10/11/2024]
Abstract
Anoikis, a form of programmed cell death induced by loss of cell contact, is closely associated with tumor invasion and metastasis, making it highly significant in lung cancer research. We examined the expression patterns and prognostic relevance of Anoikis-related genes (ARGs) in lung adenocarcinoma (LUAD) using the TCGA-LUAD database. This study identified molecular subtypes associated with Anoikis in LUAD and conducted functional enrichment analyses. We constructed an ARG risk score using univariate least absolute shrinkage and selection operator (LASSO) Cox regression, validated externally with GEO datasets and clinical samples. The clinical applicability of the prognostic model was evaluated using nomograms, calibration curves, decision curve analysis (DCA), and time-dependent AUC assessments. We identified four prognostically significant genes (PLK1, SLC2A1, CDKN3, PHLDA2) and two ARG-related molecular subtypes. ARGs were generally upregulated in LUAD and correlated with multiple pathways including the cell cycle and DNA replication. The prognostic model indicated that the low-risk group had better outcomes and significant correlations with clinicopathological features, tumor microenvironment, immune therapy responses, drug sensitivity, and pan-RNA epigenetic modification-related genes. Patients with low-risk LUAD were potential beneficiaries of immune checkpoint inhibitor (ICI) therapy. Prognostic ARGs' distribution and expression across various immune cell types were further analyzed using single-cell RNA sequencing. The pivotal role of CDKN3 in LUAD was confirmed through qRT-PCR and gene knockout experiments, demonstrating that CDKN3 knockdown inhibits tumor cell proliferation, migration, and invasion. Additionally, we constructed a ceRNA network involving CDKN3/hsa-miR-26a-5p/SNHG6, LINC00665, DUXAP8, and SLC2A1/hsa-miR-218-5p/RNASEH1-AS1, providing new insights for personalized and immune therapy decisions in LUAD patients.
Collapse
Affiliation(s)
- Haotian Qin
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen 518036, China; Shenzhen Key Laboratory of Orthopaedic Diseases and Biomaterials Research, Shenzhen 518036, China; Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Qichang Wang
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Juan Xu
- Department of Oncology, Chaohu Hospital of Anhui Medical University, Hefei 238001, China
| | - Hui Zeng
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen 518036, China; Shenzhen Key Laboratory of Orthopaedic Diseases and Biomaterials Research, Shenzhen 518036, China; Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Jixian Liu
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China.
| | - Fei Yu
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen 518036, China; Shenzhen Key Laboratory of Orthopaedic Diseases and Biomaterials Research, Shenzhen 518036, China; Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China.
| | - Jun Yang
- Department of Radiology, Peking University Shenzhen Hospital, Shenzhen 518036, China.
| |
Collapse
|
29
|
Huang P, Wolde T, Bhardwaj V, Zhang X, Pandey V. TFF3 and PVRL2 co-targeting identified by multi-omics approach as an effective cancer immunosuppression strategy. Life Sci 2024; 357:123113. [PMID: 39369842 DOI: 10.1016/j.lfs.2024.123113] [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: 07/31/2024] [Revised: 09/22/2024] [Accepted: 10/03/2024] [Indexed: 10/08/2024]
Abstract
BACKGROUND The immunosuppressive tumour microenvironment (TME) plays a critical role in cancer progression and relapse by significantly influencing cancer pathogenesis through autocrine and paracrine signalling. Trefoil factor 3 (TFF3), a secreted protein, has been implicated in modulating the TME to promote cancer advancement. Herein, we investigated the potential association between TFF3 and key immunosuppressive TME components to distinguish a co-targetable oncotherapeutic strategy. METHODS The TFF3-PVRL2 association were identified and investigated by integrating multiple bioinformatic-tools. The virtual compound screening for PVRL2 inhibitors was done with EasyVS. The TFF3-PVRL2 protein-level correlation was validated by immunoblotting, and the effectiveness of co-inhibiting TFF3 and PVRL2 was assessed using siRNA and AMPC (a TFF3 inhibitor). RESULTS Analysis of the TISIDB database revealed a positive correlation between TFF3 and PVRL2 mRNA levels across multiple cancer types. This correlation was confirmed at the protein level through immunoblot analysis. Further evaluation using TCGA pan-cancer datasets demonstrated that TFF3 and PVRL2 interact to establish an immunosuppressive TME, promoting cancer progression in BRCA, LUAD, PAAD, PRAD, and STAD. Enrichment analyses of positively correlated genes, PPI network hub proteins, and ceRNA networks involving TFF3 and PVRL2, conducted using LinkedOmics, STRING, and Cytoscape, provided insights into their potential co-functions in cancer. A cell-based assay was performed to evaluate the combined therapeutic efficacy of targeting both, TFF3 and PVRL2 and virtual screening identified potential drugs for inhibiting PVRL2. CONCLUSION PVRL2 has emerged as a promising immunoinhibitory target with significant associations with TFF3 and represents a key co-targetable molecule for effective oncotherapeutic strategies.
Collapse
Affiliation(s)
- Peng Huang
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
| | - Tesfaye Wolde
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
| | - Vipul Bhardwaj
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
| | - Xi Zhang
- Shenzhen Bay Laboratory, Shenzhen 518055, Guangdong, China.
| | - Vijay Pandey
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
| |
Collapse
|
30
|
Wang W, Jiao Y, Du X, Ye Z. Immune-related glycosylation genes based classification predicts prognosis and therapy options of osteosarcoma. Gene 2024; 933:148985. [PMID: 39369757 DOI: 10.1016/j.gene.2024.148985] [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: 07/27/2024] [Revised: 10/02/2024] [Accepted: 10/03/2024] [Indexed: 10/08/2024]
Abstract
Osteosarcoma is the most common primary bone malignancy, with a very poor prognosis. Aberrant glycosylation is close involvement in osteosarcoma. Accordingly, this study aimed at investigating the role of glycosylation genes in the prognosis and therapy options of osteosarcoma. The microenvironment of osteosarcoma was assessed using estimate algorithm. A total of 20 immune-related glycosylation genes (IRGGs) was identified using Pearson correlation analysis. Accordingly, osteosarcoma patients were divided into C1 and C2 type using consensus clustering. Multiple algorithms (Xcell, MCP-counter, ssGSEA, epic, quantiseq), cancer immune cycle analysis, and GSVA were applied to estimate the immune, molecule and metabolism characteristics of osteosarcoma, indicating that C1 type was featured with high immune infiltration, high glycosylation, enriched MEK signaling, and good prognosis, while C2 type was characterized by more metastasis, enriched immunotherapy-positive gene signatures, high tumor mutation burden, and poor prognosis. Results from TIDE algorithm and immunotherapy datasets suggested the C2 type's preference of immune checkpoint inhibitors (ICIs), while data of GDSC, CMap analysis and cell experiments indicated that C1 type was sensitivity to MEK inhibitor PD0325901. In addition, univariate Cox and Lasso analysis was combined to establish an IRGGs' risk score containing 6 genes (B3GNT8, FUT7, GAL3ST4, GALNT14, HS3ST2, and MFNG). The data of DCA and ROC indicated its well prediction of prognosis in osteosarcoma. Finally, cellular location analysis showed that the 6 genes not only distributed in tumor cells but also in immune cells. In summary, the classification and risk score based on IRGGs effectively predicted the prognosis and therapy options of osteosarcoma. Further studies on IRGGs may contribute to the understanding of cancer immunity in osteosarcoma.
Collapse
Affiliation(s)
- Wen Wang
- Zhejiang University, Hangzhou, Zhejiang 310058, China; Department of Orthopedics, Fenghua People's Hospital, 36 Gongyuan Road, Ningbo, Zhejiang 315502, China; Department of Orthopedics, Musculoskeletal Tumor Center, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Yunjia Jiao
- Clinical Laboratory, Minhang Hospital, Fudan University, No. 170, Xinsong Road, Shanghai 201199, China
| | - Xiaojing Du
- Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.
| | - Zhaoming Ye
- Zhejiang University, Hangzhou, Zhejiang 310058, China; Department of Orthopedics, Musculoskeletal Tumor Center, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.
| |
Collapse
|
31
|
Loriot Y, Kamal M, Syx L, Nicolle R, Dupain C, Mensourri N, Duquesne I, Lavaud P, Nicotra C, Ngocamus M, Lacroix L, Tselikas L, Crehange G, Friboulet L, Castel-Ajgal Z, Neuzillet Y, Borcoman E, Beuzeboc P, Marret G, Gutman T, Wong J, Radvanyi F, Dureau S, Scoazec JY, Servant N, Allory Y, Besse B, Andre F, Le Tourneau C, Massard C, Bieche I. The genomic and transcriptomic landscape of metastastic urothelial cancer. Nat Commun 2024; 15:8603. [PMID: 39366934 PMCID: PMC11452614 DOI: 10.1038/s41467-024-52915-0] [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] [Received: 03/06/2024] [Accepted: 09/20/2024] [Indexed: 10/06/2024] Open
Abstract
Metastatic urothelial carcinoma (mUC) is a lethal cancer, with limited therapeutic options. Large-scale studies in early settings provided critical insights into the genomic and transcriptomic characteristics of non-metastatic UC. The genomic landscape of mUC remains however unclear. Using Whole Exome (WES) and mRNA sequencing (RNA-seq) performed on metastatic biopsies from 111 patients, we show that driver genomic alterations from mUC were comparable to primary UC (TCGA data). APOBEC, platin, and HRD mutational signatures are the most prevalent in mUC, identified in 56%, 14%, and 9% of mUC samples, respectively. Molecular subtyping using consensus transcriptomic classification in mUC shows enrichment in neuroendocrine subtype. Paired samples analysis reveals subtype heterogeneity and temporal evolution. We identify potential therapeutic targets in 73% of mUC patients, of which FGFR3 (26%), ERBB2 (7%), TSC1 (7%), and PIK3CA (13%) are the most common. NECTIN4 and TACSTD2 are highly expressed regardless of molecular subtypes, FGFR3 alterations and sites of metastases.
