151
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Lu Y, Li H, Zhao P, Tian L, Liu Y, Sun X, Cheng Y. Dynamic phenotypic reprogramming and chemoresistance induced by lung fibroblasts in small cell lung cancer. Sci Rep 2024; 14:2884. [PMID: 38311608 PMCID: PMC10838940 DOI: 10.1038/s41598-024-52687-z] [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: 09/16/2023] [Accepted: 01/22/2024] [Indexed: 02/06/2024] Open
Abstract
Small cell lung cancer (SCLC) is heterogenous in phenotype and microenvironment. Dynamic phenotypic reprogramming, leading to heterogeneity, is prevalent in SCLC, while the mechanisms remain incompletely understood. Cancer-associated fibroblasts (CAFs) possess comprehensive roles in cancer progression, while their function in phenotypic reprogramming of SCLC remain elusive. Here, we obtained transcriptome data of SCLC tissues from publicly available databases, subsequently estimated abundance of CAFs. We found CAF-abundant SCLC exhibited non-neuroendocrine (Non-NE) characteristics. Supporting this, the positive correlation of expression level of α-SMA, the CAF marker, and expression level of REST, protein typically expressed in Non-NE type SCLC, was identified in SCLC tissue arrays. Moreover, we revealed that fibroblasts inhibited NE markers expression and cell proliferation of SCLC cells in the co-culture system comprising lung fibroblasts and SCLC cells, indicating a phenotypic reprogramming from NE to Non-NE. During this process, fibroblast-derived IL-6 activated the JAK2/STAT3 signaling, upregulated c-MYC expression, and subsequently activated the NOTCH pathway, driving phenotypic reprogramming. Moreover, CAF-enriched SCLC exhibited increased immune cell infiltration, elevated expression of immune activation-related signatures, and checkpoint molecules. Our data also highlighted the chemoresistance induced by fibroblasts in SCLC cells, which was effectively reversed by JAK inhibitor. In conclusion, fibroblasts induced phenotypic reprogramming of SCLC cells from NE to Non-NE, likely contributes to inflamed immune microenvironment and chemoresistance. These findings provide novel insights into the clinical implications of CAFs in SCLC.
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Affiliation(s)
- Yuanhua Lu
- Postdoctoral Research Workstation, Jilin Cancer Hospital, Changchun, China
| | - Hui Li
- Medical Oncology Translational Research Lab, Jilin Cancer Hospital, No. 1066, Jinhu Road, High-tech District, Changchun, 130012, Jilin, China
| | - Peiyan Zhao
- Medical Oncology Translational Research Lab, Jilin Cancer Hospital, No. 1066, Jinhu Road, High-tech District, Changchun, 130012, Jilin, China
| | - Lin Tian
- Postdoctoral Research Workstation, Jilin Cancer Hospital, Changchun, China
| | - Yan Liu
- Medical Oncology Translational Research Lab, Jilin Cancer Hospital, No. 1066, Jinhu Road, High-tech District, Changchun, 130012, Jilin, China
| | - XiaoDan Sun
- Department of 1st Gynecologic Oncology Surgery, Jilin Cancer Hospital, Changchun, China
| | - Ying Cheng
- Medical Oncology Translational Research Lab, Jilin Cancer Hospital, No. 1066, Jinhu Road, High-tech District, Changchun, 130012, Jilin, China.
- Department of Medical Thoracic Oncology, Jilin Cancer Hospital, Changchun, China.
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152
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Li R, Wen X, Lv RX, Ren XY, Cheng BL, Wang YK, Chen RZ, Hu W, Tang XR. DNA-methylome-derived epigenetic fingerprint as an immunophenotype indicator of durable clinical immunotherapeutic benefits in head and neck squamous cell carcinoma. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00917-x. [PMID: 38315286 DOI: 10.1007/s13402-024-00917-x] [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] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Cancer immunotherapy provides durable response and improves survival in a subset of head and neck squamous cell carcinoma (HNSC) patients, which may due to discriminative tumor microenvironment (TME). Epigenetic regulations play critical roles in HNSC tumorigenesis, progression, and activation of functional immune cells. This study aims to identify an epigenetic signature as an immunophenotype indicator of durable clinical immunotherapeutic benefits in HNSC patients. METHODS Unsupervised consensus clustering approach was applied to distinguish immunophenotypes based on five immune signatures in The Cancer Genome Atlas (TCGA) HNSC cohort. Two immunophenotypes (immune 'Hot' and immune 'Cold') that had different TME features, diverse prognosis, and distinct DNA methylation patterns were recognized. Immunophenotype-related methylated signatures (IPMS) were identified by the least absolute shrinkage and selector operation algorithm. Additionally, the IPMS score by deconvolution algorithm was constructed as an immunophenotype classifier to predict clinical outcomes and immunotherapeutic response. RESULTS The 'Hot' HNSC immunophenotype had higher immunoactivity and better overall survival (p = 0.00055) compared to the 'Cold' tumors. The immunophenotypes had distinct DNA methylation patterns, which was closely associated with HNSC tumorigenesis and functional immune cell infiltration. 311 immunophenotype-related methylated CpG sites (IRMCs) was identified from TCGA-HNSC dataset. IPMS score model achieved a strong clinical predictive performance for classifying immunophenotypes. The area under the curve value (AUC) of the IPMS score model reached 85.9% and 89.8% in TCGA train and test datasets, respectively, and robustness was verified in five HNSC validation datasets. It was also validated as an immunophenotype classifier for predicting durable clinical benefits (DCB) in lung cancer patients who received anti-PD-1/PD-L1 immunotherapy (p = 0.017) and TCGA-SKCM patients who received distinct immunotherapy (p = 0.033). CONCLUSIONS This study systematically analyzed DNA methylation patterns in distinct immunophenotypes to identify IPMS with clinical prognostic potential for personalized epigenetic anticancer approaches in HNSC patients. The IPMS score model may serve as a reliable epigenome prognostic tool for clinical immunophenotyping to guide immunotherapeutic strategies in HNSC.
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Affiliation(s)
- Rui Li
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong Province, China
| | - Xin Wen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong Province, China
| | - Ru-Xue Lv
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong Province, China
| | - Xian-Yue Ren
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Bing-Lin Cheng
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong Province, China
| | - Yi-Kai Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong Province, China
| | - Ru-Zhen Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong Province, China
| | - Wen Hu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong Province, China
| | - Xin-Ran Tang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong Province, China.
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153
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Liu C, Zhou C, Xia W, Zhou Y, Qiu Y, Weng J, Zhou Q, Chen W, Wang YN, Lee HH, Wang SC, Kuang M, Yu D, Ren N, Hung MC. Targeting ALK averts ribonuclease 1-induced immunosuppression and enhances antitumor immunity in hepatocellular carcinoma. Nat Commun 2024; 15:1009. [PMID: 38307859 PMCID: PMC10837126 DOI: 10.1038/s41467-024-45215-0] [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: 10/20/2023] [Accepted: 01/18/2024] [Indexed: 02/04/2024] Open
Abstract
Tumor-secreted factors contribute to the development of a microenvironment that facilitates the escape of cancer cells from immunotherapy. In this study, we conduct a retrospective comparison of the proteins secreted by hepatocellular carcinoma (HCC) cells in responders and non-responders among a cohort of ten patients who received Nivolumab (anti-PD-1 antibody). Our findings indicate that non-responders have a high abundance of secreted RNase1, which is associated with a poor prognosis in various cancer types. Furthermore, mice implanted with HCC cells that overexpress RNase1 exhibit immunosuppressive tumor microenvironments and diminished response to anti-PD-1 therapy. RNase1 induces the polarization of macrophages towards a tumor growth-promoting phenotype through activation of the anaplastic lymphoma kinase (ALK) signaling pathway. Targeting the RNase1/ALK axis reprograms the macrophage polarization, with increased CD8+ T- and Th1- cell recruitment. Moreover, simultaneous targeting of the checkpoint protein PD-1 unleashes cytotoxic CD8+ T-cell responses. Treatment utilizing both an ALK inhibitor and an anti-PD-1 antibody exhibits enhanced tumor regression and facilitates long-term immunity. Our study elucidates the role of RNase1 in mediating tumor resistance to immunotherapy and reveals an RNase1-mediated immunosuppressive tumor microenvironment, highlighting the potential of targeting RNase1 as a promising strategy for cancer immunotherapy in HCC.
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Affiliation(s)
- Chunxiao Liu
- Department of Liver Surgery, Center of Hepato-Pancreato-biliary Surgery, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Chenhao Zhou
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Weiya Xia
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Institute of Biomedical Sciences, Institute of Biochemistry and Molecular Biology, Research Center for Cancer Biology, Cancer Biology and Precision Therapeutics Center, and Center for Molecular Medicine, China Medical University, Taichung, 406, Taiwan
| | - Yifan Zhou
- Department of laboratory medicine, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yufan Qiu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jialei Weng
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Qiang Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Wanyong Chen
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Ying-Nai Wang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heng-Huan Lee
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shao-Chun Wang
- Graduate Institute of Biomedical Sciences, Institute of Biochemistry and Molecular Biology, Research Center for Cancer Biology, Cancer Biology and Precision Therapeutics Center, and Center for Molecular Medicine, China Medical University, Taichung, 406, Taiwan
| | - Ming Kuang
- Department of Liver Surgery, Center of Hepato-Pancreato-biliary Surgery, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Dihua Yu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ning Ren
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China.
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Graduate Institute of Biomedical Sciences, Institute of Biochemistry and Molecular Biology, Research Center for Cancer Biology, Cancer Biology and Precision Therapeutics Center, and Center for Molecular Medicine, China Medical University, Taichung, 406, Taiwan.
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154
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Wang F, Wang C, Li B, Wang G, Meng Z, Han J, Guo G, Yu B, Wang G. Identification of angiogenesis-related subtypes, the development of a prognosis model, and features of tumor microenvironment in colon cancer. Biotechnol Appl Biochem 2024; 71:45-60. [PMID: 37881150 DOI: 10.1002/bab.2520] [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: 03/20/2023] [Accepted: 09/26/2023] [Indexed: 10/27/2023]
Abstract
Angiogenesis is associated with tumor progression, prognosis, and treatment effect. However, the angiogenesis' underlying mechanisms in the tumor microenvironment (TME) still remain unclear. Understanding the dynamic interactions between angiogenesis and TME in colon adenocarcinoma (COAD) is necessary. We downloaded the transcriptome data and corresponding clinical data of colon cancer patients from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases, respectively. We identified two distinct angiogenesis-related molecular subtypes (subtype A and subtype B) and assessed the clinical features, prognosis, and infiltrating immune cells of patients in the two subtypes. According to the prognostic differential genes, we defined two different gene clusters to further explore the correlation between angiogenesis and tumor heterogeneity. Then, we construct the prognostic risk scoring model angiogenesis-related gene (ARG-score) including seven genes (ARMCX2, latent transforming growth factor β binding protein 1, ADAM8, FABP4, CCL11, CXCL11, ITLN1) using Lasso-multivariate cox method. We analyzed the correlation between ARG-score and prognosis, clinicopathological features, TME, molecular feature, cancer stem cells (CSCs), and microsatellite instability (MSI) status. To assess the application value of ARG-score in clinical treatment, immunophenotype score was used to predict patients' immunotherapy response in colon cancer. We found the mutations of ARGs in TCGA-COAD dataset from genetic levels and discussed their expression patterns based on TCGA and GEO datasets. We observed important differences in clinicopathological features, prognosis, immune feature, molecular feature between the two molecular subgroups. Then, we established an ARG-score for predicting OS and validated its predictive capability. A high ARG-score characterized by higher transcription level of ARGs, suggested lower MSI-high (MSI-H), lower immune score, and worse clinical stage and survival outcome. Additionally, the ARG-score was remarkably related to the CSCs index and immunotherapy sensitivity. We found two new molecular subtypes and two gene clusters based on ARGs and established an ARG-score. Multilayered analysis revealed that ARGs were remarkably correlated to the heterogeneity of colon cancer patients and explained the process of tumorigenesis and progression better. The ARG-score can help us better assess patients' survival outcomes and provide guidance for individualized treatment.
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Affiliation(s)
- Feifei Wang
- The Second Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Changjing Wang
- Department of Gastrointestinal Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Baokun Li
- The Second Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Guanglin Wang
- The Second Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zesong Meng
- The Second Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Jiachao Han
- The Second Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Ganlin Guo
- The Second Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Bin Yu
- The Second Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Guiying Wang
- Department of Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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155
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Zhang W, Liu L, Liu X, Han C, Li Q. The levels of immunosuppressive checkpoint protein PD-L1 and tumor-infiltrating lymphocytes were integrated to reveal the glioma tumor microenvironment. ENVIRONMENTAL TOXICOLOGY 2024; 39:815-829. [PMID: 37792606 DOI: 10.1002/tox.23979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/29/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023]
Abstract
In spite of significant strides in the realm of cancer biology and therapeutic interventions, the clinical prognosis for patients afflicted with glioblastoma (GBM) remains distressingly dismal. The tumor immune microenvironment (TIME), a crucial player in the progression, treatment response, and prognostic trajectory of glioma, warrants thorough exploration. Within this intricate microcosm, the immunosuppressive checkpoint protein PD-L1 and tumor-infiltrating lymphocytes (TILs) emerge as pivotal constituents, underscoring their potential role in deciphering glioma biology and informing treatment strategies. However, prognostic models based on the association between PD-L1 expression and TIL infiltration in the tumor immune microenvironment have not been established. The aim of this study was to explore TIME genes associated with PD-L1 expression and TIL invasion and to construct a risk score for predicting the overall survival (OS) of GBM patients based on these genes. The samples were separately classified according to the PD-L1 expression level and TIL score and TIME-related genes were identified using differential expression and weighted gene co-expression network analysis. The DEGs were subjected to least absolute contraction and selection operator (LASSO) -Cox regression to construct TIME associated risk score (TIMErisk). A TIMErisk was developed based on STEAP3 and CXCL13 genes. The STLEAP3 was demonstrated to be involved in glioma progression. The results showed that the patients in the high TIMErisk group had poor OS compared with subjects in the low TIMErisk group. The biological phenotypes associated with TIMErisk were analyzed in terms of functional enrichment, tumor immune profile, and tumor mutation profile. The results on tumor immune dysfunction and exclusion dysfunction (TIDE) score and immune surface score (IPS) showed that GBM patients with different TIME risks had different responses to immunotherapy. Tumor purity analysis indicated that PD-L1 and TIL scores were positively correlated with TIMErisk score and negatively correlated with tumor purity. These results show that the TIMErisk-based prognostic model had high predictive value for the prognosis and immune characteristics of GBM patients. Immunohistochemical staining images of patients in the high and low TIMErisk groups were analyzed, showing that the degree of immune cell infiltration was higher in the high TIMErisk group relative to the low TIMErisk group. The present study provides a basis for understanding glioma tumor microenvironment and a foundation for conducting comprehensive immunogenomic analysis.
