1
|
Lin L, Zhang W, Chen Y, Ren W, Zhao J, Ouyang W, He Z, Su W, Yao H, Yu Y. Immune gene patterns and characterization of the tumor immune microenvironment associated with cancer immunotherapy efficacy. Heliyon 2023; 9:e14450. [PMID: 36950600 PMCID: PMC10025929 DOI: 10.1016/j.heliyon.2023.e14450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/14/2023] Open
Abstract
Although immunotherapy has revolutionized cancer management, most patients do not derive benefits from it. Aiming to explore an appropriate strategy for immunotherapy efficacy prediction, we collected 6251 patients' transcriptome data from multicohort population and analyzed the data using a machine learning algorithm. In this study, we found that patients from three immune gene clusters had different overall survival when treated with immunotherapy (P < 0.001), and that these clusters had differential states of hypoxia scores and metabolism functions. The immune gene score showed good immunotherapy efficacy prediction (AUC was 0.737 at 20 months), which was well validated. The immune gene score, tumor mutation burden, and long non-coding RNA score were further combined to build a tumor immune microenvironment signature, which correlated more strongly with overall survival (AUC, 0.814 at 20 months) than when using a single variable. Thus, we recommend using the characterization of the tumor immune microenvironment associated with immunotherapy efficacy via a multi-omics analysis of cancer.
Collapse
Key Words
- AUC, Area under the curve
- CIs, Confidence intervals
- CTL, Cytotoxic T-lymphocyte infiltration
- Cancer
- GEO, Gene Expression Omnibus
- GO, Gene Ontology
- GSEA, Gene set enrichment analysis
- GSVA, Gene set variation analysis
- HLAs, Human leukocyte antigens
- HRs, Hazard ratios
- Immunotherapy
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- LASSO, Penalized logistic least absolute shrinkage and selector operation
- Machine learning
- NSCLC, Non-small cell lung cancer
- OS, Overall survival
- PCA, Principal componentanalysis
- PD-L1, Programmed death ligand-1
- PFS, Profession-free survival
- RNA-seq, Transcriptome RNA sequencing
- ROC, receiver operating characteristic curves
- TCGA, The Cancer Genome Atlas
- TMB, Tumor mutation burden
- TME, Tumor immunemicroenvironment
- Tumor immune microenvironment
- WGCNA, Weighted gene co-expression network analysis
- lncRNA, Long non-coding RNA
Collapse
Affiliation(s)
- Lili Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wenda Zhang
- Department of Oncology, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Yongjian Chen
- Department of Medical Oncology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wei Ren
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jianli Zhao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wenhao Ouyang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zifan He
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Weifeng Su
- Division of Science and Technology, Beijing Normal University-Hong Kong Baptist University United International College, Hong Kong Baptist University, Zhuhai, China
- Corresponding author.
| | - Herui Yao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- Corresponding author.
| | - Yunfang Yu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- Division of Science and Technology, Beijing Normal University-Hong Kong Baptist University United International College, Hong Kong Baptist University, Zhuhai, China
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao, PR China
- Corresponding author. Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
2
|
Mitra M, Shah N, Faridi MMA, Ghosh A, Sankaranarayanan VS, Aggarwal A, Chatterjee S, Bhattacharyya N, Kadhe G, Vishnoi G, Mane A. Long term follow-up study to evaluate immunogenicity and safety of a single dose of live attenuated hepatitis a vaccine in children. Hum Vaccin Immunother 2015; 11:1147-52. [PMID: 26018443 PMCID: PMC4514242 DOI: 10.4161/21645515.2014.979646] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Worldwide, viral hepatitis continues to be a cause of considerable morbidity and mortality. Mass immunization with a single dose of live attenuated HAV has been shown to significantly reduce disease burden in the community. This was a phase IV, 5-year follow up study carried out at 4 centers (Kolkata, Delhi, Mumbai and Chennai) across India. The subjects with antibody titer <20 mIU/mL at baseline were evaluated for long term immunogenicity. Of the 503 subjects enrolled, 349 subjects were baseline seronegative with an anti-HAV antibody titer <20 mIU/mL. Overall, 343 subjects could be followed up at some point of time during this 5 y post vaccination period. In the last year (60 months) of follow-up, 108 subjects (97.3%) of 111 subjects (who came for follow-up at the end of 5 y) had a protective antibody titer (anti-HAV antibody titer >20 mIU/mL). The seroconversion rates considering seroprotection levels of anti-HAV antibody titer >20 mIU/mL, following vaccination starting from 6 weeks, 6 months, 12 months, 24 months, 36 months, 48 months and 60 months were 95.1%, 97.9%, 98.3%, 96.2%, 97.8%, 92.6% and 97.3%, respectively. The geometric mean concentration (GMC) over the years increased from 64.9 mIU/mL at 6 weeks to 38.1 mIU/mL and 135.2 mIU/mL at 6 months and 12 months, respectively and was maintained at 127.1 mIU/mL at 60 months. In conclusion, the result of this 5-year follow up study showed that the single dose of live attenuated vaccine is well tolerated and provides long-term immunogenicity in healthy Indian children.