Collapse
MESH Headings
- Humans
- Receptor, Fibroblast Growth Factor, Type 3/genetics
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Transcriptome
- Mutation
- Male
- Female
- Exome Sequencing
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Urinary Bladder Neoplasms/genetics
- Urinary Bladder Neoplasms/pathology
- Nectins/genetics
- Nectins/metabolism
- Aged
- Tuberous Sclerosis Complex 1 Protein/genetics
- Tuberous Sclerosis Complex 1 Protein/metabolism
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/metabolism
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/metabolism
- Class I Phosphatidylinositol 3-Kinases/genetics
- Class I Phosphatidylinositol 3-Kinases/metabolism
- Genomics
- Middle Aged
- APOBEC Deaminases/genetics
- APOBEC Deaminases/metabolism
- Urothelium/pathology
- Urothelium/metabolism
- Gene Expression Regulation, Neoplastic
- Cytidine Deaminase/genetics
- Cytidine Deaminase/metabolism
- Neoplasm Metastasis/genetics
- Aged, 80 and over
- Carcinoma, Transitional Cell/genetics
- Carcinoma, Transitional Cell/pathology
- Urologic Neoplasms/genetics
- Urologic Neoplasms/pathology
- Gene Expression Profiling/methods
Collapse
Affiliation(s)
- Yohann Loriot
- Gustave Roussy, DITEP, Gustave Roussy, Villejuif, France.
- INSERM 981, Université Paris-Saclay, Gustave Roussy, Villejuif, France.
- PRISM, Gustave Roussy, Villejuif, France.
| | - Maud Kamal
- Department of Drug Development and Innovation (D3i), Institut Curie, 75005, Paris, France.
| | - Laurene Syx
- Bioinformatics and Computational Systems Biology of Cancer, Institut Curie, PSL Research University, Mines Paris Tech, INSERM U900, 75005, Paris, France
| | - Remy Nicolle
- Université Paris Cité, Centre de Recherche sur l'Inflammation (CRI), INSERM, U1149, CNRS, ERL 8252, F-, 75018, Paris, France
| | - Celia Dupain
- Department of Drug Development and Innovation (D3i), Institut Curie, 75005, Paris, France
| | - Naoual Mensourri
- INSERM 981, Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Igor Duquesne
- INSERM 981, Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Pernelle Lavaud
- INSERM 981, Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | | | - Maud Ngocamus
- Gustave Roussy, DITEP, Gustave Roussy, Villejuif, France
| | | | - Lambros Tselikas
- Department of interventional radiology, Gustave Roussy, Villejuif, France
| | - Gilles Crehange
- Department of Radiothérapie, Institut Curie, 75005 Paris & 92210 Saint-Cloud, Paris, France
| | - Luc Friboulet
- INSERM 981, Université Paris-Saclay, Gustave Roussy, Villejuif, France
- PRISM, Gustave Roussy, Villejuif, France
| | - Zahra Castel-Ajgal
- Department of Drug Development and Innovation (D3i), Institut Curie, 75005, Paris, France
| | | | - Edith Borcoman
- Department of Drug Development and Innovation (D3i), Institut Curie, 75005, Paris, France
| | | | - Grégoire Marret
- Department of Drug Development and Innovation (D3i), Institut Curie, 75005, Paris, France
| | - Tom Gutman
- Bioinformatics and Computational Systems Biology of Cancer, Institut Curie, PSL Research University, Mines Paris Tech, INSERM U900, 75005, Paris, France
| | - Jennifer Wong
- Department of Genetics, Institut Curie, 75005, Paris, France
| | | | - Sylvain Dureau
- Biometry unit, direction of clinical research, Institut Curie, 75005, Paris, France
| | - Jean-Yves Scoazec
- INSERM 981, Université Paris-Saclay, Gustave Roussy, Villejuif, France
- Biopath department, Gustave Roussy, Villejuif, France
| | - Nicolas Servant
- Bioinformatics and Computational Systems Biology of Cancer, Institut Curie, PSL Research University, Mines Paris Tech, INSERM U900, 75005, Paris, France
| | - Yves Allory
- Department of Pathology, Institut Curie, PSL Research University, 75005, Paris, France
| | - Benjamin Besse
- INSERM 981, Université Paris-Saclay, Gustave Roussy, Villejuif, France
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France
| | - Fabrice Andre
- INSERM 981, Université Paris-Saclay, Gustave Roussy, Villejuif, France
- PRISM, Gustave Roussy, Villejuif, France
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, 75005, Paris, France
- Bioinformatics and Computational Systems Biology of Cancer, Institut Curie, PSL Research University, Mines Paris Tech, INSERM U900, 75005, Paris, France
| | | | - Ivan Bieche
- Department of Genetics, Institut Curie, 75005, Paris, France
- INSERM U1016, Faculty of Pharmaceutical and Biological Sciences, Université Paris Cité, Paris, France
| |
Collapse
|
32
|
Tanaka A, Ogawa M, Zhou Y, Hendrickson RC, Miele MM, Li Z, Klimstra DS, Wang JY, Roehrl MHA. Proteomic basis for pancreatic acinar cell carcinoma and pancreatoblastoma as similar yet distinct entities. NPJ Precis Oncol 2024; 8:221. [PMID: 39363045 PMCID: PMC11449907 DOI: 10.1038/s41698-024-00708-5] [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: 05/03/2024] [Accepted: 09/12/2024] [Indexed: 10/05/2024] Open
Abstract
Acinar cell carcinoma (ACC) and pancreatoblastoma (PBL) are rare pancreatic malignancies with acinar differentiation. Proteogenomic profiling of ACC and PBL revealed distinct protein expression patterns compared to pancreatic ductal adenocarcinoma (PDAC) and benign pancreas. ACC and PBL exhibited similarities, with enrichment in proteins related to RNA processing, chromosome organization, and the mitoribosome, while PDACs overexpressed proteins associated with actin-based processes, extracellular matrix, and immune-active stroma. Pathway activity differences in metabolic adaptation, epithelial-to-mesenchymal transition, and DNA repair were characterized between these diseases. PBL showed upregulation of Wnt-CTNNB1 and IGF2 pathways. Seventeen ACC-specific proteins suggested connections to metabolic diseases with mitochondrial dysfunction, while 34 PBL-specific proteins marked this pediatric cancer with an embryonic stem cell phenotype and alterations in chromosomal proteins and the cell cycle. This study provides novel insights into the proteomic landscapes of ACC and PBL, offering potential targets for diagnostic and therapeutic development.