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Affiliation(s)
- Weizhong Zhang
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Li Liu
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaoyan Liu
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Cheng Han
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qun Li
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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156
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Li J, Li S, Shu M, Hu W. Unravelling the heterogeneity of oral squamous cell carcinoma by integrative analysis of single-cell and bulk transcriptome data. J Cell Mol Med 2024; 28:e18108. [PMID: 38279519 PMCID: PMC10844683 DOI: 10.1111/jcmm.18108] [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: 08/10/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 01/28/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a prevalent malignancy of the head and neck with rising global incidence. Despite advances in treatment modalities, OSCC prognosis remains diverse due to the complex molecular and cellular heterogeneity within tumours, as well as the heterogeneity in tumour microenvironment (TME). In this study, we utilized single-cell RNA sequencing (scRNA-seq) analysis to explore distinct subpopulations of tumour cells in OSCC tissues and their interaction with components in TME. We identified four major tumour cell subpopulations (C0, C1, C2 and C3) with unique molecular characteristics and functional features. Pathway enrichment analysis revealed that C0 primarily expressed genes involved in extracellular matrix interactions and C1 showed higher proliferation levels, suggesting that the two cell subpopulations exhibited tumour aggressiveness. Conversely, C2 and C3 displayed features associated with keratinization and cornified envelope formation. Accordingly, C0 and C1 subpopulations were associated with shorter overall and disease-free survival times, while C2 and C3 were weakly correlated with longer survival. Genomic analysis showed that C1 demonstrated a positive correlation with tumour mutation burden. Furthermore, C0 exhibited resistant to cisplatin treatment, while C1 showed more sensitive to cisplatin treatment, indicating that C0 might exhibit more aggressive compared to C1. Additionally, C0 had a higher level of communication with fibroblasts and endothelial cells in TME via integrin-MAPK signalling, suggesting that the function of C0 was maintained by that pathway. In summary, this study provided critical insights into the molecular and cellular heterogeneity of OSCC, with potential implications for prognosis prediction and personalized therapeutic approaches.
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Affiliation(s)
- Jia Li
- Department of ProsthodonticsShanghai Engineering Research Center of Tooth Restoration and RegenerationStomatological Hospital and Dental School of Tongji UniversityShanghaiChina
| | - Shengjiao Li
- Department of Oral and Maxillofacial SurgeryShanghai Engineering Research Center of Tooth Restoration and RegenerationStomatological Hospital and Dental School of Tongji UniversityShanghaiChina
| | - Mingyang Shu
- Department of StomatologyHuai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical UniversityHuai'anChina
| | - Weiwei Hu
- Department of StomatologyHuai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical UniversityHuai'anChina
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157
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Chen P, Long J, Zhang J, Xie F, Wu W, Tian Z, Zhang S, Yu K. Identification and validation of the association of Janus kinase 2 mutations with the response to immune checkpoint inhibitor therapy. Inflamm Res 2024; 73:263-276. [PMID: 38200372 PMCID: PMC10824873 DOI: 10.1007/s00011-023-01833-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: 07/02/2023] [Revised: 11/14/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Janus kinase 2 (JAK2) mutation plays an important role in T cell immunity. However, the effect of JAK2 mutation on immunotherapy is largely uncharacterized. METHODS In this study, we analyzed the effect of JAK2 mutation on the efficacy and outcomes of immune checkpoint inhibitor (ICI) therapy in the discovery cohort (n = 662) and the verification cohort (n = 1423). Furthermore, we explored the association of JAK2 mutation with the tumor immune microenvironment in a multiomics cohort. RESULTS In the discovery cohort (n = 662), JAK2 mutant-type patients had a better objective response rate (58.8% vs. 26.7%, P = 0.010), durable clinical benefit (64.7% vs. 38.9%, P = 0.043), progression-free survival (hazard ratio [HR] = 0.431, P = 0.015), and overall survival (HR = 0.378, P = 0.025), relative to JAK2 wild-type patients. Moreover, we further verified the prognostic significance of JAK2 mutation in an independent ICI treatment cohort with a larger sample size (n = 1423). In addition, we discovered that the JAK2 mutation was remarkably related to increased immunogenicity, such as a higher TMB, higher expression of costimulatory molecules and stimulation of antigen processing mechanisms. In addition, JAK2 mutation was positively correlated with activated anticancer immunity, such as infiltration of various immune cells and higher expression of chemokines. CONCLUSION Our study demonstrates that JAK2 mutation is a novel marker that can be used to effectively predict prognosis and response to ICI therapy.
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Affiliation(s)
- Peipei Chen
- Department of Clinical Nutrition & Health Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junyu Long
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiayang Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Fucun Xie
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wei Wu
- Department of Cardiology, Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zhuang Tian
- Department of Cardiology, Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Shuyang Zhang
- Department of Cardiology, Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Kang Yu
- Department of Clinical Nutrition & Health Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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158
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Wang X, Bai H, Zhang J, Wang Z, Duan J, Cai H, Cao Z, Lin Q, Ding X, Sun Y, Zhang W, Xu X, Chen H, Zhang D, Feng X, Wan J, Zhang J, He J, Wang J. Genetic Intratumor Heterogeneity Remodels the Immune Microenvironment and Induces Immune Evasion in Brain Metastasis of Lung Cancer. J Thorac Oncol 2024; 19:252-272. [PMID: 37717855 DOI: 10.1016/j.jtho.2023.09.276] [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: 06/06/2023] [Revised: 08/18/2023] [Accepted: 09/07/2023] [Indexed: 09/19/2023]
Abstract
INTRODUCTION Brain metastasis, with the highest incidence in patients with lung cancer, significantly worsens prognosis and poses challenges to clinical management. To date, how brain metastasis evades immune elimination remains unknown. METHODS Whole-exome sequencing and RNA sequencing were performed on 30 matched brain metastasis, primary lung adenocarcinoma, and normal tissues. Data from The Cancer Genome Atlas primary lung adenocarcinoma cohort, including multiplex immunofluorescence, were used to support the findings of bioinformatics analysis. RESULTS Our study highlights the key role of intratumor heterogeneity of genomic alterations in the metastasis process, mainly caused by homologous recombination deficiency or other somatic copy number alteration-associated mutation mechanisms, leading to increased genomic instability and genomic complexity. We further proposed a selection model of brain metastatic evolution in which intratumor heterogeneity drives immune remodeling, leading to immune escape through different mechanisms under local immune pressure. CONCLUSIONS Our findings provide novel insights into the metastatic process and immune escape mechanisms of brain metastasis and pave the way for precise immunotherapeutic strategies for patients with lung cancer with brain metastasis.
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Affiliation(s)
- Xin Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiyang Zhang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianchun Duan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongqing Cai
- Department of Neurosurgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Cao
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qingtang Lin
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Xiaosheng Ding
- Department of Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yiting Sun
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Zhang
- Department of Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Xiaoya Xu
- Department of Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Hao Chen
- Department of Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Dadong Zhang
- Department of Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Xiaoli Feng
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinghai Wan
- Department of Neurosurgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianjun Zhang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Liu G, Jin K, Liu Z, Su X, Xu Z, Li B, Xu J, Chang Y, Wang Y, Zhu Y, Xu L, Xu J, Wang Z, Liu H, Zhang W. POLQ identifies a better response subset to immunotherapy in muscle-invasive bladder cancer with high PD-L1. Cancer Med 2024; 13:e6962. [PMID: 38457207 PMCID: PMC10922026 DOI: 10.1002/cam4.6962] [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: 09/15/2023] [Revised: 12/23/2023] [Accepted: 01/12/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Though programmed cell death-ligand 1 (PD-L1) has been used in predicting the efficacy of immune checkpoint blockade (ICB), it is insufficient as a single biomarker. As a key effector of an intrinsically mutagenic microhomology-mediated end joining (MMEJ) pathway, DNA polymerase theta (POLQ) was overexpressed in various malignancies, whose expression might have an influence on genomic stability, therefore altering the sensitivity to chemotherapy and immunotherapy. METHODS A total of 1304 patients with muscle-invasive bladder cancer (MIBC) from six independent cohorts were included in this study. The Zhongshan Hospital (ZSHS) cohort (n = 134), The Cancer Genome Atlas (TCGA) cohort (n = 391), and the Neo-cohort (n = 148) were included for the investigation of chemotherapeutic response. The IMvigor210 cohort (n = 234) and the UNC-108 cohort (n = 89) were used for the assessment of immunotherapeutic response. In addition, the relationship between POLQ and the immune microenvironment was assessed, and GSE32894 (n = 308) was used only for the evaluation of the immune microenvironment. RESULTS We identified POLQhigh PD-L1high patients could benefit more from immunotherapy and platinum-based chemotherapy. Further analysis revealed that high POLQ expression was linked to chromosome instability and higher tumor mutational burden (TMB), which might elicit the production of neoantigens. Further, high POLQ expression was associated with an active tumor immune microenvironment with abundant infiltration of immune effector cells and molecules. CONCLUSIONS The study demonstrated that high POLQ expression was correlated with chromosome instability and antitumor immune microenvironment in MIBC, and the combination of POLQ and PD-L1 could be used as a superior companion biomarker for predicting the efficacy of immunotherapy.
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Affiliation(s)
- Ge Liu
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Kaifeng Jin
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
- Department of Urology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Zhaopei Liu
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Xiaohe Su
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Ziyue Xu
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Bingyu Li
- Department of Immunology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Jingtong Xu
- Department of Immunology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Yuan Chang
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Yiwei Wang
- Department of Urology, Shanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yu Zhu
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Le Xu
- Department of Urology, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Jiejie Xu
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Zewei Wang
- Department of Urology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Hailong Liu
- Department of Urology, Xinhua HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Weijuan Zhang
- Department of Immunology, School of Basic Medical SciencesFudan UniversityShanghaiChina
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160
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Liang Y, Qu X, Shah NM, Wang T. Towards targeting transposable elements for cancer therapy. Nat Rev Cancer 2024; 24:123-140. [PMID: 38228901 DOI: 10.1038/s41568-023-00653-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
Transposable elements (TEs) represent almost half of the human genome. Historically deemed 'junk DNA', recent technological advancements have stimulated a wave of research into the functional impact of TEs on gene-regulatory networks in evolution and development, as well as in diseases including cancer. The genetic and epigenetic evolution of cancer involves the exploitation of TEs, whereby TEs contribute directly to cancer-specific gene activities. This Review provides a perspective on the role of TEs in cancer as being a 'double-edged sword', both promoting cancer evolution and representing a vulnerability that could be exploited in cancer therapy. We discuss how TEs affect transcriptome regulation and other cellular processes in cancer. We highlight the potential of TEs as therapeutic targets for cancer. We also summarize technical hurdles in the characterization of TEs with genomic assays. Last, we outline open questions and exciting future research avenues.
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Affiliation(s)
- Yonghao Liang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Xuan Qu
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Nakul M Shah
- Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO, USA.
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161
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Nicolini A, Rossi G, Ferrari P. Experimental and clinical evidence in favour of an effective immune stimulation in ER-positive, endocrine-dependent metastatic breast cancer. Front Immunol 2024; 14:1225175. [PMID: 38332913 PMCID: PMC10850262 DOI: 10.3389/fimmu.2023.1225175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/04/2023] [Indexed: 02/10/2024] Open
Abstract
In ER+ breast cancer, usually seen as the low immunogenic type, the main mechanisms favouring the immune response or tumour growth and immune evasion in the tumour microenvironment (TME) have been examined. The principal implications of targeting the oestrogen-mediated pathways were also considered. Recent experimental findings point out that anti-oestrogens contribute to the reversion of the immunosuppressive TME. Moreover, some preliminary clinical data with the hormone-immunotherapy association in a metastatic setting support the notion that the reversion of immune suppression in TME is likely favoured by the G0-G1 state induced by anti-oestrogens. Following immune stimulation, the reverted immune suppression allows the boosting of the effector cells of the innate and adaptive immune response. This suggests that ER+ breast cancer is a molecular subtype where a successful active immune manipulation can be attained. If this is confirmed by a prospective multicentre trial, which is expected in light of the provided evidence, the proposed hormone immunotherapy can also be tested in the adjuvant setting. Furthermore, the different rationale suggests a synergistic activity of our proposed immunotherapy with the currently recommended regimen consisting of antioestrogens combined with cyclin kinase inhibitors. Overall, this lays the foundation for a shift in clinical practice within this most prevalent molecular subtype of breast cancer.
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Affiliation(s)
- Andrea Nicolini
- Department of Oncology, Transplantations and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Giuseppe Rossi
- Epidemiology and Biostatistics Unit, Institute of Clinical Physiology, National Research Council and Gabriele Monasterio Foundation, Pisa, Italy
| | - Paola Ferrari
- Department of Oncology, Transplantations and New Technologies in Medicine, University of Pisa, Pisa, Italy
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162
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Li J, Liu C, Su H, Dong H, Wang Z, Wang Y, Zhao P, Zhang C, Zhao Y, Ma X. Integrative analysis of LAG3 immune signature and identification of a LAG3-related genes prognostic signature in kidney renal clear cell carcinoma. Aging (Albany NY) 2024; 16:2161-2180. [PMID: 38277212 PMCID: PMC10911349 DOI: 10.18632/aging.205476] [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: 08/11/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024]
Abstract
Immune checkpoint blockade (ICB) therapy has resulted in improved overall survival in kidney renal clear cell carcinoma (KIRC), but most treated patients fail to show durable clinical responses. Lymphocyte activation gene-3 (LAG3) is a novel inhibitory immune checkpoint, but its expression pattern, prognostic value, and immunological role in KIRC remain unknown. In this study, we utilized TCGA_KIRC RNA-sequencing data to analyze the relationship between LAG3 expression and clinical features. The single-cell sequencing data and tissue immunofluorescence are employed to investigate the subcellular localization of LAG3 in KIRC. Kaplan-Meier plotter, TIMER, and TISIDB were used to assess the association between LAG3 expression and prognosis, as well as its correlation with immune-related components. We constructed the LAG3 interaction network by using STRING, GeneMANIA, BioGRID, and HitPredict databases. We found that LAG3 is upregulated and correlates with poor prognostic phenotype in KIRC. LAG3 is predominantly expressed on exhausted CD8+ T cells and shows strong co-expression with PDCD1 in KIRC. Moreover, our findings indicated that LAG3 not only inhibits T cell activation but also potentially regulates cell adhesion in KIRC. In conclusion, our study implies that LAG3 can serve as a potential prognostic biomarker for KIRC. Furthermore, blocking both LAG3 and PDCD1 may alleviate resistance to anti-PDCD1 therapy, providing novel insights for immunotherapy decision-making in KIRC patients.
