Project description:Purpose Antibody-blockade of PD-1 shows durable responses, but so far, few biomarkers accurately predict if patients with metastatic melanoma will respond. Experimental design We analyzed baseline serum samples (n=56) and tumor cell cultures (n=8), from melanoma patients treated with anti-PD1 therapy. Two approaches concentrating low abundant proteins in serum and two different mass spectrometry (MS) methods were applied: depletion of high abundant proteins with shotgun-MS, and N-glycosite enrichment combined with SWATH-MS. Tumor cell cultures were processed as whole cell lysates with subsequent shotgun-MS. Results Focusing on the non-responder proteome, we identified pathways such as inflammatory processes, cell adhesion and migration, scavenger receptor activity, RAGE receptor binding, platelet aggregation, neutrophil degranulation and integrin signaling to be upregulated. Analyzing the tumor cell proteome revealed a distinctive immunophenotype with CD antigens highly overexpressed in non-responders. Validation of a subset of these markers, performed by immunofluorescence staining of a tissue microarray, revealed a higher mean of positive cells in the tumor microenvironment of non-responders. Validation of serum proteome markers on a second baseline cohort by using a timsTOF for ion mobility MS, revealed significant differences between responder and non-responder for the proteins ORM2, SERPINA1, EFEMP1, and VASN. TCGA survival analysis demonstrated prognostic significance for multiple proteins of our signature correlating with lower overall survival in melanoma patients. Based on this study, we suggest a protein-panel for responsiveness to PD-1 blockade consisting of 14 serum and 33 tumor cell markers that will be the basis for further research.
Project description:We screened TKI-treated-CML-samples in different-phases based on < or >10% copies of BCR-ABL, undetected and control-samples for generating transcriptomics-profile. Transcriptionally, three clusters were identified which showed correlation with BCR-ABL transcript-levels i.e. <10% copies (I-cluster) , undetectable (II-cluster) and >10% copies (III-cluster). CML-new cases as well as Tyrosine kinase treated-different phases of CML
Project description:Expression of human miRNAs was analyzed in 150 ng of total RNA from nine post-transplant lymphoproliferative disorder (PTLD) patient samples, categorized as Epstein-Barr virus-positive (EBV+ , n = 4) or EBV- (n = 5) PTLD by hybridization on Affymetrix’s GeneChip miR Array 4.0 (Stanford Functional Genomics Facility, Stanford, CA). The Bioconductor ‘oligo’ package was used to perform array background subtraction, quantile normalization, and summarization by median polish. The normalized gene expression dataset was annotated with the ‘pd.mirna.4.0’ annotation library package in R (R Core Team). The expression data was fit to a linear model using the ‘stats’ package in R (R Core Team). Moderated t-statistics and log-odds of differential expression were calculated using the empirical Bayes method. False discovery rate (FDR) tests were performed with the Benjamini-Hochberg procedure for multiple testing correction in R (R Core Team).
Project description:By use of large-scale miRNA expression profiling we identified microRNAs with significantly different expressions in epithelial-mesenchymal transition (EMT)-positive tumors and selected microRNAs for training phase of the study to evaluate their diagnostic and prognostic potential. Further, microRNAs were forwarded to validation phase, where all evaluated microRNA candidates were confirmed to be significantly deregulated in tumor tissue, some of them significantly differed in metastatic tumors, correlated with clinical stage, with Fuhrman grade and with overall survival.
Project description:We screened TKI-treated-CML-samples in different-phases based on < or >10% copies of BCR-ABL, undetected and control-samples for generating transcriptomics-profile. Transcriptionally, three clusters were identified which showed correlation with BCR-ABL transcript-levels i.e. <10% copies (I-cluster) , undetectable (II-cluster) and >10% copies (III-cluster). CML-new cases as well as Tyrosiine kinase treated-different phases of CML
Project description:We evaluated blood samples from 6 patients with metastatic melanoma treated with anti-LAG3+anti-PD1 (160+480 mg) in a phase I trial (NCT01968109) using single-cell RNA and T cell receptor (TCR) sequencing (scRNA+TCRαβ-seq, 10X 5') combined with other multiomics profiling (flow, cytokine, TCRb-seq) from a larger cohort of 40 patients. This data set include three time points, including baseline, 1 month, and 3 month. The sorting is CD45+.
Project description:Transmissible gastroenteritis virus (TGEV), a member of the coronaviridae family, could cause fatal diarrhea of piglets and result in numerous economic losses. Previous studies demonstrated that TGEV infection could lead to mitochondrial damage and up-regulate miR-4331 level. So miR-4331 may play an important regulatory role in the control of mitochondrial function. To explore the potential role of miR-4331 in mitochondrial damage, we adopted a strategy consisting of quantitative proteomic analysis of porcine kidney (PK-15) cells in response to miR-4331 and TGEV infection. Eventually, 69 differentially expressed proteins were gained. The target of miR-4331 was identified. The effects of miR-4331 and its target RB1 on mitochondrial Ca2+ level, mitochondrial membrane potential (MMP), interleukin-1 receptor accessory protein (IL1RAP), p38 MAPK signaling pathway were investigated. The results showed that miR-4331 elevated mitochondrial Ca2+ level, reduced MMP, targets Retinoblastoma 1 (RB1), up-regulated IL1RAP, and induced activation of p38 MAPK pathway during TGEV infection. RB1 was identified as the direct targets of miR-4331 and down-regulated IL1RAP, suppressed the activation of p38 MPAK, and attenuated TGEV-induced mitochondrial damage. In addition, IL1RAP played a positive role in activating p38 MAPK signaling and negative role in TGEV-induced mitochondrial damage. The data indicate that miR-4331 aggravates TGEV-induced mitochondrial damage by repressing expression of RB1, promoting IL1RAP, and activating p38 MAPK pathway.
Project description:Mutations in isocitrate dehydrogenase 2 (IDH2) occur in many cancers including Acute Myeloid Leukemia (AML). In preclinical models mutant IDH2 causes partial hemopoietic differentiation arrest. Recently, we showed that single agent Enasidenib, a first-in-class, selective mutant IDH2 inhibitor, produces a 40% response in relapsed/refractory AML patients by promoting differentiation. Yet, the rate, extend and duration of the clinical benefits of Enasidenib vary from one patient to another. To investigate how the genetic mutational landscape, at baseline or at relapse, contributes in modulating response to Enasidenib, WES analyses on FACS-sorted blasts from baseline, best response and/or relapse samples from 16 Enasidenib-treated patients were performed. WES analyses were also performed on the CD3+ cells from the same patients, which may be used as germinal control samples.