Collapse
Affiliation(s)
- Atsushi Tanaka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Makiko Ogawa
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yihua Zhou
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- ICU Department, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Ronald C Hendrickson
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew M Miele
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhuoning Li
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David S Klimstra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Paige.AI, New York, NY, USA
| | | | - Michael H A Roehrl
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
33
|
Liu Z, Petinrin OO, Chen N, Toseef M, Liu F, Zhu Z, Qi F, Wong KC. Identification and evaluation of candidate COVID-19 critical genes and medicinal drugs related to plasma cells. BMC Infect Dis 2024; 24:1099. [PMID: 39363208 PMCID: PMC11451256 DOI: 10.1186/s12879-024-10000-3] [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: 12/25/2023] [Accepted: 09/25/2024] [Indexed: 10/05/2024] Open
Abstract
The ongoing COVID-19 pandemic, caused by the SARS-CoV-2 virus, represents one of the most significant global health crises in recent history. Despite extensive research into the immune mechanisms and therapeutic options for COVID-19, there remains a paucity of studies focusing on plasma cells. In this study, we utilized the DESeq2 package to identify differentially expressed genes (DEGs) between COVID-19 patients and controls using datasets GSE157103 and GSE152641. We employed the xCell algorithm to perform immune infiltration analyses, revealing notably elevated levels of plasma cells in COVID-19 patients compared to healthy individuals. Subsequently, we applied the Weighted Gene Co-expression Network Analysis (WGCNA) algorithm to identify COVID-19 related plasma cell module genes. Further, positive cluster biomarker genes for plasma cells were extracted from single-cell RNA sequencing data (GSE171524), leading to the identification of 122 shared genes implicated in critical biological processes such as cell cycle regulation and viral infection pathways. We constructed a robust protein-protein interaction (PPI) network comprising 89 genes using Cytoscape, and identified 20 hub genes through cytoHubba. These genes were validated in external datasets (GSE152418 and GSE179627). Additionally, we identified three potential small molecules (GSK-1070916, BRD-K89997465, and idarubicin) that target key hub genes in the network, suggesting a novel therapeutic approach. These compounds were characterized by their ability to down-regulate AURKB, KIF11, and TOP2A effectively, as evidenced by their low free binding energies determined through computational analyses using cMAP and AutoDock. This study marks the first comprehensive exploration of plasma cells' role in COVID-19, offering new insights and potential therapeutic targets. It underscores the importance of a systematic approach to understanding and treating COVID-19, expanding the current body of knowledge and providing a foundation for future research.
Collapse
Affiliation(s)
- Zhe Liu
- Institute for Hepatology, The Second Affiliated Hospital, School of Medicine, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, China
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | | | - Nanjun Chen
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Muhammad Toseef
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Fang Liu
- Rocgene (Beijing) Technology Co., Ltd, Beijing, Beijing, 102200, China
| | - Zhongxu Zhu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China.
| | - Furong Qi
- Institute for Hepatology, The Second Affiliated Hospital, School of Medicine, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, China.
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China.
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China.
| |
Collapse
|
34
|
Liu Y, Peng C, Brorson IS, O'Mahony DG, Kelly RL, Heng YJ, Baker GM, Grenaker Alnæs GI, Bodelon C, Stover DG, Van Allen EM, Eliassen AH, Kristensen VN, Tamimi RM, Kraft P. Germline polygenic risk scores are associated with immune gene expression signature and immune cell infiltration in breast cancer. Am J Hum Genet 2024; 111:2150-2163. [PMID: 39270649 DOI: 10.1016/j.ajhg.2024.08.009] [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: 03/29/2024] [Revised: 08/13/2024] [Accepted: 08/13/2024] [Indexed: 09/15/2024] Open
Abstract
The tumor immune microenvironment (TIME) plays key roles in tumor progression and response to immunotherapy. Previous studies have identified individual germline variants associated with differences in TIME. Here, we hypothesize that common variants associated with breast cancer risk or cancer-related traits, represented by polygenic risk scores (PRSs), may jointly influence immune features in TIME. We derived 154 immune traits from bulk gene expression profiles of 764 breast tumors and 598 adjacent normal tissue samples from 825 individuals with breast cancer in the Nurses' Health Study (NHS) and NHSII. Immunohistochemical staining of four immune cell markers were available for a subset of 205 individuals. Germline PRSs were calculated for 16 different traits including breast cancer, autoimmune diseases, type 2 diabetes, ages at menarche and menopause, body mass index (BMI), BMI-adjusted waist-to-hip ratio, alcohol intake, and tobacco smoking. Overall, we identified 44 associations between germline PRSs and immune traits at false discovery rate q < 0.25, including 3 associations with q < 0.05. We observed consistent inverse associations of inflammatory bowel disease (IBD) and Crohn disease (CD) PRSs with interferon signaling and STAT1 scores in breast tumor and adjacent normal tissue; these associations were replicated in a Norwegian cohort. Inverse associations were also consistently observed for IBD PRS and B cell abundance in normal tissue. We also observed positive associations between CD PRS and endothelial cell abundance in tumor. Our findings suggest that the genetic mechanisms that influence immune-related diseases are also associated with TIME in breast cancer.
Collapse
Affiliation(s)
- Yuxi Liu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cheng Peng
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ina S Brorson
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Denise G O'Mahony
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Rebecca L Kelly
- Cancer Prevention Fellowship Program, National Cancer Institute, Rockville, MD, USA; Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Yujing J Heng
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Gabrielle M Baker
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Grethe I Grenaker Alnæs
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Clara Bodelon
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Daniel G Stover
- Division of Medical Oncology, Stefanie Spielman Comprehensive Breast Center, Columbus, OH, USA; Department of Biomedical Informatics, Ohio State University, Columbus, OH, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - A Heather Eliassen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vessela N Kristensen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Rulla M Tamimi
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| |
Collapse
|
35
|
Oshi M, Wu R, Khoury T, Gandhi S, Yan L, Yamada A, Ishikawa T, Endo I, Takabe K. Infiltration of Common Myeloid Progenitor (CMP) Cells is Associated With Less Aggressive Tumor Biology, Lower Risk of Brain Metastasis, Better Response to Immunotherapy, and Higher Patient Survival in Breast Cancer. Ann Surg 2024; 280:557-569. [PMID: 38946549 DOI: 10.1097/sla.0000000000006428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
OBJECTIVE To investigate the clinical relevance of common myeloid progenitor (CMP) cells in breast tumor microenvironment (TME). BACKGROUND The role of rare cells in TME is less studied. In Silico transcriptomic analyses of real-world data enable us to detect and quantify rare cells, including CMP cells. METHODS A total of 5176 breast cancer (BC) patients from SCAN-B, METABRIC, and 5 single-cell sequence cohorts were analyzed using the xCell algorithm. The high group was defined as more than two-thirds of the CMP scores in each cohort. RESULTS CMP cells consist of 0.07% to 0.25% of bulk breast tumor cells, more in estrogen receptor-positive (ER+) compared with triple-negative (TN) subtype (0.1% to 0.75%, 0.18% to 0.33% of immune cells, respectively). CMP cells did not correlate with any of the myeloid lineages or stem cells in TME. CMP infiltration was higher in smaller tumors, with lower Nottingham grade, and in ER+/HER2- than in TNBC consistently in both SCAN-B and METABRIC cohorts. High CMP was significantly associated with a lower risk of brain metastasis and with better survival, particularly in ER+/HER2-. High CMP enriched epithelial-to-mesenchymal transition and angiogenesis pathways, and less cell proliferation and DNA repair gene sets. High CMP ER+/HER2- was associated with less immune cell infiltration and cytolytic activity ( P <0.001). CMP infiltration correlated with neoadjuvant chemoimmunotherapy response for both ER+/HER2- and TNBC in the ISPY-2 cohort (AUC=0.69 and 0.74, respectively). CONCLUSIONS CMP in BC is inversely associated with cell proliferation and brain metastasis, better response to immunotherapy, and survival. This is the first to report the clinical relevance of CMP infiltration in BC.
Collapse
Affiliation(s)
- Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Rongrong Wu
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, Japan
| | - Thaer Khoury
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Shipra Gandhi
- Department of Medical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Akimitsu Yamada
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY
- Department of Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Breast Surgery, Fukushima Medical University, Fukushima, Japan
| |
Collapse
|
36
|
Liu L, Hao S, Gou S, Tang X, Zhang Y, Cai D, Xiao M, Zhang X, Zhang D, Shen J, Li Y, Chen Y, Zhao Y, Deng S, Wu X, Li M, Zhang Z, Xiao Z, Du F. Potential applications of dual haptoglobin expression in the reclassification and treatment of hepatocellular carcinoma. Transl Res 2024; 272:19-40. [PMID: 38815898 DOI: 10.1016/j.trsl.2024.05.008] [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: 02/21/2024] [Revised: 05/07/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
HCC is a malignancy characterized by high incidence and mortality rates. Traditional classifications of HCC primarily rely on tumor morphology, phenotype, and multicellular molecular levels, which may not accurately capture the cellular heterogeneity within the tumor. This study integrates scRNA-seq and bulk RNA-seq to spotlight HP as a critical gene within a subgroup of HCC malignant cells. HP is highly expressed in HCC malignant cells and lowly expressed in T cells. Within malignant cells, elevated HP expression interacts with C3, promoting Th1-type responses via the C3/C3AR1 axis. In T cells, down-regulating HP expression favors the expression of Th1 cell-associated marker genes, potentially enhancing Th1-type responses. Consequently, we developed a "HP-promoted Th1 response reclassification" gene set, correlating higher activity scores with improved survival rates in HCC patients. Additionally, four predictive models for neoadjuvant treatment based on HP and C3 expression were established: 1) Low HP and C3 expression with high Th2 cell infiltration; 2) High HP and low C3 expression with high Th2 cell infiltration; 3) High HP and C3 expression with high Th1 cell infiltration; 4) Low HP and high C3 expression with high Th1 cell infiltration. In conclusion, the HP gene selected from the HCC malignant cell subgroup (Malignant_Sub 6) might serve as a potential ally against the tumor by promoting Th1-type immune responses. The establishment of the "HP-promoted Th1 response reclassification" gene set offers predictive insights for HCC patient survival prognosis and neoadjuvant treatment efficacy, providing directions for clinical treatments.