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Affiliation(s)
- Jie Li
- Department of Oncology, Affiliated Qingdao Central Hospital of Qingdao University, Qingdao Cancer Hospital, Qingdao 266042, China
| | - Chungan Liu
- Department of Oncology, Affiliated Qingdao Central Hospital of Qingdao University, Qingdao Cancer Hospital, Qingdao 266042, China
| | - Hui Su
- Department of Oncology, Liaocheng City People’s Hospital, Liaocheng 252004, China
| | - Hao Dong
- Department of Oncology, Affiliated Qingdao Central Hospital of Qingdao University, Qingdao Cancer Hospital, Qingdao 266042, China
| | - Zhiqian Wang
- Department of Oncology, Affiliated Qingdao Central Hospital of Qingdao University, Qingdao Cancer Hospital, Qingdao 266042, China
| | - Yuqi Wang
- Department of Oncology, Affiliated Qingdao Central Hospital of Qingdao University, Qingdao Cancer Hospital, Qingdao 266042, China
| | - Peng Zhao
- Department of Oncology, Affiliated Qingdao Central Hospital of Qingdao University, Qingdao Cancer Hospital, Qingdao 266042, China
| | - Chaowei Zhang
- Department of Oncology, Affiliated Qingdao Central Hospital of Qingdao University, Qingdao Cancer Hospital, Qingdao 266042, China
| | - Yi Zhao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266003, China
| | - Xuezhen Ma
- Department of Oncology, Affiliated Qingdao Central Hospital of Qingdao University, Qingdao Cancer Hospital, Qingdao 266042, China
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163
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Han T, Wu J, Liu Y, Zhou J, Miao R, Guo J, Xu Z, Xing Y, Bai Y, Hu D. Integrating bulk-RNA sequencing and single-cell sequencing analyses to characterize adenosine-enriched tumor microenvironment landscape and develop an adenosine-related prognostic signature predicting immunotherapy in lung adenocarcinoma. Funct Integr Genomics 2024; 24:19. [PMID: 38265702 DOI: 10.1007/s10142-023-01281-z] [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: 09/02/2023] [Revised: 12/19/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024]
Abstract
The adenosine-signaling axis has been recognized as an important immunomodulatory pathway in tumor immunity. However, the biological role of the adenosine-signaling axis in the remodeling of the tumor microenvironment (TME) in lung adenocarcinoma (LUAD) remains unclear. Here, we quantified adenosine signaling (ado_sig) in LUAD samples using the GSVA method and assessed the prognostic value of adenosine in LUAD. Afterward, we explored the heterogeneity of the tumor-immune microenvironment at different adenosine levels. In addition, we analyzed the potential biological pathways engaged by adenosine. Next, we established single-cell transcriptional profiles of LUAD and analyzed cellular composition and cell-cell communication analysis under different adenosine microenvironments. Moreover, we established adenosine-related prognostic signatures (ARS) based on comprehensive bioinformatics analysis and evaluated the efficacy of ARS in predicting immunotherapy. The results demonstrated that adenosine signaling adversely impacted the survival of immune-enriched LUAD. The high-adenosine microenvironment exhibited elevated pro-tumor-immune infiltration, including M2 macrophages and displayed notably increased epithelial-mesenchymal transition (EMT) transformation. Furthermore, adenosine signaling displayed significant associations with the expression patterns and prognostic value of immunomodulators within the TME. Single-cell sequencing data revealed increased fibroblast occupancy and a prominent activation of the SPP1 signaling pathway in the high adenosine-signaling microenvironment. The ARS exhibited promising effectiveness in prognostication and predicting immunotherapy response in LUAD. In summary, overexpression of adenosine can cause a worsened prognosis in the LUAD with abundant immune infiltration. Moreover, increased adenosine levels are associated with pro-tumor-immune infiltration, active EMT transformation, pro-tumor angiogenesis, and other factors promoting cancer progression, which collectively contribute to the formation of an immunosuppressive microenvironment. Importantly, the ARS developed in this study demonstrate high efficacy in evaluating the response to immunotherapy.
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Affiliation(s)
- Tao Han
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, People's Republic of China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, People's Republic of China.
| | - Jing Wu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, People's Republic of China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, People's Republic of China
| | - Yafeng Liu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, People's Republic of China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, People's Republic of China
| | - Jiawei Zhou
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, People's Republic of China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, People's Republic of China
| | - Rui Miao
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, People's Republic of China
| | - Jianqiang Guo
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, People's Republic of China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, People's Republic of China
| | - Zhi Xu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, People's Republic of China
| | - Yingru Xing
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, People's Republic of China
- Department of Clinical Laboratory, Anhui Zhongke Gengjiu Hospital, Hefei, People's Republic of China
| | - Ying Bai
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, People's Republic of China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, People's Republic of China.
| | - Dong Hu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, People's Republic of China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, People's Republic of China.
- Key Laboratory of Industrial Dust Prevention and Control & Occupational Safety and Health of the Ministry of Education, Anhui University of Science and Technology, Huainan, People's Republic of China.
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People's Republic of China.
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164
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Chou WC, Chen WT, Kuo CT, Chang YM, Lu YS, Li CW, Hung MC, Shen CY. Genetic insights into carbohydrate sulfotransferase 8 and its impact on the immunotherapy efficacy of cancer. Cell Rep 2024; 43:113641. [PMID: 38165805 DOI: 10.1016/j.celrep.2023.113641] [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: 09/14/2023] [Revised: 11/12/2023] [Accepted: 12/18/2023] [Indexed: 01/04/2024] Open
Abstract
Immune checkpoint blockade (ICB) is a promising therapy for solid tumors, but its effectiveness depends on biomarkers that are not precise. Here, we utilized genome-wide association study to investigate the association between genetic variants and tumor mutation burden to interpret ICB response. We identified 16 variants (p < 5 × 10-8) probed to 17 genes on 9 chromosomes. Subsequent analysis of one of the most significant loci in 19q13.11 suggested that the rs111308825 locus at the enhancer is causal, as its A allele impairs KLF2 binding, leading to lower carbohydrate sulfotransferase 8 (CHST8) expression. Breast cancer cells expressing CHST8 suppress T cell activation, and Chst8 loss attenuates tumor growth in a syngeneic mouse model. Further investigation revealed that programmed death-ligand 1 (PD-L1) and its homologs could be sulfated by CHST8, resulting in M2-like macrophage enrichment in the tumor microenvironment. Finally, we confirmed that low-CHST8 tumors have better ICB response, supporting the genetic effect and clinical value of rs111308825 for ICB efficacy prediction.
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Affiliation(s)
- Wen-Cheng Chou
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
| | - Wei-Ting Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chun-Tse Kuo
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yao-Ming Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yen-Shen Lu
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chia-Wei Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; College of Public Health, China Medical University, Taichung, Taiwan.
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165
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Xu B, Lian J, Pang X, Gu Y, Zhu J, Zhang Y, Lu H. Identification of colon cancer subtypes based on multi-omics data-construction of methylation markers for immunotherapy. Front Oncol 2024; 14:1335670. [PMID: 38327746 PMCID: PMC10848914 DOI: 10.3389/fonc.2024.1335670] [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: 11/09/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024] Open
Abstract
Background Being the most widely used biomarker for immunotherapy, the microsatellite status has limitations in identifying all patients who benefit in clinical practice. It is essential to identify additional biomarkers to guide immunotherapy. Aberrant DNA methylation is consistently associated with changes in the anti-tumor immune response, which can promote tumor progression. This study aims to explore immunotherapy biomarkers for colon cancers from the perspective of DNA methylation. Methods The related data (RNA sequencing data and DNA methylation data) were obtained from The Cancer Genome Atlas (TCGA) and UCSC XENA database. Methylation-driven genes (MDGs) were identified through the Pearson correlation analysis. Unsupervised consensus clustering was conducted using these MDGs to identify distinct clusters of colon cancers. Subsequently, we evaluated the immune status and predicted the efficacy of immunotherapy by tumor immune dysfunction and exclusion (Tide) score. Finally, The Quantitative Differentially Methylated Regions (QDMR) software was used to identify the specific DNA methylation markers within particular clusters. Results A total of 282 MDGs were identified by integrating the DNA methylation and RNA-seq data. Consensus clustering using the K-means algorithm revealed that the optimal number of clusters was 4. It was revealed that the composition of the tumor immune microenvironment (TIME) in Cluster 1 was significantly different from others, and it exhibited a higher level of tumor mutation burdens (TMB) and stronger anti-tumor immune activity. Furthermore, we identified three specific hypermethylation genes that defined Cluster 1 (PCDH20, APCDD1, COCH). Receiver operating characteristic (ROC) curves demonstrated that these specific markers could effectively distinguish Cluster 1 from other clusters, with an AUC of 0.947 (95% CI 0.903-0.990). Finally, we selected clinical samples for immunohistochemical validation. Conclusion In conclusion, through the analysis of DNA methylation, consensus clustering of colon cancer could effectively identify the cluster that benefit from immunotherapy along with specific methylation biomarkers.
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Affiliation(s)
- Benjie Xu
- Department of Outpatient Chemotherapy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jie Lian
- Department of Outpatient Chemotherapy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xiangyi Pang
- Department of Outpatient Chemotherapy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yue Gu
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin, China
| | - Jiahao Zhu
- Department of Outpatient Chemotherapy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yan Zhang
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin, China
- College of Pathology, Qiqihar Medical University, Qiqihar, China
| | - Haibo Lu
- Department of Outpatient Chemotherapy, Harbin Medical University Cancer Hospital, Harbin, China
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166
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Hong J, Choi E, Kim D, Seo MK, Kang H, Park B, Kim S. Immunological subtyping of salivary gland cancer identifies histological origin-specific tumor immune microenvironment. NPJ Precis Oncol 2024; 8:15. [PMID: 38245623 PMCID: PMC10799913 DOI: 10.1038/s41698-024-00501-4] [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: 06/20/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
Gene expression analysis enhances proper cancer subtyping, a better understanding of the molecular characteristics of cancer, and strategies for precision medicine. However, salivary gland cancer (SGC) subtyping remains largely unexplored because of its rarity and diverse histopathological and immunological characteristics. This study aimed to determine whether the histological origin and immunological characteristics of SGC subtypes are intrinsic tumor immunity factors. We performed immune profiling of 94 RNA-seq of SGC tissues and found that the SGCs that originated from the excretory duct (ED), such as the salivary duct and mucoepidermoid carcinomas, exhibit higher immunity than those from the intercalated duct (ID), such as the adenoid cystic and myoepithelial carcinomas, based on the computationally predicted immune score (p < 0.001), immune cell enrichment in the tumor immune microenvironment (TIME) (p < 0.001), T-cell receptor diversity (p < 0.001), and expression of signal I (major histocompatibility complex, MHC, p < 0.001) and signal II (co-stimulatory, p < 0.001 and co-inhibitory, p < 0.001) genes. Further analysis revealed that tolerogenic dendritic cell-induced dysfunctional T-cell populations and T-cell exclusion in the TIME are the major immune evasive mechanisms of the ED-and ID-derived SGCs, respectively.
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Affiliation(s)
- Jiyun Hong
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Eunwoo Choi
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Dahee Kim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Mi-Kyoung Seo
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Hyundeok Kang
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - BeumJin Park
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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167
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Fan Z, Liu Y, Li C, Jiang Y, Wang N, Wang M, Li C, Diao Y, Qiu W, Zhu X, Wang G, Cai S, Yang T, Lv G. T proliferating cells derived autophagy signature associated with prognosis and immunotherapy resistance in a pan-cancer analysis. iScience 2024; 27:108701. [PMID: 38222108 PMCID: PMC10784705 DOI: 10.1016/j.isci.2023.108701] [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: 05/25/2023] [Revised: 09/11/2023] [Accepted: 12/06/2023] [Indexed: 01/16/2024] Open
Abstract
Despite autophagy modulating tumor immunity in the tumor microenvironment (TME), the immunotherapeutic efficacy and potential mechanism of autophagy signature was not explicit. We manually curated an autophagy gene set and defined a pan-cancer autophagy signature by comparing malignant tissues and normal tissues in The Cancer Genome Atlas (TCGA) cohort. The pan-cancer autophagy signature was derived from T proliferating cells as demonstrated in multiple single-cell RNA sequencing (scRNA-seq) datasets. The pan-cancer autophagy signature could influence the cell-cell interactions in the TME and predict the responsiveness of immune checkpoint inhibitors (ICIs) in the metastatic renal cell carcinoma, non-small cell lung cancer, bladder cancer, and melanoma cohorts. Metabolism inactivation accompanied with dysregulation of autophagy was investigated with transcriptomic and proteomic data. The immunotherapeutic predictive role and mechanism regulation of the autophagy signature was validated in an in-house cohort. Our study provides valuable insights into the mechanisms of ICI resistance.
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Affiliation(s)
- Zhongqi Fan
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, First Hospital of Jilin University, Jilin, China
| | - Yutao Liu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Yanfang Jiang
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Centre, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Nanya Wang
- Phase I Clinical Trial Unit, First Hospital of Jilin University, Jilin, China
| | - Mingda Wang
- Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China
| | - Chao Li
- Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China
| | - Yongkang Diao
- Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China
| | - Wei Qiu
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, First Hospital of Jilin University, Jilin, China
| | - Xin Zhu
- Burning Rock Biotech, Guangdong, China
| | | | | | - Tian Yang
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, First Hospital of Jilin University, Jilin, China
- Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China
| | - Guoyue Lv
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, First Hospital of Jilin University, Jilin, China
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168
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Wu J, Wu C, Cai X, Li P, Lin J, Wang F. Malignant cell receptor-ligand subtypes guide the prediction of prognosis and personalized immunotherapy of liver cancer. Aging (Albany NY) 2024; 16:1712-1732. [PMID: 38244584 PMCID: PMC10866410 DOI: 10.18632/aging.205453] [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: 06/26/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024]
Abstract
OBJECTIVE Liver cancer is a prevalent disease with a dismal prognosis. The aim of the research is to identify subgroups based on malignant cell receptor ligand gene from single-cell RNA, which might lead to customized immunotherapy for patients with liver cancer. METHODS Based on scRNA-seq data, we identified the receptor-ligand genes associated with prognosis and classify patients into molecular subtypes by univariate Cox regression and consensus clustering. LASSO regression was performed to construct a prognostic model, which was validated in TCGA and ICGC datasets. Immune infiltration and prediction of immunotherapy response were analyzed using ssGSEA, ESTIMATE, TIDE, and TRS score calculation. Finally, qPCR and Western blot validation of key genes and protein levels in cell lines. RESULTS A risk model using 16-gene expression levels predicted liver cancer patients' prognosis. The RiskScore associated significantly with tumor clinical characteristics and immunity, integrated with clinicopathological features for survival prediction. Differential expression of SRXN1 was verified in hepatocellular carcinoma and normal liver cells. CONCLUSION Our study utilizes single-cell analysis to investigate the communication between malignant cells and other cell types, identifying molecular subtypes based on malignant cell receptor ligand genes, offering new insights for the development of personalized immunotherapy and prognostic prediction models.
