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Arumugam P, M SM, Jayaseelan VP. Pathogenic loss-of-function mutations in LRP1B are associated with poor survival in head and neck cancer patients. JOURNAL OF STOMATOLOGY, ORAL AND MAXILLOFACIAL SURGERY 2024:101971. [PMID: 39032644 DOI: 10.1016/j.jormas.2024.101971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 07/11/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
OBJECTIVE Head and neck squamous cell carcinoma (HNSCC) present a significant challenge in the medical field due to treatment resistance, which often hinders successful outcomes. The dysregulation of the LRP1B gene is linked to various cancers, but its specific role in HNSCC is poorly understood. METHODS This study investigated the link between pathogenic loss-of-function mutations in the LRP1B gene and survival outcomes in HNSCC patients. The Cancer Genome Atlas HNSCC cohort, comprised of 520 tumor and 44 normal tissues, was analyzed using cBioportal, and UALCAN tools. Expression patterns, survival outcomes, and clinical correlations of LRP1B were evaluated. In-depth analyses involved validation of mRNA expression using RT-qPCR and functional exploration using various in-silico tools. RESULTS Analysis of data from The Cancer Genome Atlas (TCGA) and cBioPortal revealed a high frequency (25 %) of LRP1B mutations in HNSCC patients. Notably, splice mutation, truncating mutation, and deep deletion, considered potential drivers, are commonly associated with LRP1B mutations. Patients with LRP1B mutations also exhibit poorer overall survival rates compared to those without these mutations. Furthermore, LRP1B mRNA expression is significantly reduced in HNSCC tissues compared to normal tissues and is correlated with advanced tumor stage, higher tumor grade, and nodal metastasis. CONCLUSION These findings indicate that LRP1B may function as both a prognostic biomarker and a therapeutic target in HNSCC patients.
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Affiliation(s)
- Paramasivam Arumugam
- Molecular Biology Laboratory, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India.
| | - Senthil Murugan M
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Vijayashree Priyadharsini Jayaseelan
- Clinical Genetics Laboratory, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
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Li Y, Ji L, Zhang Y, Zhang J, Reuben A, Zeng H, Huang Q, Wei Q, Tan S, Xia X, Li W, Zhang J, Tian P. The combination of tumor mutational burden and T-cell receptor repertoire predicts the response to immunotherapy in patients with advanced non-small cell lung cancer. MedComm (Beijing) 2024; 5:e604. [PMID: 38840771 PMCID: PMC11151154 DOI: 10.1002/mco2.604] [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: 10/25/2023] [Revised: 03/27/2024] [Accepted: 05/01/2024] [Indexed: 06/07/2024] Open
Abstract
Tumor mutational burden (TMB) and T-cell receptor (TCR) might predict the response to immunotherapy in patients with non-small cell lung cancer (NSCLC). However, the predictive value of the combination of TMB and TCR was not clear. Targeted DNA and TCR sequencing were performed on tumor biopsy specimens. We combined TMB and TCR diversity into a TMB-and-TCR (TMR) score using logistic regression. In total, 38 patients with advanced NSCLC were divided into a discovery set (n = 17) and validation set (n = 21). A higher TMR score was associated with better response and longer progression-free survival to immunotherapy in both the discovery set and validation set. The performance of TMR score was confirmed in the two external validation cohorts of 225 NSCLC patients and 306 NSCLC patients. Tumors with higher TMR scores were more likely to combine with LRP1B gene mutation (p = 0.027) and top 1% CDR3 sequences (p = 0.001). Furthermore, LRP1B allele frequency was negatively correlated with the top 1% CDR3 sequences (r = -0.55, p = 0.033) and positively correlated with tumor shrinkage (r = 0.68, p = 0.007). The TMR score could serve as a potential predictive biomarker for the response to immunotherapy in advanced NSCLC.
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Affiliation(s)
- Yalun Li
- Department of Pulmonary and Critical Care MedicineState Key Laboratory of Respiratory Health and MultimorbidityWest China Hospital of Sichuan University, Precision Medicine Key Laboratory of Sichuan ProvinceChengduSichuanChina
- Lung Cancer Center/Lung Cancer InstituteWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Liyan Ji
- Geneplus‐Beijing InstituteBeijingChina
| | | | - Jiexin Zhang
- Departments of Bioinformatics and Computational BiologyUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical OncologyUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Hao Zeng
- Department of Pulmonary and Critical Care MedicineWest China Hospital, West China School of Medicine, Sichuan UniversityChengduSichuanChina
| | - Qin Huang
- Department of Pulmonary and Critical Care MedicineWest China Hospital, West China School of Medicine, Sichuan UniversityChengduSichuanChina
| | - Qi Wei
- Department of Pulmonary and Critical Care MedicineWest China Hospital, West China School of Medicine, Sichuan UniversityChengduSichuanChina
| | - Sihan Tan
- Department of Pulmonary and Critical Care MedicineWest China Hospital, West China School of Medicine, Sichuan UniversityChengduSichuanChina
| | | | - Weimin Li
- Department of Pulmonary and Critical Care MedicineState Key Laboratory of Respiratory Health and MultimorbidityWest China Hospital of Sichuan University, Precision Medicine Key Laboratory of Sichuan ProvinceChengduSichuanChina
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical OncologyUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
- Department of Genomic MedicineUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
- Lung Cancer Genomics ProgramUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
- Lung Cancer Interception ProgramUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Panwen Tian
- Department of Pulmonary and Critical Care MedicineState Key Laboratory of Respiratory Health and MultimorbidityWest China Hospital of Sichuan University, Precision Medicine Key Laboratory of Sichuan ProvinceChengduSichuanChina
- Lung Cancer Center/Lung Cancer InstituteWest China Hospital, Sichuan UniversityChengduSichuanChina
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Duman ET, Sitte M, Conrads K, Mackay A, Ludewig F, Ströbel P, Ellenrieder V, Hessmann E, Papantonis A, Salinas G. A single-cell strategy for the identification of intronic variants related to mis-splicing in pancreatic cancer. NAR Genom Bioinform 2024; 6:lqae057. [PMID: 38800828 PMCID: PMC11127633 DOI: 10.1093/nargab/lqae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/24/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024] Open
Abstract
Most clinical diagnostic and genomic research setups focus almost exclusively on coding regions and essential splice sites, thereby overlooking other non-coding variants. As a result, intronic variants that can promote mis-splicing events across a range of diseases, including cancer, are yet to be systematically investigated. Such investigations would require both genomic and transcriptomic data, but there currently exist very few datasets that satisfy these requirements. We address this by developing a single-nucleus full-length RNA-sequencing approach that allows for the detection of potentially pathogenic intronic variants. We exemplify the potency of our approach by applying pancreatic cancer tumor and tumor-derived specimens and linking intronic variants to splicing dysregulation. We specifically find that prominent intron retention and pseudo-exon activation events are shared by the tumors and affect genes encoding key transcriptional regulators. Our work paves the way for the assessment and exploitation of intronic mutations as powerful prognostic markers and potential therapeutic targets in cancer.
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Affiliation(s)
- Emre Taylan Duman
- NGS-Core Unit for Integrative Genomics, Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Maren Sitte
- NGS-Core Unit for Integrative Genomics, Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Karly Conrads
- Clinic of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Göttingen, Germany
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Institute of Medical Bioinformatics, University Medical Center, Göttingen, Germany
| | - Adi Mackay
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Fabian Ludewig
- NGS-Core Unit for Integrative Genomics, Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Philipp Ströbel
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Volker Ellenrieder
- Clinic of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Göttingen, Germany
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Comprehensive Cancer Center Lower Saxony (CCC-N), Göttingen, Germany
| | - Elisabeth Hessmann
- Clinic of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Göttingen, Germany
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Comprehensive Cancer Center Lower Saxony (CCC-N), Göttingen, Germany
| | - Argyris Papantonis
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Institute of Pathology, University Medical Center, Göttingen, Germany
- Comprehensive Cancer Center Lower Saxony (CCC-N), Göttingen, Germany
| | - Gabriela Salinas
- NGS-Core Unit for Integrative Genomics, Institute of Pathology, University Medical Center, Göttingen, Germany
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
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Li T, Liu J, Zhou Y, Huang S, Wang D, Chen J, Fu Y, He P. Clinical relevance of somatic mutations in Chinese lung adenocarcinoma and their prognostic implications for survival. Cancer Med 2024; 13:e7227. [PMID: 38770632 PMCID: PMC11106684 DOI: 10.1002/cam4.7227] [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: 09/11/2023] [Revised: 04/07/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND To comprehensively elucidate the genomic and mutational features of lung cancer cases, and lung adenocarcinoma (LUAD), it is imperative to conduct ongoing investigations into the genomic landscape. In this study, we aim to analyze the somatic mutation profile and assessed the significance of these informative genes utilizing a retrospective LUAD cohort. METHODS A total of 247 Chinese samples were analyzed to exhibit the tumor somatic genomic alterations in patients with LUAD. The Cox regression analysis was employed to identify prognosis-related genes and establish a predictive model for stratifying patients with LUAD. RESULTS In the Dianjiang People's Hospital (DPH) cohort, the top five frequent mutated genes were (Epidermal growth factor receptor) EGFR (68%), TP53 (30%), RBM10 (13%), LRP1B (9%), and KRAS (9%). Of which, EGFR is a mostly altered driver gene, and most mutation sites are located in tyrosine kinase regions. Oncogene pathway alteration and mutation signature analysis demonstrated the RTK-RAS pathway alteration, and smoking was the main carcinogenic factor of the DPH cohort. Furthermore, we identified 34 driver genes in the DPH cohort, including EGFR (68%), TP53 (30.4%), RBM10 (12.6%), KRAS (8.5%), LRP1B (8.5%), and so on, and 45 Clinical Characteristic-Related Genes (CCRGs) were found to closely related to the clinical high-risk factors. We developed a Multiple Parameter Gene Mutation (MPGM) risk model by integrating critical genes and oncogenic pathway alterations in LUAD patients from the DPH cohort. Based on publicly available LUAD datasets, we identified five genes, including BRCA2, Anaplastic lymphoma kinase (ALK), BRAF, EGFR, and Platelet-Derived Growth Factor Receptor Alpha (PDGFRA), according to the multivariable Cox regression analysis. The MPGM-low group showed significantly better overall survival (OS) compared to the MPGM-high group (p < 0.0001, area under the curve (AUC) = 0.754). The robust performance was validated in 55 LUAD patients from the DPH cohort and another LUAD dataset. Immune characteristics analysis revealed a higher proportion of primarily DCs and mononuclear cells in the MPGM-low risk group, while the MPGM-high risk group showed lower immune cells and higher tumor cell infiltration. CONCLUSION This study provides a comprehensive genomic landscape of Chinese LUAD patients and develops an MPGM risk model for LUAD prognosis stratification. Further follow-up will be performed for the patients in the DPH cohort consistently to explore the resistance and prognosis genetic features.
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Affiliation(s)
- Tongxin Li
- Department of Cardiothoracic SurgeryDianjiang People's Hospital of ChongqingChongqingChina
| | - Jie Liu
- Department of Thoracic Surgery, Southwest HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Yu Zhou
- Department of Cardiothoracic SurgeryDianjiang People's Hospital of ChongqingChongqingChina
| | - Shengyuan Huang
- Department of Cardiothoracic SurgeryDianjiang People's Hospital of ChongqingChongqingChina
| | - Dong Wang
- Department of Cardiothoracic SurgeryDianjiang People's Hospital of ChongqingChongqingChina
| | - Jianrong Chen
- Department of Cardiothoracic SurgeryDianjiang People's Hospital of ChongqingChongqingChina
| | - Yong Fu
- Department of Cardiothoracic SurgeryDianjiang People's Hospital of ChongqingChongqingChina
| | - Ping He
- Department of Cardiac Surgery, Southwest HospitalArmy Medical University (Third Military Medical University)ChongqingChina
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Li Y, Pan C, Gao Y, Zhang L, Ji D, Cui X, Zhang X, Cai Y, Zhang Y, Yao Y, Wang L, Leng J, Zhan T, Wu D, Gao Z, Sun YS, Li Z, Luo H, Wu A. Total Neoadjuvant Therapy With PD-1 Blockade for High-Risk Proficient Mismatch Repair Rectal Cancer. JAMA Surg 2024; 159:529-537. [PMID: 38381429 PMCID: PMC10882505 DOI: 10.1001/jamasurg.2023.7996] [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: 07/05/2023] [Accepted: 11/25/2023] [Indexed: 02/22/2024]
Abstract
Importance Total neoadjuvant therapy (TNT) is the standard treatment for locally advanced rectal cancer, especially for patients with high-risk factors. However, the efficacy of TNT combined with immunotherapy for patients with proficient mismatch repair (pMMR) rectal cancer is unknown. Objectives To evaluate the safety and efficacy of TNT with induction chemoimmunotherapy followed by long-course chemoradiation in patients with high-risk, pMMR rectal cancer and to identify potential molecular biomarkers associated with treatment efficacy. Design, Setting, and Participants This cohort study was a single-arm phase 2 trial conducted at Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, from June 2020 to October 2021. Biopsies and plasma were collected before treatment for whole-exome sequencing and cell-free DNA sequencing, respectively. Data were analyzed from May 2022 to September 2022. Interventions Participants received 3 cycles of induction oxaliplatin and capecitabine combined with camrelizumab and radiotherapy (50.6 Gy in 22 fractions) with concurrent capecitabine. Patients without disease progression received 2 cycles of consolidation oxaliplatin/capecitabine. Main Outcomes and Measures The primary end point was pathologic complete response rate. Results Of 25 patients enrolled (19 men [76%]; 6 women [24%]; median [IQR] age, 58 [48-64] years), 22 patients (88%) completed the TNT schedule. The pathologic complete response rate was 33.3% (7/21). Twelve patients (48%) achieved clinical complete response, and 4 patients (16%) chose to watch and wait. R0 resection was achieved in 21 of 21 patients, and the major pathologic response rate was 38.1% (8/21). The most common adverse event was nausea (80%, 20/25); grade 3 toxic effects occurred in 9 of 25 patients (36%). Patients with tumor shrinkage of 50% or greater after induction oxaliplatin/capecitabine and camrelizumab or clinical complete response had higher percentages of LRP1B mutation. Mutation of LRP1B was associated with high tumor mutation burden and tumor neoantigen burden. Patients with high tumor mutation burden all benefited from therapy. Conclusions and Relevance This study found that TNT with induction chemoimmunotherapy followed by long-course chemoradiation was safe and effective for patients with high-risk rectal cancer with pMMR status. Longer follow-up and larger clinical studies are needed to validate this innovative regimen. There is also an urgent need to further validate the predictive value of LRP1B and discover other novel biomarkers with potential predictive value for rectal cancer.
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Affiliation(s)
- Yingjie Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Unit III, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing, China
| | - Chaohu Pan
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, Southern University of Science and Technology, Shenzhen, China
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology, Shenzhen, China
| | - Yuye Gao
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Unit III, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing, China
| | - Li Zhang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Pathology, Beijing Cancer Hospital and Institute, Peking University School of Oncology, Beijing, China
| | - Dengbo Ji
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Unit III, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaoli Cui
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology, Shenzhen, China
| | - Xiaoyan Zhang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Radiology, Beijing Cancer Hospital and Institute, Peking University School of Oncology, Beijing, China
| | - Yong Cai
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Radiation Oncology, Beijing Cancer Hospital and Institute, Peking University School of Oncology, Beijing, China
| | - Yangzi Zhang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Radiation Oncology, Beijing Cancer Hospital and Institute, Peking University School of Oncology, Beijing, China
| | - Yunfeng Yao
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Unit III, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing, China
| | - Lin Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Unit III, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jiahua Leng
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Unit III, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing, China
| | - Tiancheng Zhan
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Unit III, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing, China
| | - Dongfang Wu
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology, Shenzhen, China
| | - Zhibo Gao
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology, Shenzhen, China
| | - Ying-Shi Sun
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Radiology, Beijing Cancer Hospital and Institute, Peking University School of Oncology, Beijing, China
| | - Zhongwu Li
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Pathology, Beijing Cancer Hospital and Institute, Peking University School of Oncology, Beijing, China
| | - Haitao Luo
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology, Shenzhen, China
| | - Aiwen Wu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Unit III, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing, China
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Li L, Xiang T, Li X. The immune response-related genomic alterations in patients with malignant melanoma. Medicine (Baltimore) 2024; 103:e37966. [PMID: 38669390 PMCID: PMC11049764 DOI: 10.1097/md.0000000000037966] [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: 01/30/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
Immune checkpoint inhibitors (ICIs) significantly improve the survival outcomes of patients with advanced melanoma. However, response varies among from patient to patient and predictive biomarkers are urgently needed. We integrated mutational profiles from next-generation sequencing (NGS) data and clinicopathologic characteristics of melanoma patients to investigate whether tumor genomic profiling contribute to clinical benefit of ICIs treatment. The majority of genes identified with high mutation frequency have all been reported as well-known immunotherapy-related genes. Thirty-five patients (43.2%) had at least 1 BRAF/RAS/NF1 mutation. The other 46 (56.8%) melanomas without BRAF/RAS/NF1 mutation were classified as Triple-WT. We identified mutational signature 6 (known as associated with defective DNA mismatch repair) among cases in this cohort. Compared to patients with PD-L1 expression (TPS < 1%), patients with PD-L1 expression (TPS ≥ 1%) had significantly higher median progression-free survival (mPFS), but no significantly higher durable clinical benefit (DCB) rate. In contrast, FAT1, ATM, BRCA2, LRP1B, and PBRM1 mutations only occurred frequently in patients with DCB, irrespective of PD-L1 expression status. Our study explored molecular signatures of melanoma patients who respond to ICIs treatment and identified a series of mutated genes that might serve as predictive biomarker for ICIs responses in melanoma.
