1
|
Rosati D, Palmieri M, Brunelli G, Morrione A, Iannelli F, Frullanti E, Giordano A. Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review. Comput Struct Biotechnol J 2024; 23:1154-1168. [PMID: 38510977 PMCID: PMC10951429 DOI: 10.1016/j.csbj.2024.02.018] [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: 10/23/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
In recent years, the role of bioinformatics and computational biology together with omics techniques and transcriptomics has gained tremendous importance in biomedicine and healthcare, particularly for the identification of biomarkers for precision medicine and drug discovery. Differential gene expression (DGE) analysis is one of the most used techniques for RNA-sequencing (RNA-seq) data analysis. This tool, which is typically used in various RNA-seq data processing applications, allows the identification of differentially expressed genes across two or more sample sets. Functional enrichment analyses can then be performed to annotate and contextualize the resulting gene lists. These studies provide valuable information about disease-causing biological processes and can help in identifying molecular targets for novel therapies. This review focuses on differential gene expression (DGE) analysis pipelines and bioinformatic techniques commonly used to identify specific biomarkers and discuss the advantages and disadvantages of these techniques.
Collapse
Affiliation(s)
- Diletta Rosati
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Cancer Genomics & Systems Biology Lab, Dept. of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Maria Palmieri
- Cancer Genomics & Systems Biology Lab, Dept. of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Giulia Brunelli
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Andrea Morrione
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Francesco Iannelli
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisa Frullanti
- Cancer Genomics & Systems Biology Lab, Dept. of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Antonio Giordano
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| |
Collapse
|
2
|
Wu J, Sun W, Zhang Y, Mao L, Ding T, Huang X, Lin D. Impact of platinum-based chemotherapy on the tumor mutational burden and immune microenvironment in non-small cell lung cancer with postoperative recurrence. Clin Transl Oncol 2024; 26:1738-1747. [PMID: 38421562 DOI: 10.1007/s12094-024-03397-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
PURPOSE To investigate the impact of platinum-based adjuvant chemotherapy on the immunotherapeutic biomarkers of postoperative recurrent tumors in non-small cell lung cancer (NSCLC). METHODS This study involved twenty-two cases of NSCLC, all of which underwent postoperative platinum-based chemotherapy, with matched surgical samples obtained from both their primary tumors (PTs) and recurrent tumors (RTs). Multiplex immunofluorescence was performed to assess the tumor proportion score (TPS) and immune cells (IC) on whole sections. Whole exon sequencing (WES) was conducted to investigate the tumor mutational burden (TMB) and tumor neoantigen burden (TNB). RESULTS Compared to paired PTs, RTs exhibited higher PD-L1 expression, along with a slightly elevated density of intratumoral PD-L1+ cells (p = 0.082) and an increased tumor proportion score (mean TPS: 40.51% vs. 28.56%, p = 0.046). Regarding IC infiltration, RTs generally demonstrated significantly lower CD8+ cytotoxic T lymphocyte (CTL) density (p = 0.011) and lower CD68+ macrophage density (p = 0.005), with a loss of tertiary lymphoid structure (TLS). The comparison between RTs and PTs revealed no significant differences in TMB (p = 0.795), whereas the count of TNB in RTs was notably increased compared to PTs (p = 0.033). Prognosis analysis indicated that a higher density of CD8+ CTLs in RTs was positively correlated with improved overall survival (OS). CONCLUSIONS In NSCLC patients with a history of postoperative platinum-based chemotherapy, the RTs demonstrated a trend towards increased PD-L1 expression and TMB/TNB, but a state of immunosuppression characterized by decreased ICs and loss of TLS, which may potentially impact the therapeutic benefits of immunotherapy.
Collapse
Affiliation(s)
- Jianghua Wu
- Department of Pathology, Peking University Cancer Hospital & Institute, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), No. 52, Fu-Cheng Road, Beijing, 100142, China
| | - Wei Sun
- Department of Pathology, Peking University Cancer Hospital & Institute, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), No. 52, Fu-Cheng Road, Beijing, 100142, China
| | - Yanhui Zhang
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center of Cancer, Tianjin, China
| | - Luning Mao
- Department of Pathology, Peking University Cancer Hospital & Institute, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), No. 52, Fu-Cheng Road, Beijing, 100142, China
| | - Tingting Ding
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center of Cancer, Tianjin, China
| | - Xiaozheng Huang
- Department of Pathology, Peking University Cancer Hospital & Institute, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), No. 52, Fu-Cheng Road, Beijing, 100142, China
| | - Dongmei Lin
- Department of Pathology, Peking University Cancer Hospital & Institute, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), No. 52, Fu-Cheng Road, Beijing, 100142, China.
| |
Collapse
|
3
|
Shan J, Liu Z, Chen S, Du C, Li B, Ruan L, Kong M, Wang L, Du M, Shi S, Qiao G, Tian T, Tu Z. Optimizing perioperative treatment for potentially resectable stage III squamous cell lung carcinoma: promising results of a condensed four-cycle regimen with tislelizumaband chemotherapy. BMC Med 2024; 22:234. [PMID: 38853265 PMCID: PMC11163755 DOI: 10.1186/s12916-024-03462-4] [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: 07/18/2023] [Accepted: 05/30/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND The standard care for resectable non-small cell lung cancer (NSCLC) involves perioperative therapy combining chemotherapy and immune checkpoint inhibitors, typically lasting 6 to 12 months. However, the optimal treatment strategies for potentially resectable squamous cell lung carcinoma (SCC) remain unclear. This Phase 2 trial aimed to assess the efficacy and safety of a condensed four-cycle perioperative treatment regimen with tislelizumab combined with chemotherapy in patients with potentially resectable stage III SCC. METHODS Patients with potentially resectable stage IIIA-IIIB (N2) SCC received intravenous tislelizumab, albumin-bound paclitaxel, and carboplatin for up to four cycles. The primary endpoints were major pathologic response (MPR) and incidence of treatment-related adverse events. Safety and potential biomarkers for efficacy prediction were also assessed. RESULTS Among 35 enrolled patients, 32 underwent surgery with R0 resection achieved in all cases. MPR was achieved in 24 patients and pathological complete response (pCR) in 14 patients. Radiographic objective response was observed in 31 patients. The 12-month and 24-month event-free survival rate was 85.7 and 61.0%, respectively. Four patients experienced grade 3 or 4 adverse events. Tumor tissue based next-generation sequencing revealed the potential associations between several biomarkers and pathological response, including tumor neoantigen burden score, 18-gene expression profile score, CD8 + T cells, M1/M2 macrophages ratio and interferon-gamma expression level. Besides, circulating tumor DNA (ctDNA) dynamics and concentration were also associated with pathological response and the presence of ctDNA at postoperative month 1 was a strong predictor for disease relapse. Furthermore, metagenomic sequencing in bronchoalveolar lavage fluid demonstrated Streptococcus was the most abundant genus in the pCR group. CONCLUSIONS A condensed four-cycle perioperative treatment regimen of tislelizumab combined with chemotherapy demonstrated promising efficacy and manageable toxicities in potentially resectable stage III SCC. Specific biomarkers showed potential for predicting treatment efficacy and the mechanism of superior antitumor response of pCR patients was preliminarily and indirectly explored. TRIAL REGISTRATION ClinicalTrials.gov, NCT05024266. Registered August 27, 2021.