Collapse
Affiliation(s)
- Lin Liu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Siyu Hao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Shuang Gou
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Xiaolong Tang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Yao Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Dan Cai
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Mintao Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Xinyi Zhang
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, China
| | - Duoli Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Yan Li
- Public Center of Experimental Technology, Southwest Medical University, Sichuan Luzhou 646000, China
| | - Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Shuai Deng
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Zhuo Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China.
| |
Collapse
|
37
|
Ge YL, Li PJ, Bu YR, Zhang B, Xu J, He SY, Cao QL, Bai YG, Ma J, Zhang L, Zhou J, Xie MJ. TNF-α and RPLP0 drive the apoptosis of endothelial cells and increase susceptibility to high-altitude pulmonary edema. Apoptosis 2024; 29:1600-1618. [PMID: 39110356 PMCID: PMC11416372 DOI: 10.1007/s10495-024-02005-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2024] [Indexed: 09/25/2024]
Abstract
High-altitude pulmonary edema (HAPE) is a fatal threat for sojourners who ascend rapidly without sufficient acclimatization. Acclimatized sojourners and adapted natives are both insensitive to HAPE but have different physiological traits and molecular bases. In this study, based on GSE52209, the gene expression profiles of HAPE patients were compared with those of acclimatized sojourners and adapted natives, with the common and divergent differentially expressed genes (DEGs) and their hub genes identified, respectively. Bioinformatic methodologies for functional enrichment analysis, immune infiltration, diagnostic model construction, competing endogenous RNA (ceRNA) analysis and drug prediction were performed to detect potential biological functions and molecular mechanisms. Next, an array of in vivo experiments in a HAPE rat model and in vitro experiments in HUVECs were conducted to verify the results of the bioinformatic analysis. The enriched pathways of DEGs and immune landscapes for HAPE were significantly different between sojourners and natives, and the common DEGs were enriched mainly in the pathways of development and immunity. Nomograms revealed that the upregulation of TNF-α and downregulation of RPLP0 exhibited high diagnostic efficiency for HAPE in both sojourners and natives, which was further validated in the HAPE rat model. The addition of TNF-α and RPLP0 knockdown activated apoptosis signaling in endothelial cells (ECs) and enhanced endothelial permeability. In conclusion, TNF-α and RPLP0 are shared biomarkers and molecular bases for HAPE susceptibility during the acclimatization/adaptation/maladaptation processes in sojourners and natives, inspiring new ideas for predicting and treating HAPE.
Collapse
Affiliation(s)
- Yi-Ling Ge
- Department of Aerospace Physiology, Key Laboratory of Aerospace Medicine of Ministry of Education, Fourth Military Medical University, Xi'an, Shaanxi Province, 710032, China
| | - Pei-Jie Li
- Department of Aerospace Physiology, Key Laboratory of Aerospace Medicine of Ministry of Education, Fourth Military Medical University, Xi'an, Shaanxi Province, 710032, China
| | - Ying-Rui Bu
- Department of Aerospace Physiology, Key Laboratory of Aerospace Medicine of Ministry of Education, Fourth Military Medical University, Xi'an, Shaanxi Province, 710032, China
| | - Bin Zhang
- Department of Aerospace Physiology, Key Laboratory of Aerospace Medicine of Ministry of Education, Fourth Military Medical University, Xi'an, Shaanxi Province, 710032, China
| | - Jin Xu
- Department of Aerospace Physiology, Key Laboratory of Aerospace Medicine of Ministry of Education, Fourth Military Medical University, Xi'an, Shaanxi Province, 710032, China
| | - Si-Yuan He
- Department of Aerospace Physiology, Key Laboratory of Aerospace Medicine of Ministry of Education, Fourth Military Medical University, Xi'an, Shaanxi Province, 710032, China
| | - Qing-Lin Cao
- Department of Aerospace Physiology, Key Laboratory of Aerospace Medicine of Ministry of Education, Fourth Military Medical University, Xi'an, Shaanxi Province, 710032, China
| | - Yun-Gang Bai
- Department of Aerospace Physiology, Key Laboratory of Aerospace Medicine of Ministry of Education, Fourth Military Medical University, Xi'an, Shaanxi Province, 710032, China
| | - Jin Ma
- Department of Aerospace Physiology, Key Laboratory of Aerospace Medicine of Ministry of Education, Fourth Military Medical University, Xi'an, Shaanxi Province, 710032, China
| | - Lin Zhang
- Department of Aerospace Physiology, Key Laboratory of Aerospace Medicine of Ministry of Education, Fourth Military Medical University, Xi'an, Shaanxi Province, 710032, China.
| | - Jie Zhou
- Department of Endocrinology, Xijing Hospital, Air Force Medical University, No. 127 Changle West Road, Xi'an, 710032, China.
| | - Man-Jiang Xie
- Department of Aerospace Physiology, Key Laboratory of Aerospace Medicine of Ministry of Education, Fourth Military Medical University, Xi'an, Shaanxi Province, 710032, China.
| |
Collapse
|
38
|
Hiremath G, Choksi Y, Correa H, Jacobse J, Das SR, Ma S, Goettel JA, Rajagopala SV. Children with eosinophilic esophagitis non-responsive to combination therapy have distinct esophageal transcriptomic and microbiome profile. Allergy 2024; 79:2798-2811. [PMID: 38993131 DOI: 10.1111/all.16208] [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: 01/05/2024] [Revised: 04/22/2024] [Accepted: 06/03/2024] [Indexed: 07/13/2024]
Abstract
BACKGROUND A combination of proton-pump inhibitors (PPI) and topical steroids (TS) is used to treat children with eosinophilic esophagitis (EoE). However, a subset of children do not respond to this combination therapy. We aimed to identify the esophageal transcriptional, cell composition, and microbial differences between the non-responders (EoE-PPI-TSnr; n = 7) and responders (EoE-PPI-TSr; n = 7) to the combination therapy for EoE and controls (n = 9) using metatranscriptomics. METHODS Differential gene expression analysis was used to identify transcriptional differences, validated using the EoE diagnostic panel (EDP). Deconvolution analysis was performed to identify differences in their cell type composition. Microbiome analysis was conducted from esophageal biopsies RNAseq data, and microbial abundance was correlated with esophageal gene expression. RESULTS In all, 3164 upregulated and 3154 downregulated genes distinguished EoE-PPI-TSnr from EoE-PPI-TSr. Eosinophilic inflammatory response, cytokine signaling, and collagen formation pathways were significantly upregulated in EoE-PPI-TSnr. There was a 56% overlap in dysregulated genes between EoE-PPI-TSnr and EDP, with a perfect agreement in the directionality of modulation. Eosinophils, dendritic cells (DCs), immature DCs, megakaryocytic-erythroid progenitors, and T helper type 1 cells were significantly higher in EoE-PPI-TSnr. There was no significant difference in microbiome diversity. The relative abundance of Fusobacterium sp. and Acinetobacter sp. notably differed in EoE-PPI-TSnr and correlated with the key pathways. CONCLUSION Our results provide critical insights into the molecular, cellular, and microbial factors associated with the lack of response to PPI and TS combination therapy in children with EoE. This study advances our understanding of the pathobiology of EoE while guiding personalized treatment strategies.