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Affiliation(s)
- Linqing Li
- Department of Orthopedics, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan, China
| | - Tianmin Xiang
- Research and Development Department, Bioperfectus Technologies Company Limited, Jiangsu, China
| | - Xianan Li
- Department of Orthopedics, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan, China
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7
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Wang L, Chu X, Yu X, Su C. Identification of nomogram associated with durable clinical benefit gene for advanced non-small cell lung cancer with sensitivity to responsive to immunotherapy. Heliyon 2024; 10:e27801. [PMID: 38560208 PMCID: PMC10981036 DOI: 10.1016/j.heliyon.2024.e27801] [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: 07/29/2023] [Revised: 02/19/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
Background Immunotherapy has become the standard treatment for advanced non-small cell lung cancer (NSCLC). However, a subset of the most advanced NSCLC patients fails to respond adequately to Immune checkpoint inhibitors (ICIs). Developing new nomograms and integrating prognostic factors are crucial for improving the clinical predictability of NSCLC patients undergoing ICIs. Methods Clinical information and genomic data of NSCLC patients undergoing ICIs were retrieved from cBioPortal. Gene alterations associated with durable clinical benefit (DCB) were compared to those linked to no durable benefit (NDB). The Kaplan-Meier plot method was employed for survival analysis, and a novel nomogram was formulated by selecting pertinent clinical variables. Results For the NSCLC patients receiving immunotherapy, three subgroups were identified based on the treatment regimen, including anti-PD-1 monotherapy, anti-PD-1 combination with anti-CTLA-4, and first-line treatment. The mutation status of TP53, PGR, PTPRT, RELN, MUC19, LRP1B, and FAT3 was found to be associated with progression-free survival (PFS). Using the clinicopathological parameters and genomic data of the patients, we developed three novel nomograms to predict the prognosis of ICI treatment in different subgroups. Conclusion Our study revealed that PGR, PTPRD, RELN, MUC19, LRP1B, and FAT3 mutation could serve as predictive biomarkers. Our systematic nomograms demonstrate significant potential in predicting the prognosis for NSCLC patients with sensitivity to different ICI treatment strategies.
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Affiliation(s)
- Li Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Xiangling Chu
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Xin Yu
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Chunxia Su
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, PR China
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Chen LC, Lo YS, Ho HY, Lin CC, Chuang YC, Chang WC, Hsieh MJ. LDL Receptor-Related Protein 1B Polymorphisms Associated with Increased Risk of Lymph Node Metastasis in Oral Cancer Group with Diabetes Mellitus. Int J Mol Sci 2024; 25:3963. [PMID: 38612772 PMCID: PMC11012249 DOI: 10.3390/ijms25073963] [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: 03/05/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Oral cancer ranks fourth among malignancies among Taiwanese men and is the eighth most common cancer among men worldwide in terms of general diagnosis. The purpose of the current study was to investigate how low-density lipoprotein receptor-related protein 1B (LDL receptor related protein 1B; LRP1B) gene polymorphisms affect oral squamous cell carcinoma (OSCC) risk and progression in individuals with diabetes mellitus (DM). Three LRP1B single-nucleotide polymorphisms (SNPs), including rs10496915, rs431809, and rs6742944, were evaluated in 311 OSCC cases and 300 controls. Between the case and control groups, we found no evidence of a significant correlation between the risk of OSCC and any of the three specific SNPs. Nevertheless, in evaluating the clinicopathological criteria, individuals with DM who possess a minimum of one minor allele of rs10496915 (AC + CC; p = 0.046) were significantly associated with tumor size compared with those with homozygous major alleles (AA). Similarly, compared to genotypes homologous for the main allele (GG), rs6742944 genotypes (GA + AA; p = 0.010) were more likely to develop lymph node metastases. The tongue and the rs6742944 genotypes (GA + AA) exhibited higher rates of advanced clinical stages (p = 0.024) and lymph node metastases (p = 0.007) when compared to homozygous alleles (GG). LRP1B genetic polymorphisms appear to be prognostic and diagnostic markers for OSCC and DM, as well as contributing to genetic profiling research for personalized medicine.
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Affiliation(s)
- Liang-Cheng Chen
- Division of Oral & Maxillofacial Surgery, Dental Department, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Yu-Sheng Lo
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Hsin-Yu Ho
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Chia-Chieh Lin
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Yi-Ching Chuang
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Wei-Chen Chang
- Division of Oral & Maxillofacial Surgery, Dental Department, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Ming-Ju Hsieh
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
- Doctoral Program in Tissue Engineering and Regenerative Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan
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Liu D, Li B, Yang M, Xing Y, Liu Y, Yuan M, Liu F, Wu Y, Ma X, Jia Y, Wang Y, Ji M, Zhu J. A Novel Signature Based on m 6A Regulator-Mediated Genes Along Glycolytic Pathway Predicts Prognosis and Immunotherapy Responses of Gastric Cancer Patients. Adv Biol (Weinh) 2024; 8:e2300534. [PMID: 38314942 DOI: 10.1002/adbi.202300534] [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: 10/04/2023] [Revised: 12/03/2023] [Indexed: 02/07/2024]
Abstract
N6-methyladenosine (m6A) modification is involved in many aspects of gastric cancer (GC). Moreover, m6A and glycolysis-related genes (GRGs) play important roles in immunotherapeutic and prognostic implication of GC. However, GRGs involved in m6A regulation have never been analyzed comprehensively in GC. Herein, the study aims to identify and validate a novel signature based on m6A-related GRGs in GC patients. Therefore, a m6A-related GRGs signature is established, which can predict the survival of patients with GC and remain an independent prognostic factor in multivariate analyses. Clinical significance of the model is well validated in internal cohort and independent validation cohort. In addition, the expression levels of risk model-related GRGs in clinical samples are validated. Consistent with the database results, all model genes are up-regulated in expression except DCN. After regrouping the patients based on this risk model, the study can effectively distinguish between them in respect to immune-cell infiltration microenvironment and immunotherapeutic response. Additionally, candidate drugs targeting risk model-related GRGs are confirmed. Finally, a nomogram combining risk scores and clinical parameters is created, and calibration plots show that the nomogram can accurately predict survival. This risk model can serve as a reliable assessment tool for predicting prognosis and immunotherapeutic responses in GC patients.
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Affiliation(s)
- Duanrui Liu
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, 250013, P. R. China
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, P. R. China
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong First Medical University, Jinan, 250013, P. R. China
| | - Binbin Li
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, 250013, P. R. China
- Department of Clinical Laboratory, Weihai Municipal Hospital, Weihai, 264299, P. R. China
| | - Mingyue Yang
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, 250013, P. R. China
| | - Yuanxin Xing
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, 250013, P. R. China
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong First Medical University, Jinan, 250013, P. R. China
| | - Yunyun Liu
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, 250013, P. R. China
| | - Mingjie Yuan
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital, Shandong First Medical University, Jinan, 250013, P. R. China
| | - Fen Liu
- Department of Clinical Laboratory, Linyi Central Hospital, Linyi, 276400, P. R. China
| | - Yufei Wu
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, 250013, P. R. China
| | - Xiaoli Ma
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, 250013, P. R. China
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong First Medical University, Jinan, 250013, P. R. China
| | - Yanfei Jia
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, 250013, P. R. China
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong First Medical University, Jinan, 250013, P. R. China
| | - Yunshan Wang
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, 250013, P. R. China
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong First Medical University, Jinan, 250013, P. R. China
| | - Mingyu Ji
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital, Shandong First Medical University, Jinan, 250013, P. R. China
| | - Jingyu Zhu
- Department of Gastroenterology, Jinan Central Hospital, Shandong First Medical University, Jinan, 250013, P. R. China
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10
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Lee JY, Bhandare RR, Boddu SHS, Shaik AB, Saktivel LP, Gupta G, Negi P, Barakat M, Singh SK, Dua K, Chellappan DK. Molecular mechanisms underlying the regulation of tumour suppressor genes in lung cancer. Biomed Pharmacother 2024; 173:116275. [PMID: 38394846 DOI: 10.1016/j.biopha.2024.116275] [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: 11/24/2023] [Revised: 01/30/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Tumour suppressor genes play a cardinal role in the development of a large array of human cancers, including lung cancer, which is one of the most frequently diagnosed cancers worldwide. Therefore, extensive studies have been committed to deciphering the underlying mechanisms of alterations of tumour suppressor genes in governing tumourigenesis, as well as resistance to cancer therapies. In spite of the encouraging clinical outcomes demonstrated by lung cancer patients on initial treatment, the subsequent unresponsiveness to first-line treatments manifested by virtually all the patients is inherently a contentious issue. In light of the aforementioned concerns, this review compiles the current knowledge on the molecular mechanisms of some of the tumour suppressor genes implicated in lung cancer that are either frequently mutated and/or are located on the chromosomal arms having high LOH rates (1p, 3p, 9p, 10q, 13q, and 17p). Our study identifies specific genomic loci prone to LOH, revealing a recurrent pattern in lung cancer cases. These loci, including 3p14.2 (FHIT), 9p21.3 (p16INK4a), 10q23 (PTEN), 17p13 (TP53), exhibit a higher susceptibility to LOH due to environmental factors such as exposure to DNA-damaging agents (carcinogens in cigarette smoke) and genetic factors such as chromosomal instability, genetic mutations, DNA replication errors, and genetic predisposition. Furthermore, this review summarizes the current treatment landscape and advancements for lung cancers, including the challenges and endeavours to overcome it. This review envisages inspired researchers to embark on a journey of discovery to add to the list of what was known in hopes of prompting the development of effective therapeutic strategies for lung cancer.
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Affiliation(s)
- Jia Yee Lee
- School of Health Sciences, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia
| | - Richie R Bhandare
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates.
| | - Sai H S Boddu
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates
| | - Afzal B Shaik
- St. Mary's College of Pharmacy, St. Mary's Group of Institutions Guntur, Affiliated to Jawaharlal Nehru Technological University Kakinada, Chebrolu, Guntur, Andhra Pradesh 522212, India; Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, India
| | - Lakshmana Prabu Saktivel
- Department of Pharmaceutical Technology, University College of Engineering (BIT Campus), Anna University, Tiruchirappalli 620024, India
| | - Gaurav Gupta
- Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; School of Pharmacy, Suresh Gyan Vihar University, Jaipur, Rajasthan 302017, India
| | - Poonam Negi
- School of Pharmaceutical Sciences, Shoolini University, PO Box 9, Solan, Himachal Pradesh 173229, India
| | - Muna Barakat
- Department of Clinical Pharmacy & Therapeutics, Applied Science Private University, Amman-11937, Jordan
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T Road, Phagwara 144411, India; Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Sydney 2007, Australia
| | - Kamal Dua
- Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Sydney 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney 2007, Australia
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia.
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Wang Q, Xie B, Sun J, Li Z, Xiao D, Tao Y, She X. An Investigation of the Immune Microenvironment and Genome during Lung Adenocarcinoma Development. J Cancer 2024; 15:1687-1700. [PMID: 38370388 PMCID: PMC10869965 DOI: 10.7150/jca.92101] [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: 11/10/2023] [Accepted: 01/09/2024] [Indexed: 02/20/2024] Open
Abstract
Background: Adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA) are two consecutive pathological processes that occur before invasive lung adenocarcinoma (LUAD). However, our understanding of the immune editing patterns during the progression of LUAD remains limited. Furthermore, we know very little about whether alterations in driver genes are involved in forming the tumor microenvironment (TME). Therefore, it is necessary to elucidate the regulatory role of TME in LUAD development from multiple dimensions, including immune cell infiltration, molecular mutation events, and oncogenic signaling pathways. Methods: We collected 145 surgically resected pulmonary nodule specimens, including 28 cases of AIS, 52 cases of MIA, and 65 cases of LUAD. Immunohistochemistry (IHC) was used to detect the expression of immune markers CD3, CD4, CD8, CD68 and programmed death ligand 1 (PD-L1). Genomic data and TMB generated by targeted next-generation sequencing (NGS). Results: LUAD exhibited higher levels of immune cell infiltration, tumor mutation burden (TMB), and activation of oncogenic pathways compared to AIS and MIA. In LUAD, compared to epidermal growth factor receptor (EGFR) single mutation and wild-type (WT) samples, cases with EGFR co-mutations showed a more pronounced rise in the CD4/CD8 ratio and CD68 infiltration. Patients with low-density lipoprotein (LDL) receptor-related protein 1B (LRP1B) mutation have higher TMB and PD-L1 expression. The transition from AIS to LUAD tends to shift the TME towards the PD-L1+CD8+ subtype (adaptive resistance). Progression-associated mutations (PAMs) were enriched in the lymphocyte differentiation pathway and related to exhausted cells' phenotype. Conclusion: Tumor-infiltrating immune cells tend to accumulate as the depth of LUAD invasion increases, but subsequently develop into an immune exhaustion and immune escape state. Mutations in EGFR and LRP1B could potentially establish an immune niche that fosters tumor growth. PAMs in LUAD may accelerate disease progression by promoting T cell differentiation into an exhausted state.
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Affiliation(s)
- Qingyi Wang
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410078 China
| | - Bin Xie
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410078 China
| | - Jingyue Sun
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410078 China
| | - Zisheng Li
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410078 China
| | - Desheng Xiao
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410078 China
| | - Yongguang Tao
- Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Hunan, 410078, China
| | - Xiaoling She
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, 410011, China
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12
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Honoré N, van der Elst A, Dietz A, van Marcke C, Helaers R, Mendola A, Dahou H, Marbaix E, Poncin R, Seront E, Schmitz S, Limaye N, Galot R, Machiels JP. Tumour-agnostic plasma assay for circulating tumour DNA predicts outcome in recurrent and/or metastatic squamous cell carcinoma of the head and neck treated with a PD-1 inhibitor. Eur J Cancer 2023; 195:113372. [PMID: 37913682 DOI: 10.1016/j.ejca.2023.113372] [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: 08/30/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Only 15-20% of recurrent and/or metastatic squamous cell carcinoma of the head and neck (R/M SCCHN) patients derive long-term benefit from nivolumab or pembrolizumab. We developed a circulating tumour DNA (ctDNA) tumour-agnostic assay aimed at the early prediction of single agent programmed cell death 1 (PD1) inhibitor efficacy in R/M SCCHN. PATIENTS AND METHODS Our tumour-agnostic assay included 37 genes frequently mutated in R/M SCCHN and two HPV16 genes. Primary endpoint was the concordance between ctDNA kinetics (ΔctDNA) and the best overall response according to Response Evaluation Criteria in Solid Tumors version 1.1. ΔctDNA was defined as the difference in mean variant allele frequency (VAF) between the on-treatment sample harvested 6-10 weeks (FU1) after PD1 inhibitor initiation and the pre-treatment plasma sample (ΔctDNA = mean FU1 VAF - mean pre-treatment VAF). RESULTS ctDNA was detected in 35/44 (80%) of the pre-treatment plasma samples. The concordance between ΔctDNA and imaging response was observed in 74%. Median progression-free survival was 8.6 months in the favourable ΔctDNA group and 2.5 months in the unfavourable ΔctDNA group (p = 0.057). Median overall survival (OS) was 18.1 and 8.2 months in the favourable and unfavourable ΔctDNA groups, respectively (p = 0.13). In patients with PD-L1 expressing SCCHN (Combined Positive Score ≥1), OS was significantly better in patients with favourable ΔctDNA compared with patients with unfavourable ΔctDNA: median OS was 41.5 and 8.4 months (p = 0.033), respectively. CONCLUSIONS Tumour-agnostic ctDNA analysis for human papillomavirus (HPV)-negative and HPV-positive R/M SCCHN is feasible. ctDNA kinetics show promising results in predicting the efficacy of PD1 inhibitors in R/M SCCHN.
