Metagenome analysis for immunotherapy-treated patients with NSCLC
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ABSTRACT:
PROVIDER: PRJEB69295 | ENA |
REPOSITORIES: ENA
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Project description: Not available
| S-EPMC11335565 | biostudies-literature
Project description:Tumor mutation burden estimated with whole exome sequencing of 43 NSCLC patient tumors treated with anti-PD-1 + anti-CTLA-4
2018-02-15 | PRJEB24995 | EVA
Project description:Different types of therapy are currently being used to treat non-small cell lung cancer (NSCLC) depending on the stage of tumor and the presence of potentially druggable mutations. However, few biomarkers are available to guide clinicians in selecting the most effective therapy for all patients with various genetic backgrounds. To examine whether patients' mutation profiles are associated with the response to a specific treatment, we collected comprehensive clinical characteristics and sequencing data from 524 patients with stage III and IV NSCLC treated at Atrium Health Wake Forest Baptist. Overall survival based Cox-proportional hazard regression models were applied to identify mutations that were "beneficial" (HR < 1) or "detrimental" (HR > 1) for patients treated with chemotherapy (chemo), immune checkpoint inhibitor (ICI) and chemo+ICI combination therapy (Chemo+ICI) followed by the generation of mutation composite scores (MCS) for each treatment. We also found that MCS is highly treatment specific that MCS derived from one treatment group failed to predict the response in others. Receiver operating characteristics (ROC) analyses showed a superior predictive power of MCS compared to TMB and PD-L1 status for immune therapy-treated patients. Mutation interaction analysis also identified novel co-occurring and mutually exclusive mutations in each treatment group. Our work highlights how patients' sequencing data facilitates the clinical selection of optimized treatment strategies.
| S-EPMC10042886 | biostudies-literature
Project description:Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of lung cancer. However, their clinical benefit is limited to a minority of patients. To unravel immune-related factors that are predictive of sensitivity or resistance to immunotherapy, we performed a gene expression analysis by RNA-Seq using the Oncomine Immuno Response Assay (OIRRA) on a total of 33 advanced NSCLC patients treated with ICI evaluating the expression levels of 365 immune-related genes. We found four genes (CD1C, HLA-DPA1, MMP2, and TLR7) downregulated (p < 0.05) and two genes (IFNB1 and MKI67) upregulated (p < 0.05) in ICI-Responders compared to ICI-Non-Responders. The Bayesian enrichment computational analysis showed a more complex interaction network that involved 10 other genes (IFNA1, TLR4, CD40, TLR2, IL12A, IL12B, TLR9, CD1E, IFNG, and HLA-DPB1) correlated with different functional groups. Five main pathways were identified (FDR < 0.0001). High TLR7 expression levels were significantly associated with a lack of response to immunotherapy (p < 0.0001) and worse outcome in terms of both PFS (p < 0.001) and OS (p = 0.03). The multivariate analysis confirmed TLR7 RNA expression as an independent predictor for both poor PFS (HR = 2.97, 95% CI, 1.16-7.6, p = 0.023) and OS (HR = 2.2, 95% CI, 1-5.08, p = 0.049). In conclusion, a high TLR7 gene expression level was identified as an independent predictor for poor clinical benefits from ICI. These data could have important implications for the development of novel single/combinatorial strategies TLR-mediated for an efficient selection of "individualized" treatments for NSCLC in the era of immunotherapy.
| S-EPMC8303258 | biostudies-literature
Project description:Treatment with immunotherapy has made a significant impact in the outcomes for those individuals diagnosed with metastatic non-small cell lung cancer (NSCLC) and its use is currently an established treatment modality. In light of recent advances in immunotherapy, improved survival, particularly for patients with stage IV NSCLC, has been reported with durable and prolonged responses in a subset of patients. Immune check point inhibitors, which include nivolumab, pembrolizumab, and atezolizumab, are standard treatment options in the salvage setting. Nivolumab and atezolizumab are approved for patients regardless of programmed death-ligand 1 (PD-L1) expression, whereas pembrolizumab requires tumor PD-L1 expression at the cut-off ≥1%. In this review, we will outline the clinical development of immunotherapy in previously treated NSCLC, current challenges and discuss novel treatment strategies.