Collapse
Affiliation(s)
- Girish Hiremath
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Vanderbilt Children's Hospital, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yash Choksi
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Tennesee Valley Health System, Veteran's Affairs, Nashville, Tennessee, USA
| | - Hernan Correa
- Division of Pathology, Vanderbilt Children's Hospital, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Justin Jacobse
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Willem-Alexander Children's Hospital, Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Suman R Das
- Department of Medicine, Division of Infectious Disease, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Siyuan Ma
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jeremy A Goettel
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seesandra V Rajagopala
- Department of Medicine, Division of Infectious Disease, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| |
Collapse
|
39
|
Wang Z, Yu H, Bao W, Qu M, Wang Y, Zhang L, Liu X, Liu C, He M, Li J, Dong Z, Zhang Y, Yang B, Hou J, Xu C, Wang L, Li X, Gao X, Yang C. Proteomic and phosphoproteomic landscape of localized prostate cancer unveils distinct molecular subtypes and insights into precision therapeutics. Proc Natl Acad Sci U S A 2024; 121:e2402741121. [PMID: 39320917 PMCID: PMC11459144 DOI: 10.1073/pnas.2402741121] [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: 02/16/2024] [Accepted: 08/27/2024] [Indexed: 09/26/2024] Open
Abstract
Building upon our previous investigation of genomic, epigenomic, and transcriptomic profiles of prostate cancer in China, we conducted a comprehensive analysis of proteomic and phosphoproteomic profiles of 82 tumor tissues and matched adjacent normal tissues from 41 Chinese patients with localized prostate cancer. We identified three distinct proteomic subtypes with significant difference in both molecular features and clinical prognosis. Notably, these proteomic subtypes exhibited a parallel degree of heterogeneity in the phosphoproteome, featuring unique metabolism, proliferation, and immune infiltration characteristics. We further demonstrated that a combination of proteins and phosphosites serves as the most effective biomarkers in prostate cancer to predict biochemical recurrence. Through an integrated multiomics analysis, we revealed mechanistic differences underlying different proteomic subtypes and highlighted the potential significance of Serine/arginine-rich splicing factor 1 (SRSF1) phosphorylation in promoting the malignant characteristics of prostate cancer cells. Our multiomics data provide valuable resources for understanding the molecular mechanisms of prostate cancer within the Chinese population, which have the potential to inform the development of personalized treatment strategies and enhance prognostic analyses for prostate cancer patients.
Collapse
Affiliation(s)
- Zengming Wang
- Department of Urology, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai200433, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Haolan Yu
- Department of Urology, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai200433, China
- Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200031, China
| | - Wei Bao
- Department of Urology, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai200433, China
- Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200031, China
| | - Min Qu
- Department of Urology, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai200433, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai200433, China
| | - Yan Wang
- Department of Urology, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai200433, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai200433, China
| | - Liandong Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Xubing Liu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Chen Liu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Miaoxia He
- Department of Pathology, Changhai Hospital, Second Military Medical University, Shanghai200433, China
| | - Jing Li
- Center for Translational Medicine, Second Military Medical University (Naval Medical University), Shanghai200433, China
| | - Zhenyang Dong
- Department of Urology, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai200433, China
| | - Yun Zhang
- Department of Urology, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai200433, China
| | - Bo Yang
- Department of Urology, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai200433, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai200433, China
| | - Jianguo Hou
- Department of Urology, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai200433, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai200433, China
| | - Chuanliang Xu
- Department of Urology, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai200433, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai200433, China
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai200433, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai200433, China
| | - Xin Li
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Xu Gao
- Department of Urology, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai200433, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai200433, China
| | - Chenghua Yang
- Department of Urology, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai200433, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai200433, China
| |
Collapse
|
40
|
Mao Q, Qiao Z, Wang Q, Zhao W, Ju H. Construction and validation of a machine learning-based immune-related prognostic model for glioma. J Cancer Res Clin Oncol 2024; 150:439. [PMID: 39352539 PMCID: PMC11445300 DOI: 10.1007/s00432-024-05970-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 09/23/2024] [Indexed: 10/04/2024]
Abstract
BACKGROUND Glioma stands as the most prevalent primary brain tumor found within the central nervous system, characterized by high invasiveness and treatment resistance. Although immunotherapy has shown potential in various tumors, it still faces challenges in gliomas. This study seeks to develop and validate a prognostic model for glioma based on immune-related genes, to provide new tools for precision medicine. METHODS Glioma samples were obtained from a database that includes the ImmPort database. Additionally, we incorporated ten machine learning algorithms to assess the model's performance using evaluation metrics like the Harrell concordance index (C-index). The model genes were further studied using GSCA, TISCH2, and HPA databases to understand their role in glioma pathology at the genomic, molecular, and single-cell levels, and validate the biological function of IKBKE in vitro experiments. RESULTS In this study, a total of 199 genes associated with prognosis were identified using univariate Cox analysis. Subsequently, a consensus prognostic model was developed through the application of machine learning algorithms. In which the Lasso + plsRcox algorithm demonstrated the best predictive performance. The model showed a good ability to distinguish two groups in both the training and test sets. Additionally, the model genes were closely related to immunity (oligodendrocytes and macrophages), and mutation burden. The results of in vitro experiments showed that the expression level of the IKBKE gene had a significant effect on the apoptosis and migration of GL261 glioma cells. Western blot analysis showed that down-regulation of IKBKE resulted in increased expression of pro-apoptotic protein Bax and decreased expression of anti-apoptotic protein Bcl-2, which was consistent with increased apoptosis rate. On the contrary, IKBKE overexpression caused a decrease in Bax expression an increase in Bcl-2 expression, and a decrease in apoptosis rate. Tunel results further confirmed that down-regulation of IKBKE promoted apoptosis, while overexpression of IKBKE reduced apoptosis. In addition, cells with down-regulated IKBKE had reduced migration in scratch experiments, while cells with overexpression of IKBKE had increased migration. CONCLUSION This study successfully constructed a glioma prognosis model based on immune-related genes. These findings provide new perspectives for glioma prognosis assessment and immunotherapy.
Collapse
Affiliation(s)
- Qi Mao
- Department of Neurosurgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Zhi Qiao
- Department of Neurosurgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Qiang Wang
- Department of Neurosurgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Wei Zhao
- Department of Neurosurgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Haitao Ju
- Department of Neurosurgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China.
| |
Collapse
|
41
|
Wang Q, Zhang C, Pang Y, Cheng M, Wang R, Chen X, Ji T, Yang Y, Zhang J, Zhong C. Comprehensive analysis of bulk, single-cell RNA sequencing, and spatial transcriptomics revealed IER3 for predicting malignant progression and immunotherapy efficacy in glioma. Cancer Cell Int 2024; 24:332. [PMID: 39354533 PMCID: PMC11443732 DOI: 10.1186/s12935-024-03511-1] [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: 05/21/2024] [Accepted: 09/18/2024] [Indexed: 10/03/2024] Open
Abstract
BACKGROUND As part of stress-triggered molecules, immediate early response 3 (IER3) dysregulation has been reported to sustain pro-oncogenic pathways and precede malignant transformation. However, the role of IER3 in glioma pathology is ill-defined. METHODS Immunohistochemistry (IHC) assay and publicly available glioma datasets were used to calculate the IER3 expression level in glioma. Wound healing, invasion and cell counting kit-8 (CCK8) assays were applied to measure the cell viability and capacities of migration and invasion of glioma cells in vitro. The immunofluorescence (IF) assay was used to assess the expression associations of IER3 with CCL2 and TGFBI. Cox regression analysis and Kaplan-Meier (K-M) curve were introduced to compute the prognosis-predicting value of IER3. Variations in copy number (CNVs), single nucleotide (SNVs), and methylation profiles were analyzed to illustrate the epigenetic modifications of IER3. Gliomas were divided into two subgroups using the restricted cubic spline (RCS) method. RESULTS IER3: was overexpressed and hypomethylated in gliomas and significantly associated with the dismal prognosis of glioma samples. Samples in the high IER3 subgroup were characterized by increased infiltration of tumor-associated monocytes/macrophages (TAMMs), as well as the elevated sensitivity to Dabrafenib, an inhibitor of BRAF. In addition, this subgroup demonstrated a low mutation rate of IDH, high gain rates of BRAF, ELTD1, and PDGFA. Gliomas with relatively low IER3 expression demonstrated a less invasive subtype and were featured by favorable prognosis, increased response to immunotherapy, and adjuvant chemotherapy plus radiotherapy. The IF assay revealed that IER3 was co-localized and co-expressed with TGFBI. The glioma cells with small interfering RNA (siRNA)-silenced IER3 displayed lower migration, invasion, proliferation, and cell viability than the control group. CONCLUSIONS In this study, we identified IER3 upregulation as an essential biomarker that could assist in adjuvant therapy and prognosis prediction for gliomas.