Collapse
Affiliation(s)
- Jianzhen Shan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Shangcheng District, China.
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Zhen Liu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Shangcheng District, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Songan Chen
- Department of Medicine, Burning Rock Biotech, Guangzhou, China
| | - Chengli Du
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Shangcheng District, China
| | - Bing Li
- Department of Medicine, Burning Rock Biotech, Guangzhou, China
| | - Lingxiang Ruan
- Department of Radiology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mei Kong
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lingjie Wang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Shangcheng District, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Miaoyan Du
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Shangcheng District, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Shuo Shi
- Data Science Department, Burning Rock Biotech, Guangzhou, China
| | - Guoliang Qiao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Shangcheng District, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Tian Tian
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Shangcheng District, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Zhengliang Tu
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No. 79 Qingchun Road, Hangzhou, Shangcheng District, China.
| |
Collapse
|
4
|
Bajinka O, Ouedraogo SY, Golubnitschaja O, Li N, Zhan X. Energy metabolism as the hub of advanced non-small cell lung cancer management: a comprehensive view in the framework of predictive, preventive, and personalized medicine. EPMA J 2024; 15:289-319. [PMID: 38841622 PMCID: PMC11147999 DOI: 10.1007/s13167-024-00357-5] [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: 03/08/2024] [Accepted: 03/20/2024] [Indexed: 06/07/2024]
Abstract
Energy metabolism is a hub of governing all processes at cellular and organismal levels such as, on one hand, reparable vs. irreparable cell damage, cell fate (proliferation, survival, apoptosis, malignant transformation etc.), and, on the other hand, carcinogenesis, tumor development, progression and metastazing versus anti-cancer protection and cure. The orchestrator is the mitochondria who produce, store and invest energy, conduct intracellular and systemically relevant signals decisive for internal and environmental stress adaptation, and coordinate corresponding processes at cellular and organismal levels. Consequently, the quality of mitochondrial health and homeostasis is a reliable target for health risk assessment at the stage of reversible damage to the health followed by cost-effective personalized protection against health-to-disease transition as well as for targeted protection against the disease progression (secondary care of cancer patients against growing primary tumors and metastatic disease). The energy reprogramming of non-small cell lung cancer (NSCLC) attracts particular attention as clinically relevant and instrumental for the paradigm change from reactive medical services to predictive, preventive and personalized medicine (3PM). This article provides a detailed overview towards mechanisms and biological pathways involving metabolic reprogramming (MR) with respect to inhibiting the synthesis of biomolecules and blocking common NSCLC metabolic pathways as anti-NSCLC therapeutic strategies. For instance, mitophagy recycles macromolecules to yield mitochondrial substrates for energy homeostasis and nucleotide synthesis. Histone modification and DNA methylation can predict the onset of diseases, and plasma C7 analysis is an efficient medical service potentially resulting in an optimized healthcare economy in corresponding areas. The MEMP scoring provides the guidance for immunotherapy, prognostic assessment, and anti-cancer drug development. Metabolite sensing mechanisms of nutrients and their derivatives are potential MR-related therapy in NSCLC. Moreover, miR-495-3p reprogramming of sphingolipid rheostat by targeting Sphk1, 22/FOXM1 axis regulation, and A2 receptor antagonist are highly promising therapy strategies. TFEB as a biomarker in predicting immune checkpoint blockade and redox-related lncRNA prognostic signature (redox-LPS) are considered reliable predictive approaches. Finally, exemplified in this article metabolic phenotyping is instrumental for innovative population screening, health risk assessment, predictive multi-level diagnostics, targeted prevention, and treatment algorithms tailored to personalized patient profiles-all are essential pillars in the paradigm change from reactive medical services to 3PM approach in overall management of lung cancers. This article highlights the 3PM relevant innovation focused on energy metabolism as the hub to advance NSCLC management benefiting vulnerable subpopulations, affected patients, and healthcare at large. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-024-00357-5.