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Affiliation(s)
- Junzheng Wu
- Xiamen Hospital of Traditional Chinese Medicine, Xiamen Hospital, Beijing University of Chinese Medicine, Xiamen, Fujian, China
| | - Chuncheng Wu
- Xiamen Hospital of Traditional Chinese Medicine, Xiamen Hospital, Beijing University of Chinese Medicine, Xiamen, Fujian, China
| | - Xianhui Cai
- Xiamen Xianyue Hospital, Xiamen, Fujian, China
| | - Peipei Li
- Xiamen Hospital of Traditional Chinese Medicine, Xiamen Hospital, Beijing University of Chinese Medicine, Xiamen, Fujian, China
| | - Jianjun Lin
- Xiamen Hospital of Traditional Chinese Medicine, Xiamen Hospital, Beijing University of Chinese Medicine, Xiamen, Fujian, China
| | - Fuqiang Wang
- Xiamen Hospital of Traditional Chinese Medicine, Xiamen Hospital, Beijing University of Chinese Medicine, Xiamen, Fujian, China
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Zhang X, Tan J, Zhang X, Pandey K, Zhong Y, Wu G, He K. Aggrephagy-related gene signature correlates with survival and tumor-associated macrophages in glioma: Insights from single-cell and bulk RNA sequencing. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2024; 21:2407-2431. [PMID: 38454689 DOI: 10.3934/mbe.2024106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
BACKGROUND Aggrephagy is a lysosome-dependent process that degrades misfolded protein condensates to maintain cancer cell homeostasis. Despite its importance in cellular protein quality control, the role of aggrephagy in glioma remains poorly understood. OBJECTIVE To investigate the expression of aggrephagy-related genes (ARGs) in glioma and in different cell types of gliomas and to develop an ARGs-based prognostic signature to predict the prognosis, tumor microenvironment, and immunotherapy response of gliomas. METHODS ARGs were identified by searching the Reactome database. We developed the ARGs-based prognostic signature (ARPS) using data from the Cancer Genome Atlas (TCGA, n = 669) by Lasso-Cox regression. We validated the robustness of the signature in clinical subgroups and CGGA cohorts (n = 970). Gene set enrichment analysis (GSEA) was used to identify the pathways enriched in ARPS subgroups. The correlations between ARGs and macrophages were also investigated at single cell level. RESULTS A total of 44 ARGs showed heterogeneous expression among different cell types of gliomas. Five ARGs (HSF1, DYNC1H1, DYNLL2, TUBB6, TUBA1C) were identified to develop ARPS, an independent prognostic factor. GSEA showed gene sets of patients with high-ARPS were mostly enriched in cell cycle, DNA replication, and immune-related pathways. High-ARPS subgroup had higher immune cell infiltration states, particularly macrophages, Treg cells, and neutrophils. APRS had positive association with tumor mutation burden (TMB) and immunotherapy response predictors. At the single cell level, we found ARGs correlated with macrophage development and identified ARGs-mediated macrophage subtypes with distinct communication characteristics with tumor cells. VIM+ macrophages were identified as pro-inflammatory and had higher interactions with malignant cells. CONCLUSION We identified a novel signature based on ARGs for predicting glioma prognosis, tumor microenvironment, and immunotherapy response. We highlight the ARGs-mediated macrophages in glioma exhibit classical features.
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Affiliation(s)
- Xiaowei Zhang
- The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Jiayu Tan
- The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xinyu Zhang
- The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | | | - Yuqing Zhong
- The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Guitao Wu
- Guangzhou Women and Children's Hospital, Guangzhou, China
| | - Kejun He
- The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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170
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Tang X, Wang K, Yang J, Wang Y, Yan Z. A novel immunogenic cell death-related gene risk signature can identify biomarkers of gliomas and predict the immunotherapeutic response. Am J Cancer Res 2024; 14:324-343. [PMID: 38323285 PMCID: PMC10839322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 01/01/2024] [Indexed: 02/08/2024] Open
Abstract
Immunogenic cell death (ICD) is a type of cell death that plays a pivotal role in immunity. Recent studies have identified the critical role of ICD in glioma treatment. This study aimed to use ICD-associated differentially expressed genes (ICD-DEGs) to predict survival of glioma patients. We investigated the relationship between clinical prognosis and the date-to-clinical prognosis of 1,721 glioma patients by examining the expression, methylation, and mutation status of ICD-related genes (IRGs) in these patients. Our prediction of survival in glioma patients was based on three risk genes, and we explored the association between these genes and clinical outcomes. Additionally, IRG expression was used to stratify glioma patients. We further examined the relationship among the three subgroups in terms of immune microenvironment heterogeneity and immunotherapy response. In addition, this study also included analyses of histograms and sensitivity to antitumor drugs. The expression of these genes was externally validated by RT-qPCR, Western blot (WB), and immunohistochemistry (IHC) in glioma and normal brain tissue. Our findings reveal that most IRGs are overexpressed in glioma tumor tissues, and this high expression was confirmed through histological validation. We successfully developed predictive models for three prognostic genes associated with ICD. These models not only predict survival in glioma but also correlate with the tumor's immune microenvironment. Finally, using consensus clustering, we identified three ICD-associated subtypes. Notably, patients with the C3 subtype showed high levels of immune cell infiltration, whereas those with the C1 subtype exhibited lower levels of immune cell infiltration. We successfully developed an innovative IRG-based systematic approach for evaluating glioma patients. This stratification in experimental studies opens new avenues for prognosis and assessing immunotherapy responses in glioma patients. Our study demonstrates the effectiveness of this approach in treating glioma, potentially paving the way for more promising and effective therapeutic strategies in the future.
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Affiliation(s)
- Xuewu Tang
- Longgang District Maternity and Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)Shenzhen, Guangdong, China
- Department of Hematology and Oncology, Shenzhen Children’s HospitalShenzhen, Guangdong, China
| | - Kan Wang
- Department of Neurosurgery, Harbin Medical UniversityHarbin, Heilongjiang, China
| | - Jinchao Yang
- Longgang District Maternity and Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)Shenzhen, Guangdong, China
- Department of Hematology and Oncology, Shenzhen Children’s HospitalShenzhen, Guangdong, China
| | - Yuting Wang
- Department of Hematology and Oncology, Shenzhen Children’s HospitalShenzhen, Guangdong, China
| | - Zhiteng Yan
- Longgang District Maternity and Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)Shenzhen, Guangdong, China
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171
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Chida K, Oshi M, An N, Kanazawa H, Roy AM, Mann GK, Yan L, Endo I, Hakamada K, Takabe K. Gastric cancer with enhanced myogenesis is associated with less cell proliferation, enriched epithelial-to-mesenchymal transition and angiogenesis, and poor clinical outcomes. Am J Cancer Res 2024; 14:355-367. [PMID: 38323295 PMCID: PMC10839307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
Gastric cancer (GC) remains a lethal disease, with over 26,000 new cases and more than 11,000 deaths annually in the US. Thus, a deeper understanding of GC biology is critical to improve survival. Myogenesis is the formation of muscle fibers, which is a mesodermal tissue. In cancer, epithelial-to-mesenchymal transition (EMT) is a known phenomenon that promotes metastasis and poor survival. Given that myogenesis produces mesenchymal cells, we hypothesized that GC with increased myogenesis is linked to aggressive tumor behaviors and less favorable outcomes. In this study, three GC patient cohorts: TCGA (n=375), GSE26253 (n=432), and GSE84437 (n=482), were analyzed. The "MYOGENESIS" set in the Hallmark collection which comprises 200 myogenesis-related genes was analyzed to perform gene set variation analysis to create a score to quantify the myogenesis activity. Our results showed that T category of AJCC cancer staging that reflects the tumor invasion to stomach wall consistently correlated with myogenesis activity in two GC cohorts. High myogenesis GC was associated with lower cell proliferation, evidenced by reduced proliferation scores, decreased Ki67 gene expression, and less enrichment of E2F Targets, G2M checkpoint, MYC Targets V1, and V2 gene sets. High myogenesis tumors showed increased stromal cells (fibroblasts and adipocytes) infiltration within the tumor microenvironment, as well as less silent and non-silent mutation rates and copy number alterations. Higher lymphocyte infiltration, leukocyte fraction, T-cell receptor richness, and B-cell receptor richness were associated with high myogenesis GC. However, infiltration of CD4 cells, T helper type 1 and 2 cells, Natural Killer cells, regulatory T cells, and plasma cells was lower, with increased infiltration of dendritic cells in high myogenesis GC. High myogenesis GC enriched EMT, Hedgehog, TGF-β, and KRAS gene sets. Furthermore, it was associated with enhanced angiogenesis, evidenced by enrichment of Angiogenesis, Coagulation, and Hypoxia gene sets, and increased infiltration of microvascular and lymphatic endothelial cells and pericytes. High myogenesis GC consistently correlated with worse overall survival in all three cohorts, and worse disease-specific and progression-free survival in the TCGA cohort. Hence, our findings suggest that GC with enhanced myogenesis is associated with decreased cell proliferation, increased EMT and angiogenesis, and worse prognosis.
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Affiliation(s)
- Kohei Chida
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
- Department of Gastroenterological Surgery, Hirosaki University Graduate School of MedicineHirosaki 036-8562, Japan
| | - Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa 236-0004, Japan
| | - Nan An
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
| | - Hirofumi Kanazawa
- The University of Texas Health Science Center at Tyler School of MedicineTyler, TX 11937, USA
| | - Arya M Roy
- Department of Hematology and Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
| | - Gabriella K Mann
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa 236-0004, Japan
| | - Kenichi Hakamada
- Department of Gastroenterological Surgery, Hirosaki University Graduate School of MedicineHirosaki 036-8562, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa 236-0004, Japan
- Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New YorkBuffalo, NY 14263, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental SciencesNiigata 951-8510, Japan
- Department of Breast Surgery, Fukushima Medical University School of MedicineFukushima 960-1295, Japan
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172
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Wang Q, Shang Y, Li Y, Li X, Wang X, He Y, Ma J, Ning S, Chen H. Identification of cuproptosis-related diagnostic biomarkers in idiopathic pulmonary fibrosis. Medicine (Baltimore) 2024; 103:e36801. [PMID: 38215148 PMCID: PMC10783416 DOI: 10.1097/md.0000000000036801] [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: 09/16/2023] [Accepted: 12/06/2023] [Indexed: 01/14/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease with clinical and pathological heterogeneity. Recent studies have identified cuproptosis as a novel cell death mechanism. However, the role of cuproptosis-related genes in the pathogenesis of IPF is still unclear. Two IPF datasets of the Gene Expression Omnibus database were studied. Mann-Whitney U test, correlation analysis, functional enrichment analyses, single-sample gene set enrichment analysis, CIBERSORT, unsupervised clustering, weighted gene co-expression network analysis, and receiver operating characteristic curve analysis were used to conduct our research. The dysregulated cuproptosis-related genes and immune responses were identified between IPF patients and controls. Two cuproptosis-related molecular clusters were established in IPF, the high immune score group (C1) and the low immune score group (C2). Significant heterogeneity in immunity between clusters was revealed by functional analyses results. The module genes with the strongest correlation to the 2 clusters were identified by weighted gene co-expression network analysis results. Seven hub genes were found using the Cytoscape software. Ultimately, 2 validated diagnostic biomarkers of IPF, CDKN2A and NEDD4, were obtained. Subsequently, the results were validated in GSE47460. Our investigation illustrates that CDKN2A and NEDD4 may be valid biomarkers that were useful for IPF diagnosis and copper-related clustering.
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Affiliation(s)
- Qi Wang
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yu Shang
- Department of Respiration, The First Hospital of Harbin, Harbin, China
| | - Yupeng Li
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xincheng Li
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xue Wang
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yaowu He
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jing Ma
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hong Chen
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
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173
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Sharma P, Zhang X, Ly K, Kim JH, Wan Q, Kim J, Lou M, Kain L, Teyton L, Winau F. Hyperglycosylation of prosaposin in tumor dendritic cells drives immune escape. Science 2024; 383:190-200. [PMID: 38207022 DOI: 10.1126/science.adg1955] [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: 12/07/2022] [Accepted: 11/27/2023] [Indexed: 01/13/2024]
Abstract
Tumors develop strategies to evade immunity by suppressing antigen presentation. In this work, we show that prosaposin (pSAP) drives CD8 T cell-mediated tumor immunity and that its hyperglycosylation in tumor dendritic cells (DCs) leads to cancer immune escape. We found that lysosomal pSAP and its single-saposin cognates mediated disintegration of tumor cell-derived apoptotic bodies to facilitate presentation of membrane-associated antigen and T cell activation. In the tumor microenvironment, transforming growth factor-β (TGF-β) induced hyperglycosylation of pSAP and its subsequent secretion, which ultimately caused depletion of lysosomal saposins. pSAP hyperglycosylation was also observed in tumor-associated DCs from melanoma patients, and reconstitution with pSAP rescued activation of tumor-infiltrating T cells. Targeting DCs with recombinant pSAP triggered tumor protection and enhanced immune checkpoint therapy. Our studies demonstrate a critical function of pSAP in tumor immunity and may support its role in immunotherapy.
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Affiliation(s)
- Pankaj Sharma
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaolong Zhang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin Ly
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Ji Hyung Kim
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Qi Wan
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jessica Kim
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Mumeng Lou
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Lisa Kain
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Luc Teyton
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Florian Winau
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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174
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Dai Z, Wang Y, Sun N, Zhang C. Characterizing ligand-receptor interactions and unveiling the pro-tumorigenic role of CCL16-CCR1 axis in the microenvironment of hepatocellular carcinoma. Front Immunol 2024; 14:1299953. [PMID: 38274805 PMCID: PMC10808667 DOI: 10.3389/fimmu.2023.1299953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Background The heterogeneity of the tumor microenvironment significantly influences the prognosis of hepatocellular carcinoma (HCC) patients, with cell communication through ligand-receptor complexes playing a central role. Methods We conducted single-cell transcriptomic analysis on ten HCC tissues to identify ligand-receptor genes involved in malignant HCC cell communication using CellChat. Leveraging RNA-Seq data from the TCGA Liver Cancer (TCGA-LIHC) and Liver Cancer - RIKEN, JP (LIRI-JP) cohorts, we employed Cox regression analysis to screen for prognosis-related genes. Prognostic risk models were constructed through unsupervised clustering and differential gene expression analysis. Subsequently, a co-culture system involving tumor cells and macrophages was established. A series of experiments, including Transwell assays, immunofluorescence staining, immunoprecipitation, flow cytometry, and immunohistochemistry, were conducted to elucidate the mechanism through which HCC cells recruit macrophages via the CCL16-CCR1 axis. Results Single-cell analysis unveiled significant interactions between malignant HCC cells and macrophages, identifying 76 related ligand-receptor genes. Patients were classified into three subtypes based on the expression patterns of eight prognosis-related ligand-receptor genes. The subtype with the worst prognosis exhibited reduced infiltration of T cell-related immune cells, downregulation of immune checkpoint genes, and increased M2-like tumor-associated macrophage scores. In vitro experiments confirmed the pivotal role of the CCL16-CCR1 axis in the recruitment and M2 polarization of tumor-associated macrophages. Clinical samples demonstrated a significant association between CCL16 protein expression levels and advanced stage, lymph node metastasis, and distant metastasis. Immunohistochemistry and immunofluorescence staining further confirmed the correlation between CCL16 and CCR1, CD68, and CD206, as well as CD68+CCR1+ macrophage infiltration. Conclusions Our study identified molecular subtypes, a prognostic model, and immune microenvironment features based on ligand-receptor interactions in malignant HCC cell communication. Moreover, we revealed the pro-tumorigenic role of HCC cells in recruiting M2-like tumor-associated macrophages through the CCL16-CCR1 axis.
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Affiliation(s)
- Zongbo Dai
- Hepabobiliary Surgery Department, First Hospital of China Medical University, Shenyang, China
| | - Yu Wang
- Department of General Surgery, Anshan Central Hospital, Anshan, China
| | - Ning Sun
- Hepabobiliary Surgery Department, First Hospital of China Medical University, Shenyang, China
| | - Chengshuo Zhang
- Hepabobiliary Surgery Department, First Hospital of China Medical University, Shenyang, China
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175
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Liu Y, Altreuter J, Bodapati S, Cristea S, Wong CJ, Wu CJ, Michor F. Predicting patient outcomes after treatment with immune checkpoint blockade: A review of biomarkers derived from diverse data modalities. CELL GENOMICS 2024; 4:100444. [PMID: 38190106 PMCID: PMC10794784 DOI: 10.1016/j.xgen.2023.100444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/12/2023] [Accepted: 10/24/2023] [Indexed: 01/09/2024]
Abstract
Immune checkpoint blockade (ICB) therapy targeting cytotoxic T-lymphocyte-associated protein 4, programmed death 1, and programmed death ligand 1 has shown durable remission and clinical success across different cancer types. However, patient outcomes vary among disease indications. Studies have identified prognostic biomarkers associated with immunotherapy response and patient outcomes derived from diverse data types, including next-generation bulk and single-cell DNA, RNA, T cell and B cell receptor sequencing data, liquid biopsies, and clinical imaging. Owing to inter- and intra-tumor heterogeneity and the immune system's complexity, these biomarkers have diverse efficacy in clinical trials of ICB. Here, we review the genetic and genomic signatures and image features of ICB studies for pan-cancer applications and specific indications. We discuss the advantages and disadvantages of computational approaches for predicting immunotherapy effectiveness and patient outcomes. We also elucidate the challenges of immunotherapy prognostication and the discovery of novel immunotherapy targets.