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Affiliation(s)
- Natasha Honoré
- Pôle Oncologie, Institut de Recherche Clinique et Expérimentale, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 10, 1200 Brussels, Belgium; Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Athenaïs van der Elst
- Pôle Oncologie, Institut de Recherche Clinique et Expérimentale, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 10, 1200 Brussels, Belgium; Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Anna Dietz
- Department of Radiology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Cédric van Marcke
- Pôle Oncologie, Institut de Recherche Clinique et Expérimentale, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 10, 1200 Brussels, Belgium; Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Raphael Helaers
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Antonella Mendola
- Pôle Oncologie, Institut de Recherche Clinique et Expérimentale, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 10, 1200 Brussels, Belgium
| | - Hajar Dahou
- Pôle Oncologie, Institut de Recherche Clinique et Expérimentale, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 10, 1200 Brussels, Belgium
| | - Etienne Marbaix
- Department of Pathology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Renaud Poncin
- Department of Medical Oncology, Cliniques Saint-Pierre, Ottignies, Belgium
| | - Emanuel Seront
- Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Department of Medical Oncology, Jolimont Hospital, La Louviere, Belgium
| | - Sandra Schmitz
- Pôle Oncologie, Institut de Recherche Clinique et Expérimentale, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 10, 1200 Brussels, Belgium; Department of ENT and Maxillo-facial Surgery, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Nisha Limaye
- Genetics of Autoimmune Diseases and Cancer, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Rachel Galot
- Pôle Oncologie, Institut de Recherche Clinique et Expérimentale, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 10, 1200 Brussels, Belgium; Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Jean-Pascal Machiels
- Pôle Oncologie, Institut de Recherche Clinique et Expérimentale, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 10, 1200 Brussels, Belgium; Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, Brussels, Belgium.
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13
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He J, Luan T, Zhao G, Yang Y. Fusing WGCNA and Machine Learning for Immune-Related Gene Prognostic Index in Lung Adenocarcinoma: Precision Prognosis, Tumor Microenvironment Profiling, and Biomarker Discovery. J Inflamm Res 2023; 16:5309-5326. [PMID: 38026246 PMCID: PMC10658954 DOI: 10.2147/jir.s436431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023] Open
Abstract
Background The objective is to create an IRGPI (Immune-related genes prognostic index), which could predict the survival and effectiveness of immune checkpoint inhibitor (ICI) treatment for lung adenocarcinoma (LUAD). Methods By applying weighted gene co-expression network analysis (WGCNA), we ascertained 13 genes associated with immune functions. An IRGPI was constructed using four genes through multicox regression, and its validity was assessed in the GEO dataset. Next, we explored the immunological and molecular attributes and advantages of ICI treatment in subcategories delineated by IRGPI. The model genes were also validated by the random forest tree, and functional experiments were conducted to validate it. Results The IRGPI relied on the genes CD79A, IL11, CTLA-4, and CD27. Individuals categorized as low-risk exhibited significantly improved overall survival in comparison to those classified as high-risk. Extensive findings indicated that the low-risk category exhibited associations with immune pathways, significant infiltration of CD8 T cells, M1 macrophages, and CD4 T cells, a reduced rate of gene mutations, and improved sensitivity to ICI therapy. Conversely, the higher-risk group displayed metabolic signals, elevated frequencies of TP53, KRAS, and KEAP1 mutations, escalated levels of NK cells, M0, and M2 macrophage infiltration, and a diminished response to ICI therapy. Additionally, our study unveiled that the downregulation of IL11 effectively impedes the proliferation and migration of lung carcinoma cells, while also inducing cell cycle arrest. Conclusion IRGPI is a biomarker with significant potential for predicting the effectiveness of ICI treatment in LUAD patients and is closely related to the microenvironment and clinicopathological characteristics.
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Affiliation(s)
- Jiaming He
- Laboratory of Stem Cells and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Tiankuo Luan
- Department of Anatomy, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Gang Zhao
- Department of Gastroenterology, Wushan County People’s Hospital of Chongqing, Chongqing, 404700, People’s Republic of China
| | - Yingxue Yang
- Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
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14
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Kolb S, Hoffmann I, Monjé N, Dragomir MP, Jank P, Bischoff P, Keunecke C, Pohl J, Kunze CA, Marchenko S, Schmitt WD, Kulbe H, Sers C, Sehouli J, Braicu EI, Denkert C, Darb-Esfahani S, Horst D, Sinn BV, Taube ET. LRP1B-a prognostic marker in tubo-ovarian high-grade serous carcinoma. Hum Pathol 2023; 141:158-168. [PMID: 37742945 DOI: 10.1016/j.humpath.2023.09.001] [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: 07/30/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Abstract
Low-density lipoprotein (LDL) receptor-related protein 1B (LRP1B) is a member of the LDL receptor family and has often been discussed as a tumor suppressor gene, as its down-regulation is correlated with a poor prognosis in multiple carcinoma entities. Due to the high metastasis rate into the fatty peritoneal cavity and current research findings showing a dysregulation of lipid metabolism in tubo-ovarian high-grade serous carcinoma (HGSC), we questioned the prognostic impact of the LRP1B protein expression. We examined a well-characterized large cohort of 571 patients with primary HGSC and analyzed the LRP1B protein expression via immunohistochemical staining (both in tumor and stroma cells separately), performed precise bioimage analysis with QuPath, and calculated the prognostic impact using SPSS. Our results demonstrate that LRP1B functions as a significant prognostic marker for overall survival (OS) and progression-free survival (PFS) in HGSC on the protein level. High cytoplasmic expression of LRP1B in tumor, stroma, and combined tumor and stroma cells has a significantly positive association with a mean prolongation of the OS by 42 months (P = .005), 29 months (P = .005), and 25 months (P = .001), respectively. Additionally, the mean PFS was 18 months longer in tumor (P = .002), 19 months in stroma (P = .004), and 19 months in both cell types combined (P = .01). Our results remained significant in multivariate analysis. We envision LRP1B as a potential prognostic tool that could help us understand the functional role of lipid metabolism in advanced HGSC, especially regarding liposomal medications.
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Affiliation(s)
- Svenja Kolb
- Department of Gynecology, Vivantes Netzwerk für Gesundheit GmbH Berlin, Vivantes Hospital Neukölln, 12351, Berlin, Germany
| | - Inga Hoffmann
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Nanna Monjé
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Mihnea P Dragomir
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Paul Jank
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, 35043 Marburg, Germany
| | - Philip Bischoff
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Carlotta Keunecke
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Jonathan Pohl
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Catarina Alisa Kunze
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Sofya Marchenko
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Wolfgang D Schmitt
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Hagen Kulbe
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Tumorbank Ovarian Cancer Network, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Christine Sers
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Jalid Sehouli
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Tumorbank Ovarian Cancer Network, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Elena Ioana Braicu
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Tumorbank Ovarian Cancer Network, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Carsten Denkert
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, 35043 Marburg, Germany
| | - Silvia Darb-Esfahani
- MVZ Pathologie Spandau, 13589 Berlin, Spandau, Germany; MVZ Pathologie Berlin-Buch, 13125 Berlin, Germany
| | - David Horst
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Bruno V Sinn
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Eliane T Taube
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany.
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15
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Hijazo-Pechero S, Muñoz-Pinedo C, Nadal E. A Transcriptomic Approach Outperforms Mutational Analysis to Identify KEAP1/NFE2L2 Pathway Activation in Patients With NSCLC. J Thorac Oncol 2023; 18:1431-1433. [PMID: 37879763 DOI: 10.1016/j.jtho.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 10/27/2023]
Affiliation(s)
- Sara Hijazo-Pechero
- Preclinical and Experimental Research in Thoracic Tumors (PRETT), Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Spain
| | - Cristina Muñoz-Pinedo
- Preclinical and Experimental Research in Thoracic Tumors (PRETT), Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Spain
| | - Ernest Nadal
- Preclinical and Experimental Research in Thoracic Tumors (PRETT), Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Spain; Department of Medical Oncology, Catalan Institute of Oncology, L'Hospitalet, Barcelona, Spain.
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Karolová J, Kazantsev D, Svatoň M, Tušková L, Forsterová K, Maláriková D, Benešová K, Heizer T, Dolníková A, Klánová M, Winkovska L, Svobodová K, Hojný J, Krkavcová E, Froňková E, Zemanová Z, Trněný M, Klener P. Sequencing-based analysis of clonal evolution of 25 mantle cell lymphoma patients at diagnosis and after failure of standard immunochemotherapy. Am J Hematol 2023; 98:1627-1636. [PMID: 37605345 DOI: 10.1002/ajh.27044] [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: 05/18/2023] [Revised: 07/03/2023] [Accepted: 07/16/2023] [Indexed: 08/23/2023]
Abstract
Our knowledge of genetic aberrations, that is, variants and copy number variations (CNVs), associated with mantle cell lymphoma (MCL) relapse remains limited. A cohort of 25 patients with MCL at diagnosis and the first relapse after the failure of standard immunochemotherapy was analyzed using whole-exome sequencing. The most frequent variants at diagnosis and at relapse comprised six genes: TP53, ATM, KMT2D, CCND1, SP140, and LRP1B. The most frequent CNVs at diagnosis and at relapse included TP53 and CDKN2A/B deletions, and PIK3CA amplifications. The mean count of mutations per patient significantly increased at relapse (n = 34) compared to diagnosis (n = 27). The most frequent newly detected variants at relapse, LRP1B gene mutations, correlated with a higher mutational burden. Variant allele frequencies of TP53 variants increased from 0.35 to 0.76 at relapse. The frequency and length of predicted CNVs significantly increased at relapse with CDKN2A/B deletions being the most frequent. Our data suggest, that the resistant MCL clones detected at relapse were already present at diagnosis and were selected by therapy. We observed enrichment of genetic aberrations of DNA damage response pathway (TP53 and CDKN2A/B), and a significant increase in MCL heterogeneity. We identified LRP1B inactivation as a new potential driver of MCL relapse.
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Affiliation(s)
- J Karolová
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
- First Department of Medicine - Hematology, University General Hospital Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - D Kazantsev
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - M Svatoň
- CLIP - Childhood Leukaemia Investigation Prague, Department of Pediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - L Tušková
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - K Forsterová
- First Department of Medicine - Hematology, University General Hospital Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - D Maláriková
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
- First Department of Medicine - Hematology, University General Hospital Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - K Benešová
- First Department of Medicine - Hematology, University General Hospital Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - T Heizer
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - A Dolníková
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - M Klánová
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
- First Department of Medicine - Hematology, University General Hospital Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - L Winkovska
- CLIP - Childhood Leukaemia Investigation Prague, Department of Pediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - K Svobodová
- Center for Oncocytogenetics, Institute of Medical Biochemistry and Laboratory Diagnostics, Charles University and General University Hospital, Prague, Czech Republic
| | - J Hojný
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - E Krkavcová
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - E Froňková
- CLIP - Childhood Leukaemia Investigation Prague, Department of Pediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Z Zemanová
- Center for Oncocytogenetics, Institute of Medical Biochemistry and Laboratory Diagnostics, Charles University and General University Hospital, Prague, Czech Republic
| | - M Trněný
- First Department of Medicine - Hematology, University General Hospital Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - P Klener
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
- First Department of Medicine - Hematology, University General Hospital Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
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17
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Jiang Y, Zhang T, Yang L, Du Z, Wang Q, Hou J, Liu Y, Song Q, Zhao J, Wu Y. Downregulation of FTO in the hippocampus is associated with mental disorders induced by fear stress during pregnancy. Behav Brain Res 2023; 453:114598. [PMID: 37506852 DOI: 10.1016/j.bbr.2023.114598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/23/2023] [Accepted: 07/22/2023] [Indexed: 07/30/2023]
Abstract
Mental disorders (MD), such as anxiety, depression, and cognitive impairment, are very common during pregnancy and predispose to adverse pregnancy outcomes; however, the underlying mechanisms are still under intense investigation. Although the most common RNA modification in epigenetics, N6-methyladenosine (m6A) has been widely studied, its role in MD has not been investigated. Here, we observed that fat mass and obesity-associated protein (FTO) are downregulated in the hippocampus of pregnant rats with MD induced by fear stress and demonstrated that FTO participates in and regulates MD induced by fear stress. In addition, we identified four genes with anomalous modifications and expression (double aberrant genes) that were directly regulated by FTO, namely Angpt2, Fgf10, Rpl21, and Adcy7. Furthermore, we found that these genes might induce MD by regulating the PI3K/Akt and Rap1 signaling pathways. It appears that FTO-mediated m6A modification is a key regulatory mechanism in MD caused by fear stress during pregnancy.
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Affiliation(s)
- Yu Jiang
- Medicine College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Tong Zhang
- Medicine College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Liping Yang
- Medicine College, Henan University of Chinese Medicine, Zhengzhou, China.
| | - Zhixin Du
- Medicine College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Qiyang Wang
- Medicine College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Junlin Hou
- Medicine College, Henan University of Chinese Medicine, Zhengzhou, China.
| | - Yuexuan Liu
- Medicine College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Qi Song
- Medicine College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Jiajia Zhao
- Medicine College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Yongye Wu
- Medicine College, Henan University of Chinese Medicine, Zhengzhou, China
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18
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Gui C, Wei J, Mo C, Liang Y, Cen J, Chen Y, Wang D, Luo J. Therapeutic implications for localized prostate cancer by multiomics analyses of the ageing microenvironment landscape. Int J Biol Sci 2023; 19:3951-3969. [PMID: 37564213 PMCID: PMC10411471 DOI: 10.7150/ijbs.85209] [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: 04/12/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023] Open
Abstract
Background: Numerous studies have substantiated the association between aging and the progression of malignant tumors in humans, notably prostate cancer (PCa). Nevertheless, to the best of our knowledge, no studies have comprehensively elucidated the intricate characteristics of the aging microenvironment (AME) in PCa. Methods: AME regulatory patterns were determined using the NMF algorithm. Then an ageing microenvironment index (AMI) was constructed, with excellent prognostic and immunotherapy prediction ability, and its' clinical relevance was surveyed through spatial transcriptomics. Further, the drug response was analysed using the Genomics of Drug Sensitivity in Cancer (GDSC), the Connectivity Map (CMap) and CellMiner database for patients with PCa. Finally, the AME was studied using in vitro and vivo experiments. Results: Three different AME regulatory patterns were identified across 813 PCa patients, associated with distinct clinical prognosis and physiological pathways. Based on the AMI, patients with PCa were divided into the high-score and low-score subsets. Higher AMI score was significantly infiltrated with more immune cells, higher rate of biochemical recurrence (BCR) and worse response to immunotherapy, antiandrogen therapy and chemotherapy in PCa. In addition, we found that the combination of bicalutamide and embelin was capable of suppressing tumor growth of PCa. Besides, as the main components of AMI, COL1A1 and BGLAP act as oncogenes and were verified via in vivo and in vitro experiments. Conclusions: AME regulation is significantly associated with the diversity and complexity of TME. Quantitative evaluation of the AME regulatory patterns may provide promising novel molecular markers for individualised therapy in PCa.
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Affiliation(s)
- Chengpeng Gui
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jinhuan Wei
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Chengqiang Mo
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanping Liang
- Department of Laboratory Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Junjie Cen
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuhang Chen
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Daohu Wang
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Junhang Luo
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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19
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Ye C, Chong W, Liu Y, Zhu X, Ren H, Xu K, Xie X, Du F, Zhang Z, Wang M, Ma T, Shang L, Li L, Chen H. Suppression of tumorigenesis in LUAD by LRP1B through regulation of the IL-6-JAK-STAT3 pathway. Am J Cancer Res 2023; 13:2886-2905. [PMID: 37560001 PMCID: PMC10408488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/20/2023] [Indexed: 08/11/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common type of lung cancer. LRP1B was initially identified as a cancer suppressor in several cancers. However, the potential biological phenotypes and molecular mechanisms of LRP1B in LUAD have not been fully investigated. In our study, we showed that the expression of LRP1B in LUAD tissues was lower than that in normal tissues. Knockdown of LRP1B markedly enhanced malignancy of LUAD cells. Genomic analysis indicated that the population expressing low-levels of LRP1B had higher genomic instability, which accounted for a larger proportion of aneuploidy and inflammation subtyping. Enrichment analysis of bulk and cell-line transcriptomic data both showed that the low expression of LRP1B could induce the activation of IL-6-JAK-STAT3, chemokine, cytokine, and other inflammation signaling pathways. Moreover, our findings revealed that knockdown LRP1B enhanced the secretion of IL-6 and IL-8, as confirmed by ELISA assays. Further validation using PCR and WB confirmed that downregulation of LRP1B mRNA significantly upregulated the activity of the IL-6-JAK-STAT3 pathway. Collectively, this study highlights LRP1B as a tumor suppressor gene and reveals that LRP1B knockdown promotes malignant progression in LUAD by inducing inflammation through the IL-6-JAK-STAT3 pathway.