Collapse
Affiliation(s)
- Ousman Bajinka
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Serge Yannick Ouedraogo
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Olga Golubnitschaja
- Predictive, Preventive and Personalised (3P) Medicine, University Hospital Bonn, Venusberg Campus 1, Rheinische Friedrich-Wilhelms-University of Bonn, 53127 Bonn, Germany
| | - Na Li
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| |
Collapse
|
5
|
Kaira K, Ichiki Y, Imai H, Kawasaki T, Hashimoto K, Kuji I, Kagamu H. Potential predictors of the pathologic response after neoadjuvant chemoimmunotherapy in resectable non-small cell lung cancer: a narrative review. Transl Lung Cancer Res 2024; 13:1137-1149. [PMID: 38854945 PMCID: PMC11157365 DOI: 10.21037/tlcr-24-142] [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: 02/10/2024] [Accepted: 03/27/2024] [Indexed: 06/11/2024]
Abstract
Background and Objective Neoadjuvant chemoimmunotherapy (NACI) is the standard of care for patients with resectable non-small cell lung cancer (NSCLC). Although the pathological complete response (pCR) after NACI reportedly exceeds 20%, an optimal predictor of pCR is yet to be established. This review aims to examine the possible predictors of pCR after NACI. Methods We identified research article published between 2018 and 2022 in English by the PubMed database. Fifty research studies were considered as relevant article, and were examined to edit information for this narrative review. Key Content and Findings Recently, several studies have explored potential biomarkers for the pathological response after NACI. For example, 18F-fluorodeoxyglucose positron emission tomography (18F-FDG-PET) imaging, tumor microenvironment (TME), genetic alternation such as circulating tumor DNA (ctDNA), and clinical markers such as neutrophil-to-lymphocyte ratio (NLR) and smoking signature were assessed in patients with resectable NSCLC to predict the pathological response after NACI. Based on the PET response criteria, the complete metabolic response (CMR) achieved a positive predictive value (PPV) of 71.4% for predicting pCR, and the decreasing rate of post-therapy maximum standardized uptake value (SUVmax) after NACI substantially correlated with the major pathological response (MPR). TME, as a significant marker for MPR in tumor specimens, was identified as an increase in CD8+ T cells and decrease in CD3+ T cells or Foxp3 T cells. Considering blood samples, TME comprised an increase in CD4+PD-1+ cells or natural killer cells and a decrease in CD3+CD56+CTLA4+ cells, total T cells, Th cells, myeloid-derived suppressor cells (MDSCs), or regulatory T cells. Although low pretreatment levels of ctDNA and undetectable ctDNA levels after NACI were markedly associated with survival, the relationship between ctDNA levels and pCR remains elusive. Moreover, the patients with a high baseline NLR had a low incidence of pCR. Heavy smoking (>40 pack-years) was favorable for predicting pathological response. Conclusions A reduced rate of 18F-FDG uptake post-NACI and TME-related surface markers on lymphocytes could be optimal predictors for pCR. However, the role of these pCR predictors for NACI remains poorly validated, warranting further investigations. This review focuses on predictive biomarkers for pathological response after NACI in patients with resectable NSCLC.
Collapse
Affiliation(s)
- Kyoichi Kaira
- Department of Respiratory Medicine, International Medical Center, Saitama Medical University, Hidaka, Saitama, Japan
| | - Yoshinobu Ichiki
- Department of General Thoracic Surgery, International Medical Center, Saitama Medical University, Hidaka, Saitama, Japan
| | - Hisao Imai
- Department of Respiratory Medicine, International Medical Center, Saitama Medical University, Hidaka, Saitama, Japan
| | - Tomonori Kawasaki
- Department of Diagnostic Pathology, International Medical Center, Saitama Medical University, Hidaka, Saitama, Japan
| | - Kosuke Hashimoto
- Department of Respiratory Medicine, International Medical Center, Saitama Medical University, Hidaka, Saitama, Japan
| | - Ichiei Kuji
- Department of Nuclear Medicine, International Medical Center, Saitama Medical University, Hidaka, Saitama, Japan
| | - Hiroshi Kagamu
- Department of Respiratory Medicine, International Medical Center, Saitama Medical University, Hidaka, Saitama, Japan
| |
Collapse
|
6
|
D'Aiello A, Stiles B, Ohri N, Levy B, Cohen P, Halmos B. Perioperative Immunotherapy for Non-Small Cell Lung Cancer: Practical Application of Emerging Data and New Challenges. Clin Lung Cancer 2024; 25:197-214. [PMID: 38462413 DOI: 10.1016/j.cllc.2024.02.004] [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: 10/02/2023] [Revised: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 03/12/2024]
Abstract
Immune checkpoint inhibition, with or without chemotherapy, is an established standard of care for metastatic non-small cell lung cancer (NSCLC). For locally advanced NSCLC treated with chemoradiotherapy, consolidation immunotherapy has dramatically improved outcomes. Recently, immunotherapy has also been established as a valuable component of treatment for resectable NSCLC with pembrolizumab, atezolizumab, and nivolumab all approved for use in this setting. As more results read out from ongoing perioperative clinical trials, navigating treatment options will likely become increasingly complex for the practicing oncologist. In this paper, we distill key outcomes from major perioperative trials and highlight current knowledge gaps. In addition, we provide practical considerations for incorporating perioperative immunotherapy into the clinical management of operable NSCLC.
Collapse
Affiliation(s)
- Angelica D'Aiello
- Department of Oncology, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY.
| | - Brendon Stiles
- Division of Thoracic Surgery and Surgical Oncology, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY
| | - Nitin Ohri
- Department of Radiation Oncology, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY
| | - Benjamin Levy
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Perry Cohen
- Division of Anatomic and Clinical Pathology, Department of Pathology, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY
| | - Balazs Halmos
- Department of Oncology, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY.
| |
Collapse
|
7
|
Sun X, Teng X, Liu C, Tian W, Cheng J, Hao S, Jin Y, Hong L, Zheng Y, Dai X, Wu L, Liu L, Teng X, Shi Y, Zhao P, Fang W, Shi Y, Bao X. A Pathologically Friendly Strategy for Determining the Organ-specific Spatial Tumor Microenvironment Topology in Lung Adenocarcinoma Through the Integration of snRandom-seq and Imaging Mass Cytometry. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308892. [PMID: 38682485 DOI: 10.1002/advs.202308892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 03/24/2024] [Indexed: 05/01/2024]
Abstract
Heterogeneous organ-specific responses to immunotherapy exist in lung cancer. Dissecting tumor microenvironment (TME) can provide new insights into the mechanisms of divergent responses, the process of which remains poor, partly due to the challenges associated with single-cell profiling using formalin-fixed paraffin-embedded (FFPE) materials. In this study, single-cell nuclei RNA sequencing and imaging mass cytometry (IMC) are used to dissect organ-specific cellular and spatial TME based on FFPE samples from paired primary lung adenocarcinoma (LUAD) and metastases. Single-cell analyses of 84 294 cells from sequencing and 250 600 cells from IMC reveal divergent organ-specific immune niches. For sites of LUAD responding well to immunotherapy, including primary LUAD and adrenal gland metastases, a significant enrichment of B, plasma, and T cells is detected. Spatially resolved maps reveal cellular neighborhoods recapitulating functional units of the tumor ecosystem and the spatial proximity of B and CD4+ T cells at immunogenic sites. Various organ-specific densities of tertiary lymphoid structures are observed. Immunosuppressive sites, including brain and liver metastases, are deposited with collagen I, and T cells at these sites highly express TIM-3. This study originally deciphers the single-cell landscape of the organ-specific TME at both cellular and spatial levels for LUAD, indicating the necessity for organ-specific treatment approaches.
