scholarly journals Plasma-derived extracellular vesicle analysis and deconvolution enable prediction and tracking of melanoma checkpoint blockade outcome

2020 ◽  
Vol 6 (46) ◽  
pp. eabb3461
Author(s):  
Alvin Shi ◽  
Gyulnara G. Kasumova ◽  
William A. Michaud ◽  
Jessica Cintolo-Gonzalez ◽  
Marta Díaz-Martínez ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Immune Checkpoint Inhibitors ◽  
Immune Status ◽  
Checkpoint Inhibitors ◽  
Extracellular Vesicle ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Non Invasive ◽  
Tumor Persistence ◽  
Immune Changes

Immune checkpoint inhibitors (ICIs) show promise, but most patients do not respond. We identify and validate biomarkers from extracellular vesicles (EVs), allowing non-invasive monitoring of tumor- intrinsic and host immune status, as well as a prediction of ICI response. We undertook transcriptomic profiling of plasma-derived EVs and tumors from 50 patients with metastatic melanoma receiving ICI, and validated with an independent EV-only cohort of 30 patients. Plasma-derived EV and tumor transcriptomes correlate. EV profiles reveal drivers of ICI resistance and melanoma progression, exhibit differentially expressed genes/pathways, and correlate with clinical response to ICI. We created a Bayesian probabilistic deconvolution model to estimate contributions from tumor and non-tumor sources, enabling interpretation of differentially expressed genes/pathways. EV RNA-seq mutations also segregated ICI response. EVs serve as a non-invasive biomarker to jointly probe tumor-intrinsic and immune changes to ICI, function as predictive markers of ICI responsiveness, and monitor tumor persistence and immune activation.

Abstract 128: RNA-seq Based Non-Invasive Endovascular Biopsy of Brain Arteriovenous Malformations

Stroke ◽  
2020 ◽  
Vol 51 (Suppl_1) ◽  
Author(s):  
Ethan Winkler ◽  
David McCoy ◽  
Zhengda Sun ◽  
Daniel Cooke
Keyword(s):  
Differentially Expressed Genes ◽  
Pearson Correlation ◽  
Rna Extraction ◽  
Correlation Coefficients ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Detachable Coil ◽  
Illumina Hiseq ◽  
Non Invasive

Introduction: To-date, there is no accurate means to identify which bAVMs will bleed and treatment remains controversial. Hypothesis: We developed an endovascular biopsy (EB) technique to isolate endothelial cells (ECs) from bAVMs in patients. We hypothesized this technique would allow RNA-seq analysis of relevant bAVM-related molecular pathways. Methods: EB was performed during angiography for bAVM patients undergoing resection. Cells were obtained from a bAVM juxta-nidal feeding artery and iliac artery (control) with a detachable coil and 0.035 inch wire. ECs were isolated with fluorescence assisted cell sorting (FACS). bAVM tissue was obtained from surgery, dissociated and underwent FACS sorting. Total RNA extraction and library preparation was performed, and samples sequenced on an Illumina HiSeq 4000 sequencer. Reads were aligned with Kallisto, and differentially expressed genes identified between bAVM and control with Sleuth using likelihood ratio tests. Correlations between EB and resected tissues were calculated with Pearson correlation coefficients. Principle Component Analysis (PCA) was used to assess for cell clustering. Results: EB was performed in 4 patients without complication or adverse event. PCA showed separation of bAVM ECs from controls. Analysis demonstrated 106 differentially expressed genes (FDR p ≤ 0.05). KEGG pathway analysis on these genes revealed enrichment in bAVM-related RAS/MAPK cell signaling functionally related to trophic factor, chemokine and gap junction signaling pathways. Detected genes were strongly correlated between EB and ECs isolated from resected tissues (R 2 = 0.77 for artery, nidus, and vein tissue). Results shown in Figure 1 . Conclusions: EB is a safe technique to permit non-invasive sequencing of bAVMs. These results implicate dysregulated KRAS/MAPK signaling in adult bAVMs. Whether this technique will allow for better natural history prediction or targeted medical therapies requires future study.

scholarly journals Plasma-derived exosomal analysis and deconvolution enables prediction and tracking of melanoma checkpoint blockade response

2019 ◽  
Author(s):  
Alvin Shi ◽  
Gyulnara G. Kasumova ◽  
William A. Michaud ◽  
Jessica Cintolo-Gonzales ◽  
Marta Díaz Martínez ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Immune Checkpoint ◽  
Peripheral Blood ◽  
Predictive Biomarkers ◽  
Response To Therapy ◽  
Checkpoint Blockade ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Discovery Cohort ◽  
Non Invasive