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Affiliation(s)
- Chunshui Ye
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong UniversityJinan, Shandong, China
| | - Wei Chong
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong UniversityJinan, Shandong, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical SciencesJinan, Shandong, China
| | - Yuan Liu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong UniversityJinan, Shandong, China
| | - Xingyu Zhu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong UniversityJinan, Shandong, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical SciencesJinan, Shandong, China
| | - Huicheng Ren
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong UniversityJinan, Shandong, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical SciencesJinan, Shandong, China
| | - Kang Xu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong UniversityJinan, Shandong, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical SciencesJinan, Shandong, China
| | - Xiaozhou Xie
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong UniversityJinan, Shandong, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical SciencesJinan, Shandong, China
| | - Fengying Du
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong UniversityJinan, Shandong, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical SciencesJinan, Shandong, China
| | - Zihao Zhang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong UniversityJinan, Shandong, China
| | - Mingfei Wang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong UniversityJinan, Shandong, China
| | - Tianrong Ma
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong UniversityJinan, Shandong, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical SciencesJinan, Shandong, China
| | - Liang Shang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong UniversityJinan, Shandong, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical SciencesJinan, Shandong, China
| | - Leping Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong UniversityJinan, Shandong, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical SciencesJinan, Shandong, China
| | - Hao Chen
- Clinical Research Center of Shandong University, Clinical Epidemiology Unit, Qilu Hospital of Shandong UniversityJinan, Shandong, China
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Peixoto J, Príncipe C, Pestana A, Osório H, Pinto MT, Prazeres H, Soares P, Lima RT. Using a Dual CRISPR/Cas9 Approach to Gain Insight into the Role of LRP1B in Glioblastoma. Int J Mol Sci 2023; 24:11285. [PMID: 37511044 PMCID: PMC10379115 DOI: 10.3390/ijms241411285] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
LRP1B remains one of the most altered genes in cancer, although its relevance in cancer biology is still unclear. Recent advances in gene editing techniques, particularly CRISPR/Cas9 systems, offer new opportunities to evaluate the function of large genes, such as LRP1B. Using a dual sgRNA CRISPR/Cas9 gene editing approach, this study aimed to assess the impact of disrupting LRP1B in glioblastoma cell biology. Four sgRNAs were designed for the dual targeting of two LRP1B exons (1 and 85). The U87 glioblastoma (GB) cell line was transfected with CRISPR/Cas9 PX459 vectors. To assess LRP1B-gene-induced alterations and expression, PCR, Sanger DNA sequencing, and qRT-PCR were carried out. Three clones (clones B9, E6, and H7) were further evaluated. All clones presented altered cellular morphology, increased cellular and nuclear size, and changes in ploidy. Two clones (E6 and H7) showed a significant decrease in cell growth, both in vitro and in the in vivo CAM assay. Proteomic analysis of the clones' secretome identified differentially expressed proteins that had not been previously associated with LRP1B alterations. This study demonstrates that the dual sgRNA CRISPR/Cas9 strategy can effectively edit LRP1B in GB cells, providing new insights into the impact of LRP1B deletions in GBM biology.
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Grants
- PTDC/MEC-ONC/31520/2017 FEEI, FEDER through COMPETE 2020 -POCI, Portugal 2020, and by Portuguese funds through FCT/Ministério da Ciência, Tecnologia e Ensino Superior
- POCI-01-0145-FEDER-028779 (PTDC/BIA-MIC/28779/2017) FEEI, FEDER through COMPETE 2020 -POCI, Portugal 2020, and by Portuguese funds through FCT/Ministério da Ciência, Tecnologia e Ensino Superior
- project "Institute for Research and Innovation in Health Sciences" (UID/BIM/04293/2019) FEEI, FEDER through COMPETE 2020 -POCI, Portugal 2020, and by Portuguese funds through FCT/Ministério da Ciência, Tecnologia e Ensino Superior
- "Cancer Research on Therapy Resistance: From Basic Mechanisms to Novel Targets"-NORTE-01-0145-FEDER-000051 Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF
- The Porto Comprehensive Cancer Center" with the reference NORTE-01-0145-FEDER-072678 - Consórcio PORTO.CCC - Porto.Comprehensive Cancer Center Raquel Seruca European Regional Development Fund
- ROTEIRO/0028/2013; LISBOA-01-0145-FEDER-022125 Portuguese Mass Spectrometry Network, integrated in the National Roadmap of Research Infra-structures of Strategic Relevance
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Affiliation(s)
- Joana Peixoto
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
| | - Catarina Príncipe
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
- Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Ana Pestana
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
| | - Hugo Osório
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- FMUP-Department of Pathology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Marta Teixeira Pinto
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
| | - Hugo Prazeres
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
| | - Paula Soares
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- FMUP-Department of Pathology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Raquel T Lima
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- FMUP-Department of Pathology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
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Tsai YS, Chareddy YS, Price BA, Parker JS, Pecot CV. An integrated model for predicting KRAS dependency. PLoS Comput Biol 2023; 19:e1011095. [PMID: 37141389 DOI: 10.1371/journal.pcbi.1011095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 05/16/2023] [Accepted: 04/10/2023] [Indexed: 05/06/2023] Open
Abstract
The clinical approvals of KRAS G12C inhibitors have been a revolutionary advance in precision oncology, but response rates are often modest. To improve patient selection, we developed an integrated model to predict KRAS dependency. By integrating molecular profiles of a large panel of cell lines from the DEMETER2 dataset, we built a binary classifier to predict a tumor's KRAS dependency. Monte Carlo cross validation via ElasticNet within the training set was used to compare model performance and to tune parameters α and λ. The final model was then applied to the validation set. We validated the model with genetic depletion assays and an external dataset of lung cancer cells treated with a G12C inhibitor. We then applied the model to several Cancer Genome Atlas (TCGA) datasets. The final "K20" model contains 20 features, including expression of 19 genes and KRAS mutation status. In the validation cohort, K20 had an AUC of 0.94 and accurately predicted KRAS dependency in both mutant and KRAS wild-type cell lines following genetic depletion. It was also highly predictive across an external dataset of lung cancer lines treated with KRAS G12C inhibition. When applied to TCGA datasets, specific subpopulations such as the invasive subtype in colorectal cancer and copy number high pancreatic adenocarcinoma were predicted to have higher KRAS dependency. The K20 model has simple yet robust predictive capabilities that may provide a useful tool to select patients with KRAS mutant tumors that are most likely to respond to direct KRAS inhibitors.
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Affiliation(s)
- Yihsuan S Tsai
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yogitha S Chareddy
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Brandon A Price
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joel S Parker
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Chad V Pecot
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Hematology & Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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22
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Wang CX, Yan J, Lin S, Ding Y, Qin YR. Mutant-allele dispersion correlates with prognosis risk in patients with advanced non-small cell lung cancer. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04801-3. [PMID: 37093348 DOI: 10.1007/s00432-023-04801-3] [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: 11/29/2022] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
BACKGROUND Intra-tumor heterogeneity (ITH) contributes to lung cancer progression and resistance to therapy. To evaluate ITH and determine whether it may be employed as a predictive biomarker of prognosis in patients with advanced non-small cell lung cancer (NSCLC), we used a novel algorithm called mutant-allele dispersion (MAD). METHODS In the study, 103 patients with advanced NSCLC were enrolled. Using a panel of 425 cancer-related genes, next-generation sequencing (NGS) was performed on tumor specimens that had been collected. From NGS data, we derived MAD values, and we next looked into their relationships with clinical variables and different mutation subtypes. RESULTS The median MAD among 103 NSCLC patients was 0.73. EGFR mutation, tyrosine kinase inhibitor (TKI) therapy, radiotherapy, and chemotherapy cycles were all substantially correlated with the MAD score. In patients with lung adenocarcinoma (LUAD), correlation analysis revealed that the MAD score was substantially linked with Notch pathway mutation (P = 0.021). A significant relationship between high MAD and shorter progression-free survival (PFS) was found (HR = 2.004, 95%CI 1.269-3.163, P = 0.003). In patients with advanced NSCLC, histological type (P = 0.004), SMARCA4 mutation (P = 0.038), and LRP1B mutation (P = 0.006) were all independently associated with prognosis. The disease control rate was considerably greater in the low MAD group compared to the high MAD group in 19 LUAD patients receiving immunotherapy (92.9% vs. 40%, P = 0.037). TKI-PFS was longer in 37 patients with low MAD who received first-line TKI therapy (P = 0.014). CONCLUSION Our findings suggested that MAD is a practical and simple algorithm for assessing ITH, and populations with high MAD values are more likely to have EGFR mutations. MAD can be used as a potential biomarker to predict not only the prognosis of NSCLC but also the efficacy of immunotherapy and TKI therapy in patients with advanced NSCLC.
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Affiliation(s)
- Chen-Xu Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jie Yan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Shan Lin
- Department of Oncology, Zhongshan Hospital Affiliated to Xiamen University, Xiamen, 361004, Fujian, China
| | - Yi Ding
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yan-Ru Qin
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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Zhang R, Wei B, Hu Y, Lv W, Adilai A, Yang F, Zhang J, Cheng G. Whole-Exome Sequencing Revealed the Mutational Profiles of Primary Central Nervous System Lymphoma. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2023; 23:291-302. [PMID: 36725383 DOI: 10.1016/j.clml.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/31/2022] [Accepted: 01/08/2023] [Indexed: 01/13/2023]
Abstract
BACKGROUND Primary central nervous system lymphoma (PCNSL) is a highly aggressive type of extranodal non-Hodgkin lymphoma, of which approximately 90% of the cases are diffuse large B-cell lymphoma (DLBCL). In recent years, the incidence of PCNSL has significantly increased in women and older men. Although advanced treatments such as high-dose methotrexate (HD-MTX) and targeted agents have been introduced, the prognosis of these patients remains poorer than those with other forms of non-Hodgkin's lymphoma. METHODS Twelve cases of Chinese PCNSL were analyzed to detect their genetic alterations using whole-exome sequencing (WES). We identified 448 potential somatic single nucleotide variants (SNVs) with a median of 12 SNVs per PCNSL sample and 35 small indels with potentially protein-changing features in 9 PCNSL samples. RESULTS We found that myeloid differentiation factor 88 (MYD88) had the highest mutation frequency, which affected the activity of the nuclear factor-κB (NF-κB) pathway. PCNSL samples with low-density lipoprotein receptor-related protein 1B (LRP1B) mutations had a higher mutation rate than samples with wild-type LRP1B. Polycystic kidney and hepatic disease 1 (PKHD1), the causal gene of autosomal recessive polycystic kidney disease (ARPKD), was identified in 2 PCNSL cases and exhibited missense mutations. Pathway analysis revealed enrichment in pathways associated with central carbon metabolism in cancer, renal cell carcinoma, nicotine addiction, bladder cancer, and long-term depression. CONCLUSIONS WES revealed significantly mutated genes associated with the molecular mechanisms of PCNSL, which could serve as therapeutic targets to improve patient outcomes.
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Affiliation(s)
- Rui Zhang
- Department of Neurosurgery, the First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Boyuan Wei
- Department of Neurosurgery, the First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Yiyang Hu
- Department of Medical Genetics and Developmental Biology, Fourth Military Medical University, Xi'an, China
| | - Wenying Lv
- Department of Neurosurgery, the Sixth Medical Centre, Chinese PLA General Hospital, Beijing,China
| | - Abudurexiti Adilai
- Department of Neurosurgery, the First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Fan Yang
- Department of Neurosurgery, the First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Jianning Zhang
- Department of Neurosurgery, the First Medical Centre, Chinese PLA General Hospital, Beijing, China.
| | - Gang Cheng
- Department of Neurosurgery, the First Medical Centre, Chinese PLA General Hospital, Beijing, China.
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Xu X, Ding C, Zhong H, Qin W, Shu D, Yu M, Abuduaini N, Zhang S, Yang X, Feng B. Integrative analysis revealed that distinct cuprotosis patterns reshaped tumor microenvironment and responses to immunotherapy of colorectal cancer. Front Immunol 2023; 14:1165101. [PMID: 37006250 PMCID: PMC10060625 DOI: 10.3389/fimmu.2023.1165101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
BackgroundCuprotosis is a novel form of programmed cell death that involves direct targeting of key enzymes in the tricarboxylic acid (TCA) cycle by excess copper and may result in mitochondrial metabolic dysfunction. However, whether cuprotosis may mediate the tumor microenvironment (TME) and immune regulation in colorectal cancer (CRC) remains unclear.MethodsTen cuprotosis-related genes were selected and unsupervised consensus clustering was performed to identify the cuprotosis patterns and the correlated TME characteristics. Using principal component analysis, a COPsig score was established to quantify cuprotosis patterns in individual patients. The top 9 most important cuprotosis signature genes were analyzed using single-cell transcriptome data.ResultsThree distinct cuprotosis patterns were identified. The TME cell infiltration characteristics of three patterns were associated with immune-excluded, immune-desert, and immune-inflamed phenotype, respectively. Based on individual cuprotosis patterns, patients were assigned into high and low COPsig score groups. Patients with a higher COPsig score were characterized by longer overall survival time, lower immune cell as well as stromal infiltration, and greater tumor mutational burden. Moreover, further analysis demonstrated that CRC patients with a higher COPsig score were more likely to respond to immune checkpoint inhibitors and 5-fluorouracil chemotherapy. Single-cell transcriptome analysis indicated that cuprotosis signature genes recruited tumor-associated macrophages to TME through the regulation of TCA and the metabolism of glutamine and fatty acid, thus influencing the prognosis of CRC patients.ConclusionThis study indicated that distinct cuprotosis patterns laid a solid foundation to the explanation of heterogeneity and complexity of individual TME, thus guiding more effective immunotherapy as well as adjuvant chemotherapy strategies.
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Affiliation(s)
| | | | | | | | | | | | | | - Sen Zhang
- *Correspondence: Bo Feng, ; Xiao Yang, ; Sen Zhang,
| | - Xiao Yang
- *Correspondence: Bo Feng, ; Xiao Yang, ; Sen Zhang,
| | - Bo Feng
- *Correspondence: Bo Feng, ; Xiao Yang, ; Sen Zhang,
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Wu S, Li M, Su R, Shen H, He Y, Zhou Y. Modification of m5C regulators in sarcoma can guide different immune infiltrations as well as immunotherapy. Front Surg 2023; 9:948371. [PMID: 36684288 PMCID: PMC9853431 DOI: 10.3389/fsurg.2022.948371] [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: 05/19/2022] [Accepted: 09/09/2022] [Indexed: 01/09/2023] Open
Abstract
Background Recent studies have found that 5-methylcytosine (m5C) modulators are associated with the prognosis and treatment of cancer. However, the relevance of m5C modulators in sarcoma prognosis and the tumour microenvironment is unclear. Methods We selected 15 m5C regulators and performed unsupervised clustering to identify m5C modification patterns and differentially expressed genes associated with the m5C phenotype in The Cancer Genome Atlas (TCGA) sarcomas. The extent of immune cell infiltration in different clustering groups was explored using single-sample gene set enrichment analysis and estimation algorithms. A principal component analysis algorithm-based m5C scoring protocol was performed to assess the m5C modification patterns of individual tumors. Results We identified two distinct m5C modification patterns in the TCGA sarcoma cohort, which possess different clinical outcomes and biological processes. Tumour microenvironment analysis revealed two groups of immune infiltration patterns highly consistent with m5C modification patterns, classified as immune inflammatory and immune desert types. We constructed m5C scores and found that high m5C scores were closely associated with leiomyosarcoma and other subtypes, and were associated with poorer prognosis, lower PD-L1 expression, and poorer immunotherapy outcomes. The best application was validated against the m5C database. Conclusion We constructed an m5C score for sarcoma based on the TCGA database and identified a poorer prognosis in the high m5c score group. The stability and good prognostic predictive power of the m5C score was verified by an external database. We found that sarcomas in the low m5C score group may have a better response to immunotherapy.