Collapse
Affiliation(s)
- Xuqi Sun
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Xiao Teng
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Chuan Liu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Weihong Tian
- Changzhou Third People's Hospital, Changzhou Medical Center, Nanjing Medical University, 140 Hanzhong Rd, Gulou, Nanjing, Jiangsu, 210029, China
| | - Jinlin Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Shuqiang Hao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yuzhi Jin
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Libing Hong
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yongqiang Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Xiaomeng Dai
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Linying Wu
- Department of Respiratory Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Lulu Liu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Xiaodong Teng
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yi Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China
| | - Peng Zhao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Weijia Fang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yu Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Xuanwen Bao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| |
Collapse
|
8
|
Wu S, Sheng Q, Liu P, Jiao Z, Lv J, Qiao R, Xie D, Wang Z, Ge J, Li P, Wei T, Lei J, Fan J, Wang L. M1 macrophage-related gene model for NSCLC immunotherapy response prediction. Acta Biochim Biophys Sin (Shanghai) 2024; 56:379-392. [PMID: 38379417 PMCID: PMC10984861 DOI: 10.3724/abbs.2023262] [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: 08/15/2023] [Accepted: 10/09/2023] [Indexed: 02/22/2024] Open
Abstract
Patients diagnosed with non-small cell lung cancer (NSCLC) have a limited lifespan and exhibit poor immunotherapy outcomes. M1 macrophages have been found to be essential for antitumor immunity. This study aims to develop an immunotherapy response evaluation model for NSCLC patients based on transcription. RNA sequencing profiles of 254 advanced-stage NSCLC patients treated with immunotherapy are downloaded from the POPLAR and OAK projects. Immune cell infiltration in NSCLC patients is examined, and thereafter, different coexpressed genes are identified. Next, the impact of M1 macrophage-related genes on the prognosis of NSCLC patients is investigated. Six M1 macrophage coexpressed genes, namely, NKX2-1, CD8A , SFTA3, IL2RB, IDO1, and CXCL9, exhibit a strong association with the prognosis of NSCLC and serve as effective predictors for immunotherapy response. A response model is constructed using a Cox regression model and Lasso Cox regression analysis. The M1 genes are validated in our TD-FOREKNOW NSCLC clinical trial by RT-qPCR. The response model shows excellent immunotherapy response prediction and prognosis evaluation value in advanced-stage NSCLC. This model can effectively predict advanced NSCLC prognosis and aid in identifying patients who could benefit from customized immunotherapy as well as sensitive drugs.
Collapse
Affiliation(s)
- Sifan Wu
- State Key Laboratory of Cancer BiologyDepartment of Medical Genetics and Developmental BiologyFourth Military Medical UniversityXi’an710032China
| | - Qiqi Sheng
- State Key Laboratory of Cancer BiologyDepartment of Medical Genetics and Developmental BiologyFourth Military Medical UniversityXi’an710032China
- Department of Thoracic Surgerythe Second Affiliated Hospital of Air Force Medical UniversityXi’an710038China
| | - Pengjun Liu
- State Key Laboratory of Cancer BiologyDepartment of Medical Genetics and Developmental BiologyFourth Military Medical UniversityXi’an710032China
| | - Zhe Jiao
- State Key Laboratory of Cancer BiologyDepartment of Medical Genetics and Developmental BiologyFourth Military Medical UniversityXi’an710032China
- Department of Thoracic Surgerythe Second Affiliated Hospital of Air Force Medical UniversityXi’an710038China
| | - Jinru Lv
- State Key Laboratory of Cancer BiologyDepartment of Medical Genetics and Developmental BiologyFourth Military Medical UniversityXi’an710032China
- Department of Thoracic Surgerythe Second Affiliated Hospital of Air Force Medical UniversityXi’an710038China
| | - Rong Qiao
- State Key Laboratory of Cancer BiologyDepartment of Medical Genetics and Developmental BiologyFourth Military Medical UniversityXi’an710032China
| | - Dongkun Xie
- State Key Laboratory of Cancer BiologyDepartment of Medical Genetics and Developmental BiologyFourth Military Medical UniversityXi’an710032China
| | - Zanhan Wang
- State Key Laboratory of Cancer BiologyDepartment of Medical Genetics and Developmental BiologyFourth Military Medical UniversityXi’an710032China
| | - Jiamei Ge
- State Key Laboratory of Cancer BiologyDepartment of Medical Genetics and Developmental BiologyFourth Military Medical UniversityXi’an710032China
| | - Penghui Li
- State Key Laboratory of Cancer BiologyDepartment of Medical Genetics and Developmental BiologyFourth Military Medical UniversityXi’an710032China
| | - Tiaoxia Wei
- State Key Laboratory of Cancer BiologyDepartment of Medical Genetics and Developmental BiologyFourth Military Medical UniversityXi’an710032China
| | - Jie Lei
- Department of Thoracic Surgerythe Second Affiliated Hospital of Air Force Medical UniversityXi’an710038China
| | - Jieyi Fan
- Department of Aerospace MedicineFourth Military Medical UniversityXi’an710032China
| | - Liang Wang
- State Key Laboratory of Cancer BiologyDepartment of Medical Genetics and Developmental BiologyFourth Military Medical UniversityXi’an710032China
| |
Collapse
|
9
|
Yu H, Bian Q, Wang X, Wang X, Lai L, Wu Z, Zhao Z, Ban B. Bone marrow stromal cell antigen 2: Tumor biology, signaling pathway and therapeutic targeting (Review). Oncol Rep 2024; 51:45. [PMID: 38240088 PMCID: PMC10828922 DOI: 10.3892/or.2024.8704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
Bone marrow stromal cell antigen 2 (BST2) is a type II transmembrane protein that serves critical roles in antiretroviral defense in the innate immune response. In addition, it has been suggested that BST2 is highly expressed in various types of human cancer and high BST2 expression is related to different clinicopathological parameters in cancer. The molecular mechanism underlying BST2 as a potential tumor biomarker in human solid tumors has been reported on; however, to the best of our knowledge, there has been no review published on the molecular mechanism of BST2 in human solid tumors. The present review focuses on human BST2 expression, structure and functions; the molecular mechanisms of BST2 in breast cancer, hepatocellular carcinoma, gastrointestinal tumor and other solid tumors; the therapeutic potential of BST2; and the possibility of BST2 as a potential marker. BST2 is involved in cell membrane integrity and lipid raft formation, which can activate epidermal growth factor receptor signaling pathways, providing a potential mechanistic link between BST2 and tumorigenesis. Notably, BST2 may be considered a universal tumor biomarker and a potential therapeutical target.