AbstractPurposeImmune checkpoint inhibitors (ICI) have demonstrated promising therapeutic benefit although a majority will not respond. Here we identify and validate predictive biomarkers from plasma-derived exosomes that allow non-invasive monitoring of tumor intrinsic and host immune status and prediction of ICI success.Experimental DesignTranscriptomic profiling of peripheral blood bulk exosomes and tumors from a discovery cohort of 50 patients with metastatic melanoma treated with ICI was undertaken; a further validation cohort of 30 patients was utilized to validate findings from the discovery cohort. We designed a Bayesian probabilistic model to partition bulk exosomes into tumor-specific and non-tumor-specific proportions.ResultsExosomal RNA signatures exhibit significant correlations with tumor transcriptomes. Exosomal profiles reflect several key biological drivers of ICI resistance or melanoma progression, exhibit significantly differentially expressed genes and pathways, and correlate with and are predictive of clinical response to therapy. Our deconvolution model estimates contributions from tumor and non-tumor sources, enabling more precise interpretation of differentially-expressed genes and pathways. Exosomal RNA-seq mutational information can be used to segregate responders and non-responders.ConclusionsPeripheral blood-derived exosomes can serve as a non-invasive biomarker to jointly probe tumor-intrinsic and immune changes to ICI, and can potentially function as predictive markers of ICI responsiveness and a monitoring tool for tumor persistence and immune activation.Statement of SignificanceWe use transcriptomic analysis of bulk, non-selected, peripheral blood derived exosomes to reveal both tumor-intrinsic and immune-derived signatures predictive of early response to immune checkpoint inhibitor therapy. We develop a novel computational model to classify exosomal transcripts into tumor and non-tumor components and establish relevance in immune checkpoint blockade therapy. We show that tumor driver load from RNA-seq mutational calls are significantly different between responders and non-responders.

scholarly journals Exon-level estimates improve the detection of differentially expressed genes in RNA-seq studies

RNA Biology ◽  
2021 ◽  
pp. 1-8
Author(s):  
Arfa Mehmood ◽  
Asta Laiho ◽  
Laura L. Elo
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Exon Level

scholarly journals HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 244 ◽  
Author(s):  
Antonio Victor Campos Coelho ◽  
Rossella Gratton ◽  
João Paulo Britto de Melo ◽  
José Leandro Andrade-Santos ◽  
Rafael Lima Guimarães ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Differentially Expressed Genes ◽  
Cd4 T Cells ◽  
Expression Profiles ◽  
Meta Analysis ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Infected Cells ◽  
Hiv 1

HIV-1 infection elicits a complex dynamic of the expression various host genes. High throughput sequencing added an expressive amount of information regarding HIV-1 infections and pathogenesis. RNA sequencing (RNA-Seq) is currently the tool of choice to investigate gene expression in a several range of experimental setting. This study aims at performing a meta-analysis of RNA-Seq expression profiles in samples of HIV-1 infected CD4+ T cells compared to uninfected cells to assess consistently differentially expressed genes in the context of HIV-1 infection. We selected two studies (22 samples: 15 experimentally infected and 7 mock-infected). We found 208 differentially expressed genes in infected cells when compared to uninfected/mock-infected cells. This result had moderate overlap when compared to previous studies of HIV-1 infection transcriptomics, but we identified 64 genes already known to interact with HIV-1 according to the HIV-1 Human Interaction Database. A gene ontology (GO) analysis revealed enrichment of several pathways involved in immune response, cell adhesion, cell migration, inflammation, apoptosis, Wnt, Notch and ERK/MAPK signaling.

scholarly journals Phytophthora infestans Sporangia Produced in Culture and on Tomato Leaflet Lesions Show Marked Differences in Indirect Germination Rates, Aggressiveness, and Global Transcription Profiles

2019 ◽  
Vol 32 (5) ◽  
pp. 515-526 ◽  
Author(s):  
William E. Fry ◽  
Sean P. Patev ◽  
Kevin L. Myers ◽  
Kan Bao ◽  
Zhangjun Fei
Keyword(s):  
Phytophthora Infestans ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Moist Chamber ◽  
Field Isolates ◽  
Rxlr Effectors ◽  
Transcription Profiles ◽  
Independent Field ◽  
Pure Cultures