Collapse
Affiliation(s)
- Qi Wang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Chunyu Zhang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ying Pang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Meng Cheng
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Rui Wang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xu Chen
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Tongjie Ji
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yuntong Yang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jing Zhang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute for Advanced Study, Tongji University, Shanghai, China
| | - Chunlong Zhong
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China.
| |
Collapse
|
42
|
Lim CY, Ng GWY, Goh CK, Lee MKC, Cheong I, Ooi EE, Liu J, West RB, Loh KS, Tay JK. Impact of high-risk EBV strains on nasopharyngeal carcinoma gene expression. Oral Oncol 2024; 157:106941. [PMID: 39024697 DOI: 10.1016/j.oraloncology.2024.106941] [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: 04/12/2024] [Revised: 06/20/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024]
Abstract
Nasopharyngeal carcinoma (NPC) is closely associated with Epstein-Barr Virus infection (EBV). Despite ubiquitous EBV infection worldwide, NPC displays a unique geographical distribution in Southern China and Southeast Asia. This observed phenomenon can be attributed to the interplay of different strains of EBV infection with host genetics and environmental factors. Polymorphisms on the EBV BALF2 gene have been shown to influence risk of nasopharyngeal carcinoma (NPC). Notably, two non-synonymous EBV polymorphisms (162476T>C, 163364C>T) account for majority of NPC risk in endemic regions. These polymorphisms confer amino acid changes (I1613V, V317M) within the BALF2 protein. However, their impact on NPC tumor biology is unknown. We evaluated the distribution of BALF2 risk polymorphisms in five independent genomic datasets comprising 351 NPC clinical samples, confirming the high prevalence of high-risk EBV strains in NPC. Importantly, we observed two biologically distinct groups of tumors based on their gene expression profiles when grouped by their EBV risk strains. NPC tumors with the V317M substitution demonstrated increased proliferation processes including cell cycle (NES = 1.71, p = 5.64x10-24) and keratinization (NES = 2.42, p = 6.95x10-17). In contrast, NPC tumors without the V317M substitution demonstrated increased immune-related processes, including cell activation (NES = 1.85, p = 8.29x10-31), myeloid leukocyte activation (NES = 2.16, p = 6.51x10-24) and leukocyte mediated immunity (NES = 1.99, p = 1.05x10-23). These findings provide further insight on the influence of BALF2 variants on NPC tumor biology. EBV risk strains may have the potential to define biologically important groups in NPC.
Collapse
Affiliation(s)
- Chee Yit Lim
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Otolaryngology - Head & Neck Surgery, National University of Singapore, Singapore
| | - Gwyneth W Y Ng
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chuan Keng Goh
- Department of Otolaryngology - Head & Neck Surgery, National University of Singapore, Singapore
| | - Melvin Kiang Chua Lee
- Department of Head and Neck and Thoracic Oncology, Division of Radiation Oncology, National Cancer Centre, Singapore
| | - Ian Cheong
- Temasek Life Sciences Laboratory, Singapore; Department of Biological Sciences, National University of Singapore, Singapore
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jianjun Liu
- Human Genomics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, USA
| | - Kwok Seng Loh
- Department of Otolaryngology - Head & Neck Surgery, National University of Singapore, Singapore
| | - Joshua K Tay
- Department of Otolaryngology - Head & Neck Surgery, National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, National University of Singapore, Singapore.
| |
Collapse
|
43
|
Ma H, Shi L, Zheng J, Zeng L, Chen Y, Zhang S, Tang S, Qu Z, Xiong X, Zheng X, Yin Q. Advanced machine learning unveils CD8 + T cell genetic markers enhancing prognosis and immunotherapy efficacy in breast cancer. BMC Cancer 2024; 24:1222. [PMID: 39354417 PMCID: PMC11446097 DOI: 10.1186/s12885-024-12952-w] [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: 05/19/2024] [Accepted: 09/13/2024] [Indexed: 10/03/2024] Open
Abstract
BACKGROUND Breast cancer (BC) is the most common cancer in women and poses a significant health burden, especially in China. Despite advances in diagnosis and treatment, patient variability and limited early detection contribute to poor outcomes. This study examines the role of CD8 + T cells in the tumor microenvironment to identify new biomarkers that improve prognosis and guide treatment strategies. METHODS CD8 + T-cell marker genes were identified using single-cell RNA sequencing (scRNA-seq), and a CD8 + T cell-related gene prognostic signature (CTRGPS) was developed using 10 machine-learning algorithms. The model was validated across seven independent public datasets from the GEO database. Clinical features and previously published signatures were also analyzed for comparison. The clinical applications of CTRGPS in biological function, immune microenvironment, and drug selection were explored, and the role of hub genes in BC progression was further investigated. RESULTS We identified 71 CD8 + T cell-related genes and developed the CTRGPS, which demonstrated significant prognostic value, with higher risk scores linked to poorer overall survival (OS). The model's accuracy and robustness were confirmed through Kaplan-Meier and ROC curve analyses across multiple datasets. CTRGPS outperformed existing prognostic signatures and served as an independent prognostic factor. The role of the hub gene TTK in promoting malignant proliferation and migration of BC cells was validated. CONCLUSION The CTRGPS enhances early diagnosis and treatment precision in BC, improving clinical outcomes. TTK, a key gene in the signature, shows promise as a therapeutic target, supporting the CTRGPS's potential clinical utility.
Collapse
Affiliation(s)
- Haodi Ma
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - LinLin Shi
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, China
| | - Jiayu Zheng
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Li Zeng
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Youyou Chen
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Shunshun Zhang
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Siya Tang
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Zhifeng Qu
- Radiology Department, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Xin Xiong
- Department of Pathology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xuewei Zheng
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China.
- School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China.
| | - Qinan Yin
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China.
- School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China.
| |
Collapse
|
44
|
Oh JM, Kim Y, Lee HS, Son H, Heo HJ, Baek SE, Kim EK, Lee JY, Lee KE, Kim YH, Kim HJ. Paired Transcriptional Analysis of Periodontitis and Peri-Implantitis within same host: a Pilot study. J Dent 2024:105366. [PMID: 39357620 DOI: 10.1016/j.jdent.2024.105366] [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: 06/28/2024] [Revised: 09/15/2024] [Accepted: 09/23/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Peri-implantitis, a plaque-associated pathological condition, has been on the rise with the increasing prevalence of dental implants. Despite its similarities to periodontitis, peri-implantitis is difficult to control completely and has high relapse rates. This has sparked interest in exploring the pathogenic differences between the two conditions. METHODS This cross-sectional study involved 10 participants to concurrently examine periodontitis and peri-implantitis within the same patients, thereby minimizing inter-individual variation. Gingival tissue samples were collected from each participant, comprising 10 periodontitis and 10 peri-implantitis tissues, and RNAs were extracted. Using RNA sequencing and bioinformatics analysis, we investigated complex gene interactions, immune responses, and the role of the extracellular matrix in both conditions. We identified hub genes in each enhanced Protein-Protein Interaction network, providing crucial insights into these diseases' pathogenesis. RESULTS Our findings highlighted the potential involvement of activated fibroblasts in the pathogenesis of peri-implantitis, identifying three marker genes (ACTA2, FAP, and PDGFRβ) overexpressed in peri-implantitis, thus highlighting their potential as disease-specific biomarkers. CONCLUSIONS Our study uncovered a novel connection between peri-implantitis and activated fibroblasts, examining specific markers and microbial differences between periodontitis and peri-implantitis. These insights improve our understanding of peri-implantitis pathogenesis, encouraging future research for better management and prevention strategies. CLINICAL SIGNIFICANCE This study identifies key insights into the pathogenesis of peri-implantitis compared to periodontitis. These findings promise to advance clinical approaches for better managing and preventing peri-implantitis, addressing its complexities and high relapse rates effectively.
Collapse
Affiliation(s)
- Jung-Min Oh
- Department of Oral Biochemistry, School of Dentistry, Pusan National University, Yangsan, Republic of Korea; Periodontal Disease Signaling Network Research Center, School of Dentistry, Pusan National University, Yangsan, Republic of Korea.
| | - Yeongjoo Kim
- Institute for Future Earth, Pusan National University, Busan, Republic of Korea.
| | - Hae Seul Lee
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea.
| | - Hyojae Son
- Department of Oral Biochemistry, School of Dentistry, Pusan National University, Yangsan, Republic of Korea; Periodontal Disease Signaling Network Research Center, School of Dentistry, Pusan National University, Yangsan, Republic of Korea.
| | - Hye Jin Heo
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea.
| | - Seung Eun Baek
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea.
| | - Eun Kyoung Kim
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea.
| | - Ju-Young Lee
- Department of Periodontology, Dental and Life Science Institute, Pusan National University, School of Dentistry, Yangsan, Republic of Korea; Department of Periodontics and Dental Research Institute, Pusan National University Dental Hospital, Yangsan, Republic of Korea.
| | - Kyoung Eun Lee
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Yun Hak Kim
- Periodontal Disease Signaling Network Research Center, School of Dentistry, Pusan National University, Yangsan, Republic of Korea; Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea; Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea.
| | - Hyun-Joo Kim
- Periodontal Disease Signaling Network Research Center, School of Dentistry, Pusan National University, Yangsan, Republic of Korea; Department of Periodontology, Dental and Life Science Institute, Pusan National University, School of Dentistry, Yangsan, Republic of Korea; Department of Periodontics and Dental Research Institute, Pusan National University Dental Hospital, Yangsan, Republic of Korea.