| S-EPMC5861264 | biostudies-literature
Project description:BACKGROUND:Recent evidence suggests that immunotherapy efficacy in melanoma is modulated by gut microbiota. Few studies have examined this phenomenon in humans, and none have incorporated metatranscriptomics, important for determining expression of metagenomic functions in the microbial community. METHODS:In melanoma patients undergoing immunotherapy, gut microbiome was characterized in pre-treatment stool using 16S rRNA gene and shotgun metagenome sequencing (n = 27). Transcriptional expression of metagenomic pathways was confirmed with metatranscriptome sequencing in a subset of 17. We examined associations of taxa and metagenomic pathways with progression-free survival (PFS) using 500 × 10-fold cross-validated elastic-net penalized Cox regression. RESULTS:Higher microbial community richness was associated with longer PFS in 16S and shotgun data (p < 0.05). Clustering based on overall microbiome composition divided patients into three groups with differing PFS; the low-risk group had 99% lower risk of progression than the high-risk group at any time during follow-up (p = 0.002). Among the species selected in regression, abundance of Bacteroides ovatus, Bacteroides dorei, Bacteroides massiliensis, Ruminococcus gnavus, and Blautia producta were related to shorter PFS, and Faecalibacterium prausnitzii, Coprococcus eutactus, Prevotella stercorea, Streptococcus sanguinis, Streptococcus anginosus, and Lachnospiraceae bacterium 3 1 46FAA to longer PFS. Metagenomic functions related to PFS that had correlated metatranscriptomic expression included risk-associated pathways of L-rhamnose degradation, guanosine nucleotide biosynthesis, and B vitamin biosynthesis. CONCLUSIONS:This work adds to the growing evidence that gut microbiota are related to immunotherapy outcomes, and identifies, for the first time, transcriptionally expressed metagenomic pathways related to PFS. Further research is warranted on microbial therapeutic targets to improve immunotherapy outcomes.
| S-EPMC6785875 | biostudies-other
Project description:Approximately 40% of unselected non-small cell lung cancer (NSCLC) patients develop brain metastases (BMs) during their disease, with considerable morbidity and mortality. The management of BMs in patients with NSCLC is a clinical challenge and requires a multidisciplinary approach to gain effective intracranial disease control. Over the last decade, immune checkpoint inhibitors (ICIs) have emerged as a game-changer in the treatment landscape of advanced NSCLC, with significant improvements in survival outcomes, although patients with BMs are mostly underrepresented in randomized clinical trials. Moreover, the safety and activity of ICIs and radiotherapy combinations compared with single-agent or sequential modalities is still under evaluation to establish the optimal management of these patients. The aim of this review is to summarize the state-of-the-art of clinical evidence of ICIs intracranial activity and the main challenges of incorporating these agents in the treatment armamentarium of NSCLC patients with BMs.
| S-EPMC9267075 | biostudies-literature
Project description:BackgroundSeveral biomarkers have been separately described to select patients for immunotherapy (IO), but few studies integrate these markers. Di Maio, EPSILoN and the plasma microRNA signature classifier (MSC), are three different clinico, biochemical and molecular markers able to independently predict prognosis in non-small cell lung cancer (NSCLC).MethodsComplete data such as sex, histology, ECOG-PS, stage, smoking status, presence of liver metastasis, LDH and neutrophils-to-lymphocyte ratio were collected to generate Di Maio and EPSILoN. The MSC risk level was prospectively assessed in plasma samples collected at baseline IO. The 3 markers were integrated into the DEMo score system prospectively tested in a cohort of 200 advanced NSCLC patients treated with IO. Endpoints were overall survival (OS), progression-free survival (PFS) and overall response rate (ORR).ResultsDEMo separated patients in 7-risk groups whose median OS had a trend ranging from 29.7 to 1.5 months (P<0.0001). When comparing patients with the lowest (n=29) and the highest (n=35) DEMo scores ORR was 45% and 3%, respectively (P<0.0001). Considering the 53 PD-L1 ≥50% patients, DEMo identified a group of 13 (25%) patients who benefit less from IO in terms of both OS (HR: 8.81; 95% CI: 2.87-20.01) and PFS (HR: 6.82; 95% CI: 2.57-18.10). Twelve out of 111 (11%) patients who most benefit from IO according to OS (HR: 0.21; 95% CI: 0.07-0.62) and PFS (HR: 0.28; 95% CI: 0.12-0.65) were identified by DEMo in the PD-L1 <50% group.ConclusionsThe DEMo prognostic score system stratified NSCLC patients treated with IO better than each single marker. The proper use of DEMo according to PD-L1 could improve selection in IO regimens.