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Affiliation(s)
- Yang Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jennifer Altreuter
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Sudheshna Bodapati
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Simona Cristea
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Cheryl J Wong
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 20115, USA
| | - Catherine J Wu
- Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 20115, USA; The Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02138, USA; The Ludwig Center at Harvard, Boston, MA 02115, USA.
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176
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Sun Y, Wu P, Zhang Z, Wang Z, Zhou K, Song M, Ji Y, Zang F, Lou L, Rao K, Wang P, Gu Y, Gu J, Lu B, Chen L, Pan X, Zhao X, Peng L, Liu D, Chen X, Wu K, Lin P, Wu L, Su Y, Du M, Hou Y, Yang X, Qiu S, Shi Y, Sun H, Zhou J, Huang X, Peng DH, Zhang L, Fan J. Integrated multi-omics profiling to dissect the spatiotemporal evolution of metastatic hepatocellular carcinoma. Cancer Cell 2024; 42:135-156.e17. [PMID: 38101410 DOI: 10.1016/j.ccell.2023.11.010] [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: 02/16/2023] [Revised: 09/27/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
Comprehensive molecular analyses of metastatic hepatocellular carcinoma (HCC) are lacking. Here, we generate multi-omic profiling of 257 primary and 176 metastatic regions from 182 HCC patients. Primary tumors rich in hypoxia signatures facilitated polyclonal dissemination. Genomic divergence between primary and metastatic HCC is high, and early dissemination is prevalent. The remarkable neoantigen intratumor heterogeneity observed in metastases is associated with decreased T cell reactivity, resulting from disruptions to neoantigen presentation. We identify somatic copy number alterations as highly selected events driving metastasis. Subclones without Wnt mutations show a stronger selective advantage for metastasis than those with Wnt mutations and are characterized by a microenvironment rich in activated fibroblasts favoring a pro-metastatic phenotype. Finally, metastases without Wnt mutations exhibit higher enrichment of immunosuppressive B cells that mediate terminal exhaustion of CD8+ T cells via HLA-E:CD94-NKG2A checkpoint axis. Collectively, our results provide a multi-dimensional dissection of the complex evolutionary process of metastasis.
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Affiliation(s)
- Yunfan Sun
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China.
| | - Pin Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200032, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, Shenzhen 518083, China
| | - Zefan Zhang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Zejian Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200032, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaiqian Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Minfang Song
- Research Center for Intelligent Computing Platforms, Zhejiang Lab, Hangzhou, Zhejiang 311121, China
| | - Yuan Ji
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Fenglin Zang
- Department of Pathology, Liver Cancer Research Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Limu Lou
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200032, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Keqiang Rao
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Pengxiang Wang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Yutong Gu
- Department of Orthopaedic Surgery, Zhongshan Hospital Fudan University, Shanghai 200032, China
| | - Jie Gu
- Department of Thoracic Surgery, Zhongshan Hospital Fudan University, Shanghai 200032, China
| | - Binbin Lu
- Dunwill Med-Tech, Shanghai 200032, China
| | | | - Xiuqi Pan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200032, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Xiaojing Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200032, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Lihua Peng
- BGI Research, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Dongbing Liu
- BGI Research, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Xiaofang Chen
- BGI Research, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Kui Wu
- BGI Research, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Penghui Lin
- BGI Research, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Liang Wu
- BGI Research, Shenzhen 518083, China
| | - Yulin Su
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200032, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Min Du
- Department of Pathology, Huadong Hospital, Fudan University, Shanghai 200032, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xinrong Yang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Shuangjian Qiu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Yinghong Shi
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Huichuan Sun
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Jian Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Xingxu Huang
- Research Center for Intelligent Computing Platforms, Zhejiang Lab, Hangzhou, Zhejiang 311121, China
| | | | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200032, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China.
| | - Jia Fan
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China.
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Long JY, Li RZ, Wang DX, Liu H, Tian J, Ding ZN, Yan LJ, Dong ZR, Hong JG, Tian BW, Han CL, Zhao HT, Li T. Comprehensive molecular analysis identifies RET alterations association with response of ICIs in multi-immunotherapy cohorts. Int Immunopharmacol 2024; 126:111281. [PMID: 38061115 DOI: 10.1016/j.intimp.2023.111281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND The RET gene, which is frequently mutated across many types of cancer, has been proven to be critically involved in tumorigenesis and tumour development; however, its prediction of the therapeutic efficacy of immune checkpoint inhibitor (ICI) therapy remains to be elucidated. The present research aims to investigate the association between RET mutations and the efficiency of ICI therapy. METHOD We analysed the role of RET mutations in predicting the prognosis of patients receiving ICIs therapy in the discovery cohort and validated it in the validation cohort. Then, multi-omics data from TCGA pan-cancer cohort was employed to propose the association between RET mutations and tumour inflamed anti-tumour immune response and tumour antigenicity. RESULTS Our study revealed that among 606 cases and across five types of cancer, RET mutation was associated with better clinical outcomes for ICIs therapy, including elevated response rate, longer progression-free survival PFS, and longer overall survival OS. Multivariate analysis showed that RET mutation could independently predict the prognosis of patients treated with ICIs, after adjusting cancer types. The predictive value of RET status for the OS of patients treated with ICIs immunotherapy was further validated in the validation cohort (n = 1,409). Subgroup analysis suggested that only the monotherapy group showed significant differences in OS(P < 0.05) and PFS(P < 0.05) between RET-wildtype tumours and RET-mutant tumours. Multi-omics data analysis revealed potential anti-tumour immunity mechanisms of RET mutations, suggesting that RET-mutant tumours have enhanced immunogenicity, higher expression of immune checkpoints and chemokines, and higher immune cell infiltration than those observed in RET-wildtype tumours; thus, potentially indicating a more favourable response to immunotherapy. CONCLUSIONS RET mutation may be a predictive biomarker of enhanced response to ICIs therapy. Extensive investigation of the underlying molecular mechanisms and prospective studies are needed in the future.
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Affiliation(s)
- Jun-Yu Long
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, PR China
| | - Rui-Zhe Li
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan 250012, PR China
| | - Dong-Xu Wang
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan 250012, PR China
| | - Hui Liu
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan 250012, PR China
| | - Jincheng Tian
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan 250012, PR China
| | - Zi-Niu Ding
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan 250012, PR China
| | - Lun-Jie Yan
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan 250012, PR China
| | - Zhao-Ru Dong
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan 250012, PR China
| | - Jian-Guo Hong
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan 250012, PR China
| | - Bao-Wen Tian
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan 250012, PR China
| | - Cheng-Long Han
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan 250012, PR China
| | - Hai-Tao Zhao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, PR China.
| | - Tao Li
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan 250012, PR China.
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Liu Q, Zhang J, Guo C, Wang M, Wang C, Yan Y, Sun L, Wang D, Zhang L, Yu H, Hou L, Wu C, Zhu Y, Jiang G, Zhu H, Zhou Y, Fang S, Zhang T, Hu L, Li J, Liu Y, Zhang H, Zhang B, Ding L, Robles AI, Rodriguez H, Gao D, Ji H, Zhou H, Zhang P. Proteogenomic characterization of small cell lung cancer identifies biological insights and subtype-specific therapeutic strategies. Cell 2024; 187:184-203.e28. [PMID: 38181741 DOI: 10.1016/j.cell.2023.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 09/25/2023] [Accepted: 12/01/2023] [Indexed: 01/07/2024]
Abstract
We performed comprehensive proteogenomic characterization of small cell lung cancer (SCLC) using paired tumors and adjacent lung tissues from 112 treatment-naive patients who underwent surgical resection. Integrated multi-omics analysis illustrated cancer biology downstream of genetic aberrations and highlighted oncogenic roles of FAT1 mutation, RB1 deletion, and chromosome 5q loss. Two prognostic biomarkers, HMGB3 and CASP10, were identified. Overexpression of HMGB3 promoted SCLC cell migration via transcriptional regulation of cell junction-related genes. Immune landscape characterization revealed an association between ZFHX3 mutation and high immune infiltration and underscored a potential immunosuppressive role of elevated DNA damage response activity via inhibition of the cGAS-STING pathway. Multi-omics clustering identified four subtypes with subtype-specific therapeutic vulnerabilities. Cell line and patient-derived xenograft-based drug tests validated the specific therapeutic responses predicted by multi-omics subtyping. This study provides a valuable resource as well as insights to better understand SCLC biology and improve clinical practice.
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Affiliation(s)
- Qian Liu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China; Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Chenchen Guo
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mengcheng Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yilv Yan
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Liangdong Sun
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Di Wang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Lele Zhang
- Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Huansha Yu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Likun Hou
- Department of Pathology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Yuming Zhu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Gening Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Hongwen Zhu
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanting Zhou
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shanhua Fang
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tengfei Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Hu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Junqiang Li
- D1 Medical Technology, Shanghai 201800, China
| | - Yansheng Liu
- Cancer Biology Institute, Yale University School of Medicine, West Haven, CT 06516, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Li Ding
- Department of Medicine, McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Daming Gao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 200120, China.
| | - Hu Zhou
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Peng Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China.
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Braune EB, Geist F, Tang X, Kalari K, Boughey J, Wang L, Leon-Ferre RA, D'Assoro AB, Ingle JN, Goetz MP, Kreis J, Wang K, Foukakis T, Seshire A, Wienke D, Lendahl U. Identification of a Notch transcriptomic signature for breast cancer. Breast Cancer Res 2024; 26:4. [PMID: 38172915 PMCID: PMC10765899 DOI: 10.1186/s13058-023-01757-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Dysregulated Notch signalling contributes to breast cancer development and progression, but validated tools to measure the level of Notch signalling in breast cancer subtypes and in response to systemic therapy are largely lacking. A transcriptomic signature of Notch signalling would be warranted, for example to monitor the effects of future Notch-targeting therapies and to learn whether altered Notch signalling is an off-target effect of current breast cancer therapies. In this report, we have established such a classifier. METHODS To generate the signature, we first identified Notch-regulated genes from six basal-like breast cancer cell lines subjected to elevated or reduced Notch signalling by culturing on immobilized Notch ligand Jagged1 or blockade of Notch by γ-secretase inhibitors, respectively. From this cadre of Notch-regulated genes, we developed candidate transcriptomic signatures that were trained on a breast cancer patient dataset (the TCGA-BRCA cohort) and a broader breast cancer cell line cohort and sought to validate in independent datasets. RESULTS An optimal 20-gene transcriptomic signature was selected. We validated the signature on two independent patient datasets (METABRIC and Oslo2), and it showed an improved coherence score and tumour specificity compared with previously published signatures. Furthermore, the signature score was particularly high for basal-like breast cancer, indicating an enhanced level of Notch signalling in this subtype. The signature score was increased after neoadjuvant treatment in the PROMIX and BEAUTY patient cohorts, and a lower signature score generally correlated with better clinical outcome. CONCLUSIONS The 20-gene transcriptional signature will be a valuable tool to evaluate the response of future Notch-targeting therapies for breast cancer, to learn about potential effects on Notch signalling from conventional breast cancer therapies and to better stratify patients for therapy considerations.
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Affiliation(s)
- Eike-Benjamin Braune
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Xiaojia Tang
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Krishna Kalari
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Judy Boughey
- Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | | | | | - James N Ingle
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Matthew P Goetz
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | | | - Kang Wang
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Theodoros Foukakis
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Urban Lendahl
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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180
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Ding JH, Xiao Y, Yang F, Song XQ, Xu Y, Ding XH, Ding R, Shao ZM, Di GH, Jiang YZ. Guanosine diphosphate-mannose suppresses homologous recombination repair and potentiates antitumor immunity in triple-negative breast cancer. Sci Transl Med 2024; 16:eadg7740. [PMID: 38170790 DOI: 10.1126/scitranslmed.adg7740] [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: 01/22/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer with poor prognosis. TNBCs with high homologous recombination deficiency (HRD) scores benefit from DNA-damaging agents, including platinum drugs and poly(ADP-ribose) polymerase (PARP) inhibitors, whereas those with low HRD scores still lack therapeutic options. Therefore, we sought to exploit metabolic alterations to induce HRD and sensitize DNA-damaging agents in TNBCs with low HRD scores. We systematically analyzed TNBC metabolomics and identified a metabolite, guanosine diphosphate (GDP)-mannose (GDP-M), that impeded homologous recombination repair (HRR). Mechanistically, the low expression of the upstream enzyme GDP-mannose-pyrophosphorylase-A (GMPPA) led to the endogenous up-regulation of GDP-M in TNBC. The accumulation of GDP-M in tumor cells further reduced the interaction between breast cancer susceptibility gene 2 (BRCA2) and ubiquitin-specific peptidase 21 (USP21), which promoted the ubiquitin-mediated degradation of BRCA2 to inhibit HRR. Therapeutically, we illustrated that the supplementation of GDP-M sensitized DNA-damaging agents to impair tumor growth in both in vitro (cancer cell line and patient-derived organoid) and in vivo (xenograft in immunodeficient mouse) models. Moreover, the combination of GDP-M with DNA-damaging agents activated STING-dependent antitumor immunity in immunocompetent syngeneic mouse models. Therefore, GDP-M supplementation combined with PARP inhibition augmented the efficacy of anti-PD-1 antibodies. Together, these findings suggest that GDP-M is a crucial HRD-related metabolite and propose a promising therapeutic strategy for TNBCs with low HRD scores using the combination of GDP-M, PARP inhibitors, and anti-PD-1 immunotherapy.
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Affiliation(s)
- Jia-Han Ding
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 201203, P. R. China
| | - Yi Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Fan Yang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Xiao-Qing Song
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Ying Xu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Xiao-Hong Ding
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Rui Ding
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Gen-Hong Di
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
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Chen Z, Zeng L, Chen Z, Xu J, Zhang X, Ying H, Zeng Y, Yu F. Combined OLA1 and CLEC3B Gene Is a Prognostic Signature for Hepatocellular Carcinoma and Impact Tumor Progression. Technol Cancer Res Treat 2024; 23:15330338241241935. [PMID: 38564315 PMCID: PMC11007312 DOI: 10.1177/15330338241241935] [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: 09/27/2023] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Hepatocellular carcinoma (HCC), partly because of its complexity and high heterogeneity, has a poor prognosis and an extremely high mortality rate. In this study, mRNA sequencing expression profiles and relevant clinical data of HCC patients were gathered from different public databases. Kaplan-Meier survival curves as well as ROC curves validated that OLA1|CLEC3B was an independent predictor with better predictive capability of HCC prognosis compared to OLA1 and CLEC3B separately. Further, the cell transfection experiment verified that knockdown of OLA1 inhibited cell proliferation, facilitated apoptosis, and improved sensitivity of HCC cells to gemcitabine. In this study, the prognostic model of HCC composed of OLA1/CLEC3B genes was constructed and verified, and the prediction ability was favorable. A higher level of OLA1 along with a lower level of CEC3B is a sign of poor prognosis in HCC. We revealed a novel gene pair OLA1|CLEC3B overexpressed in HCC patients, which may serve as a promising independent predictor of HCC survival and an approach for innovative diagnostic and therapeutic strategies.
