Blood platelet RNA profiles do not enable for nivolumab response prediction at baseline in patients with non-small-cell lung cancer
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE216297 | GEO | 2023/07/10
REPOSITORIES: GEO
Similar Datasets
Project description:Double anti-platelet therapy (DAPT) has wide inter-individual variabilities in coronary heart disease (CHD) patients’ responses, which undermines the prognosis effect in clinical practice. Noncoding RNAs are present in platelets, albeit their potential roles in platelet responses to DAPT largely remains in the realm of the unknown. This study aims to screen differential noncoding RNAs responsible for low residual platelet reactivities under DAPT. We enrolled 144 CHD patients that received DAPT and assigned them to high platelet reactivity (HPR) group and baseline group according to their residual platelet reactivities. Through microarray analysis, we detected a total of 22,424 kinds of co-expressed lncRNAs in three pairs of the patients between the HPR and baseline groups.
2020-01-01 | GSE130492 | GEO
Project description:Novel perioperative strategies are needed to reduce recurrence rates in patients undergoing nephrectomy for high-risk, non-metastatic clear cell renal cell carcinoma (ccRCC). We conducted a prospective, phase I trial of neoadjuvant nivolumab prior to nephrectomy in 15 evaluable patients with non-metastatic ccRCC. We leveraged tissue from that cohort to elucidate the effects of PD-1 inhibition on immune cell populations in ccRCC and correlate the evolving immune milieu with anti-PD-1 response. We found that nivolumab durably induces a pro-inflammatory state within the primary tumor, and baseline immune infiltration within the primary tumor correlates with nivolumab responsiveness. Nivolumab increases CTLA-4 expression in the primary tumor, and subsequent nephrectomy increases circulating concentrations of sPD-L1, sPD-L3 (sB7-H3), and s4-1BB. These findings form the basis to consider neoadjuvant immune checkpoint inhibition (ICI) for high-risk ccRCC while the tumor remains in situ and provide the rationale for perioperative strategies of novel ICI combinations.
2023-12-18 | GSE245372 | GEO
Project description:Background: Preclinical work has demonstrated that ibrutinib inhibits the generation, migration and immunosuppressive function of myeloid-derived suppressor cells (MDSC). A pilot study tested the combination of ibrutinib and nivolumab in patients with metastatic solid tumors. Methods: Sixteen patients with metastatic solid malignancies were treated with ibrutinib (420 mg) daily and nivolumab (240 mg) IV on days 1 and 15 of 28 day cycles. Ibrutinib dosing started 7 days before cycle 1 of nivolumab and was given until cycle 1, day 8 of nivolumab. The effect of ibrutinib alone and in combination with nivolumab on circulating MDSC and immune subsets and cytokine/chemokine levels were measured. Single-cell RNA and TCR sequencing was also performed. Results: The most common treatment-related AEs were fatigue (31%) and anorexia (31%). Five patients had a clinical response (4 partial, 1 complete). Four patients had stable disease at 3 months. Median progression-free survival was 3.5 months and median overall survival 10.8 months. MDSC levels increased following 7 days of single-agent ibrutinib compared to baseline (21.91% vs. 27.67%). There was increased T cell proliferation in response (33.9% vs. 40.06%, p<0.01) to the combination regimen. Plasma levels of CCL2, CCL3, CCL4, CCL13, IL- 8, and VEGF-α decreased with ibrutinib treatment. Ibrutinib treatment altered the transcriptional state of the myeloid cell compartment and led to increased cancer-associated TCR clonotypes. Conclusion: The combination of ibrutinib and nivolumab was well tolerated and ibrutinib significantly impacted MDSC and T cell function in patients with solid metastatic tumors.
2022-06-24 | GSE178882 | GEO
Project description:Expression profiling of tumor samples obtained during CA209-038 (ClinicalTrials.gov Identifier: NCT01621490). The purpose of this study is to evaluate pharmacodynamic changes of nivolumab and nivolumab in combination with ipilimumab treatment on the biomarkers measured in the peripheral blood and tumor tissues of subjects with advanced melanoma (unresectable or advanced). Samples are rumor core needle biopsies obtained at trial enrolment (i.e. Screen) and/or at Cycle 1 Day 29 (i.e.Week 4) from Subjects With Advanced Melanoma (Unresectable or Metastatic) treated with nivolumab (BMS-936558,MDX-1106) 3 mg/kg solution intravenously every 2 weeks on Bristol-Myers Squibb clinical trial protocol CA209-038 Part 1 . Cohort 2 patients have progressed on anti-CTLA4 (ipilimumab) monoclonal antibody therapy. Values are from an interim lock of the trial data in July 2014. Best overall response (BOR) was defined using RECIST 1.1 criteria: tumor assessments between date of first dose and the date of first objectively documented progression, or the date of non-missing subsequent anti-cancer therapy (whichever occurs first) were used to derive BOR. MPCT is Maximum reduction in tumor size (index lesions only) up to first progression, and is the value typically shown on a waterfall plot.