| S-EPMC7354114 | biostudies-literature
Project description:Lung cancer is the most commonly diagnosed cancer among men and it is the third ranked in women. There are two major types of lung cancer, namely, small cell lung cancer (SCLC), which accounts for ~20% of the cases, and non-small cell lung cancer (NSCLC), which is the most common. Chemotherapy and chemoradiotherapy have been used as the first-line therapies but suffer from lack of efficacy and also of several toxic adverse effects. Immunotherapeutic approaches including tumor antigen vaccination, monoclonal antibodies targeting checkpoint pathways and also activated immune cells are being developed and have been shown to be effective in treating NSCLC. Despite their promise, efficacy of several immunotherapies has not been consistent. We undertook this meta-analysis study to analyze results from clinical trials that compared efficacy and safety of immunotherapies with placebo or chemotherapy/radiotherapy in improving overall survival (OS) and progression-free survival (PFS) of NSCLC patients. Various databases were searched to identify randomized clinical studies examining the efficacy and safety of antibody- and vaccine-based immunotherapies in NSCLC patients in comparison to chemotherapy or chemoradiotherapy or placebo. Effects on OS and PFS and also adverse events have been compared. In accordance with the selection criteria, a total of 13 studies with 3,513 patients in immunotherapy and 3,072 patients in chemotherapy/placebo, were selected. PFS (odds ratio 1.81, 95% CI 1.36, 2.42; P<0.0001) and OS (P<0.0001) are found to be greatly improved by immunotherapies. Immunotherapy of NSCLC patients was also found to prevent several adverse effects and to improve daily living ability of the patients. The present meta-analysis strongly suggests that immunotherapy improves OS and PFS of patients with NSCLC.
| S-EPMC5529907 | biostudies-other
Project description:Immunotherapy has now been integrated as a treatment strategy for most patients with non-small cell lung cancer (NSCLC). However, the pivotal clinical trials that demonstrated its impressive efficacy often did not include patients with active, untreated brain metastases or leptomeningeal carcinomatosis. Nevertheless, NSCLC is the most common tumor to metastasize to the brain, and patients develop brain and meningeal involvement in approximately 40 and 10% of cases, respectively. Consequently, the appropriate care of these patients is a recurrent clinical concern. Although there are many aspects that would merit further investigation to explain the mechanism of intracranial response to immune checkpoint inhibitors (ICPs), some data suggest that they are able to cross the blood-brain barrier, resulting in local tumor microenvironment modification. This results in a similar clinical benefit in patients with stable, previously treated brain metastases compared to the general population. Despite important limitations, some real-life studies have described that the ICPs' efficacy was maintained also in less selected patients with untreated or symptomatic brain metastases. In contrast, few data are available about patients with leptomeningeal carcinomatosis. Nevertheless, neurological complications due to ICP treatment in patients with brain metastases have to be evaluated and carefully monitored. Despite the fact that limited data are available in the literature, the purpose of this review is to show that the multimodal treatment of these patients with brain metastases and/or leptomeningeal disease should be discussed during tracing of the history of the disease, participating in the local and possibly systemic control of NSCLC.
| S-EPMC9039308 | biostudies-literature