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Affiliation(s)
- Zhoufeng Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Liuwei Zeng
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhuoyan Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jun Xu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiangting Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Huiya Ying
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuan Zeng
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fujun Yu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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182
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Mao M, Jiang F, Han R, Xiang Y. Identification of the prognostic immune subtype in copy-number high endometrial cancer. J Gynecol Oncol 2024; 35:e8. [PMID: 37857563 PMCID: PMC10792215 DOI: 10.3802/jgo.2024.35.e8] [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: 06/07/2023] [Revised: 08/21/2023] [Accepted: 09/04/2023] [Indexed: 10/21/2023] Open
Abstract
OBJECTIVE The TCGA molecular subtype of endometrial cancer (EC) is widely applied, among which the copy-number high (CNH) subtype has the poorest prognosis. However, the heterogeneity of this subtype remains elusive. In this study, we aimed to identify heterogeneous immune subtypes in CNH EC and explore their prognostic significance. METHODS We collected 60 CNH EC cases in the TCGA database and performed unsupervised cluster analysis based on the enrichment scores of immune-related gene signatures to identify immune subtypes. We described their immune characteristics and prognoses and conducted differential gene analysis and lasso regression to identify a prognostic biomarker, GZMM. For experimental validation, we performed immunohistochemical staining of GZMM in 39 p53-positive EC surgical samples. RESULTS We defined two immune subtypes, immune-hot (IH) and immune-cold (IC), which differed in immune cell infiltration, cytokine and chemokine expression and prognosis. The IH subtype has significantly stronger immune activation than the IC subtype, showing a significant infiltration of immune effector cells and high expression of relevant chemokines, with better prognosis. Moreover, the immunohistochemical staining of GZMM in a cohort of 39 p53-positive EC surgical samples confirmed GZMM as a unique prognostic biomarker, with high expression in both tumor cells and lymphocytes predicting a better prognosis. CONCLUSION Our study revealed heterogeneous immune subtypes in CNH EC and identified GZMM as a prognostic biomarker. The stratified classification strategy combining molecular and immune subtypes provides valuable insights for future clinical practice.
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Affiliation(s)
- Mingyi Mao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China
| | - Fang Jiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China.
| | - Ruiqin Han
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Xiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China
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Wang J, Shu J. Construction of RNA Methylation Modification-immune-related lncRNA Molecular Subtypes and Prognostic Scoring System in Lung Adenocarcinoma. Curr Med Chem 2024; 31:1539-1560. [PMID: 37680151 DOI: 10.2174/0929867331666230901110629] [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: 05/31/2023] [Revised: 07/13/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND RNA methylation modification is not only intimately interrelated with cancer development and progression but also actively influences immune cell infiltration in the tumor microenvironment (TME). RNA methylation modification genes influence the therapeutic progression of lung adenocarcinoma (LUAD), and mining RNA methylation modification prognosis-related markers in LUAD is crucial for its precise prognosis. METHODS RNA-Seq data and Gene sets were collected from online databases or published literature. Genomic variation analysis was conducted by the Maftools package. RNA methylation-immune-related lncRNAs were obtained by Pearson correlation analysis. Then, Consistent clustering analysis was performed to obtain RNA methylation modification- immune molecular subtypes (RMM-I Molecular subtypes) in LUAD based on selected lncRNAs. COX and random survival forest analysis were carried out to construct the RMM-I Score. The receiver operating characteristic (ROC) curve and Kaplan Meier survival analysis were used to assess survival differences. Tumor immune microenvironment was assessed through related gene signatures and CIBERSORT algorithm. In addition, drug sensitivity analysis was executed by the pRRophetic package. RESULTS Four RNA methylation modified-immune molecular subtypes (RMM-I1, RMM- I2, RMM-I3, RMM-I4) were presented in LUAD. Patients in RMM-I4 exhibited excellent survival advantages and immune activity. HAVCR2, CD274, and CTLA-4 expression were activated in RMM-I4, which might be heat tumors and a potential beneficial group for immunotherapy. OGFRP1, LINC01116, DLGAP1-AS2, CRNDE, LINC01137, MIR210HG, and CYP1B1-AS1 comprised the RMM-I Score. The RMM-I Score exhibited excellent accuracy in the prognostic assessment of LUAD, as patients with a low RMM- I Score exhibited remarkable survival advantage. Patients with a low RMM-I score might be more sensitive to treatment with Docetaxel, Vinorelbine, Paclitaxel, Cisplatin, and immunotherapy. CONCLUSION The RMM-I molecular subtype constituted the novel molecular characteristic subtype of LUAD, which complemented the existing pathological typing. More refined and accurate molecular subtypes provide help to reveal the mechanism of LUAD development. In addition, the RMM-I score offers a reliable tool for accurate prognosis of LUAD.
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Affiliation(s)
- Jiajing Wang
- Department of Clinical Laboratory, Beilun People's Hospital, Ningbo, 315000, China
| | - Jianfeng Shu
- Huamei Hospital, University of Chinese Academy of Sciences, Ningbo, 315000, China
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Gao Z, Wan Z, Yu P, Shang Y, Zhu G, Jiang H, Chen Y, Wang S, Lei F, Huang W, Zeng Q, Wang Y, Rong W, Hong Y, Gao Q, Niu P, Zhai Z, An K, Ding C, Wang Y, Gu G, Wang X, Meng Q, Ye S, Liu H, Gu J. A recurrence-predictive model based on eight genes and tumor mutational burden/microsatellite instability status in Stage II/III colorectal cancer. Cancer Med 2024; 13:e6720. [PMID: 38111983 PMCID: PMC10807589 DOI: 10.1002/cam4.6720] [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: 03/16/2023] [Revised: 06/18/2023] [Accepted: 10/27/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Although adjuvant chemotherapy (ACT) is widely used to treat patients with Stage II/III colorectal cancer (CRC), administering ACT to specific patients remains a challenge. The decision to ACT requires an accurate assessment of recurrence risk and absolute treatment benefit. However, the traditional TNM staging system does not accurately assess a patient's individual risk of recurrence. METHODS To identify recurrence risk-related genetic factors for Stage II/III CRC patients after radical surgery, we conducted an analysis of whole-exome sequencing of 47 patients with Stage II/III CRC who underwent radical surgery at five institutions. Patients were grouped into non-recurrence group (NR, n = 24, recurrence-free survival [RFS] > 5 years) and recurrence group (R, n = 23, RFS <2 years). The TCGA-COAD/READ cohort was employed as the validation dataset. RESULTS A recurrence-predictive model (G8plus score) based on eight gene (CUL9, PCDHA12, HECTD3, DCX, SMARCA2, FAM193A, AATK, and SORCS2) mutations and tumor mutation burden/microsatellite instability (TMB/MSI) status was constructed, with 97.87% accuracy in our data and 100% negative predictive value in the TCGA-COAD/READ cohort. For the TCGA-COAD/READ cohort, the G8plus-high group had better RFS (HR = 0.22, p = 0.024); the G8plus-high tumors had significantly more infiltrated immune cell types, higher tertiary lymphoid structure signature scores, and higher immunological signature scores. The G8plus score was also a predict biomarker for immunotherapeutic in advanced CRC in the PUCH cohort. CONCLUSIONS In conclusion, the G8plus score is a powerful biomarker for predicting the risk of recurrence in patients with stage II/III CRC. It can be used to stratify patients who benefit from ACT and immunotherapy.
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Affiliation(s)
- Zhaoya Gao
- Department of General SurgeryPeking University First HospitalBeijingChina
| | - Zhiyi Wan
- Genecast Biotechnology Co., Ltd.Wuxi CityJiangsu ProvinceChina
| | - Pengfei Yu
- Department of General SurgeryAir Force Medical Center, Chinese People's Liberation ArmyBeijingChina
| | - Yan Shang
- Department of Colorectal SurgeryCancer Hospital of China Medical University, Liaoning Cancer Hospital and InstituteShenyangLiaoning ProvinceChina
| | - Guangsheng Zhu
- Department of Gastrointestinal SurgeryHubei Cancer HospitalWuhanHubei ProvinceChina
| | - Huiyuan Jiang
- Department of Colorectal and Anal SurgeryShanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanShanxi ProvinceChina
| | - Yawei Chen
- Genecast Biotechnology Co., Ltd.Wuxi CityJiangsu ProvinceChina
| | - Shengzhou Wang
- Genecast Biotechnology Co., Ltd.Wuxi CityJiangsu ProvinceChina
| | - Fuming Lei
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Wensheng Huang
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Qingmin Zeng
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Yanzhao Wang
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Wanshui Rong
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Yuming Hong
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Qingkun Gao
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Pengfei Niu
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Zhichao Zhai
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Ke An
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Changmin Ding
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
| | - Yunfan Wang
- Department of PathologyPeking University Shougang HospitalBeijingChina
| | - Guoli Gu
- Department of General SurgeryAir Force Medical Center, Chinese People's Liberation ArmyBeijingChina
| | - Xin Wang
- Department of General SurgeryPeking University First HospitalBeijingChina
| | - Qingkai Meng
- Department of Colorectal SurgeryCancer Hospital of China Medical University, Liaoning Cancer Hospital and InstituteShenyangLiaoning ProvinceChina
| | - Shengwei Ye
- Department of Gastrointestinal SurgeryHubei Cancer HospitalWuhanHubei ProvinceChina
| | - Haiyi Liu
- Department of Colorectal and Anal SurgeryShanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanShanxi ProvinceChina
| | - Jin Gu
- Department of Gastrointestinal SurgeryPeking University Shougang HospitalBeijingChina
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal SurgeryPeking University Cancer Hospital & InstituteBeijingChina
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
- Peking University International Cancer InstituteBeijingChina
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185
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Morris LGT. Loss of Human Leukocyte Antigen and Immune Escape in Head and Neck Cancer. Laryngoscope 2024; 134:160-165. [PMID: 37249223 PMCID: PMC10687312 DOI: 10.1002/lary.30761] [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: 02/26/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/31/2023]
Abstract
OBJECTIVES/HYPOTHESIS Cancer cells evade recognition by the immune system to survive. Head and neck squamous cell carcinoma (HNSCC) is characterized by high levels of immune infiltration and mutation-associated neoantigens; therefore, immune evasion is likely to be an important mechanism in HNSCC tumorigenesis and progression. A commonly employed mechanism of immune evasion is downregulation of human leukocyte antigen (HLA) or loss of heterozygosity (LOH) in tumor cells. The objective of this study was to integrate multi-dimensional genomic and transcriptomic data from HNSCC tumors to better understand the clinical and immunologic implications of HLA LOH. STUDY TYPE/DESIGN Cross-sectional integrated clinical and genomic analysis. METHODS Whole-exome sequencing and RNA-sequencing data from 522 tumors profiled in The Cancer Genome Atlas HNSCC cohort were analyzed and integrated with secondary analyses including immune cell deconvolution data. Associations were analyzed with categorical hypothesis testing and multivariable logistic and Cox regression. RESULTS HLA LOH was a prevalent event that was identified in 53% of HNSCC tumors; in many cases, more than one class I HLA gene was targeted for LOH. HLA LOH was more common in advanced-stage tumors. Tumors with somatic HLA LOH had tumor microenvironments defined by decreased lymphocyte and T cell infiltration. CONCLUSIONS HLA LOH is one of the most prevalent genetic alterations in HNSCC, and is associated with a cold immune microenvironment, suggesting that HLA LOH is a means of immune evasion. It may have value as a predictive biomarker or potential as a cancer cell-specific therapeutic target. LEVEL OF EVIDENCE 3 Laryngoscope, 134:160-165, 2024.
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Affiliation(s)
- Luc G T Morris
- Department of Surgery (Head and Neck Service), Memorial Sloan Kettering Cancer Center, New York, New York, USA
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186
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Saliby RM, Saad E, Kashima S, Schoenfeld DA, Braun DA. Update on Biomarkers in Renal Cell Carcinoma. Am Soc Clin Oncol Educ Book 2024; 44:e430734. [PMID: 38207251 DOI: 10.1200/edbk_430734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Immune checkpoint inhibitors have significantly transformed the treatment paradigm for metastatic renal cell carcinoma (RCC), offering prolonged overall survival and achieving remarkable deep and durable responses. However, given the multiple ICI-containing, standard-of-care regimens approved for RCC, identifying biomarkers that predict therapeutic response and resistance is of critical importance. Although tumor-intrinsic features such as pathological characteristics, genomic alterations, and transcriptional signatures have been extensively investigated, they have yet to provide definitive, robust predictive biomarkers. Current research is exploring host factors through in-depth characterization of the immune system. Additionally, innovative technological approaches are being developed to overcome challenges presented by existing techniques, such as tumor heterogeneity. Promising avenues in biomarker discovery include the study of the microbiome, radiomics, and spatial transcriptomics.
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Affiliation(s)
- Renée M Saliby
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
- Yale Center of Cellular and Molecular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT
| | - Eddy Saad
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Soki Kashima
- Yale Center of Cellular and Molecular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT
| | - David A Schoenfeld
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - David A Braun
- Yale Center of Cellular and Molecular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
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187
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Sheng N, He C, Jin X, Meng Q, Gu P, Ding S, Liu H, Xu Y. A comprehensive study of oxidative stress-related effects on the prognosis and drug therapy of cervical cancer. J Gene Med 2024; 26:e3581. [PMID: 37605936 DOI: 10.1002/jgm.3581] [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: 05/13/2023] [Revised: 07/18/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Cervical cancer (CC) is a serious global disease with poor prognoses and a significant recurrence rate in patients with advanced disease. Oxidative stress (OS) greatly influences many types of human cancers, making it crucial to understand the functional mechanisms of OS-related genes in CC. METHODS The transcriptome and clinical data of three normal samples and 306 patients with CC were obtained from The Cancer Genome Atlas dataset. The GSE44001 dataset was acquired from the Gene Expression Omnibus database. OS-related subtypes in the cohort with CC were identified using unsupervised hierarchical clustering, univariate Cox analysis, gene set enrichment analysis (GSEA), and least absolute shrinkage and selection operator regression analysis. Additionally, molecular pathways that differ across subtypes were determined and OS-related genes linked to the prognosis of patients of CC were determined. Finally, a clinical prognostic gene signature was developed and validated. The relative infiltration level of immune cell subpopulations in different risk groups and subtypes was evaluated using the cell-type identification by estimating relative subsets of RNA transcripts (CIBERPORT) algorithm and single-sample GSEA (ssGSEA) techniques. RESULTS The present study established two distinct OS subtypes (OS clusters A and B). Analysis using ssGSEA and CIBERSPORT revealed that OS cluster B exhibited a significant level of immune infiltration. A clinical prognostic gene signature was established using OS-related characteristic genes identified by examining the differentially expressed genes across both subtypes. Furthermore, patients with CC were grouped into high- and low-risk groups, with the low-risk group showing higher survival rates. Additionally, these individuals exhibited significant advantages in terms of survival and immunotherapy. Receiver operating characteristic curve analysis demonstrated the higher predictive value of the clinical prognostic gene signature. The outcomes of the validation group depicted congruence with those recorded in the training group. CONCLUSIONS A new model was constructed based on eight OS-related characteristic genes to aid the prediction of the survival rates of individuals with CC. The present study contributes to the existing literature on the mechanisms of OS genes in CC and offers a fresh perspective for future advancements in immunotherapy for such individuals.