Collapse
Affiliation(s)
- Honglian Yu
- Department of Endocrinology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272029, P.R. China
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
- Collaborative Innovation Center, Jining Medical University, Jining, Shandong 272067, P.R. China
| | - Qiang Bian
- Collaborative Innovation Center, Jining Medical University, Jining, Shandong 272067, P.R. China
- Department of Pathophysiology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Xin Wang
- Department of Urology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Xinzhe Wang
- Department of Urology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Luhao Lai
- Collaborative Innovation Center, Jining Medical University, Jining, Shandong 272067, P.R. China
| | - Zhichun Wu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
| | - Zhankui Zhao
- Department of Urology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Bo Ban
- Department of Endocrinology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272029, P.R. China
| |
Collapse
|
10
|
Tian C, Yu Y, Wang Y, Yang L, Tang Y, Yu C, Feng G, Zheng D, Wang X. Neoadjuvant Immune Checkpoint Inhibitors in hepatocellular carcinoma: a meta-analysis and systematic review. Front Immunol 2024; 15:1352873. [PMID: 38440727 PMCID: PMC10909934 DOI: 10.3389/fimmu.2024.1352873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 01/29/2024] [Indexed: 03/06/2024] Open
Abstract
Background Neoadjuvant immunotherapy has demonstrated beneficial outcomes in various cancer types; however, standardized protocols for neoadjuvant immunotherapy in hepatocellular carcinoma (HCC) are currently lacking. This systematic review and meta-analysis aims to investigate the reliability of neoadjuvant immunotherapy's efficacy and safety in the context of HCC. Methods A systematic search was conducted across PubMed (MEDLINE), EMBASE, the Web of Science, the Cochrane Library, and conference proceedings to identify clinical trials involving resectable HCC and neoadjuvant immunotherapy. Single-arm meta-analyses were employed to compute odds ratios and 95% confidence intervals (CIs). Heterogeneity analysis, data quality assessment, and subgroup analyses based on the type of immunotherapy drugs and combination therapies were performed. This meta-analysis is registered in PROSPERO (identifier CRD42023474276). Results This meta-analysis included 255 patients from 11 studies. Among resectable HCC patients, neoadjuvant immunotherapy exhibited an overall major pathological response (MPR) rate of 0.47 (95% CI 0.31-0.70) and a pathological complete response (pCR) rate of 0.22 (95% CI 0.14-0.36). The overall objective response rate (ORR) was 0.37 (95% CI 0.20-0.69), with a grade 3-4 treatment-related adverse event (TRAE) incidence rate of 0.35 (95% CI 0.24-0.51). Furthermore, the combined surgical resection rate was 3.08 (95% CI 1.66-5.72). Subgroup analysis shows no significant differences in the efficacy and safety of different single-agent immunotherapies; the efficacy of dual ICIs (Immune Checkpoint Inhibitors) combination therapy is superior to targeted combined immunotherapy and monotherapy, while the reverse is observed in terms of safety. Discussion Neoadjuvant immunotherapy presents beneficial outcomes in the treatment of resectable HCC. However, large-scale, high-quality experiments are warranted in the future to provide robust data support.
Collapse
Affiliation(s)
- Chunhong Tian
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yifan Yu
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuqing Wang
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lunwei Yang
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ying Tang
- Institute of Tumor, Guangzhou University of Chinese Medicine, Guangzhou, China
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chengyang Yu
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Gaofei Feng
- Department of Oncology, Shenzhen Hospital, Beijing University of Chinese Medicine, Shenzhen, China
| | - Dayong Zheng
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatopancreatobiliary, Cancer Center, Southern Medical University, Guangzhou, China
- Department of Oncology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiongwen Wang
- Beibei District Traditional Chinese Medicine Hospital (Chongqing Hospital, The First Affiliated Hospital of Guangzhou University of Chinese Medicine), Chongqing, China
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| |
Collapse
|
11
|
Gu Y, Chen Q, Yin H, Zeng M, Gao S, Wang X. Cancer-associated fibroblasts in neoadjuvant setting for solid cancers. Crit Rev Oncol Hematol 2024; 193:104226. [PMID: 38056580 DOI: 10.1016/j.critrevonc.2023.104226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/15/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
Therapeutic approaches for cancer have become increasingly diverse in recent times. A comprehensive understanding of the tumor microenvironment (TME) holds great potential for enhancing the precision of tumor therapies. Neoadjuvant therapy offers the possibility of alleviating patient symptoms and improving overall quality of life. Additionally, it may facilitate the reduction of inoperable tumors and prevent potential preoperative micrometastases. Within the TME, cancer-associated fibroblasts (CAFs) play a prominent role as they generate various elements that contribute to tumor progression. Particularly, extracellular matrix (ECM) produced by CAFs prevents immune cell infiltration into the TME, hampers drug penetration, and diminishes therapeutic efficacy. Therefore, this review provides a summary of the heterogeneity and interactions of CAFs within the TME, with a specific focus on the influence of neoadjuvant therapy on the microenvironment, particularly CAFs. Finally, we propose several potential and promising therapeutic strategies targeting CAFs, which may efficiently eliminate CAFs to decrease stroma density and impair their functions.
Collapse
Affiliation(s)
- Yanan Gu
- Department of Radiology, Zhongshan Hospital and Shanghai Institute of Medical Imaging, Fudan University, Shanghai 200032, China; Department of Interventional Radiology, Zhongshan Hospital Fudan University Shanghai, 200032, China
| | - Qiangda Chen
- Department of Pancreatic Surgery, Zhongshan Hospital Fudan University, Shanghai 200032, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Hanlin Yin
- Department of Pancreatic Surgery, Zhongshan Hospital Fudan University, Shanghai 200032, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Mengsu Zeng
- Department of Radiology, Zhongshan Hospital and Shanghai Institute of Medical Imaging, Fudan University, Shanghai 200032, China
| | - Shanshan Gao
- Department of Radiology, Zhongshan Hospital and Shanghai Institute of Medical Imaging, Fudan University, Shanghai 200032, China.