| |
Collapse
|
45
|
Zhang Y, He J, Xie F, Shan S, Qin J, Wang C, Li Q, Xie Y, Fang B. Spatial transcriptomic analysis deciphers adipocyte-to-fibroblast transformation in bleomycin-induced murine skin fibrosis. Chin Med J (Engl) 2024:00029330-990000000-01264. [PMID: 39345020 DOI: 10.1097/cm9.0000000000003219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND Scleroderma is characterized by inflammation and fibrosis, predominantly occurring in the skin and extending to various parts of the body. The pathophysiology of scleroderma is multifaceted, with the current understanding including endothelial damage, inflammatory cell infiltration, and fibroblast activation in its progression. Nonetheless, the mechanism of cellular interactions and the precise spatial distribution of these cellular events within the fibrotic tissues remain elusive, highlighting a critical gap in our comprehensive understanding of scleroderma's pathogenesis. METHODS In this study, we administered bleomycin intradermally to the dorsal skin of four individual murine models. Subsequently, skin tissues were harvested at predetermined intervals for comprehensive spatial transcriptomic analysis to determine the spatial dynamics influencing scleroderma pathogenesis. To validate the possible results from bioinformatic analysis, further in vitro and in vivo experiments were conducted. RESULTS Analysis of the spatial transcriptome revealed significant alterations in cell clusters during the progression of scleroderma. Gene Ontology analysis identified disruptions in lipid metabolism as the disease advanced. Pseudotime analysis provided evidence for a phenotypic transition from adipocytes to fibroblasts. In vitro studies demonstrated increased expression of Col1a1 and α-SMA as the disease progressed. These fibroblasts have been identified as key contributors to the increasing inflammation. Co-culturing TGF-β induced adipocytes with RAW264.7 cells resulted in overexpression of pro-inflammatory cytokines in the RAW264.7 cells. Both in vitro and in vivo experiments confirmed adipocyte loss and fibroblast formation, with transformed fibroblasts showing pronounced pro-inflammatory characteristics, highlighting their crucial role in the disease mechanism. CONCLUSIONS Our study showed the spatial distribution and dynamic alterations of various cell types during scleroderma progression. Crucially, we identified the transformation of adipocytes into fibroblasts as a key factor promoting disease advancement. These emergent fibroblasts intensify inflammation, indicating that research on these cell clusters could reveal key scleroderma mechanisms and guide future therapies.
Collapse
Affiliation(s)
- Yixiang Zhang
- Department of Plastic & Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Jiahao He
- Shanghai Institute for Plastic and Reconstructive Surgery, Shanghai, China. Department of Plastic & Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Fangzhou Xie
- Department of Plastic & Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Shengzhou Shan
- Department of Plastic & Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Jiaqi Qin
- Department of Plastic & Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Chuandong Wang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200092, China
| | - Qingfeng Li
- Department of Plastic & Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Yun Xie
- Shanghai Institute for Plastic and Reconstructive Surgery, Shanghai, China. Department of Plastic & Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Bin Fang
- Department of Plastic & Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| |
Collapse
|
46
|
Zhu Z, Li J, Fa Z, Xu X, Wang Y, Zhou J, Xu Y. Functional gene signature offers a powerful tool for characterizing clinicopathological features and depicting tumor immune microenvironment of colorectal cancer. BMC Cancer 2024; 24:1199. [PMID: 39342165 PMCID: PMC11437988 DOI: 10.1186/s12885-024-12996-y] [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: 04/26/2024] [Accepted: 09/26/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND Colorectal cancer, a prevalent malignancy worldwide, poses a significant challenge due to the lack of effective prognostic tools. In this study, we aimed to develop a functional gene signature to stratify colorectal cancer patients into different groups with distinct characteristics, which will greatly facilitate disease prediction. RESULTS Patients were stratified into high- and low-risk groups using a prediction model built based on the functional gene signature. This innovative approach not only predicts clinicopathological features but also reveals tumor immune microenvironment types and responses to immunotherapy. The study reveals that patients in the high-risk group exhibit poorer pathological features, including invasion depth, lymph node metastasis, and distant metastasis, as well as unfavorable survival outcomes in terms of overall survival and disease-free survival. The underlying mechanisms for these observations are attributed to upregulated tumor-related signaling pathways, increased infiltration of pro-tumor immune cells, decreased infiltration of anti-tumor immune cells, and a lower tumor mutation burden. Consequently, patients in the high-risk group exhibit a diminished response to immunotherapy. Furthermore, the high-risk group demonstrates enrichment in extracellular matrix-related functions and significant infiltration of cancer-associated fibroblasts (CAFs). Single-cell transcriptional data analysis identifies CAFs as the primary cellular type expressing hub genes, namely ACTA2, TPM2, MYL9, and TAGLN. This finding is further validated through multiple approaches, including multiplex immunohistochemistry (mIHC), polymerase chain reaction (PCR), and western blot analysis. Notably, TPM2 emerges as a potential biomarker for identifying CAFs in colorectal cancer, distinguishing them from both colorectal cancer cell lines and normal colon epithelial cell lines. Co-culture of CAFs and colorectal cancer cells revealed that CAFs could enhance the tumorigenic biofunctions of cancer cells indirectly, which could be partially inhibited by knocking down CAF original TPM2 expression. CONCLUSIONS This study introduces a functional gene signature that effectively and reliably predicts clinicopathological features and the tumor immune microenvironment in colorectal cancer. Moreover, the identification of TPM2 as a potential biomarker for CAFs holds promising implications for future research and clinical applications in the field of colorectal cancer.
Collapse
Affiliation(s)
- Ziyan Zhu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jikun Li
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenzhong Fa
- Department of General Surgery, Wujin Hospital Affiliated With Jiangsu University, Changzhou, Jiangsu Province, China
- Department of General Surgery, the Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu Province, China
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou, Jiangsu Province, China
| | - Xuezhong Xu
- Department of General Surgery, Wujin Hospital Affiliated With Jiangsu University, Changzhou, Jiangsu Province, China
- Department of General Surgery, the Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu Province, China
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou, Jiangsu Province, China
| | - Yue Wang
- Department of General Surgery, Wujin Hospital Affiliated With Jiangsu University, Changzhou, Jiangsu Province, China
- Department of General Surgery, the Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu Province, China
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou, Jiangsu Province, China
| | - Jie Zhou
- Department of General Surgery, Wujin Hospital Affiliated With Jiangsu University, Changzhou, Jiangsu Province, China
- Department of General Surgery, the Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu Province, China
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou, Jiangsu Province, China
| | - Yixin Xu
- Department of General Surgery, Wujin Hospital Affiliated With Jiangsu University, Changzhou, Jiangsu Province, China.
- Department of General Surgery, the Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu Province, China.
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou, Jiangsu Province, China.
| |
Collapse
|
47
|
Li S, Peng Y, Chen M, Zhao Y, Xiong Y, Li J, Luo P, Wang H, Zhao F, Zhao Q, Cui Y, Chen S, Zhou JG, Wang S. Facilitating integrative and personalized oncology omics analysis with UCSCXenaShiny. Commun Biol 2024; 7:1200. [PMID: 39341906 PMCID: PMC11439031 DOI: 10.1038/s42003-024-06891-2] [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: 04/02/2024] [Accepted: 09/12/2024] [Indexed: 10/01/2024] Open
Abstract
The continuous generation of multi-omics and phenotype data is propelling advancements in precision oncology. UCSCXenaShiny was developed as an interactive tool for exploring thousands of cancer datasets available on UCSC Xena. However, its capacity for comprehensive and personalized pan-cancer data analysis is being challenged by the growing demands. Here, we introduce UCSCXenaShiny v2, a milestone update through a variety of improvements. Firstly, by integrating multidimensional data and implementing adaptable sample settings, we create a suite of robust TPC (TCGA, PCAWG, CCLE) analysis pipelines. These pipelines empower users to conduct in-depth analyses of correlation, comparison, and survival in three modes: Individual, Pan-cancer and Batch screen. Additionally, the tool includes download interfaces that enable users to access diverse data and outcomes, several features also facilitate the joint analysis of drug sensitivity and multi-omics of cancer cell lines. UCSCXenaShiny v2 is an open-source R package and a web application, freely accessible at https://github.com/openbiox/UCSCXenaShiny .
Collapse
Affiliation(s)
- Shensuo Li
- West China School of Public Health and West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, PR China
| | - Yuzhong Peng
- School of Pharmacy, Macau University of Science and Technology, Macau, SAR, PR China
| | - Minjun Chen
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, PR China
| | - Yankun Zhao
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, PR China
| | - Yi Xiong
- Xiangya School of Medicine, Central South University, Changsha, 410013, PR China
| | - Jianfeng Li
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, PR China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Haitao Wang
- Center for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau, SAR, PR China
- Thoracic Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA
| | - Fei Zhao
- University of the Chinese Academy of Sciences, Beijing, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Yanru Cui
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Sujun Chen
- West China School of Public Health and West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, PR China.
| | - Jian-Guo Zhou
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, PR China.
- Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Shixiang Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
- Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, PR China.
| |
Collapse
|
48
|
Zhang Q, Xu Z, Han R, Wang Y, Ye Z, Zhu J, Cai Y, Zhang F, Zhao J, Yao B, Qin Z, Qiao N, Huang R, Feng J, Wang Y, Rui W, He F, Zhao Y, Ding C. Proteogenomic characterization of skull-base chordoma. Nat Commun 2024; 15:8338. [PMID: 39333076 PMCID: PMC11436687 DOI: 10.1038/s41467-024-52285-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 08/29/2024] [Indexed: 09/29/2024] Open
Abstract
Skull-base chordoma is a rare, aggressive bone cancer with a high recurrence rate. Despite advances in genomic studies, its molecular characteristics and effective therapies remain unknown. Here, we conduct integrative genomics, transcriptomics, proteomics, and phosphoproteomics analyses of 187 skull-base chordoma tumors. In our study, chromosome instability is identified as a prognostic predictor and potential therapeutic target. Multi-omics data reveals downstream effects of chromosome instability, with RPRD1B as a putative target for radiotherapy-resistant patients. Chromosome 1q gain, associated with chromosome instability and upregulated mitochondrial functions, lead to poorer clinical outcomes. Immune subtyping identify an immune cold subtype linked to chromosome 9p/10q loss and immune evasion. Proteomics-based classification reveals subtypes (P-II and P-III) with high chromosome instability and immune cold features, with P-II tumors showing increased invasiveness. These findings, confirmed in 17 paired samples, provide insights into the biology and treatment of skull-base chordoma.
Collapse
Affiliation(s)
- Qilin Zhang
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neuroendocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ziyan Xu
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China
| | - Rui Han
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yunzhi Wang
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China
| | - Zhen Ye
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiajun Zhu
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China
| | - Yixin Cai
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fan Zhang
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China
| | - Jiangyan Zhao
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China
| | - Boyuan Yao
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhaoyu Qin
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China
| | - Nidan Qiao
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ruofan Huang
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Oncology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Jinwen Feng
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China
| | - Yongfei Wang
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenting Rui
- Department of Radiology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fuchu He
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China.
- Research Unit of Proteomics Driven Cancer Precision Medicine. Chinese Academy of Medical Sciences, Beijing, 102206, China.
| | - Yao Zhao
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China.
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China.
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, 200040, China.
- Neurosurgical Institute of Fudan University, Shanghai, 200040, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Chen Ding
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200433, China.
- Departments of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Xinjiang Key Laboratory of Translational Biomedical Engineering, Urumqi, 830000, China.
| |
Collapse
|
49
|
Zhang Z, Wang C, Shi W, Wang Z, Fu W. Construction of store-operated calcium entry-related gene signature for predicting prognosis and indicates immune microenvironment infiltration in stomach adenocarcinomas. Sci Rep 2024; 14:22342. [PMID: 39333689 PMCID: PMC11436956 DOI: 10.1038/s41598-024-73324-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 09/16/2024] [Indexed: 09/29/2024] Open
Abstract
Gastric adenocarcinoma (STAD) is the most prevalent malignancy of the human digestive system and the fourth leading cause of cancer-related death. Calcium pools, especially Ca2+ entry (SOCE) for storage operations, play a crucial role in maintaining intracellular and extracellular calcium balance, influencing cell activity, and facilitating tumor progression. Nevertheless, the prognostic and immunological value of SOCE in STAD has not been systematically studied. The objective of this study was to develop a risk model for SOCE signature and to explore its correlation with clinical characteristics, prognosis, tumor microenvironment (TME), as well as response to immunotherapy, chemotherapy, and targeted drugs. We used the TCGA, GEO (GSE84437 and GSE159929), cBioPortal and TIMER databases to acquire mRNA expression data for STAD, along with patient clinical indicators, single-cell sequencing data, genomic variation information, and correlations of immune cell infiltration. An analysis of SOCE genes based on tumor vs. normal tissue comparisons, pan-cancer dimension, single-cell sequencing, DNA mutation, and copy number variation revealed that SOCE genes significantly impact the survival of STAD patients and are differentially involved in the immune response. SOCE co-expressed genes were identified by Pearson analysis, and subsequently protein-protein interaction (PPI) and gene function enrichment analysis indicated that coexpressed genes were associated with multicellular pathways. Based on TCGA and GSE84437 datasets, a multifactor Cox proportional hazard regression analysis was conducted to identify SOCE co-expressed genes associated with overall survival in STAD patients. Several mRNA prognostic genes, including PTPRJ, GPR146, LTBP3, FBLN1, EFEMP2, ADAMTS7 and LBH, were identified, which could be used as effective prognostic predictors for STAD patients. In both training and test datasets, receiver operating characteristic (ROC) curves were utilized to evaluate and illustrate the predictive capability of this characteristic in forecasting overall survival of STAD patients. The qPCR and human protein atlas (HPA) were employed to assess mRNA expression and protein levels. Furthermore, the ESTIMATE, TIMER, CIBERSORT, QUANTISEQ, MCPCOUNTER, xCell and EPIC algorithms were utilized to perform immune score and analyze immune cell infiltration. It effectively revealed the difference in prognosis and immune cell infiltration in TME between high-risk and low-risk groups based on the risk signature associated with SOCE. Notably, significant differences in tumor immune dysfunction and rejection (TIDE) scores between the two groups, suggesting that patients in the low-risk group may exhibit a more favorable response to ICIS treatment. The GDSC database and R packages for predictive analysis were utilized to analyze responses to chemotherapy and targeted drugs in high-risk and low-risk groups. In summary, the 7-gene signature associated with SOCE serves as a significant biomarker for evaluating the TME and predicting the prognosis of STAD patients. In addition, it may provide valuable insights for developing effective immunotherapy and chemotherapy regiments for patients with STAD.
Collapse
Affiliation(s)
- Zichao Zhang
- Department of General Surgery, The First Hospital of Tsinghua University, Beijing, 100016, People's Republic of China
- Department of General Surgery, Tianjin Medical University General Hospital, No. 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Chenglong Wang
- Department of Otolaryngology, The First Hospital of Tsinghua University, Beijing, 100016, People's Republic of China
| | - Wenzheng Shi
- Department of General Surgery, The First Hospital of Tsinghua University, Beijing, 100016, People's Republic of China
| | - Zhihui Wang
- Department of General Surgery, Tianjin Medical University General Hospital, No. 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Weihua Fu
- Department of General Surgery, Tianjin Medical University General Hospital, No. 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China.
| |
Collapse
|
50
|
Wu C, Qin W, Lu W, Lin J, Yang H, Li C, Mao Y. Unraveling the immune landscape of lung adenocarcinoma: insights for tailoring therapeutic approaches. Discov Oncol 2024; 15:470. [PMID: 39331252 PMCID: PMC11436577 DOI: 10.1007/s12672-024-01396-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 09/24/2024] [Indexed: 09/28/2024] Open
Abstract
Lung adenocarcinoma (LUAD), a prevalent type of non-small cell lung cancer (NSCLC), was known for its diversity and intricate tumor microenvironment (TME). Comprehending the interaction among human immune-related genes (IRGs) and the TME is vital in the creation of accurate predictive models and specific treatments. We created a risk score based on IRGs and designed a nomogram to predict the prognosis of LUAD accurately. This involved a thorough examination of TME and the infiltration of immune cells in both high-risk and low-risk LUAD groups. Furthermore, the examination of the association between characteristic genes (BIRC5 and BMP5) and immune cells, along with immune checkpoints in the TME, was also conducted. The findings of our research unveiled unique immune profiles and interactions among individuals in the high- and low-risk categories, which contribute to variations in prognosis. LUAD demonstrated significant associations between BIRC5, BMP5, immune cells, and checkpoints, suggesting their involvement in disease advancement and resistance to medication. Furthermore, by correlating our findings with a multidrug database, we identified specific LUAD patient subsets that might benefit from tailored treatments. Our study establishes a groundbreaking prognostic model for LUAD, which not only underscores the importance of the immune context in LUAD but also paves the way for advancing precision medicine strategies in this complex malignancy.
Collapse
Affiliation(s)
- Changjiang Wu
- Department of Intensive Care Unit, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, 215028, Jiangsu, China
| | - Wangshang Qin
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530003, Guangxi, China
| | - Wenqiang Lu
- Department of Thoracic Surgery, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, 215028, Jiangsu, China
| | - Jingyu Lin
- Department of Science & Education, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, 215028, Jiangsu, China
| | - Hongwei Yang
- Department of Clinical Laboratory, Suzhou BOE Hospital, Suzhou, 215028, Jiangsu, China
| | - Chunhong Li
- Central Laboratory, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, Guangxi, China.
- Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, Guangxi, China.
| | - Yiming Mao
- Department of Thoracic Surgery, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, 215028, Jiangsu, China.
| |
Collapse
|