Sporangia of Phytophthora infestans from pure cultures on agar plates are typically used in lab studies, whereas sporangia from leaflet lesions drive natural infections and epidemics. Multiple assays were performed to determine if sporangia from these two sources are equivalent. Sporangia from plate cultures showed much lower rates of indirect germination and produced much less disease in field and moist-chamber tests. This difference in aggressiveness was observed whether the sporangia had been previously incubated at 4°C (to induce indirect germination) or at 21°C (to prevent indirect germination). Furthermore, lesions caused by sporangia from plates produced much less sporulation. RNA-Seq analysis revealed that thousands of the >17,000 P. infestans genes with a RPKM (reads per kilobase of exon model per million mapped reads) >1 were differentially expressed in sporangia obtained from plate cultures of two independent field isolates compared with sporangia of those isolates from leaflet lesions. Among the significant differentially expressed genes (DEGs), putative RxLR effectors were overrepresented, with almost half of the 355 effectors with RPKM >1 being up- or downregulated. DEGs of both isolates include nine flagellar-associated genes, and all were down-regulated in plate sporangia. Ten elicitin genes were also detected as DEGs in both isolates, and nine (including INF1) were up-regulated in plate sporangia. These results corroborate previous observations that sporangia produced from plates and leaflets sometimes yield different experimental results and suggest hypotheses for potential mechanisms. We caution that use of plate sporangia in assays may not always produce results reflective of natural infections and epidemics.

scholarly journals Bioinformatics-based Screening of Key Genes for Saponin Metabolism in Quinoa

2021 ◽  
Author(s):  
Chengang Guo ◽  
Zhimin wei ◽  
Wei Lyu ◽  
Yanlou Geng
Keyword(s):  
Differentially Expressed Genes ◽  
Principal Component ◽  
Enrichment Analysis ◽  
Hierarchical Cluster ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Differential Analysis ◽  
Rna Seq ◽  
Protein Coding ◽  
Key Genes

Abstract Quinoa saponins have complex, diverse and evident physiologic activities. However, the key regulatory genes for quinoa saponin metabolism are not yet well studied. The purpose of this study was to explore genes closely related to quinoa saponin metabolism. In this study, the significantly differentially expressed genes in yellow quinoa were firstly screened based on RNA-seq technology. Then, the key genes for saponin metabolism were selected by gene set enrichment analysis (GSEA) and principal component analysis (PCA) statistical methods. Finally, the specificity of the key genes was verified by hierarchical clustering. The results of differential analysis showed that 1654 differentially expressed genes were achieved after pseudogenes deletion. Therein, there were 142 long non-coding genes and 1512 protein-coding genes. Based on GSEA analysis, 116 key candidate genes were found to be significantly correlated with quinoa saponin metabolism. Through PCA dimension reduction analysis, 57 key genes were finally obtained. Hierarchical cluster analysis further demonstrated that these key genes can clearly separate the four groups of samples. The present results could provide references for the breeding of sweet quinoa and would be helpful for the rational utilization of quinoa saponins.

scholarly journals 522 Transcriptomic changes in cancer patients treated with immune-checkpoint inhibitors

2021 ◽  
Vol 9 (Suppl 3) ◽  
pp. A552-A552
Author(s):  
Dmitrii Shek ◽  
Bo Gao ◽  
Joey Lai ◽  
Won-Hee Yoon ◽  
Tania Moujaber ◽  
...  
Keyword(s):  
Cancer Patients ◽  
Differentially Expressed Genes ◽  
Immune Checkpoint ◽  
Functional Annotation ◽  
Immune Checkpoint Inhibitors ◽  
Checkpoint Inhibitors ◽  
Link Type ◽  
Pre Treatment ◽  
Grade 3 ◽  
Transcriptomic Changes