| | - Xiaolin Wang
- Department of Radiology, Zhongshan Hospital and Shanghai Institute of Medical Imaging, Fudan University, Shanghai 200032, China; Department of Interventional Radiology, Zhongshan Hospital Fudan University Shanghai, 200032, China.
| |
Collapse
|
12
|
Woodard GA, Cho C, Chen L. Increased Lymphocyte Infiltration in NSCLC Neoadjuvant Chemo-Immunotherapy Non-responders: A Biomarker of T-Cell Dysfunction and Prognosis? Ann Surg Oncol 2024; 31:25-27. [PMID: 37899411 DOI: 10.1245/s10434-023-14388-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023]
Affiliation(s)
- Gavitt A Woodard
- Division of Thoracic Surgery, Department of Surgery, Yale University School of Medicine, Yale University, New Haven, CT, USA.
| | - Christina Cho
- Department of Immunobiology, Yale University School of Medicine, Yale University, New Haven, CT, USA
| | - Lieping Chen
- Department of Immunobiology, Yale University School of Medicine, Yale University, New Haven, CT, USA
| |
Collapse
|
13
|
Liu QQ, Yu XH, Tang QB, Chen D, Zhang R, Liu C, Shi XD. Complete response of recurrent perihilar cholangiocarcinoma following sintilimab combined with lenvatinib plus S-1: a case report and review of literature. Anticancer Drugs 2024; 35:81-85. [PMID: 37227031 DOI: 10.1097/cad.0000000000001519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Perihilar cholangiocarcinoma is a refractory malignancy with an unfavorable prognosis and a high probability of recurrence. Systemic chemotherapy is critical for palliative treatment, but effective therapeutic strategies for perihilar cholangiocarcinoma after first-line chemotherapy failure are scarce. Here, we introduced a sustained benefit following sintilimab combined with lenvatinib plus S-1 in a patient with recurrent perihilar cholangiocarcinoma. A 52-year-old female patient was admitted to our hospital due to yellow skin and sclera, and further radiological examination revealed perihilar cholangiocarcinoma. The patient underwent surgery and histopathological results confirmed moderately differentiated adenocarcinoma with metastatic lymph nodes. Postoperative adjuvant chemotherapy with gemcitabine and S-1 was given. One year after surgery, the patient experienced hepatic recurrence. Then, she received radiofrequency ablation combined with gemcitabine and cisplatin. Unfortunately, radiological assessment revealed progressive disease with multiple liver metastases after treatment. Subsequently, she received sintilimab combined with lenvatinib plus S-1 and the lesions were completely regressed following 14 cycles of combination therapy. The patient recovered well without disease recurrence at the last follow-up. Sintilimab combined with lenvatinib plus S-1 may be an alternative therapeutic option for chemotherapy-refractory perihilar cholangiocarcinoma, and further evaluation in a larger number of patients is needed.
Collapse
Affiliation(s)
- Qin-Qin Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation and Department of Biliary-Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | | | | | | | | | | | | |
Collapse
|
14
|
Tostes K, Siqueira AP, Reis RM, Leal LF, Arantes LMRB. Biomarkers for Immune Checkpoint Inhibitor Response in NSCLC: Current Developments and Applicability. Int J Mol Sci 2023; 24:11887. [PMID: 37569262 PMCID: PMC10418476 DOI: 10.3390/ijms241511887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Lung cancer has the highest mortality rate among all cancer types, resulting in over 1.8 million deaths annually. Immunotherapy utilizing immune checkpoint inhibitors (ICIs) has revolutionized the treatment of non-small cell lung cancer (NSCLC). ICIs, predominantly monoclonal antibodies, modulate co-stimulatory and co-inhibitory signals crucial for maintaining immune tolerance. Despite significant therapeutic advancements in NSCLC, patients still face challenges such as disease progression, recurrence, and high mortality rates. Therefore, there is a need for predictive biomarkers that can guide lung cancer treatment strategies. Currently, programmed death-ligand 1 (PD-L1) expression is the only established biomarker for predicting ICI response. However, its accuracy and robustness are not consistently reliable. This review provides an overview of potential biomarkers currently under development or in the validation stage that hold promise in improving the classification of responders and non-responders to ICI therapy in the near future.
Collapse
Affiliation(s)
- Katiane Tostes
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, São Paulo, Brazil; (K.T.)
| | - Aléxia Polo Siqueira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, São Paulo, Brazil; (K.T.)
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, São Paulo, Brazil; (K.T.)
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s-PT Government Associate Laboratory, 4806-909 Guimarães, Portugal
| | - Leticia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, São Paulo, Brazil; (K.T.)
- Barretos School of Health Sciences, Dr. Paulo Prata-FACISB, Barretos 14785-002, São Paulo, Brazil
| | | |
Collapse
|
15
|
Fortis SP, Batsaki P, Stokidis S, Moschandreou D, Grouzi E, Baxevanis CN, Gritzapis AD, Goulielmaki M. A Blood-Based Immune Gene Signature with Prognostic Significance in Localized Prostate Cancer. Cancers (Basel) 2023; 15:3697. [PMID: 37509358 PMCID: PMC10377824 DOI: 10.3390/cancers15143697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Prostate cancer (PCa) is one of the most common male cancers worldwide and one of the deadliest if unsuccessfully treated. Τhe need for reliable, easily accessible immune-related molecular biomarkers that could be combined with clinically defined criteria, including PSA and Gleason score, to accurately predict PCa patients' clinical outcomes is emerging. Herein, we describe for the first time a blood-identified immune-related gene signature comprising eight upregulated multi-functional genes associated with poor prognosis. Next-generation sequencing (NGS) analysis of PCa patients' peripheral blood samples revealed a more than three-fold upregulation of each of the eight genes as compared to samples originating from healthy donors. The construction of gene and protein interaction networks revealed different extents of the functional implications of these genes in the regulation of cell proliferation and immune responses. Analysis of the available data from The Cancer Genome Atlas (TCGA) regarding gene expression and survival of prostate adenocarcinoma (PRAD) and pan-cancer (PANCAN) patients revealed that intra-tumoral upregulation of this eight-gene signature (8-GS) was associated with poor 5-year progression-free intervals in PCa patients, even in those with high Gleason scores, and also with an unfavorable prognosis for cancer patients irrespective of the cancer type and even in the early stages. These observations suggest that further investigation of the 8-GS prospectively in randomized clinical trials, in which clinical benefit in terms of evaluating time to disease progression can be assessed, is warranted.