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Affiliation(s)
- Shusheng Wu
- Department of Medical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Mengge Li
- Department of Medical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Rixin Su
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China
| | - Hao Shen
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China
| | - Yifu He
- Department of Medical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China,Correspondence: Yangfan Zhou Yifu He
| | - Yangfan Zhou
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, China,Correspondence: Yangfan Zhou Yifu He
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26
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Duan XP, Liu K, Jiao XD, Qin BD, Li B, He X, Ling Y, Wu Y, Chen SQ, Zang YS. Prognostic value of tumor mutation burden in patients with advanced gastric cancer receiving first-line chemotherapy. Front Oncol 2023; 12:1007146. [PMID: 36686739 PMCID: PMC9847361 DOI: 10.3389/fonc.2022.1007146] [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: 07/30/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Background Tumor mutation burden (TMB) is a promising biomarker positively associated with the benefit of immunotherapy and that might predict the outcome of chemotherapy. We described the prognostic value of TMB in advanced gastric cancer and explored the underlying mechanism. Methods We enrolled 155 TMB-evaluated advanced gastric cancer patients and analyzed the relationship between clinicopathological characteristics and both overall survival (OS) and progression-free survival (PFS) among 40 patients treated with first-line chemotherapy. We further verified the distribution of TMB and analyzed the potential mechanism underlying the prognosis based on The Cancer Genome Atlas (TCGA) database. Results Among the 155 patients, 29 (18.7%) were TMB-high (TMB ≥ 10), roughly the same as the proportion in the TCGA data. Of the 40 patients receiving first-line chemotherapy, the median OS (7.9 vs. 12.1 months; HR 3.18; p = 0.0056) and PFS (4.4 vs. 6.2 months; HR 2.94; p = 0.0099) of the tissue-tested TMB (tTMB)-high patients were inferior to those of the tTMB-low patients. Similarly, unfavorable median OS (9.9 vs. 12.1 months; HR 2.11; p = 0.028) and PFS (5.3 vs. 6.5 months; HR 2.49; p = 0.0054) were shown in the blood-tested TMB (bTMB)-high than in the bTMB-low patients. The Cox analysis demonstrated that both tTMB-high and bTMB-high were significant independent predictors of dreadful OS and PFS. The differentially expressed genes (DEGs) according to TMB status were most significantly enriched in the downregulated metabolic pathway among the TMB-high patients. Conclusions TMB-high advanced gastric cancer patients accounted for around one-sixth and had a poorer prognosis than TMB-low patients when treated with first-line chemotherapy. The potential mechanism might be the downregulated metabolic activity in TMB-high patients.
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Affiliation(s)
- Xiao-Peng Duan
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Ke Liu
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xiao-Dong Jiao
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Bao-Dong Qin
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Bing Li
- Burning Rock Biotech, Shanghai, China
| | - Xi He
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yan Ling
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Ying Wu
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Shi-Qi Chen
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yuan-Sheng Zang
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China,*Correspondence: Yuan-Sheng Zang,
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Wang M, Zhu L, Yang X, Li J, Liu Y, Tang Y. Targeting immune cell types of tumor microenvironment to overcome resistance to PD-1/PD-L1 blockade in lung cancer. Front Pharmacol 2023; 14:1132158. [PMID: 36874015 PMCID: PMC9974851 DOI: 10.3389/fphar.2023.1132158] [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: 12/26/2022] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Lung cancer is the common malignant tumor with the highest mortality rate. Lung cancer patients have achieved benefits from immunotherapy, including immune checkpoint inhibitors (ICIs) therapy. Unfortunately, cancer patients acquire adaptive immune resistance, leading to poor prognosis. Tumor microenvironment (TME) has been demonstrated to play a critical role in participating in acquired adaptive immune resistance. TME is associated with molecular heterogeneity of immunotherapy efficacy in lung cancer. In this article, we discuss how immune cell types of TME are correlated with immunotherapy in lung cancer. Moreover, we describe the efficacy of immunotherapy in driven gene mutations in lung cancer, including KRAS, TP53, EGFR, ALK, ROS1, KEAP1, ZFHX3, PTCH1, PAK7, UBE3A, TNF-α, NOTCH, LRP1B, FBXW7, and STK11. We also emphasize that modulation of immune cell types of TME could be a promising strategy for improving adaptive immune resistance in lung cancer.
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Affiliation(s)
- Man Wang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Lijie Zhu
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Xiaoxu Yang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Jiahui Li
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yu'e Liu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, Tongji University, Shanghai, China
| | - Ying Tang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin, China
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Lei T, Yang Y, Shi Y, Deng X, Peng Y, Wang H, Chen T. Clinicopathological features and genomic profiles of a group of secretory breast carcinomas in which progressive cases have more complex genomic features. Diagn Pathol 2022; 17:101. [PMID: 36585729 PMCID: PMC9805283 DOI: 10.1186/s13000-022-01284-7] [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: 08/15/2022] [Accepted: 12/19/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Secretory breast carcinoma (SBC) is a rare malignant breast neoplasm with distinct histological features, including solid, microcystic, tubular, and rarely papillary structures, traditionally characterized by a t (12;15) (p13:q25) translocation, which usually leads to ETV6-NTRK3 fusion, suggesting an early event in tumorigenesis. Due to the rarity of this disease, very few genome sequencing studies have been performed on a series of cases, especially progressive cases. METHODS Seven lesions from 5 patients diagnosed at the Third Affiliated Hospital of Soochow University from 2007 to 2021 were included. Clinicopathological features and prognosis/survival data were collected. Next-generation DNA sequencing was performed on six of the seven lesions. RESULTS In total, 3/7 (42.9%) lesions demonstrated estrogen receptor (ER) expression, including weak, moderate to strong staining, and no lesion demonstrated progesterone receptor (PR) expression. There were no cases of human epidermal growth factor (HER2) overexpression, and the Ki-67 index was low. S-100 and pan-TRK protein were diffusely positively expressed in all cases. All lesions were characterized by a t(12;15) (p13:q25) translocation, leading to ETV6-NTRK3 fusion confirmed by fluorescence in situ hybridization (FISH). The sequencing results showed that ETV6-NTRK3 fusion was the main driver of early tumorigenesis, while SBC with invasive biological behavior had more complex genomic variation in which TERT promoter mutation was detected. CONCLUSIONS Immunohistochemical staining of a biomarker panel, including ER, PR, HER2, Ki-67, S-100 and pan-TRK, can be used as an auxiliary diagnostic tool, and FISH detection can be used as a diagnostic tool. ETV6-NTRK3 gene fusion involving multiple sites may drive tumorigenesis, while mutations in the TERT promoter region may be a factor driving tumor progression.
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Affiliation(s)
- Ting Lei
- grid.452253.70000 0004 1804 524XDepartment of Pathology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213003 P.R. China
| | - Yuyan Yang
- grid.412648.d0000 0004 1798 6160Department of Pathology, The Second Hospital of Tianjin Medical University, Tianjin, 300211 P.R. China
| | - Yongqiang Shi
- grid.452253.70000 0004 1804 524XDepartment of Pathology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213003 P.R. China
| | - Xu Deng
- grid.452253.70000 0004 1804 524XDepartment of Pathology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213003 P.R. China
| | - Yan Peng
- grid.452253.70000 0004 1804 524XDepartment of Pathology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213003 P.R. China
| | - Hui Wang
- grid.452253.70000 0004 1804 524XDepartment of Pathology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213003 P.R. China
| | - Tongbing Chen
- grid.452253.70000 0004 1804 524XDepartment of Pathology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213003 P.R. China
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Li J, Wu J, Han J. Analysis of Tumor Microenvironment Heterogeneity among Breast Cancer Subtypes to Identify Subtype-Specific Signatures. Genes (Basel) 2022; 14:44. [PMID: 36672784 PMCID: PMC9858482 DOI: 10.3390/genes14010044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/18/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Breast cancer is one of the most frequent malignancies in women worldwide. According to 50-gene signature, Prediction Analysis of Microarray 50 (PAM50), breast cancer can be categorized into five molecular subtypes, and these subtypes are highly heterogeneous in different molecular characteristics. However, the landscape of their tumor microenvironment (TME) heterogeneity has not been fully researched. Using the multi-omics dataset of breast cancer from the METABRIC cohort (n = 1699), we conducted extensive analyses of TME-related features to investigate TME heterogeneity in each breast cancer subtype. We then developed a cell-based subtype set enrichment analysis to identify the subtype-specific TME cells, and further evaluate their prognostic effects. Our results illustrate that different breast cancer subtypes exhibit different TME patterns. Basal-like and HER2-enriched subtypes are associated with high immune scores, expression of most immune regulatory targets, and immune cell infiltration, suggesting that these subtypes could be defined as "immune hot" tumors and suitable for immune checkpoint blockade (ICB) therapy. In contrast, Luminal A and Luminal B subtypes are associated with low immune scores and immune cell infiltration, suggesting that these subtypes could be defined as "immune cold" tumors. Additionally, the Normal-like subtype has relatively high levels of both immune and stromal features, which indicates that the Normal-like subtype may be suitable for more diverse treatment strategies. Our study reveals the breast cancer tumor microenvironment heterogeneity across subtypes. The comprehensive analysis of breast cancer TME-related characteristics may help us to adopt a tailored treatment strategy for different subtypes of patients.
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Affiliation(s)
- Ji Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Jiashuo Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Junwei Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
- Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150086, China
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Zhang W, Shang X, Liu N, Ma X, Yang R, Xia H, Zhang Y, Zheng Q, Wang X, Liu Y. ANK2 as a novel predictive biomarker for immune checkpoint inhibitors and its correlation with antitumor immunity in lung adenocarcinoma. BMC Pulm Med 2022; 22:483. [PMID: 36539782 PMCID: PMC9768990 DOI: 10.1186/s12890-022-02279-2] [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: 08/13/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) have been shown to significantly improve the survival of patients with advanced lung adenocarcinoma (LUAD). However, only limited proportion of patients could benefit from ICIs. Novel biomarkers with strong predictability are needed for clinicians to maximize the efficacy of ICIs. Our study aimed to identify potential biomarkers predicting ICIs efficacy in LUAD. METHODS The Cancer Genome Atlas (TCGA) PanCancer Atlas studies in cBioportal were used to evaluate the mutation frequency of ANK2 across multiple cancers. Clinical and mutational data for LUAD from ICIs-treated cohorts (Hellmann et al. and Rizvi et al.) were collected to explore the correlation between ANK2 mutation and clinical outcomes. In addition, the relationship between ANK2 expression and clinical outcomes was analyzed using LUAD data from TCGA and Gene Expression Omnibus. Furthermore, the impact of ANK2 mutation and expression on the tumor immune microenvironment of LUAD was analyzed using TCGA and TISIDB databases. RESULTS Patients with ANK2 mutation benefited more from ICIs. In ICIs-treated cohort, prolonged progression-free survival (PFS) (median PFS: NR (not reached) vs. 5.42 months, HR (hazard ratio) 0.31, 95% CI 0.18-0.54; P = 0.0037), improved complete response rate (17.65% vs. 1.85%, P = 0.0402), and improved objective response rate (64.71% vs. 24.07%, P = 0.0033) were observed in LUAD patients with ANK2 mutation compared to their wild-type counterparts. Regarding ANK2 expression, it was observed that ANK2 expression was decreased in LUAD (P < 0.05) and a higher level of ANK2 expression was associated with longer overall survival (HR 0.69, 95% CI 0.52-0.92; P = 0.012) in TCGA LUAD cohort. Moreover, ANK2 mutation or higher ANK2 expression correlated with enhanced antitumor immunity and "hot" tumor microenvironment in LUAD, which could be potential mechanisms that ANK2 mutation facilitated ICIs therapy and patients with higher ANK2 expression survived longer. CONCLUSION Our findings suggest that ANK2 mutation or increased ANK2 expression may serve as a favorable biomarker for the efficacy of ICIs in patients with LUAD.
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Affiliation(s)
- Wengang Zhang
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Xiaoling Shang
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Ni Liu
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Xinchun Ma
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Rui Yang
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Handai Xia
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Yuqing Zhang
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Qi Zheng
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Xiuwen Wang
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Yanguo Liu
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
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Xu F, Cui W, Liu C, Feng F, Liu R, Zhang J, Sun C. Prognostic biomarkers correlated with immune infiltration in non-small cell lung cancer. FEBS Open Bio 2022; 13:72-88. [PMID: 36282125 PMCID: PMC9811604 DOI: 10.1002/2211-5463.13501] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 10/17/2022] [Accepted: 10/24/2022] [Indexed: 01/07/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related mortality in men and women globally. Non-small cell lung cancer (NSCLC) is the most prevalent subtype, accounting for 85-90% of all cancers. Although there have been dramatic advances in therapeutic approaches in recent decades, the recurrence and metastasis rates of NSCLC are as high as 30-40% with the 5-year overall survival rate being less than 15%. Therefore, it is necessary to explore the pathogenesis of NSCLC at the genetic level and identify prognostic biomarkers and novel therapeutic targets. Here, we aimed to identify mutated genes with high frequencies in Chinese NSCLC patients using next-generation sequencing and to investigate their relationships with the tumor mutation burden (TMB) and tumor immune microenvironment. A total of 110 NSCLC patients were enrolled to profile the genetic variations. Mutations in EGFR (62.37%), TP53 (61.29%), LRP1B (13.98%), FAT1 (12.90%), KMT2D (11.83%), CREBBP (10.75%), and RB1 (9.68%) were most prevalent. TP53, LRP1B, KMT2D, and CREBBP mutations were all significantly associated with high TMB (P < 0.05 or P < 0.01). The infiltrating levels of immune cells and immune molecules were enriched significantly in the LRP1B mutation group. LRP1B mutations significantly correlated with stimulating and inhibitory immunoregulators. Gene set enrichment analysis revealed that cell cycle, the Notch signaling pathway, the insulin signaling pathway, and the mTOR signaling pathway are related to LRP1B mutations in the immune system. LRP1B mutations may be of clinical importance in enhancing the anti-tumor immune response and may be a promising biomarker for predicting immunotherapy responsiveness.
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Affiliation(s)
- Fei Xu
- Department of Geriatric MedicineAffiliated Hospital of Shandong University of Traditional Chinese MedicineJinanChina,First Clinical Medical CollegeShandong University of Traditional Chinese MedicineJinanChina
| | - Wen‐qiang Cui
- Department of NeurologyAffiliated Hospital of Shandong University of Traditional Chinese MedicineJinanChina
| | - Cun Liu
- College of Traditional Chinese MedicineShandong University of Traditional Chinese MedicineJinanChina
| | - Fubin Feng
- Department of OncologyWeifang Traditional Chinese HospitalChina
| | - Ruijuan Liu
- Department of OncologyWeifang Traditional Chinese HospitalChina
| | - Jingtao Zhang
- College of Traditional Chinese MedicineShandong University of Traditional Chinese MedicineJinanChina
| | - Chang‐gang Sun
- Department of OncologyWeifang Traditional Chinese HospitalChina,Qingdao Academy of Chinese Medical SciencesShandong University of Traditional Chinese MedicineQingdaoChina
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Liu J, Li Z, Lu T, Pan J, Li L, Song Y, Hu D, Zhuo Y, Chen Y, Xu Q. Genomic landscape, immune characteristics and prognostic mutation signature of cervical cancer in China. BMC Med Genomics 2022; 15:231. [PMID: 36333792 PMCID: PMC9636686 DOI: 10.1186/s12920-022-01376-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
Purpose This study aimed to analyse the genomic alteration profiles and immune characteristics of a cohort of Chinese cervical cancer patients to understand why certain patients benefited from molecular targeted therapies and immunotherapy as well as their prognostic significance. Methods PD-L1 expression and clinicopathological information were obtained from 98 cervical cancer patients. Differences in PD-L1 expression and gene mutations between squamous cell carcinoma (SCC) and adenocarcinoma (AC) were analysed by the chi-square test or Fisher's exact test. Differences in gene mutations between our cohort and The Cancer Genome Atlas (TCGA) cohort were tested by Fisher's exact test. Logistic regression was used to analyse factors influencing TMB-high. Results Positive PD-L1 expression was significantly higher in cervical SCC than in cervical AC (87% vs. 39%, p < 0.001). Frequently mutated genes in cervical cancer included the PIK3CA, KMT2D, and KMT2C genes, among others. PIK3CA gene mutation rates were significantly higher in SCC than in AC (p = 0.004). The TERT gene mutation rate was significantly higher in our cohort than in the TCGA cohort (12% vs. 1%, p < 0.001). The independent predictors of high TMB were KMT2C and LRP1B gene mutations (p < 0.05). We also found that PTEN mutations were associated with worse survival (median PFS, 12.16 vs. 21.75 months, p = 0.0024). Conclusion Cervical SCC and AC have different molecular profiles and immune characteristics, suggesting that targeted treatments for SCC and AC patients may improve clinical outcomes. KMT2C and LRP1B gene mutations are independent predictors of TMB-high status in cervical cancer. We also proposed the prognostic value of PTEN mutations. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01376-9.