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Affiliation(s)
- Nan Sheng
- Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Nantong, China
| | - Chenyun He
- Department of Gynecology Oncology, Nantong Tumor Hospital, Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Xiaoxia Jin
- Department of Pathology, Nantong Tumor Hospital, Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Qi Meng
- Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Nantong, China
| | - Panyun Gu
- Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Nantong, China
| | - Shu Ding
- Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Nantong, China
| | - Hong Liu
- Department of Hematology, Affiliated Hospital of Nantong University, Nantong, China
| | - Yunzhao Xu
- Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Nantong, China
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188
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Bestion E, Rachid M, Tijeras-Raballand A, Roth G, Decaens T, Ansaldi C, Mezouar S, Raymond E, Halfon P. Ezurpimtrostat, A Palmitoyl-Protein Thioesterase-1 Inhibitor, Combined with PD-1 Inhibition Provides CD8 + Lymphocyte Repopulation in Hepatocellular Carcinoma. Target Oncol 2024; 19:95-106. [PMID: 38133710 DOI: 10.1007/s11523-023-01019-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Palmitoyl-protein thioesterase-1 (PPT1) is a clinical stage druggable target for inhibiting autophagy in cancer. OBJECTIVE We aimed to determine the cellular and molecular activity of targeting PPT1 using ezurpimtrostat, in combination with an anti-PD-1 antibody. METHODS In this study we used a transgenic immunocompetent mouse model of hepatocellular carcinoma. RESULTS Herein, we revealed that inhibition of PPT1 using ezurpimtrostat decreased the liver tumor burden in a mouse model of hepatocellular carcinoma by inducing the penetration of lymphocytes into tumors when combined with anti-programmed death-1 (PD-1). Inhibition of PPT1 potentiates the effects of anti-PD-1 immunotherapy by increasing the expression of major histocompatibility complex (MHC)-I at the surface of liver cancer cells and modulates immunity through recolonization and activation of cytotoxic CD8+ lymphocytes. CONCLUSIONS Ezurpimtrostat turns cold tumors into hot tumors and, thus, could improve T cell-mediated immunotherapies in liver cancer.
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Affiliation(s)
- Eloïne Bestion
- Genoscience Pharma, 10, Rue d'Iéna, 13006, Marseille, France
| | - Madani Rachid
- Genoscience Pharma, 10, Rue d'Iéna, 13006, Marseille, France
| | | | - Gael Roth
- Centre hospitalouniversitaire Grenoble Alpes/Institute for Advanced Biosciences, Centre national de la recherché scienti-fique, Unité mixte de recherche 5309-Institut national de la santé et de la recherche médicale U1209, University Grenoble Alpes/Hepato-Gastroenterology and Digestive Oncology Department, 38043, Grenoble, France
| | - Thomas Decaens
- Centre hospitalouniversitaire Grenoble Alpes/Institute for Advanced Biosciences, Centre national de la recherché scienti-fique, Unité mixte de recherche 5309-Institut national de la santé et de la recherche médicale U1209, University Grenoble Alpes/Hepato-Gastroenterology and Digestive Oncology Department, 38043, Grenoble, France
| | | | - Soraya Mezouar
- Genoscience Pharma, 10, Rue d'Iéna, 13006, Marseille, France
- Etablissement français du sang, Centre national de la recherche scientifique, Anthropologie bio-culturelle, droit, éthique et santé, "Biologie des Groupes Sanguins", Aix-Marseille University, Marseille, France
| | - Eric Raymond
- Genoscience Pharma, 10, Rue d'Iéna, 13006, Marseille, France
- Oncology Department, Groupe Hospitalier Paris Saint Joseph, Paris, France
| | - Philippe Halfon
- Genoscience Pharma, 10, Rue d'Iéna, 13006, Marseille, France.
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189
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Ling L, Li B, Wu H, Zhang K, Li S, Ke B, Zhu Z, Liu T, Liu P, Zhang B. Construction and validation of molecular subtype and signature of immune cell-related telomeric genes and prediction of prognosis and immunotherapy efficacy in ovarian cancer patients. J Gene Med 2024; 26:e3606. [PMID: 38282157 DOI: 10.1002/jgm.3606] [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: 07/13/2023] [Revised: 08/26/2023] [Accepted: 09/20/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Ovarian cancer (OVC) has emerged as a fatal gynecological malignancy as a result of a lack of reliable methods for early detection, limited biomarkers and few treatment options. Immune cell-related telomeric genes (ICRTGs) show promise as potential biomarkers. METHODS ICRTGs were discovered using weighted gene co-expression network analysis (WGCNA). ICRTGs were screened for significant prognosis using one-way Cox regression analysis. Subsequently, molecular subtypes of prognosis-relevant ICRTGs were constructed and validated for OVC, and the immune microenvironment's landscape across subtypes was compared. OVC prognostic models were built and validated using prognosis-relevant ICRTGs. Additionally, chemotherapy susceptibility drugs for OVC patients in the low- and high-risk groups of ICRTGs were screened using genomics of drug susceptibility to cancer (GDSC). Finally, the immunotherapy response in the low- and high-risk groups was detected using the data from GSE78220. We conducted an immune index correlation analysis of ICRTGs with significant prognoses. The MAP3K4 gene, for which the prognostic correlation coefficient is the highest, was validated using tissue microarrays for a prognostic-immune index correlation. RESULTS WGCNA analysis constructed a gene set of ICRTGs and screened 22 genes with prognostic significance. Unsupervised clustering analysis revealed the best molecular typing for two subtypes. The Gene Set Variation Analysis algorithm was used to calculate telomere scores and validate the molecular subtyping. A prognostic model was constructed using 17 ICRTGs. In the The Cancer Genome Atlas-OVC training set and the Gene Expression Omnibus validation set (GSE30161), the risk score model's predicted risk groups and the actual prognosis were shown to be significantly correlated. GDSC screened Axitinib, Bexarotene, Embelin and the GSE78220 datasets and demonstrated that ICRTGs effectively distinguished the group that responds to immunotherapy from the non-responsive group. Additionally, tissue microarray validation results revealed that MAP3K4 significantly predicted patient prognosis. Furthermore, MAP3K4 exhibited a positive association with PD-L1 and a negative relationship with the M1 macrophage markers CD86 and INOS. CONCLUSIONS ICRTGs may be reliable biomarkers for the molecular typing of patients with OVC, enabling the prediction of prognosis and immunotherapy efficacy.
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Affiliation(s)
- Lele Ling
- Department of Acupuncture and Moxibustion, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bingrong Li
- Department of Acupuncture and Moxibustion, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huijing Wu
- Department of Medical Affairs, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kaiyong Zhang
- Department of Acupuncture and Moxibustion, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siwen Li
- Department of Acupuncture and Moxibustion, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Boliang Ke
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengyang Zhu
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Te Liu
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Peng Liu
- Department of Acupuncture and Moxibustion, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bimeng Zhang
- Department of Acupuncture and Moxibustion, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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190
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Bai Y, Li Y, Qin Y, Yang X, Tseng GC, Kim S, Park HJ. The microRNA target site profile is a novel biomarker in the immunotherapy response. Front Oncol 2023; 13:1225221. [PMID: 38188295 PMCID: PMC10771317 DOI: 10.3389/fonc.2023.1225221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
MicroRNAs (miRNAs) bind on the 3' untranslated region (3'UTR) of messenger RNAs (mRNAs) and regulate mRNA expression in physiological and pathological conditions, including cancer. Thus, studies have identified miRNAs as potential biomarkers by correlating the miRNA expression with the expression of important mRNAs and/or clinical outcomes in cancers. However, tumors undergo pervasive 3'UTR shortening/lengthening events through alternative polyadenylation (APA), which varies the number of miRNA target sites in mRNA, raising the number of miRNA target sites (numTS) as another important regulatory axis of the miRNA binding effects. In this study, we developed the first statistical method, BIOMATA-APA, to identify predictive miRNAs based on numTS features. Running BIOMATA-APA on The Cancer Genome Atlas (TCGA) and independent cohort data both with immunotherapy and no immunotherapy, we demonstrated for the first time that the numTS feature 1) distinguishes different cancer types, 2) predicts tumor proliferation and immune infiltration status, 3) explains more variation in the proportion of tumor-infiltrating immune cells, 4) predicts response to immune checkpoint blockade (ICB) therapy, and 5) adds prognostic power beyond clinical and miRNA expression. To the best of our knowledge, this is the first pan-cancer study to systematically demonstrate numTS as a novel type of biomarker representing the miRNA binding effects underlying tumorigenesis and pave the way to incorporate miRNA target sites for miRNA biomarker identification. Another advantage of examining the miRNA binding effect using numTS is that it requires only RNA-Seq data, not miRNAs, thus resulting in high power in the miRNA biomarker identification.
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Affiliation(s)
- Yulong Bai
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Yujia Li
- Statistics-Oncology, Eli Lilly and Company, Indianapolis, IN, United States
| | - Yidi Qin
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Xinshuo Yang
- Department of Operations Research and Financial Engineering, Princeton University, Princeton, NJ, United States
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Soyeon Kim
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Hyun Jung Park
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, United States
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191
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Chen C, Lin CJ, Pei YC, Ma D, Liao L, Li SY, Fan L, Di GH, Wu SY, Liu XY, Wang YJ, Hong Q, Zhang GL, Xu LL, Li BB, Huang W, Shi JX, Jiang YZ, Hu X, Shao ZM. Comprehensive genomic profiling of breast cancers characterizes germline-somatic mutation interactions mediating therapeutic vulnerabilities. Cell Discov 2023; 9:125. [PMID: 38114467 PMCID: PMC10730692 DOI: 10.1038/s41421-023-00614-3] [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: 07/13/2023] [Accepted: 10/08/2023] [Indexed: 12/21/2023] Open
Abstract
Germline-somatic mutation interactions are universal and associated with tumorigenesis, but their role in breast cancer, especially in non-Caucasians, remains poorly characterized. We performed large-scale prospective targeted sequencing of matched tumor-blood samples from 4079 Chinese females, coupled with detailed clinical annotation, to map interactions between germline and somatic alterations. We discovered 368 pathogenic germline variants and identified 5 breast cancer DNA repair-associated genes (BCDGs; BRCA1/BRCA2/CHEK2/PALB2/TP53). BCDG mutation carriers, especially those with two-hit inactivation, demonstrated younger onset, higher tumor mutation burden, and greater clinical benefits from platinum drugs, PARP inhibitors, and immune checkpoint inhibitors. Furthermore, we leveraged a multiomics cohort to reveal that clinical benefits derived from two-hit events are associated with increased genome instability and an immune-activated tumor microenvironment. We also established an ethnicity-specific tool to predict BCDG mutation and two-hit status for genetic evaluation and therapeutic decisions. Overall, this study leveraged the large sequencing cohort of Chinese breast cancers, optimizing genomics-guided selection of DNA damaging-targeted therapy and immunotherapy within a broader population.
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Affiliation(s)
- Chao Chen
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cai-Jin Lin
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu-Chen Pei
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ding Ma
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Li Liao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Si-Yuan Li
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lei Fan
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gen-Hong Di
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Song-Yang Wu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi-Yu Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yun-Jin Wang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Qi Hong
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Guo-Liang Zhang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lin-Lin Xu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Bei-Bei Li
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wei Huang
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Jin-Xiu Shi
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Xin Hu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China.
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Deneuve S, Fervers B, Senkin S, Bouaoun L, Pérol O, Chavanel B, Lu L, Coste I, Renno T, Zavadil J, Virard F. Molecular landscapes of oral cancers of unknown etiology. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.15.23299866. [PMID: 38168303 PMCID: PMC10760302 DOI: 10.1101/2023.12.15.23299866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The incidence of the mobile tongue cancer in young patients has been rising. This oral cancer (OC) type has no identified risk factors (NIRF), no established molecular markers and is not yet recognized as a distinct clinical entity. To understand this emerging malignancy, we innovatively analyzed the public head and neck cancer multi-omics data. We identified mutational signatures that successfully stratified 307 OC and 109 laryngeal cancer cases according to their clinico-pathological characteristics. The NIRF OCs exhibited significantly increased activities of endogenous clock-like and APOBEC-associated mutagenesis, alongside specific cancer driver gene mutations, distinct methylome patterns and prominent antimicrobial transcriptomic responses. Furthermore, we show that mutational signature SBS16 in OCs reflects the combined effects of alcohol drinking and tobacco smoking. Our study characterizes the unique disease histories and molecular programs of the NIRF OCs revealing that this emerging cancer subtype is likely driven by increased endogenous mutagenesis correlated with responses to microbial insults.
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193
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Sun X, Meng F, Nong M, Fang H, Lu C, Wang Y, Zhang P. Single-cell dissection reveals the role of aggrephagy patterns in tumor microenvironment components aiding predicting prognosis and immunotherapy on lung adenocarcinoma. Aging (Albany NY) 2023; 15:14333-14371. [PMID: 38095634 PMCID: PMC10756128 DOI: 10.18632/aging.205306] [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: 07/17/2023] [Accepted: 11/06/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is one of the leading malignant cancers. Aggrephagy plays a critical role in key genetic events for various cancers; yet, how aggrephagy functions within the tumor microenvironment (TME) in LUAD remains to be elucidated. METHODS In this study, by sequential non-negative matrix factorization (NMF) algorithm, pseudotime analysis, cell-cell interaction analysis, and SCENIC analysis, we have shown that aggrephagy genes demonstrated various patterns among different cell types in LUAD TME. LUAD and Immunotherapy cohorts from public repository were used to determine the prognosis and immune response of aggrephagy TME subtypes. The aggrephagy-deprived prognostic score (ADPS) was quantified based on machine learning algorithms. RESULTS The cancer-associated fibroblasts (CAFs), tumor-associated macrophages (TAMs), and CD8+ T cells have various aggrephagy patterns, which enhance the intensity of intercellular communication and transcription factor activation. Furthermore, based on the signatures of the newly defined aggrephagy cell subtypes and expression profiles of large cohorts in LUAD patients, we determine that DYNC1I2+CAF-C1, DYNLL1+CAF-C2, PARK7+CAF-C3, VIM+Mac-C1, PARK7+Mac-C2, VIM+CD8+T_cells-C1, UBA52+CD8+T_cells-C2, TUBA4A+CD8+T_ cells-C3, and TUBA1A+CD8+T_cells-C4 are crucial prognostic factors for LUAD patients. The developed ADPS could predict survival outcomes and immunotherapeutic response across ten cohorts (n = 1838), and patients with low ADPS owned a better prognosis, lower genomic alterations, and are more sensitive to immunotherapy. Meanwhile, based on PRISM, CTRP, and CMAP databases, PLK inhibitor BI-2536, may be a potential agent for patients with high ADPS. CONCLUSIONS Taken together, our novel and systematic single-cell analysis has revealed the unique role of aggrephagy in remodeling the TME of LUAD. As a newly demonstrated biomarker, the ADPS facilitates the clinical management and individualized treatment of LUAD.