Collapse
Affiliation(s)
- Sotirios P Fortis
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, 11522 Athens, Greece
| | - Panagiota Batsaki
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, 11522 Athens, Greece
| | - Savvas Stokidis
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, 11522 Athens, Greece
| | - Dimitra Moschandreou
- Department of Transfusion Service and Clinical Hemostasis, Saint Savas Cancer Hospital, 11522 Athens, Greece
| | - Elisavet Grouzi
- Department of Transfusion Service and Clinical Hemostasis, Saint Savas Cancer Hospital, 11522 Athens, Greece
| | - Constantin N Baxevanis
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, 11522 Athens, Greece
| | - Angelos D Gritzapis
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, 11522 Athens, Greece
| | - Maria Goulielmaki
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, 11522 Athens, Greece
| |
Collapse
|
16
|
Tian Y, Wang Z, Liang F, Wang Y. Identifying Immune Cell Infiltration and Hub Genes During the Myocardial Remodeling Process After Myocardial Infarction. J Inflamm Res 2023; 16:2893-2906. [PMID: 37456781 PMCID: PMC10349602 DOI: 10.2147/jir.s416914] [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: 04/12/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023] Open
Abstract
Purpose Myocardial remodeling after myocardial infarction (MI) is a complex repair process following myocardial injury, characterized by the infiltration of multiple types of immune cells. However, the underlying molecular mechanism of myocardial remodeling after MI remains obscure. This study aimed to identify the hub differential expression genes (DEGs) of myocardial remodeling after MI and determine the distribution of immune cells infiltrating the pathology. Methods We downloaded GSE132143, GSE151834, and GSE176092 data from the GEO database. The GSE132143 dataset was used to identify DEGs, perform functional annotation, and screen hub genes based on protein-protein interaction (PPI) analysis. The GSE151834 dataset was used to validate the expression of hub genes. CIBERSORTx analysis was performed to explore the immune microenvironment in myocardial remodeling after MI. After conducting a literature review, we selected P3H3 to confirm the expression by utilizing immunohistochemistry and qRT-PCR. Finally, the snRNA-seq data in dataset GSE176092 was used for clarifying the expression of these hub genes in various cell clusters. Results We found 975 DEGs in myocardial remodeling after MI. Four hub genes (P3H3, COL15A1, COL16A1, COL27A1) were identified and were verified in the GSE151834 dataset. According to immune infiltration analysis, CD4+ naive T cells, regulatory T cells, monocytes, M2 macrophages, and neutrophils were involved in the pathological process of myocardial remodeling after MI. Additionally, in vitro experiments verified that P3h3 expression was significantly elevated in myocardial remodeling after MI. The snRNA-seq data analyzed that P3h3, Col15a1, Col16a1, and Col27a1 were highly expressed in fibroblasts of post-MI. Conclusion This study identified four hub genes P3H3, COL15A1, COL16A1, and COL27A1, particularly P3H3, as potential targets for targeted therapy in MI patients.
Collapse
Affiliation(s)
- Yuan Tian
- Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, People’s Republic of China
| | - Zilin Wang
- Department of Radiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, People’s Republic of China
| | - Feng Liang
- Heart Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, People’s Republic of China
| | - Yi Wang
- Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, People’s Republic of China
| |
Collapse
|
17
|
Tao Y, Li X, Liu B, Wang J, Lv C, Li S, Wang Y, Chen J, Yan S, Wu N. Association of early immune-related adverse events with treatment efficacy of neoadjuvant Toripalimab in resectable advanced non-small cell lung cancer. Front Oncol 2023; 13:1135140. [PMID: 37256186 PMCID: PMC10225556 DOI: 10.3389/fonc.2023.1135140] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
Background Neoadjuvant immunotherapy with anti-PD-1 was proved promising in resectable non-small cell lung cancer (NSCLC). Immune-related adverse events (irAEs) have been preliminarily implicated their association with treatment efficacy. Here we elucidated the early onset of irAEs associated with better clinical outcomes in a prospective study (Renaissance study). Methods We conducted the prospective study of NSCLC patients treated by neoadjuvant Toripalimab (240mg, every 3 weeks) plus double platinum-based chemotherapy from December 2020 to March 2022 at Peking University Cancer Hospital. Patients were enrolled if they have resectable IIB-IIIB NSCLC without EGFR/ALK mutation. Data were analyzed to explore the relationship between clinical outcome and irAEs after neoadjuvant treatment. A multidisciplinary team including physicians, surgeons, and radiologists, confirmed the irAEs according to the clinical manifestation. The relationship between irAEs and pathological outcomes was analyzed. The Renaissance study was approved by the Peking University Ethic board (2020YJZ58) and registered at https://clinicaltrials.gov/ as NCT04606303. Results Fifty-five consecutive patients were enrolled with a male-to-female ratio of 10:1, the median age was 62 years old (IQR: 45-76), of which 44 patients (80%) were diagnosed with squamous cell carcinoma. Forty-eight of 55 patients finally received thoracic surgery with a median preoperative waiting time of 67 days (IQR 39-113 days). Pathological results demonstrated that 31 (64.6%) patients achieved major pathological response (MPR) and 24 (50.0%) achieved complete pathological response (pCR). Among 48 patients who received R0 resection, immunotherapy-related thyroid dysfunction, rash/pruritus and enteritis occurred in 11 patients (22.9%), 7 patients (14.6%), and 1 patient (2.1%), respectively. Six patients (54.5%) with thyroid dysfunction achieved MPR with 5 (45.5%) achieved pCR, and a median time to onset was 45 days (IQR 21-91 days). Six patients (85.7%) with rash or pruritus achieved MPR and 5 patients (71.4%) achieved pCR, with median time to onset being 8 days (IQR 6-29 days). Furthermore, irAEs had no significant influence on operation time (170.6 min vs 165.7 min, P=0.775), intraoperative blood loss (67.4 mL vs 64.3 mL, P=0.831) and preoperative waiting time (93 days vs 97 days, P=0.630) when comparing with patients without irAEs (Figure 1).Figure 1Comparison of operation time (A), intraoperative blood loss (B), and preoperative waiting time (C) between "with irAEs" and "without irAEs". Conclusion The immunotherapy-related rash is potentially associated with pathological outcomes in NSCLC patients after neoadjuvant chemo-immunotherapy, suggesting easy-to-find irAEs, such as rash, can be used as indicators to predict response to neoadjuvant chemo-immunotherapy.Clinical trial registration: clinicaltrials.gov/, identifier NCT04606303.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Shi Yan