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Affiliation(s)
- Jing Liu
- grid.415110.00000 0004 0605 1140Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No. 420 Fuma Road, Jinan District, Fuzhou, 350014 China
| | - Zirong Li
- grid.256112.30000 0004 1797 9307Department of Radiation Oncology, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan, Fujian China
| | - Ting Lu
- grid.459516.aDepartment of Pathology, Fujian Women and Children Hospital, Fuzhou, Fujian China
| | - Junping Pan
- grid.415110.00000 0004 0605 1140Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No. 420 Fuma Road, Jinan District, Fuzhou, 350014 China
| | - Li Li
- grid.415110.00000 0004 0605 1140Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No. 420 Fuma Road, Jinan District, Fuzhou, 350014 China
| | - Yanwen Song
- grid.415110.00000 0004 0605 1140Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No. 420 Fuma Road, Jinan District, Fuzhou, 350014 China
| | - Dan Hu
- grid.415110.00000 0004 0605 1140Department of Pathology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No. 420 Fuma Road, Jinan District, Fuzhou, 350014 China
| | - Yanhong Zhuo
- grid.256112.30000 0004 1797 9307Department of Radiotherapy, Zhangzhou Hospital, Teaching Hospital of Fujian Medical University, Zhangzhou, 363000 Fujian China
| | - Ying Chen
- grid.415110.00000 0004 0605 1140Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No. 420 Fuma Road, Jinan District, Fuzhou, 350014 China
| | - Qin Xu
- grid.415110.00000 0004 0605 1140Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No. 420 Fuma Road, Jinan District, Fuzhou, 350014 China
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Wang L, Hu X, Liu X, Feng Y, Zhang Y, Han J, Liu X, Meng F. m7G regulator-mediated methylation modification patterns define immune cell infiltration and patient survival. Front Immunol 2022; 13:1022720. [DOI: 10.3389/fimmu.2022.1022720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous studies have demonstrated the important roles of epigenetic modifications in tumorigenesis, progression and prognosis. However, in hepatocellular carcinoma, the potential link between N7-methylguanosine (m7G) modification and molecular heterogeneity and tumor microenvironment (TME) remains unclear.MethodWe performed a comprehensive evaluation of m7G modification patterns in 816 hepatocellular carcinoma samples based on 24 m7G regulatory factors, identified different m7G modification patterns, and made a systematic correlation of these modification patterns with the infiltration characteristics of immunocytes. Then, we built and validated a scoring tool called m7G score.ResultsIn this study, we revealed the presence of three distinct m7G modification patterns in liver cancer, with remarkable differences in the immunocyte infiltration characteristics of these three subtypes. The m7G scoring system of this study could assess m7G modification patterns in individual hepatocellular carcinoma patients, could predict TME infiltration characteristics, genetic variants and patient prognosis. We also found that the m7G scoring system may be useful in guiding patients’ clinical use of medications.ConclusionsThis study revealed that m7G methylation modifications exerted a significant role in formation of TME in hepatocellular carcinoma. Assessing the m7G modification patterns of single patients would help enhance our perception of TME infiltration characteristics and give significant insights into immunotherapy efficacy.
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Wu H, Yu Z, Liu Y, Guo L, Teng L, Guo L, Liang L, Wang J, Gao J, Li R, Yang L, Nie X, Su D, Liang Z. Genomic characterization reveals distinct mutation landscapes and therapeutic implications in neuroendocrine carcinomas of the gastrointestinal tract. CANCER COMMUNICATIONS (LONDON, ENGLAND) 2022; 42:1367-1386. [PMID: 36264285 PMCID: PMC9759768 DOI: 10.1002/cac2.12372] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/24/2022] [Accepted: 10/08/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND Neuroendocrine carcinomas of the gastrointestinal tract (GI-NECs) remain a disease of grim prognosis with limited therapeutic options. Their molecular characteristics are still undefined. This study aimed to explore the underlying genetic basis and heterogeneity of GI-NECs. METHODS Comprehensive genomic analysis using whole-exome sequencing was performed on 143 formalin-fixed, paraffin-embedded samples of surgically resected GI-NEC with a thorough histological evaluation. Mutational signatures, somatic mutations, and copy number aberrations were analyzed and compared across anatomic locations and histological subtypes. Survival analysis was conducted to identify the independent factors. RESULTS In total, 143 GI-NECs were examined: the stomach, 87 cases (60.8%); the esophagus, 29 cases (20.3%); the colorectum, 20 cases (14.0%); and the small intestine, 7 cases (4.9%). Eighty-three (58.0%) and 60 (42.0%) cases were subclassified into small cell and large cell subtypes, respectively. GI-NECs showed distinct genetic alterations from their lung counterparts and non-neuroendocrine carcinomas in the same locations. Obvious heterogeneity of mutational signatures, somatic mutations, and copy number variations was revealed across anatomic locations rather than histological subtypes. Except for tumor protein p53 (TP53) and retinoblastoma 1 (RB1), the most frequently mutated genes in the stomach, esophagus, colorectum, and small intestine were low-density lipoprotein receptor-related protein 1B (LRP1B), notch receptor 1 (NOTCH1), adenomatosis polyposis coli (APC), catenin beta 1 (CTNNB1), respectively. Mutations in the WNT-β-catenin, NOTCH and erythroblastic leukemia viral oncogene B (ERBB) pathways were prevalently identified in gastric, esophageal, and colorectal NECs, respectively. Importantly, 104 (72.7%) GI-NECs harbored putative clinically relevant alterations, and non-gastric location and RB1 bi-allelic inactivation with copy number alterations were identified as two independent poor prognostic factors. Furthermore, we found that tumor cells in GI-NECs first gain clonal mutations in TP53, RB1, NOTCH1 and APC, followed by subsequent whole-genome doubling (WGD) and post-WGD clonal mutations in LRP1B, CUB and Sushi multiple domains 3 (CSMD3), FAT tumor suppressor homolog 4 (FAT4) and erb-b2 receptor tyrosine kinase 4 (ERBB4), and finally develop subclonal mutations. CONCLUSIONS GI-NECs harbor distinct genomic landscapes and demonstrate significant genetic heterogeneity across different anatomic locations. Moreover, potentially actionable alterations and prognostic factors were revealed for GI-NECs.
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Affiliation(s)
- Huanwen Wu
- Department of PathologyState Key Laboratory of Complex Severe and Rare DiseasesMolecular Pathology Research CenterPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100730P. R. China
| | - Zicheng Yu
- Geneplus‐BeijingBeijing102200P. R. China
| | - Yueping Liu
- Department of PathologyThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebei050011P. R. China
| | - Lei Guo
- Department of PathologyCancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Lianghong Teng
- Department of PathologyXuanwu HospitalCapital Medical UniversityBeijing100053P. R. China
| | - Lingchuan Guo
- Department of PathologyThe First Affiliated Hospital of Soochow UniversitySuzhouJiangsu215000P. R. China
| | - Li Liang
- Department of PathologySouthern Medical UniversityGuangzhouGuangdong510515P. R. China
| | - Jing Wang
- Department of PathologyState Key Laboratory of Complex Severe and Rare DiseasesMolecular Pathology Research CenterPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100730P. R. China
| | - Jie Gao
- Department of PathologyState Key Laboratory of Complex Severe and Rare DiseasesMolecular Pathology Research CenterPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100730P. R. China
| | - Ruiyu Li
- Department of PathologyState Key Laboratory of Complex Severe and Rare DiseasesMolecular Pathology Research CenterPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100730P. R. China
| | - Ling Yang
- Geneplus‐BeijingBeijing102200P. R. China
| | - Xiu Nie
- Department of PathologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430022P. R. China
| | - Dan Su
- Department of PathologyThe Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital)Institute of Basic Medicine and Cancer (IBMC)Chinese Academy of SciencesHangzhouZhejiang310022P. R. China
| | - Zhiyong Liang
- Department of PathologyState Key Laboratory of Complex Severe and Rare DiseasesMolecular Pathology Research CenterPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100730P. R. China
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Khoury LM, Burcher KM, Ng RT, Song AH, Chang MJ, Gavrila E, Bloomer CH, Robinson MB, Kouri BE, Waltonen JD, Bunch PM, Lauer UM, Porosnicu M. Serendipitous synergism - an exceptional response to treatment with pembrolizumab in the course of a natural immunovirotherapy: a case report and review of the literature. Ther Adv Med Oncol 2022; 14:17588359221122729. [PMID: 36312814 PMCID: PMC9597005 DOI: 10.1177/17588359221122729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/11/2022] [Indexed: 11/06/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs) are the current guideline recommended treatment for many malignancies considered to be terminal. Despite considerable advances, their utility remains limited, and the field requires synergistic partners to further improve outcomes. Oncolytic viruses (OV) are emerging as contenders for the role of the synergistic agent of choice due to their multi-mechanistic effect on activating the tumor 'cold' immune microenvironment. Herpes simplex virus 1, a naturally selective OV, is the most advanced virotherapeutic compound in clinical applications for use in combination with ICI. We here present the case of a 72 year-old patient with a heavily pre-treated, advanced maxillary sinus squamous cell cancer with distant metastases who developed complete response (CR) with only three administrations of a programmed death 1 inhibitor after treatment interference by a severe herpes zoster infection, based on the related alpha-herpesvirus varicella zoster virus (VZV). This exceptional response has been followed and confirmed with imaging studies over more than 5 years. Although the patient had several favorable predictors for response to immunotherapy, we reason that the exceptional response may in part be secondary to the serendipitous VZV infection. Documented cases of cancer patients that achieved CR after few administrations of treatment with ICI are rare, with most reporting follow up of just over 1 year or less. In this case, it is conceivable that the interference of the infection with VZV, soon after the start of immunotherapy with ICI, led to a lasting antitumor immunity and sustained CR. This hypothesis is supported by the concept of 'oncolytic immunotherapy' which is reviewed in this manuscript. In addition, persistence of a TP53 mutation found in a liquid biopsy, despite clinical and radiologic remission, is discussed.
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Affiliation(s)
- Lara M. Khoury
- Department of Internal Medicine, Wake Forest
University School of Medicine, Winston-Salem, NC, USA
| | - Kimberly M. Burcher
- Department of Internal Medicine, Wake Forest
University School of Medicine, Winston-Salem, NC, USA
| | - Ronald T. Ng
- Department of Internal Medicine, Wake Forest
University School of Medicine, Winston-Salem, NC, USA
| | - Alexander H. Song
- Department of Internal Medicine, Section on
Hematology and Oncology, Wake Forest University School of Medicine,
Winston-Salem, NC, USA
| | - Mark J. Chang
- Department of Internal Medicine, Wake Forest
University School of Medicine, Winston-Salem, NC, USA
| | - Elena Gavrila
- Wake Forest University School of Medicine,
Winston-Salem, NC, USA
| | - Chance H. Bloomer
- Department of Internal Medicine, Wake Forest
University School of Medicine, Winston-Salem, NC, USA
| | - Mac B. Robinson
- Wake Forest Baptist Comprehensive Cancer
Center, Winston-Salem, NC, USA
| | - Brian E. Kouri
- Department of Radiology, Wake Forest University
School of Medicine, Winston-Salem, NC, USA
| | - Joshua D. Waltonen
- Department of Otolaryngology, Wake Forest
University School of Medicine, Winston-Salem, NC, USA
| | - Paul M. Bunch
- Department of Radiology, Wake Forest
University School of Medicine, Winston-Salem, NC, USA
| | - Ulrich M. Lauer
- Department of Internal Medicine VIII, Medical
Oncology and Pneumology, University Hospital Tuebingen, Germany German
Cancer Research Center (DKFZ), Tuebingen, Germany
| | - Mercedes Porosnicu
- Department of Internal Medicine, Section on
Hematology and Oncology, Wake Forest University School of Medicine, Medical
Center Blvd, Winston-Salem, NC 27101-4135, USA
- Wake Forest Baptist Comprehensive Cancer
Center, Winston-Salem, NC, USA
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Li SS, Zhai XH, Liu HL, Liu TZ, Cao TY, Chen DM, Xiao LX, Gan XQ, Cheng K, Hong WJ, Huang Y, Lian YF, Xiao J. Whole-exome sequencing analysis identifies distinct mutational profile and novel prognostic biomarkers in primary gastrointestinal diffuse large B-cell lymphoma. Exp Hematol Oncol 2022; 11:71. [PMID: 36243813 PMCID: PMC9569083 DOI: 10.1186/s40164-022-00325-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
Background Diffuse large B-cell lymphoma (DLBCL) is the most common aggressive non-Hodgkin lymphoma, and about 10% of DLBCL cases primarily occur in the gastrointestinal tract. Previous reports have revealed that primary gastrointestinal-DLBCL (pGI-DLBCL) harbors different genetic mutations from other nodal or extranodal DLBCL. However, the exonic mutation profile of pGI-DLBCL has not been fully addressed. Methods We performed whole-exome sequencing of matched tumor tissues and blood samples from 53 pGI-DLBCL patients. The exonic mutation profiles were screened, and the correlations between genetic mutations and clinicopathological characteristics were analyzed. Results A total of 6,588 protein-altering events were found and the five most frequent mutated genes in our pGI-DLBCL cohort were IGLL5 (47%), TP53 (42%), BTG2 (28%), P2RY8 (26%) and PCLO (23%). Compared to the common DLBCL, significantly less or absence of MYD88 (0%), EZH2 (0%), BCL2 (2%) or CD79B (8%) mutations were identified in pGI-DLBCL. The recurrent potential driver genes were mainly enriched in pathways related to signal transduction, infectious disease and immune regulation. In addition, HBV infection had an impact on the mutational signature in pGI-DLBCL, as positive HBsAg was significantly associated with the TP53 and LRP1B mutations, two established tumor suppressor genes in many human cancers. Moreover, IGLL5 and LRP1B mutations were significantly correlated with patient overall survival and could serve as two novel prognostic biomarkers in pGI-DLBCL. Conclusions Our study provides a comprehensive view of the exonic mutation profile of the largest pGI-DLBCL cohort to date. The results could facilitate the clinical development of novel therapeutic and prognostic biomarkers for pGI-DLBCL. Supplementary Information The online version contains supplementary material available at 10.1186/s40164-022-00325-7.
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Affiliation(s)
- Shan-Shan Li
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Xiao-Hui Zhai
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Hai-Ling Liu
- Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Ting-Zhi Liu
- Department of Hematology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Tai-Yuan Cao
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Dong-Mei Chen
- Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Le-Xin Xiao
- Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Xiao-Qin Gan
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Ke Cheng
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Wan-Jia Hong
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Yan Huang
- Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China. .,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
| | - Yi-Fan Lian
- Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Jian Xiao
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China. .,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
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Bronk JK, Kapadia C, Wu X, Chapman BV, Wang R, Karpinets TV, Song X, Futreal AM, Zhang J, Klopp AH, Colbert LE. Feasibility of a novel non-invasive swab technique for serial whole-exome sequencing of cervical tumors during chemoradiation therapy. PLoS One 2022; 17:e0274457. [PMID: 36201462 PMCID: PMC9536567 DOI: 10.1371/journal.pone.0274457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/29/2022] [Indexed: 11/06/2022] Open
Abstract
Background Clinically relevant genetic predictors of radiation response for cervical cancer are understudied due to the morbidity of repeat invasive biopsies required to obtain genetic material. Thus, we aimed to demonstrate the feasibility of a novel noninvasive cervical swab technique to (1) collect tumor DNA with adequate throughput to (2) perform whole-exome sequencing (WES) at serial time points over the course of chemoradiation therapy (CRT). Methods Cervical cancer tumor samples from patients undergoing chemoradiation were collected at baseline, at week 1, week 3, and at the completion of CRT (week 5) using a noninvasive swab-based biopsy technique. Swab samples were analyzed with whole-exome sequencing (WES) with mutation calling using a custom pipeline optimized for shallow whole-exome sequencing with low tumor purity (TP). Tumor mutation changes over the course of treatment were profiled. Results 216 samples were collected and successfully sequenced for 70 patients (94% of total number of tumor samples collected). A total of 33 patients had a complete set of samples at all four time points. The mean mapping rate was 98% for all samples, and the mean target coverage was 180. Estimated TP was greater than 5% for all samples. Overall mutation frequency decreased during CRT but mapping rate and mean target coverage remained at >98% and >180 reads at week 5. Conclusion This study demonstrates the feasibility and application of a noninvasive swab-based technique for WES analysis which may be applied to investigate dynamic tumor mutational changes during treatment to identify novel genes which confer radiation resistance.