Collapse
Affiliation(s)
- Monjori Mitra
- Institute of Child Health; Kolkata, India
- Correspondence to: Monjori Mitra;
| | - Nitin Shah
- Department of Pediatrics; Lion's Tarachand Bapa Hospital; Sion West, Mumbai, India
| | - MMA Faridi
- Department of Pediatrics; University College of Medical Sciences; GTB Hospital, Dilshad Garden; Delhi, India
| | | | | | - Anju Aggarwal
- Department of Pediatrics; University College of Medical Sciences; GTB Hospital; Delhi, India
| | - Suparna Chatterjee
- Deptartment of Pharmacology; Institute of Postgraduate Medical Education & Research; Kolkata, India
| | | | - Ganesh Kadhe
- Medical Affairs; Wockhardt Limited, Wockhardt Towers; Bandra–Kurla Complex; Bandra–East, Mumbai
| | - Gaurav Vishnoi
- Medical Affairs; Wockhardt Limited, Wockhardt Towers; Bandra–Kurla Complex; Bandra–East, Mumbai
| | - Amey Mane
- Medical Affairs; Wockhardt Limited, Wockhardt Towers; Bandra–Kurla Complex; Bandra–East, Mumbai
| |
Collapse
|
3
|
Li X, Ma SJ, Liu X, Jiang LN, Zhou JH, Xiong YQ, Ding H, Chen Q. Immunogenicity and safety of currently available Japanese encephalitis vaccines: a systematic review. Hum Vaccin Immunother 2014; 10:3579-93. [PMID: 25668666 PMCID: PMC4514081 DOI: 10.4161/21645515.2014.980197] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/26/2014] [Accepted: 09/05/2014] [Indexed: 11/19/2022] Open
Abstract
A number of Japanese encephalitis (JE) vaccines have been used for preventing Japanese encephalitis around the world. We here reviewed the immunogenicity and safety of the currently available Japanese encephalitis vaccines. We searched Pubmed, Embase, Web of Science, the Cochrane Library and other online databases up to March 25, 2014 for studies focusing on currently used JE vaccines in any language. The primary outcomes were the seroconversion rate against JEV and adverse events. Meta-analysis was performed for the primary outcome when available. A total of 51 articles were included. Studies were grouped on the basic types of vaccines. This systematic review led to 2 aspects of the conclusions. On one hand, all the currently available JE vaccines are safe and effective. On the other hand, the overall of JE vaccine evaluation is disorganized, the large variation in study designs, vaccine types, schedules, doses, population and few hand-to-hand trails, make direct comparisons difficult. In order to make a more evidence-based decision on optimizing the JE vaccine, it is warranted to standardize the JE vaccine evaluation research.
Collapse
Key Words
- ACIP, The Advisory Committee on Immunization Practices
- AEs, Adverse events
- CENTRAL, Cochrane Central Register of Controlled Trials
- CIs, Confidence intervals
- DARE, Database of Abstracts of Reviews of Effects
- GMTs, Geometric mean titers
- HAART, Highly active antiretroviral therapy
- JE, Japanese encephalitis
- JE-CV, Chimeric live-attenuated JE vaccine
- JEV, Japanese encephalitis virus
- Japanese encephalitis vaccine
- LILACS, Latin American and Caribbean Health Sciences Literature
- MBJEV, Mouse brain–derived inactivated vaccines
- MMR, Measles mumps rubella vaccine
- NIP, National Immunization Program
- NOS, Newcastle–Ottawa scale
- ORs, Odd ratios
- PHK, Primary hamster kidney cells
- PRNT50, Plaque-reduction neutralization tests
- RCTs, Randomized controlled trials
- TBE, Tick-borne encephalitis vaccine
- TGPO, Thai Governmental Pharmaceutical Organization
- WHO, World Health Organization
- YF-VAX, Yellow fever vaccine
- YFV, Yellow fever virus
- YFV17D, Yellow fever virus 17D vaccine strain
- immunogenicity
- meta-analysis
- safety
- systematic review
Collapse
Affiliation(s)
- Xing Li
- Department of Epidemiology; School of Public Health and Tropical Medicine; Southern Medical University; Guangzhou, China
| | - Shu-Juan Ma
- Department of Epidemiology; School of Public Health and Tropical Medicine; Southern Medical University; Guangzhou, China
| | - Xie Liu
- Department of Epidemiology; School of Public Health and Tropical Medicine; Southern Medical University; Guangzhou, China
| | - Li-Na Jiang
- Department of Epidemiology; School of Public Health and Tropical Medicine; Southern Medical University; Guangzhou, China
| | - Jun-Hua Zhou
- Department of Epidemiology; School of Public Health and Tropical Medicine; Southern Medical University; Guangzhou, China
| | - Yi-Quan Xiong
- Department of Epidemiology; School of Public Health and Tropical Medicine; Southern Medical University; Guangzhou, China
| | - Hong Ding
- Department of Epidemiology; School of Public Health and Tropical Medicine; Southern Medical University; Guangzhou, China
| | - Qing Chen
- Department of Epidemiology; School of Public Health and Tropical Medicine; Southern Medical University; Guangzhou, China
| |
Collapse
|