BackgroundImmune-checkpoint inhibitors (ICIs) are monoclonal antibodies that block inhibitory CTLA-4/PD-1 signalling pathways and thus boost cytotoxic T cell antitumor activity. ICIs have been proven effective in various malignancies, but there is a lack of knowledge regarding factors associated with ICI efficacy and safety. This study aims to examine transcriptomic changes in cancer patients treated with ICIs and their potential association with related clinical outcomes.MethodsThis is a prospective multicentre cohort study (NCT04631731) recruiting cancer patients treated with (1) ICI monotherapy; (2) ICI dual therapy; (3) ICI + kinase inhibitor; (4) ICI + platinum-doublet chemotherapy. Peripheral blood is collected at baseline and 6–8 weeks after first ICI treatment as well as after the development of immune-related adverse events (irAEs, grade 2 and higher). Whole transcriptome sequencing (Novaseq S4 300 cycle lane, Illumina) was performed and followed by functional annotation using the ConsensusPath-DB platform.Results22 patients were recruited to the study and had paired blood taken. Two patients had developed grade 3–4 irAEs. RNA sequencing analysis identified 3,000 genes that were significantly dysregulated at week 6–8 after ICI commencement as compared to pre-treatment in n=20 recruited patients without irAEs (figure 1). Functional annotation established that 132 pathways were associated with the identified set of dysregulated genes. Among them: (1) pre-NOTCH processing in Golgi, (2) Interleukin-15 signalling; (3) STAT5 activation, and (4) RORA activation of gene expression possessed a gene set enrichment of at least 80% and p<0.01. In 2 patients with grade 3 immune-mediated hepatitis, both treated with combination of CTLA-4/PD-1 inhibitors, analysis revealed that 360 and 325 were 2-fold up- and downregulated respectively upon onset of toxicity as compared to both pre-treatment and 1-week post-steroid treatment. Interestingly, this gene set possessed minimal overlap when compared to genes dysregulated in patients without irAEs. Moreover, functional annotation established different pathways that were associated with toxicity. The highest enrichment scores belonged to pathways regulating cell cycle and apoptotic pathways driven by CDC25A, p53 and BCL-2, among others.Abstract 522 Figure 1Volcano plot representing the differentially expressed genesThe figure representing differentially expressed genes elucidated in this pilot study. N=3000 genes were significantly dysregulated between pre- and week 6–8 post-IO commencement.ConclusionsThe preliminary analysis of the first 22 patients recruited to NCT04631731 confirms that ICI treatment interferes with expression of coding and non-coding RNAs. Importantly, patients with and without irAEs show different patterns of transcriptomic changes as well as variability among activated cellular pathways. This data emphasises the need for further exploration and validation of transcriptomic changes in a larger cohort. In the near future, RNA signatures may be utilised as biomarkers to rapidly and accurately diagnose irAEs.AcknowledgementsN/ATrial RegistrationClinicalTrials.Gov identification number: NCT04631731ReferencesN/AEthics ApprovalThis study has been approved by the Western Sydney Local Health District (WSLHD) Human Research Ethics Committee on the November 9th, 2020 to be conducted at Blacktown and Westmead Public Hospitals of the WSLHD, Sydney, NSW, Australia.ConsentEach participant recruited to this translational study has provided written consent approved on the November 6th, 2020 (MASTER version) by the WSLHD HREC.

Expression profile analysis of Differentially Expressed Genes in Human Coronary Artery Endothelial Cells Induced by Serum from Kawasaki Disease: A preliminary study

2020 ◽  
Author(s):  
Xue Fan ◽  
Meng Li ◽  
Min Xiao ◽  
Cong Liu ◽  
Mingguo Xu
Keyword(s):  
Endothelial Cells ◽  
Coronary Artery ◽  
Kawasaki Disease ◽  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Healthy Children ◽  
Rna Seq ◽  
Human Coronary Artery

Abstract Background: Kawasaki disease (KD) leads to coronary artery damage and the etiology of KD is unknown. The present study was designed to explore the differentially expressed genes (DEGs) in KD serum-induced human coronary artery endothelial cells (HCAECs) by RNA-sequence (RNA-seq). Methods: HCAECs were stimulated with serum (15% (v/v)), which were collected from 20 healthy children and 20 KD patients, for 24 hours. DEGs were then detected and analyzed by RNA-seq and bioinformatics analysis. Results: The expression of SMAD1, SMAD6, CD34, CXCL1, PITX2, and APLN was validated by qPCR. 102 genes, 59 up-regulated and 43 down-regulated genes, were significantly differentially expressed in KD groups. GO enrichment analysis showed that DEGs were enriched in cellular response to cytokines, cytokine-mediated signaling pathway, and regulation of immune cells migration and chemotaxis. KEGG signaling pathway analysis showed that DEGs were mainly involved in cytokine−cytokine receptor interaction, chemokine signaling pathway, and TGF−β signaling pathway. Besides, the mRNA expression levels of SMAD1, SMAD6, CD34, CXCL1, and APLN in the KD group were significantly up-regulated compared with the normal group, whilePITX2 was significantly down-regulated. Conclusion: 102 DEGs in KD serum-induced HCAECs were identified, and six new targets were proposed as potential indicators of KD.

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