2022-01-01 | E-MTAB-4030 | biostudies-arrayexpress
Project description:Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis
| PRJEB45262 | ENA
Project description:MicroRNAs (miRNAs) regulate cell physiology by altering protein expression, but the biology of platelet miRNAs is largely unexplored. We tested whether platelet miRNA levels were associated with platelet reactivity by genome-wide profiling using platelet RNA from 19 healthy subjects. We found that human platelets express 284 miRNAs. Unsupervised hierarchical clustering of miRNA profiles resulted in 2 groups of subjects that appeared to cluster by platelet aggregation phenotypes. Seventy-four miRNAs were differentially expressed (DE) between subjects grouped according to platelet aggregation to epinephrine, a subset of which predicted the platelet reactivity response. Using whole genome mRNA expression data on these same subjects, we computationally generated a high-priority list of miRNA-mRNA pairs in which the DE platelet miRNAs had binding sites in 3'UTRs of DE mRNAs, and the levels were negatively correlated. Three miRNA-mRNA pairs (miR-200b:PRKAR2B, miR-495:KLHL5 and miR-107:CLOCK) were selected from this list and all 3 miRNAs knocked down protein expression from the target mRNA. Reduced activation from platelets lacking PRKAR2B supported these findings. In summary, (1) platelet miRNAs are able to repress expression of platelet proteins, (2) miRNA profiles are associated with and may predict platelet reactivity, and (3) bioinformatic approaches can successfully identify functional miRNAs in platelets. Total RNA from the platelets of 19 donors was harvested and labeled with Hy3. Reference RNA (a pool of all samples) was labeled with Hy5. This submission represents the miRNA expression component of the study.
2011-09-26 | E-GEOD-27917 | biostudies-arrayexpress
Project description:To identify critical tumor-secreting factors that may contribute to immunotherapy efficacy against HCC, we subjected tumor samples from 10 HCC patients to whole-transcriptome sequencing, and categorized the patients into two groups according to clinical response to nivolumab. We then performed gene expression profiling analysis using data obtained from RNA-seq of Nivolumab reponders and non-reponsers.
2023-12-06 | GSE215011 | GEO
Project description:Platelet-rich plasma (PRP) has been obtained by centrifuging whole blood at 160 g for 15 min at room temperature. Platelets have been activated with 2 different physiologic agonists, namely collagen (60ug/mL) or Thrombin Receptor Activating Peptide (TRAP 25uM) under continuous stirring. An aliquot of platelets has been obtained at 120 minutes following collagen and TRAP and then processed to determine mRNA expression profiles. Time 0, indicating samples before any agonist treatment, was used as baseline. Total RNA was extracted using the mirVana PARIS kit (LifeTechnologies), according to manufacturers instruction. Indexed libraries were prepared using 500 ng of total RNA as starting material and sequenced on HiSeq 1500 (Illumina, USA) at a concentration of 8pM for 2x100 plus 7 additional cycles for indexes sequencing. Standard workflow for quality control through RTA and bcl2fastq conversion tool was applied.
2015-04-27 | E-MTAB-2355 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) regulate cell physiology by altering protein expression, but the biology of platelet miRNAs is largely unexplored. We tested whether platelet miRNA levels were associated with platelet reactivity by genome-wide profiling using platelet RNA from 19 healthy subjects. We found that human platelets express 284 miRNAs. Unsupervised hierarchical clustering of miRNA profiles resulted in 2 groups of subjects that appeared to cluster by platelet aggregation phenotypes. Seventy-four miRNAs were differentially expressed (DE) between subjects grouped according to platelet aggregation to epinephrine, a subset of which predicted the platelet reactivity response. Using whole genome mRNA expression data on these same subjects, we computationally generated a high-priority list of miRNA-mRNA pairs in which the DE platelet miRNAs had binding sites in 3'UTRs of DE mRNAs, and the levels were negatively correlated. Three miRNA-mRNA pairs (miR-200b:PRKAR2B, miR-495:KLHL5 and miR-107:CLOCK) were selected from this list and all 3 miRNAs knocked down protein expression from the target mRNA. Reduced activation from platelets lacking PRKAR2B supported these findings. In summary, (1) platelet miRNAs are able to repress expression of platelet proteins, (2) miRNA profiles are associated with and may predict platelet reactivity, and (3) bioinformatic approaches can successfully identify functional miRNAs in platelets.
2011-09-27 | GSE27917 | GEO
Project description:The purpose of this study was to perform an unbiased RNA expression profile in platelets from HIV subjects under ART and healthy controls to identify a gene signature for the HIV hyperactive phenotype. Methods: Rna-Sequencing was performed in leukocyte-depleted platelet RNA from 6 HIV subjects and 3 healthy controls. qRT–PCR validation was performed to validate our candidate transcripts. Results: Across the 9 platelet samples, there was an average of 28.3 million mapped reads per sample with an average unique mapping rate of 91.6 %. Using a cut-off of normalized counts ≥1 across the 9 samples, we found 11988 expressed transcripts. Conclusions: Our study represents a detailed analysis of platelet transcriptome generated by RNA-seq technology in HIV patients under ART. Further experiments identified the mechanism of our transcript target in mediating platelet activity and platelet cell effector function.
2018-06-10 | GSE99737 | GEO