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Affiliation(s)
- Julianna K. Bronk
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Chiraag Kapadia
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiaogang Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Bhavana V. Chapman
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Rui Wang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Tatiana V. Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Andrew M. Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ann H. Klopp
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail: (LEC); (AHK)
| | - Lauren E. Colbert
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail: (LEC); (AHK)
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Luo H, Ye M, Hu Y, Wu M, Cheng M, Zhu X, Huang K. DNA methylation regulator-mediated modification patterns and tumor microenvironment characterization in glioma. Aging (Albany NY) 2022; 14:7824-7850. [PMID: 36152044 PMCID: PMC9596205 DOI: 10.18632/aging.204291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022]
Abstract
Growing evidences indicate DNA methylation plays a crucial regulatory role in inflammation, innate immunity, and immunotherapy. However, the overall landscape of various DNA methylation regulatory genes and their relationship with the infiltration of immune cells into the tumor microenvironment (TME) as well as the response to immunotherapy in gliomas is still not clear. Therefore, we comprehensively analyzed the correlation between DNA methylation regulator patterns, infiltration of immune cell-types, and tumor immune response status in gather glioma cohorts. Furthermore, we calculated the DNA methylation score (DMS) for individual glioma samples, then evaluated the relationship between DMS, clinicopathological characteristics, and overall survival (OS) in patients with gliomas. Our results showed three distinct DNA methylation regulator patterns among the glioma patients which correlated with three distinct tumor immune response phenotypes, namely, immune-inflamed, immune-excluded, and immune desert. We then calculated DMS for individual glioma samples based on the expression of DNA methylation-related gene clusters. Furthermore, DMS, tumor mutation burden (TMB), programmed death 1 (PD-1) expression, immune cell infiltration status in the TME, and Tumor Immune Dysfunction and Exclusion (TIDE) scores were associated with survival outcomes and clinical responses to immune checkpoint blockade therapy. We also validated the predictive value of DMS in two independent immunotherapy cohorts. In conclusion, our results demonstrated that three DNA methylation regulator patterns that correlated with three tumor immune response phenotypes. Moreover, we demonstrated that DMS was an independent predictive biomarker that correlated with survival outcomes of glioma patients and their responses to immunotherapy therapeutic regimens.
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Affiliation(s)
- Haitao Luo
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi Province, China
| | - Minhua Ye
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi Province, China
| | - Yan Hu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,East China Institute of Digital Medical Engineering, Shangrao, Jiangxi Province, China
| | - Miaojing Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China
| | - Mengqi Cheng
- Department of Obstetrics and Gynecology, Suizhou Central Hospital, Hubei University of Medicine, Suizhou, Hubei Province, China
| | - Xingen Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi Province, China
| | - Kai Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi Province, China
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Miao YR, Liu CJ, Hu H, Yang M, Guo AY. Biological Pathway-Derived TMB Robustly Predicts the Outcome of Immune Checkpoint Blockade Therapy. Cells 2022; 11:cells11182802. [PMID: 36139377 PMCID: PMC9496944 DOI: 10.3390/cells11182802] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/22/2022] [Accepted: 09/02/2022] [Indexed: 11/28/2022] Open
Abstract
Although immune checkpoint blockade (ICB) therapies have achieved great progress, the patient response varies among cancers. In this study, we analyzed the potential genomic indicators contributing to ICB therapy response. The results showed that high tumor mutation burden (TMB) failed to predict response in anti-PD1 treated melanoma. SERPINB3 was the most significant response-related gene in melanoma and mutations in either SERPINB3 or PEG3 can serve as an independent risk factor in melanoma. Some recurrent mutations in CSMD3 were only in responders or non-responders, indicating their diverse impacts on patient response. Enrichment scores (ES) of gene mutations in 12 biological pathways were significantly higher in responders or non-responders. Next, the P-TMB calculated from genes in these pathways was significantly related to patient response with prediction AUC 0.74–0.82 in all collected datasets. In conclusion, our work provides new insights into the application of TMB in predicting patient response, which will benefit to immunotherapy research.
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Affiliation(s)
- Ya-Ru Miao
- Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chun-Jie Liu
- Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hui Hu
- Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mei Yang
- Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - An-Yuan Guo
- Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Research Institute of Huazhong University of Science and Technology in Shenzhen, Shenzhen 518000, China
- Correspondence:
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Insight into the potential candidate genes and signaling pathways involved in lymphoma disease in dogs using a comprehensive whole blood transcriptome analysis. Gene 2022; 838:146735. [PMID: 35835403 DOI: 10.1016/j.gene.2022.146735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/20/2022] [Accepted: 07/08/2022] [Indexed: 11/04/2022]
Abstract
Lymphoma is one of the most prevalent hematological cancers, accounting for 15-20 % of new cancer diagnoses in dogs. Therefore, this study aims to explore the important genes and pathways involved in canine lymphoma progression and understand the underlying molecular mechanisms using RNA sequencing. In this study, RNAs acquired from seven pairs of lymphoma and non-lymphoma blood samples were sequenced from different breeds of dogs. Sequencing reads were preprocessed, aligned with the reference genome, assembled and expressions were estimated through bioinformatics approaches. At a false discovery rate (FDR) < 0.05 and fold change (FC) ≥ 1.5, a total of 625 differentially expressed genes (DEGs) were identified between lymphoma and non-lymphoma samples, including 347 up-regulated DEGs such as SLC38A11, SCN3A, ZIC5 etc. and 278 down-regulated DEGs such as LOC475937, CSMD1, KRT14 etc. GO enrichment analysis showed that these DEGs were highly enriched for molecular function of ATP binding and calcium ion binding, cellular process of focal adhesion, and biological process of immune response, and defense response to virus. Similarly, KEGG pathways analysis revealed 11 significantly enriched pathways such as ECM-receptor interaction, cell cycle, PI3K-Akt signaling pathway, ABC transporters etc. In the protein-protein interaction (PPI) network, CDK1 was found to be a top hub gene with highest degree of connectivity. Three modules selected from the PPI network showed that canine lymphoma was highly associated with cell cycle, ECM-receptor interaction, hypertrophic cardiomyopathy, dilated cardiomyopathy and RIG-I-like receptor signaling pathway. Overall, our findings highlighted new candidate therapeutic targets for further testing in canine lymphoma and facilitate the understanding of molecular mechanism of lymphoma's progression in dogs.
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Xing P, Jiang Z, Liu Y. Construction and validation of a gene signature related to bladder urothelial carcinoma based on immune gene analysis. BMC Cancer 2022; 22:926. [PMID: 36030212 PMCID: PMC9419388 DOI: 10.1186/s12885-022-09794-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/15/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND This study developed a gene signature associated with a malignant and common tumor of the urinary system, the Bladder Urothelial Carcinoma (BLCA). METHODS The Cancer Genome Atlas (TCGA) database was searched to obtain 414 BLCA samples and the expression spectra of 19 normal samples. Single-sample Gene Set Enrichment Analysis (ssGSEA) was conducted to determine the enrichment levels in the BLCA samples of the 29 immune genes. Unsupervised hierarchical clustering, gene set enrichment analysis (GSEA), single-factor Cox analysis, least absolute shrinkage and selection operator (LASSO) regression models, and GEO queues were used to determine the BLCA immune gene subtype, analyze the biological pathway differences between immune gene subtypes, determine the characteristic genes of BLCA associated with prognosis, identify the BLCA-related genes, and verify the gene signature, respectively. RESULTS We identified two immune gene subtypes (immunity_L and immunity_H). The latter was significantly related to receptors, JAK STAT signaling pathways, leukocyte interleukin 6 generation, and cell membrane signal receptor complexes. Four characteristic genes (RBP1, OAS1, LRP1, and AGER) were identified and constituted the gene signature. Significant survival advantages, higher mutation frequency, and superior immunotherapy were observed in the low-risk group patients. The gene signature had good predictive ability. The results of the validation group were consistent with TCGA queue results. CONCLUSIONS We constructed a 4-gene signature that helps monitor BLCA occurrence and prognosis, providing an important basis for developing personalized BLCA immunotherapy.
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Affiliation(s)
- Peng Xing
- Department of Urology, The First Hospital of China Medical University, Shenyang, 110013, P.R. China
| | - Zhengming Jiang
- Department of Urology, The First Hospital of China Medical University, Shenyang, 110013, P.R. China
| | - Yang Liu
- Department of Urology, The First Hospital of China Medical University, Shenyang, 110013, P.R. China.
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Ma T, Jiao J, Huo R, Li X, Fang G, Zhao Q, Liu W, Han X, Xi C, Wang Y, Shang Y. PD-L1 expression, tumor mutational burden, and immune cell infiltration in non-small cell lung cancer patients with epithelial growth factor receptor mutations. Front Oncol 2022; 12:922899. [PMID: 35992815 PMCID: PMC9389166 DOI: 10.3389/fonc.2022.922899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundImmunotherapy using programmed cell death protein 1/programmed death-ligand 1 (PD-1/PD-L1) inhibitors seems less effective in non-small cell lung cancer (NSCLC) patients with epithelial growth factor receptor (EGFR) mutations. Varied responses to PD-1/PD-L1 inhibitors have recently been observed in NSCLC patients harboring different types of EGFR mutations. Some EGFR-mutated NSCLC patients may benefit from PD-1/PD-L1 inhibitors. At present, PD-L1 expression, tumor mutational burden (TMB), and tumor immune microenvironment (TIME) are biomarkers for predicting the efficacy of PD-1/PD-L1 inhibitors in NSCLC patients. We retrospectively evaluated PD-L1 expression, TMB, and immune cell infiltration in NSCLC patients with EGFR mutation subtypes.MethodsPD-L1 expression, TMB, and the abundance of immune cell infiltration in NSCLC patients were evaluated in public databases and clinical samples. TMB was detected using the NGS technique, PD-L1 was detected using immunohistochemistry, and the abundance of immune cell infiltration in NSCLC samples was detected using multiple immunohistochemistry.ResultsPD-L1 expression and TMB were lower in EGFR-mutated NSCLCs than in wild-type patients. Differences in the abundance of immune cell infiltration were also observed between EGFR-mutated and wild-type NSCLC. The expression of PD-L1, TMB, and abundance of immune cell infiltration were different in patients harboring different subtypes of EGFR mutations. Patients with uncommon EGFR mutations, especially the G719X mutation, showed higher TMB and expressions of PD-L1 than classical EGFR mutations. M1 macrophages were higher in uncommon EGFR mutations than classical EGFR mutations.ConclusionsThe expression of PD-L1 and TMB in uncommon EGFR-mutated NSCLCs, especially the G719X mutation, were higher than those for classical EGFR-mutated NSCLCs and similar to EGFR wild-type. The abundance of immune cell infiltration in uncommon EGFR-mutated NSCLCs was similar to that in EGFR wild-type. Our findings suggest that uncommon EGFR-mutated NSCLCs may benefit from PD-1/PD-L1 inhibitors.
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Affiliation(s)
- Tiantian Ma
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, China
| | - Jin Jiao
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, China
| | - Ran Huo
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, China
| | - Xiaofang Li
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, China
| | - Guotao Fang
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, China
| | - Qi Zhao
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, China
| | - Weiwei Liu
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, China
| | - Xiao Han
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, China
| | - Chenglin Xi
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, China
| | - Yanan Wang
- Department of Pathology, Affiliated Hospital of Hebei University, Baoding, China
| | - Yanhong Shang
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, China
- *Correspondence: Yanhong Shang,
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Zhou J, Bao M, Gao G, Cai Y, Wu L, Lei L, Zhao J, Ji X, Huang Y, Su C. Increased blood-based intratumor heterogeneity (bITH) is associated with unfavorable outcomes of immune checkpoint inhibitors plus chemotherapy in non-small cell lung cancer. BMC Med 2022; 20:256. [PMID: 35902848 PMCID: PMC9335993 DOI: 10.1186/s12916-022-02444-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/17/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The combination of immune checkpoint inhibitors (ICIs) and chemotherapy has been the standard first-line treatment for advanced non-small cell lung cancer (NSCLC) patients with driver-gene negative. However, efficacy biomarkers for ICIs-based combination therapy are lacking. We aimed to identify potential factors associated with outcomes of ICIs plus chemotherapy at baseline and dynamic changes in peripheral blood. METHODS We collected plasma samples of 51 advanced NSCLC patients without EGFR/ALK/ROS1 alteration at baseline and/or after two treatment cycles of ICIs plus chemotherapy. A blood-based intratumor heterogeneity (bITH) score was calculated based on the allele frequencies of somatic mutations using a 520-gene panel. bITH-up was defined as a ≥ 10% increase in bITH score from baseline, with a second confirmatory measurement after treatment. RESULTS At baseline, the number of metastatic organs and lung immune prognostic index (LIPI) were significantly associated with shorter progression-free survival (PFS) of ICIs plus chemotherapy, while bITH and other common molecular biomarkers, including ctDNA level, blood-based tumor mutational burden (bTMB), and PD-L1 expression, had no effect on PFS. LRP1B mutation at baseline was significantly associated with favorable outcomes to ICIs plus chemotherapy. There were 37 patients who had paired samples at baseline and after two cycles of treatment, with the median interval of 53 days. Intriguingly, patients with bITH-up had significant shorter PFS (HR, 4.92; 95% CI, 1.72-14.07; P = 0.001) and a lower durable clinical benefit rate (0 vs 41.38%, P = 0.036) than those with bITH-stable or down. Case studies indicated that bITH was promising to predict disease progression. CONCLUSIONS The present study is the first to report that increased bITH is associated with unfavorable outcomes of ICIs plus chemotherapy in advanced NSCLC patients.
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Affiliation(s)
- Juan Zhou
- Department of Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China
| | - Minwei Bao
- Department of Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China
| | - Guanghui Gao
- Department of Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China
| | - Yiran Cai
- Burning Rock Biotech, Guangzhou, China
| | - Lihong Wu
- Burning Rock Biotech, Guangzhou, China
| | - Lei Lei
- Burning Rock Biotech, Guangzhou, China
| | - Jing Zhao
- Department of Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China
| | - Xianxiu Ji
- Department of Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China
| | - Ying Huang
- Department of Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China
| | - Chunxia Su
- Department of Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China.
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Liao K, Hu J, Huang Y, Yu S, Yang Q, Sun F, Wu C, Cheng Y, Zhang W, Zhang X, Li H, Wang X. m 6A Regulator-Based Methylation Modification Patterns Characterized by Distinct Tumor Microenvironment Immune Profiles in Rectal Cancer. Front Oncol 2022; 12:879405. [PMID: 35875124 PMCID: PMC9299953 DOI: 10.3389/fonc.2022.879405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/23/2022] [Indexed: 12/24/2022] Open
Abstract
Background Previous studies reported the related role of RNA n6-methyladenosine (m6A) modification in tumorigenesis and development. However, it is not clear whether m6A modification also plays a potential role in the immune regulation of rectal cancer (RC) and the formation of tumor microenvironment. Methods In this study, we screened 23 m6A regulatory factors from 369 rectal cancer specimens, further determined the modification patterns of m6A in RC, and systematically linked these modification patterns with the characteristics of TME cell infiltration. The principal component analysis (PCA) algorithm was used to evaluate the m6A modification pattern of a single tumor related to immune response. Results Three different m6A modification patterns were found in the measurement results, which are related to different clinical results and biological pathways. TME identification results show that the identified m6A pattern is closely related to immune characteristics. According to the m6Ascore extracted from m6A-related signature genes, RC patients were divided into high and low score subgroups combined with tumor mutation burden. Patients with high tumor mutation burden and higher m6Ascore have a significant survival advantage and enhanced immune infiltration. Further analysis showed that patients with higher m6Ascore had higher PD-L1 expression levels and showed better immune response and lasting clinical benefits. Conclusions M6A modification plays a crucial role in the formation of TME diversity and complexity. The evaluation of the m6A modification mode will help us to enhance our understanding of the characteristics of TME infiltration and provide new insights for more effective immunotherapy strategies.