- *Correspondence: Shi Yan, ; Nan Wu,
| | - Nan Wu
- *Correspondence: Shi Yan, ; Nan Wu,
| |
Collapse
|
18
|
Lazzari C, Spagnolo CC, Ciappina G, Di Pietro M, Squeri A, Passalacqua MI, Marchesi S, Gregorc V, Santarpia M. Immunotherapy in Early-Stage Non-Small Cell Lung Cancer (NSCLC): Current Evidence and Perspectives. Curr Oncol 2023; 30:3684-3696. [PMID: 37185393 PMCID: PMC10136903 DOI: 10.3390/curroncol30040280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 03/12/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023] Open
Abstract
Lung cancer is the leading cause of cancer deaths in the world. Surgery is the most potentially curative therapeutic option for patients with early-stage non-small cell lung cancer (NSCLC). The five-year survival for these patients remains poor and variable, depending on the stage of disease at diagnosis, and the risk of recurrence following tumor resection is high. During the last 20 years, there has been a modest improvement in the therapeutic strategies for resectable NSCLC. Immune checkpoint inhibitors (ICIs), alone or in combination with chemotherapy, have become the cornerstone for the treatment of metastatic NSCLC patients. Recently, their clinical development has been shifted in the neoadjuvant and adjuvant settings where they have demonstrated remarkable efficacy, leading to improved clinical outcomes. Based on the positive results from phase III trials, ICIs have become a therapeutic option in neoadjuvant and adjuvant settings. On October 2021 the Food and Drug Administration (FDA) approved atezolizumab as an adjuvant treatment following surgery and platinum-based chemotherapy for patients with NSCLC whose tumors express PD-L1 ≥ 1%. In March 2022, nivolumab in combination with platinum-doublet chemotherapy was approved for adult patients with resectable NSCLC in the neoadjuvant setting. The current review provides an updated overview of the clinical trials exploring the role of immunotherapy in patients with early-stage NSCLC, focusing on the biological rationale for their use in the perioperative setting. We will also discuss the role of potential predictive biomarkers to personalize therapy and optimize the incorporation of immunotherapy into the multimodality management of stage I-III NSCLC.
Collapse
|
19
|
Wu X, Chau YF, Bai H, Zhuang X, Wang J, Duan J. Progress on neoadjuvant immunotherapy in resectable non-small cell lung cancer and potential biomarkers. Front Oncol 2023; 12:1099304. [PMID: 36761426 PMCID: PMC9902866 DOI: 10.3389/fonc.2022.1099304] [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: 11/15/2022] [Accepted: 12/31/2022] [Indexed: 01/25/2023] Open
Abstract
Immune checkpoint inhibitors (ICIs) are highly concerned in the treatment of non-small cell lung cancer (NSCLC), represented by inhibitors of programmed death protein 1 (PD-1) and its ligand (PD-L1), and inhibitors of cytotoxic T lymphocyte-associated antigen-4 (CTLA-4). The introduction of immunotherapy in the treatment of perioperative NSCLC has improved the prognosis to a great extent, as demonstrated by several phase II and III clinical trials. The target population for immunotherapy in early-stage NSCLC is still under discussion, and the biomarkers for neoadjuvant immunotherapy population selection are the next pending problem. The predictive efficacy of many potential makers is still being explored, including PD-L1 expression levels, tumor mutation burden, circulating tumor DNA, components of the tumor microenvironment, and several clinical factors. We summarize key findings on the utility of ICIs in clinical trials of preoperative NSCLC patients and conclude analyses of relevant biomarkers to provide a better understanding of potentially predictive biomarkers in neoadjuvant immunotherapy.
Collapse
Affiliation(s)
- Xinyu Wu
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing, China
| | - Yi Fung Chau
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing, China
| | - Hua Bai
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing, China
| | - Xiaofei Zhuang
- Department of Thoracic Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jie Wang
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing, China
| | - Jianchun Duan
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing, China,Department of Medical Oncology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China,*Correspondence: Jianchun Duan,
| |
Collapse
|
20
|
Rangamuwa K, Aloe C, Christie M, Asselin-Labat ML, Batey D, Irving L, John T, Bozinovski S, Leong TL, Steinfort D. Methods for assessment of the tumour microenvironment and immune interactions in non-small cell lung cancer. A narrative review. Front Oncol 2023; 13:1129195. [PMID: 37143952 PMCID: PMC10151669 DOI: 10.3389/fonc.2023.1129195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/28/2023] [Indexed: 05/06/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is one of the leading causes of cancer death worldwide. Immunotherapy with immune checkpoint inhibitors (ICI) has significantly improved outcomes in some patients, however 80-85% of patients receiving immunotherapy develop primary resistance, manifesting as a lack of response to therapy. Of those that do have an initial response, disease progression may occur due to acquired resistance. The make-up of the tumour microenvironment (TME) and the interaction between tumour infiltrating immune cells and cancer cells can have a large impact on the response to immunotherapy. Robust assessment of the TME with accurate and reproducible methods is vital to understanding mechanisms of immunotherapy resistance. In this paper we will review the evidence of several methodologies to assess the TME, including multiplex immunohistochemistry, imaging mass cytometry, flow cytometry, mass cytometry and RNA sequencing.
Collapse
Affiliation(s)
- Kanishka Rangamuwa
- Department of Respiratory Medicine, Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine Royal Melbourne Hospital (RMH), University of Melbourne, Parkville, VIC, Australia
- *Correspondence: Kanishka Rangamuwa,
| | - Christian Aloe
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Michael Christie
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | | | - Daniel Batey
- Personalised Oncology Division, Walter Eliza Hall Institute, Melbourne, VIC, Australia
| | - Lou Irving
- Department of Respiratory Medicine, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Thomas John
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Steven Bozinovski
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Tracy L. Leong
- Personalised Oncology Division, Walter Eliza Hall Institute, Melbourne, VIC, Australia
- Department of Respiratory Medicine, Austin Hospital, Heidelberg, VIC, Australia
| | - Daniel Steinfort
- Department of Respiratory Medicine, Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine Royal Melbourne Hospital (RMH), University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|