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Affiliation(s)
- Xinti Sun
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Fei Meng
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Minyu Nong
- School of Clinical Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Hao Fang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Chenglu Lu
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yan Wang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Peng Zhang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
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Shi A, Yan M, Pang B, Pang L, Wang Y, Lan Y, Zhang X, Xu J, Ping Y, Hu J. Dissecting cellular states of infiltrating microenvironment cells in melanoma by integrating single-cell and bulk transcriptome analysis. BMC Immunol 2023; 24:52. [PMID: 38082384 PMCID: PMC10714533 DOI: 10.1186/s12865-023-00587-8] [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] [Received: 05/25/2022] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Cellular states of different immune cells can affect the activity of the whole immune microenvironment. METHODS Here, leveraging reference profiles of microenvironment cell states that were constructed based on single-cell RNA-seq data of melanoma, we dissected the composition of microenvironment cell states across 463 skin cutaneous melanoma (SKCM) bulk samples through CIBERSORT-based deconvolution of gene expression profiles and revealed high heterogeneity of their distribution. Correspondence analysis on the estimated cellular fractions of melanoma bulk samples was performed to identify immune phenotypes. Based on the publicly available clinical survival and therapy data, we analyzed the relationship between immune phenotypes and clinical outcomes of melanoma. RESULTS By analysis of the relationships among those cell states, we further identified three distinct tumor microenvironment immune phenotypes: "immune hot/active", "immune cold-suppressive" and "immune cold-exhausted". They were characterized by markedly different patterns of cell states: most notably the CD8 T Cytotoxic state, CD8 T Mixed state, B non-regulatory state and cancer-associated fibroblasts (CAFs), depicting distinct types of antitumor immune response (or immune activity). These phenotypes had prognostic significance for progression-free survival and implications in response to immune therapy in an independent cohort of anti-PD1 treated melanoma patients. CONCLUSIONS The proposed strategy of leveraging single-cell data to dissect the composition of microenvironment cell states in individual bulk tumors can also extend to other cancer types, and our results highlight the importance of microenvironment cell states for the understanding of tumor immunity.
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Affiliation(s)
- Aiai Shi
- School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin, 541100, Guangxi, China
| | - Min Yan
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, 400010, China
| | - Bo Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yihan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Jinyuan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Jing Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
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195
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Heiser CN, Simmons AJ, Revetta F, McKinley ET, Ramirez-Solano MA, Wang J, Kaur H, Shao J, Ayers GD, Wang Y, Glass SE, Tasneem N, Chen Z, Qin Y, Kim W, Rolong A, Chen B, Vega PN, Drewes JL, Markham NO, Saleh N, Nikolos F, Vandekar S, Jones AL, Washington MK, Roland JT, Chan KS, Schürpf T, Sears CL, Liu Q, Shrubsole MJ, Coffey RJ, Lau KS. Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors. Cell 2023; 186:5620-5637.e16. [PMID: 38065082 PMCID: PMC10756562 DOI: 10.1016/j.cell.2023.11.006] [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: 02/22/2023] [Revised: 08/23/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023]
Abstract
Colorectal cancer exhibits dynamic cellular and genetic heterogeneity during progression from precursor lesions toward malignancy. Analysis of spatial multi-omic data from 31 human colorectal specimens enabled phylogeographic mapping of tumor evolution that revealed individualized progression trajectories and accompanying microenvironmental and clonal alterations. Phylogeographic mapping ordered genetic events, classified tumors by their evolutionary dynamics, and placed clonal regions along global pseudotemporal progression trajectories encompassing the chromosomal instability (CIN+) and hypermutated (HM) pathways. Integrated single-cell and spatial transcriptomic data revealed recurring epithelial programs and infiltrating immune states along progression pseudotime. We discovered an immune exclusion signature (IEX), consisting of extracellular matrix regulators DDR1, TGFBI, PAK4, and DPEP1, that charts with CIN+ tumor progression, is associated with reduced cytotoxic cell infiltration, and shows prognostic value in independent cohorts. This spatial multi-omic atlas provides insights into colorectal tumor-microenvironment co-evolution, serving as a resource for stratification and targeted treatments.
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Affiliation(s)
- Cody N Heiser
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Alan J Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Frank Revetta
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Eliot T McKinley
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Marisol A Ramirez-Solano
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Jiawei Wang
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Harsimran Kaur
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Justin Shao
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Computer Science, Vanderbilt University, Nashville, TN 37235, USA
| | - Gregory D Ayers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yu Wang
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Sarah E Glass
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Naila Tasneem
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Zhengyi Chen
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yan Qin
- Incendia Therapeutics, Inc., Boston, MA 02135, USA
| | - William Kim
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Andrea Rolong
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Bob Chen
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Paige N Vega
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Julia L Drewes
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas O Markham
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nabil Saleh
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Fotis Nikolos
- Department of Urology, Neal Cancer Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Simon Vandekar
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Angela L Jones
- Vanderbilt Technologies for Advanced Genomics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Joseph T Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Keith S Chan
- Department of Urology, Neal Cancer Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | | | - Cynthia L Sears
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Qi Liu
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Martha J Shrubsole
- Department of Medicine, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robert J Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| | - Ken S Lau
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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196
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Coley AK, Lu C, Pankaj A, Emmett MJ, Lang ER, Song Y, Xu KH, Xu N, Patel BK, Chougule A, Nieman LT, Aryee MJ, Ferrone CR, Deshpande V, Franses JW, Ting DT. Dysregulated Repeat Element Viral-like Immune Response in Hepatocellular Carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.570014. [PMID: 38105940 PMCID: PMC10723373 DOI: 10.1101/2023.12.04.570014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Purpose Dysregulation of viral-like repeat RNAs are a common feature across many malignancies that are linked with immunological response, but the characterization of these in hepatocellular carcinoma (HCC) is understudied. In this study, we performed RNA in situ hybridization (RNA-ISH) of different repeat RNAs, immunohistochemistry (IHC) for immune cell subpopulations, and spatial transcriptomics to understand the relationship of HCC repeat expression, immune response, and clinical outcomes. Experimental Design RNA-ISH for LINE1, HERV-K, HERV-H, and HSATII repeats and IHC for T-cell, Treg, B-cell, macrophage, and immune checkpoint markers were performed on 43 resected HCC specimens. Spatial transcriptomics on tumor and vessel regions of interest was performed on 28 specimens from the same cohort. Results High HERV-K and high LINE1 expression were both associated with worse overall survival. There was a positive correlation between LINE1 expression and FOXP3 T-regulatory cells (r = 0.51 p < 0.001) as well as expression of the TIM3 immune checkpoint (r = 0.34, p = 0.03). Spatial transcriptomic profiling of HERV-K high and LINE-1 high tumors identified elevated expression of multiple genes previously associated with epithelial mesenchymal transition, cellular proliferation, and worse overall prognosis in HCC including SSX1, MAGEC2, and SPINK1. Conclusion Repeat RNAs may serve as useful prognostic biomarkers in HCC and may also serve as novel therapeutic targets. Additional study is needed to understand the mechanisms by which repeat RNAs impact HCC tumorigenesis.
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Affiliation(s)
- Avril K. Coley
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Surgery, Massachusetts General Hospital Harvard Medical School; Boston, MA, USA
| | - Chenyue Lu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Health Sciences and Technology Program; Cambridge, MA, USA
| | - Amaya Pankaj
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Matthew J. Emmett
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Evan R. Lang
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Yuhui Song
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Katherine H. Xu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Nova Xu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Bidish K. Patel
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Abhijit Chougule
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Linda T. Nieman
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Martin J. Aryee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health; Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA, USA
- Broad Institute of Harvard and MIT; Cambridge, MA, USA
| | | | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School; Boston, MA, USA
| | - Joseph W. Franses
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
- Health Sciences and Technology Program; Cambridge, MA, USA
- Section of Hematology-Oncology, Department of Medicine, University of Chicago; Chicago, IL, USA
| | - David T. Ting
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
- Health Sciences and Technology Program; Cambridge, MA, USA
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197
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Wu X, Li T, Jiang R, Yang X, Guo H, Yang R. Targeting MHC-I molecules for cancer: function, mechanism, and therapeutic prospects. Mol Cancer 2023; 22:194. [PMID: 38041084 PMCID: PMC10693139 DOI: 10.1186/s12943-023-01899-4] [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: 08/29/2023] [Accepted: 11/12/2023] [Indexed: 12/03/2023] Open
Abstract
The molecules of Major histocompatibility class I (MHC-I) load peptides and present them on the cell surface, which provided the immune system with the signal to detect and eliminate the infected or cancerous cells. In the context of cancer, owing to the crucial immune-regulatory roles played by MHC-I molecules, the abnormal modulation of MHC-I expression and function could be hijacked by tumor cells to escape the immune surveillance and attack, thereby promoting tumoral progression and impairing the efficacy of cancer immunotherapy. Here we reviewed and discussed the recent studies and discoveries related to the MHC-I molecules and their multidirectional functions in the development of cancer, mainly focusing on the interactions between MHC-I and the multiple participators in the tumor microenvironment and highlighting the significance of targeting MHC-I for optimizing the efficacy of cancer immunotherapy and a deeper understanding of the dynamic nature and functioning mechanism of MHC-I in cancer.
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Affiliation(s)
- Xiangyu Wu
- Department of Urology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Tianhang Li
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Rui Jiang
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Xin Yang
- Department of Urology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Hongqian Guo
- Department of Urology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
| | - Rong Yang
- Department of Urology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
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198
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Kato M, Uchida J. Recent advances in immune checkpoint inhibitors in the treatment of urothelial carcinoma: A review. Int J Urol 2023; 30:1068-1077. [PMID: 37602512 DOI: 10.1111/iju.15278] [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: 05/30/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023]
Abstract
Treatment options for urothelial carcinoma were limited until the emergence of immune checkpoint inhibitors, and even now, the prognosis of metastatic disease is poor compared with the other two major genitourinary cancers, renal cell carcinoma and prostate cancer. Despite the increasing use of immune checkpoint inhibitors in the sequential treatment of urothelial carcinoma, conflicting results from similar randomized clinical trials call into question the efficacy of this treatment. In addition, physicians must be aware of the clinical characteristics of immune checkpoint inhibitors, including immune-related adverse events, pseudo- and hyperprogression. This review summarizes the conflicting results of recent clinical trials and provides insights into the role of immune checkpoint inhibitors in the treatment of urothelial carcinoma.
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Affiliation(s)
- Minoru Kato
- Department of Urology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Junji Uchida
- Department of Urology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
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199
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Vos JL, Burman B, Jain S, Fitzgerald CWR, Sherman EJ, Dunn LA, Fetten JV, Michel LS, Kriplani A, Ng KK, Eng J, Tchekmedyian V, Haque S, Katabi N, Kuo F, Han CY, Nadeem Z, Yang W, Makarov V, Srivastava RM, Ostrovnaya I, Prasad M, Zuur CL, Riaz N, Pfister DG, Klebanoff CA, Chan TA, Ho AL, Morris LGT. Nivolumab plus ipilimumab in advanced salivary gland cancer: a phase 2 trial. Nat Med 2023; 29:3077-3089. [PMID: 37620627 PMCID: PMC11293616 DOI: 10.1038/s41591-023-02518-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
Salivary gland cancers (SGCs) are rare, aggressive cancers without effective treatments when metastasized. We conducted a phase 2 trial evaluating nivolumab (nivo, anti-PD-1) and ipilimumab (ipi, anti-CTLA-4) in 64 patients with metastatic SGC enrolled in two histology-based cohorts (32 patients each): adenoid cystic carcinoma (ACC; cohort 1) and other SGCs (cohort 2). The primary efficacy endpoint (≥4 objective responses) was met in cohort 2 (5/32, 16%) but not in cohort 1 (2/32, 6%). Treatment safety/tolerability and progression-free survival (PFS) were secondary endpoints. Treatment-related adverse events grade ≥3 occurred in 24 of 64 (38%) patients across both cohorts, and median PFS was 4.4 months (95% confidence interval (CI): 2.4, 8.3) and 2.2 months (95% CI: 1.8, 5.3) for cohorts 1 and 2, respectively. We present whole-exome, RNA and T cell receptor (TCR) sequencing data from pre-treatment and on-treatment tumors and immune cell flow cytometry and TCR sequencing from peripheral blood at serial timepoints. Responding tumors universally demonstrated clonal expansion of pre-existing T cells and mutational contraction. Responding ACCs harbored neoantigens, including fusion-derived neoepitopes, that induced T cell responses ex vivo. This study shows that nivo+ipi has limited efficacy in ACC, albeit with infrequent, exceptional responses, and that it could be promising for non-ACC SGCs, particularly salivary duct carcinomas. ClinicalTrials.gov identifier: NCT03172624 .
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Affiliation(s)
- Joris L Vos
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bharat Burman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Swati Jain
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Conall W R Fitzgerald
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric J Sherman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lara A Dunn
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James V Fetten
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Loren S Michel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anuja Kriplani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth K Ng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juliana Eng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vatche Tchekmedyian
- Department of Medicine, Maine Medical Center-Tufts University School of Medicine, Portland, ME, USA
| | - Sofia Haque
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nora Katabi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fengshen Kuo
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Catherine Y Han
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zaineb Nadeem
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Yang
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vladimir Makarov
- Center for Immunotherapy and Precision Immuno-oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Raghvendra M Srivastava
- Center for Immunotherapy and Precision Immuno-oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Manu Prasad
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte L Zuur
- Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Department of Otorhinolaryngology Head and Neck Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David G Pfister
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher A Klebanoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Center for Immunotherapy and Precision Immuno-oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Alan L Ho
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Luc G T Morris
- Head and Neck Service and Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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He Y, Wang X. Identifying biomarkers associated with immunotherapy response in melanoma by multi-omics analysis. Comput Biol Med 2023; 167:107591. [PMID: 37875043 DOI: 10.1016/j.compbiomed.2023.107591] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/26/2023] [Accepted: 10/17/2023] [Indexed: 10/26/2023]
Abstract
Despite immune checkpoint inhibitors (ICIs) have shown the greatest success in melanoma treatment, only a subset of melanoma patients responds well to ICIs. Thus, identifying predictive biomarkers for immunotherapy response is crucial. In this study, we took complementary advantages of immunotherapy data and The Cancer Genome Atlas (TCGA) multi-omics data to explore the predictive biomarkers for the response to immunotherapy in melanoma. We first predicted responsive and non-responsive melanomas in the TCGA skin cutaneous melanoma (SKCM) cohort based on both somatic mutation and transcriptome datasets which involved immunotherapy data for melanoma. This method identified 170 responsive and 56 non-responsive melanomas in TCGA-SKCM. Based on the TCGA-SKCM data, we performed a comprehensive comparison of multi-omics molecular features between responsive and non-responsive melanomas. We identified the molecular features significantly associated with immunotherapy response in melanoma at the genome, transcriptome, epigenome, and proteome levels, respectively. Our analysis confirmed certain immunotherapy response-associated biomarkers, such as tumor mutation burden (TMB), copy number alteration (CNA), intratumor heterogeneity (ITH), PD-L1 expression, and tumor immunity. Moreover, we identified some novel molecular features associated with immunotherapy response: (1) the activation of mast cells and dendritic cells correlating negatively with immunotherapy response; (2) the enrichment of many oncogenic pathways correlating positively with immunotherapy response, such as JAK-STAT, RAS, MAPK, HIF-1, PI3K-Akt, and VEGF pathways; and (3) a number of microRNAs and proteins whose expression correlates with immunotherapy response. In addition, the mTOR signaling pathway has a negative association with immunotherapy response. The novel biomarkers have potential predictive values in immunotherapy response and warrant further investigation.
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Affiliation(s)
- Yin He
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China.
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