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Affiliation(s)
- Kaili Liao
- Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jialing Hu
- Department of Emergency medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yu Huang
- School of Advanced Manufacturing of Nanchang University, Nanchang, China
| | - Siji Yu
- School of Advanced Manufacturing of Nanchang University, Nanchang, China
| | - Qijun Yang
- Queen Mary College of Nanchang University, Xuefu Road, Nanchang, Nanchang, China
| | - Fan Sun
- Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chengfeng Wu
- Department of Vascular Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yunqi Cheng
- Queen Mary College of Nanchang University, Xuefu Road, Nanchang, Nanchang, China
| | - Wenyige Zhang
- Queen Mary College of Nanchang University, Xuefu Road, Nanchang, Nanchang, China
| | - Xue Zhang
- Queen Mary College of Nanchang University, Xuefu Road, Nanchang, Nanchang, China
| | - Hongyu Li
- Queen Mary College of Nanchang University, Xuefu Road, Nanchang, Nanchang, China
| | - Xiaozhong Wang
- Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Ma H, Zhang Q, Zhao Y, Zhang Y, Zhang J, Chen G, Tan Y, Zhang Q, Duan Q, Sun T, Qi C, Li F. Molecular and Clinicopathological Characteristics of Lung Cancer Concomitant Chronic Obstructive Pulmonary Disease (COPD). Int J Chron Obstruct Pulmon Dis 2022; 17:1601-1612. [PMID: 35860812 PMCID: PMC9293488 DOI: 10.2147/copd.s363482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/25/2022] [Indexed: 11/23/2022] Open
Abstract
Introduction Chronic obstructive pulmonary disease (COPD) and lung cancer often coexist, but its pathophysiology and genomics features are still unclear. Methods In this study, we retrospectively collected lung cancer concomitant COPD (COPD-LC) and non-COPD lung cancer (non-COPD-LC) patients, who performed next generation sequencing (NGS) and had clinicopathological information simultaneously. The COPD-LC data from the TCGA cohort were collected to conduct further analysis. Results A total of 51 COPD-LC patients and 88 non-COPD-LC patients were included in the study. Clinicopathological analysis showed that proportion of male gender, older age, and smoking patients were all substantially higher in COPD-LC group than in non-COPD-LC group (all P<0.01). Comparing the genomic data of the two groups in our cohort, COPD-LC had higher mutation frequency of LRP1B (43% vs 9%, P = 0.001), EPHA5 (24% vs 1%, P = 0.002), PRKDC (14% vs 1%, P = 0.039), PREX2 (14% vs 0%, P = 0.012), and FAT1 (14% vs 0%, P = 0.012), which had a relationship with improved tumor immunity. Immunotherapy biomarker of PD-L1 positive expression (62.5% vs 52.0%, P = 0.397) and tumor mutation burden (TMB, median TMB: 7.09 vs 2.94, P = 0.004) also were higher in COPD-LC. In addition, RNA data from TCGA further indicated tumor immunity increased in COPD-LC. Whereas, COPD-LC had lower frequency of EGFR mutation (19% vs 50%, P = 0.013) and EGFR mutant COPD-LC treated with EGFR-TKI had worse progression-free survival (PFS) (HR = 3.52, 95% CI: 1.27–9.80, P = 0.01). Conclusion In this retrospective study, we first explored molecular features of COPD-LC in a Chinese population. Although COPD-LC had lower EGFR mutant frequency and worse PFS with target treatment, high PD-L1 expression and TMB indicated these patients may benefit from immunotherapy.
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Affiliation(s)
- Hongxia Ma
- Pneumology Department, The Fourth Affiliated Hospital of Xinjiang Medical University, Urumqi, The Xinjiang Uygur Autonomous Region, People's Republic of China
| | - Qian Zhang
- Pneumology Department, The Fourth Affiliated Hospital of Xinjiang Medical University, Urumqi, The Xinjiang Uygur Autonomous Region, People's Republic of China
| | - Yanwen Zhao
- Pneumology Department, The Fourth Affiliated Hospital of Xinjiang Medical University, Urumqi, The Xinjiang Uygur Autonomous Region, People's Republic of China
| | - Yaohui Zhang
- Pneumology Department, The Fourth Affiliated Hospital of Xinjiang Medical University, Urumqi, The Xinjiang Uygur Autonomous Region, People's Republic of China
| | - Jingjing Zhang
- Pneumology Department, The Fourth Affiliated Hospital of Xinjiang Medical University, Urumqi, The Xinjiang Uygur Autonomous Region, People's Republic of China
| | - Guoqing Chen
- Pneumology Department, The Fourth Affiliated Hospital of Xinjiang Medical University, Urumqi, The Xinjiang Uygur Autonomous Region, People's Republic of China
| | - Yuan Tan
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China.,Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China.,The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China
| | - Qin Zhang
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China.,Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China.,The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China
| | - Qianqian Duan
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China.,Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China.,The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China
| | - Tingting Sun
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China.,Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China.,The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China
| | - Chuang Qi
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China.,Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China.,The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu Province, People's Republic of China
| | - Fengsen Li
- Pneumology Department, The Fourth Affiliated Hospital of Xinjiang Medical University, Urumqi, The Xinjiang Uygur Autonomous Region, People's Republic of China
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Gong XY, Chen HB, Zhang LQ, Chen DS, Li W, Chen DH, Xu J, Zhou H, Zhao LL, Song YJ, Xiao MZ, Deng WL, Qi C, Wang XR, Chen X. NOTCH1 mutation associates with impaired immune response and decreased relapse-free survival in patients with resected T1-2N0 laryngeal cancer. Front Immunol 2022; 13:920253. [PMID: 35911687 PMCID: PMC9336464 DOI: 10.3389/fimmu.2022.920253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Background Patients with early-stage laryngeal cancer, even stage T1-2N0, are at considerable risk of recurrence and death. The genetic and immunologic characteristics of recurrent laryngeal cancer remain unclear. Methods A total of 52 T1-2N0 laryngeal cancer patients were enrolled. Of these, 42 tissue samples were performed by targeted DNA sequencing, and 21 cases were performed by NanoString immuno-oncology targeted RNA sequencing to identify the distinct molecular bases and immunologic features associated with relapse in patients with early laryngeal cancer, respectively. Results To the best to our knowledge, we present for the first time an overview of the genomic mutation spectrum of early-stage laryngeal cancers. A total of 469 genomic alterations were detected in 211 distinct cancer-relevant genes, and the genes found to be mutated in more than five patients (>10%) included tumor protein p53 (TP53, 78.5%), FAT atypical cadherin 1 (FAT1, 26%), LDL receptor related protein 1B (LRP1B, 19%), cyclin dependent kinase inhibitor 2A (CDKN2A, 17%), tet methylcytosine dioxygenase 2 (TET2, 17%), notch receptor 1 (NOTCH1, 12%) and neuregulin 1 (NRG1, 12%). Recurrent laryngeal cancer demonstrated a higher tumor mutation burden (TMB), as well as higher LRP1B mutation and NOTCH1 mutation rates. Univariate and multivariate analyses revealed that high TMB (TMB-H) and NOTCH1 mutation are independent genetic factors that are significantly associated with shorter relapse-free survival (RFS). Simultaneously, the results of the transcriptome analysis presented recurrent tumors with NOTCH1 mutation displayed upregulation of the cell cycle pathway, along with decreased B cells score, T cells score, immune signature score and tumor-infiltrating lymphocytes (TILs) score. The Cancer Genome Atlas (TCGA)-laryngeal cancer dataset also revealed weakened immune response and impaired adhesion functions in NOTCH1-mutant patients. Conclusions Genomic instability and impaired immune response are key features of the immunosurveillance escape and recurrence of early laryngeal cancer after surgery. These findings revealed immunophenotypic attenuation in recurrent tumors and provided valuable information for improving the management of these high-risk patients. Due to the small number of patients in this study, these differences need to be further validated in a larger cohort.
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Affiliation(s)
- Xiao-yang Gong
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Hai-bin Chen
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Li-qing Zhang
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Dong-sheng Chen
- Jiangsu Simcere Diagnostics Co., Ltd, The State Key Laboratory of Translational Medicine and Innovative Drug Development, Nanjing, China
| | - Wang Li
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Dong-hui Chen
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Jin Xu
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Han Zhou
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Le-le Zhao
- Jiangsu Simcere Diagnostics Co., Ltd, The State Key Laboratory of Translational Medicine and Innovative Drug Development, Nanjing, China
| | - Yun-jie Song
- Jiangsu Simcere Diagnostics Co., Ltd, The State Key Laboratory of Translational Medicine and Innovative Drug Development, Nanjing, China
| | - Ming-zhe Xiao
- Jiangsu Simcere Diagnostics Co., Ltd, The State Key Laboratory of Translational Medicine and Innovative Drug Development, Nanjing, China
| | - Wang-long Deng
- Jiangsu Simcere Diagnostics Co., Ltd, The State Key Laboratory of Translational Medicine and Innovative Drug Development, Nanjing, China
| | - Chuang Qi
- Jiangsu Simcere Diagnostics Co., Ltd, The State Key Laboratory of Translational Medicine and Innovative Drug Development, Nanjing, China
| | - Xue-rong Wang
- Department of Pharmacology, Nanjing Medical University, Nanjing, China
- *Correspondence: Xi Chen, ; Xue-rong Wang,
| | - Xi Chen
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
- *Correspondence: Xi Chen, ; Xue-rong Wang,
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TP53 and LRP1B Co-Wild Predicts Improved Survival for Patients with LUSC Receiving Anti-PD-L1 Immunotherapy. Cancers (Basel) 2022; 14:cancers14143382. [PMID: 35884443 PMCID: PMC9320428 DOI: 10.3390/cancers14143382] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/02/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
Immunotherapy brought long-term benefits for partial patients with lung squamous cell carcinoma (LUSC). The predictor of anti-PD-L1 therapy was controversial and limited in LUSC. We aimed to explore novel biomarker for LUSC immunotherapy and the potential mechanism. Five hundred and twenty-five Chinese patients (Geneplus cohort) with LUSC underwent targeted sequencing and were involved to explore the genomic profiling. TP53 and LRP1B were the most frequently recurrent genes and correlated to higher tumor mutational burden (TMB). We observed that LUSC patients with TP53 and LRP1B co-wild (co-wild type) were associated with better survival of anti-PD-L1 therapy compared with TP53 mutant or LRP1B mutant (mutant type) in POPAR/OAK cohort. Copy-number variation (CNV) and whole genome doubling (WGD) data from TCGA LUSC cohort were obtained to assess the CNV events. There were fewer CNV alterations and lower chromosome instability in patients with TP53/LRP1B co-wild compared with those with TP53/LRP1B mutant. RNA expression data from the TCGA LUSC cohort were collected to explore the differences in RNA expression and tumor immune microenvironment (TIME) between mutant and co-wild groups. The TP53/LRP1B co-wild type had a significantly increased proportion of multiple tumor-infiltrating lymphocytes (TILs), including activated CD8 T cell, activated dendritic cell (DC), and effector memory CD8 T cell. Immune-related gene sets including checkpoint, chemokine, immunostimulatory, MHC and receptors were enriched in the co-wild type. In conclusion, TP53/LRP1B co-wild LUSC conferred an elevated response rate in anti-PD-L1 therapy and improved survival, which was associated with a chromosome-stable phenotype and an activated immune microenvironment.
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Orexin A Suppresses the Expression of Exosomal PD-L1 in Colon Cancer and Promotes T Cell Activity by Inhibiting JAK2/STAT3 Signaling Pathway. Dig Dis Sci 2022; 67:2173-2181. [PMID: 34097168 DOI: 10.1007/s10620-021-07077-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/26/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Colon cancer, ranked third in cancer related mortality, is the most common malignant cancer of digestive tract. Though immune checkpoint inhibitors show promising efficacy in colon cancer, a rather high unresponsive rate and recurrence rate requires further elucidation of the underlying regulatory mechanism of cancer-related immunity. AIMS To study the regulatory function of Orexin A in the expression of exosomal PD-L1 and T cell activity. METHODS Orthotopic colon cancer transplantation mice model were established to study the cancer growth and immune infiltration between Orexin A treated group and untreated group. In vitro studies using mouse CT-26 and human HCT-116 colon cancer cell model studied the effect of Orexin A on cellular and exosomal PD-L1 expression. Co-culturing Jurkat cells with exosomes delivered by cancer cells treated with Orexin A, PD-L1 knockdown and PBS studied different effects on T cell. Comparing Orexin A with WP1066, a JAK2/STAT3 inhibitor verified the mechanism of these changes. RESULTS The growth rate of orthotopic transplanted colon cancer was slower in Orexin A treated group, with lower PD-L1 expression and higher immune infiltration. Orexin A could inhibit cellular and exosomal PD-L1 expression. The decreased expression of PD-L1 in exosomes could promote the activity of Jurkat cells secreting higher level of IFN-γ and IL-2. Orexin A showed a similar effect like WP1066 which proved JAK2/STAT3 signaling pathway was its downstream signaling pathway. CONCLUSIONS Orexin A could suppress the expression of exosomal PD-L1 in colon cancer cells and promote T cells activity by inhibiting JAK2/STAT3 signaling pathway.
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Cui Y, Jiang N. Identification of a seven-gene signature predicting clinical outcome of liver cancer based on tumor mutational burden. Hum Cell 2022; 35:1192-1206. [PMID: 35622212 DOI: 10.1007/s13577-022-00708-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/20/2022] [Indexed: 12/13/2022]
Abstract
The total number of somatic mutations may affect the prognosis of cancer, so we applied bioinformatics methods to investigate the association between the TMB (tumor mutational burden)-related differentially expressed genes (DEGs) and the prognosis of hepatocellular carcinoma (HCC). We calculated the TMB value of the patients with HCC in TCGA database and identified the differentially expressed genes between the high-TMB and low-TMB patients. We performed functional enrichment analysis and LASSO Cox regression analysis of the DEGs, and seven genes were screened to establish a risk score model. A nomogram based on the risk scores was drawn to assess the predictive outcomes compared to the actual outcomes. The expression level of the seven genes was verified in cancer cell lines. Moreover, we explored the difference in immune cells infiltration and immune checkpoints between the high-risk and low-risk groups. The results showed that the DEGs between the high-TMB and low-TMB patients were enriched in extracellular matrix organization. A seven-gene risk score model (PAGE1, CHGA, OGN, MMP7, TRIM55, MAGEA6, and MAGEA12) was established for predicting HCC prognosis. Patients with lower risk scores had longer survival time and lower mortality rate. The nomogram based on risk scores and TNM staging showed good performance and reliability in predicting the clinical outcomes. Significant differences in cell infiltration and checkpoints were found between the high-risk and low-risk groups. Our study demonstrated a seven-gene signature and a nomogram based on the risk score model to predict the prognosis of HCC. Some of the newly identified DEGs may be potential biomarkers or therapeutic targets.
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Affiliation(s)
- Yunlong Cui
- Department of Hepatobiliary Surgery, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, People's Republic of China
| | - Ning Jiang
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, Tianjin University of Sport, 301617, Tianjin, People's Republic of China.
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Liu J, Zhao Z, Wei S, Li B, Zhao Z. Genomic features of Chinese small cell lung cancer. BMC Med Genomics 2022; 15:117. [PMID: 35596192 PMCID: PMC9123817 DOI: 10.1186/s12920-022-01255-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/22/2022] [Indexed: 11/12/2022] Open
Abstract
Background Small cell lung cancer (SCLC) is an aggressive disease with poor survival. Although molecular and clinical characteristics have been established for SCLC in western patients, limited investigation has been performed for Chinese SCLC patients. Objective In this study, we investigated the genomic features of Chinese SCLC patients. Methods A total of 75 SCLC patients were enrolled. Genomic alterations in 618 selected genes were analyzed by targeted next-generation sequencing. Results Here, we showed that TP53 (77.30%) and RB1 (30.70%) were the most prevalent genes alterations, followed by KMT2D, ALK, LRP1B, EGFR, NOTCH3, AR, CREBBP, ROS1, and BRCA2. And the most common genetic alterations were enriched in the cell cycle signaling pathway (84.00%) of Chinese SCLC patients. DNA damage repair (DDR) pathway analysis showed that the most frequently enriched DDR pathways were fanconi anaemia (FA, 29.41%) and homology recombination (HR, 21.57%). Notably, 9.33% SCLC patients in our cohort had pathogenic or likely pathogenic germline gene variants. Compared with the U Cologne cohort, a higher prevalence in EGFR, AR, BRCA2, TSC1, ATXN3, MET, MSH2, ERBB3 and FOXA1 were found in our cohort; while compared to the data from the Johns Hopkins cohort, a higher mutated frequency in TP53, KMT2D, ALK, and EGFR were found in our cohort. Moreover, a significant association was found between high tumor mutation burden (TMB) and mutations involved in TP53, CREBBP, EPHA3, KMT2D, ALK and RB1. Approximately 33.33% of patients with SCLC harbored at least one actionable alteration annotated by OncoKB, of which one patient had alterations of level 1; seventeen patients had level 3; fifteen patients possessed level 4. Conclusion Our data might provide an insightful meaning in targeted therapy for Chinese SCLC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01255-3.
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Affiliation(s)
- Jun Liu
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of South China University of Technology, Guangzhou, 510000, China
| | - Zhuxiang Zhao
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of South China University of Technology, Guangzhou, 510000, China
| | - Shuquan Wei
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of South China University of Technology, Guangzhou, 510000, China
| | - Binkai Li
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of South China University of Technology, Guangzhou, 510000, China
| | - Ziwen Zhao
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of South China University of Technology, Guangzhou, 510000, China.
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