Pluto Bioinformatics

GSE148476: Transcriptome analysis of purified T cells from chronic lymphocytic leukemia patients treated with avadomide alone or in combination with immune checkpoint blocking antibodies

Bulk RNA sequencing

Cancer treatment has been transformed by checkpoint blockade therapies, with the highest anti-tumor activities of anti-programmed death 1 (PD-1) antibody (Ab) therapy seen in Hodgkin lymphoma. Disappointingly, response rates have been low in the non-Hodgkin lymphomas, with no activity seen in relapsed chronic lymphocytic leukemia (CLL) with anti-PD-1 Ab. Thus, identifying more powerful combination therapy is required for these patients. Here, we pre-clinically demonstrate enhanced T cell mediated anti-CLL activity following combinational therapy with anti-PD-1 or anti-PD-1 ligand (PD-L1) Ab and avadomide, a cereblon-modulating agent.; Next-generation RNA sequencing was performed on highly purified T cells from treatment nave CLL patients treated for 18 hours with avadomide or anti-PD-1 (nivolumab) or PD-L1 (durvalumab) alone or in combinations. Patient samples were selected to represent extremes of prognosis (n=6 good and n=6 poor prognostic groups). Total RNA was extracted using the RNeasy isolation kit (Qiagen) while the library preparation of extracted mRNA was performed by utilizing the TruSeq stranded mRNA kit (Illumina) and the resulting library sequencing was performed on an Illumina HiSeq 2500 system. In all analyses the primary assembly of hg38 was used (ENCODE version) and the annotation from Gencode v24. Alignment was performed using a two-pass mode with STAR (v2.5.2b) on the full genome and counts were obtained using the quantmode GeneCounts option. Salmon (v 0.7) was used to obtain pseudoalignments on transcripts and genes on the trimmed fastq files. Differentially expressed genes were identified by application of the voom R package. Each treatment group was compared to vehicle to estimate the effect size and statistical significance of gene expression changes between treatment and control.; Differential expression pathway analysis revealed that the top functional gene categories common for all the avadomide and combination treated patient samples were related to the response to both type I and II interferon (IFN) signalling, as well as inflammatory, TNF- signalling, IL-6/JAK/STAT3 and IL-2/STAT5 signalling responses. Pathway analysis revealed a strong enrichment of genes involved in T cell proliferation, cytokine and chemokine signalling, F-actin polymerization, T cell differentiation and co-stimulation. Notably, avadomide induced the expression of IFN type I inducible chemokines Cxcl9, Cxcl10 and Cxcl11 that have been associated with activation of Th1 immunity and favourable response to immunotherapy in solid cancer. In addition, genes associated with IFN-induced counter-regulatory pathways including Cd274 (PD-L1), Lag3 (lymphocyte-activation gene 3) and Ido1 (indoleamine 2,3 deoxygenase) were also upregulated by avadomide. Our analysis revealed that avadomide and the combination treatments induced IFN signaling in both good and poor prognostic disease subtypes, suggesting that therapies targeting patient T cells could be effective for all CLL patients. Thus, these results demonstrate the ability of avadomide to normalize dysfunctional IFN and chemokine responses in patient T cells that are linked to anti-tumor immunity. SOURCE: Nikolaos Ioannou ( - The Rayne Institute King’s College London

View this experiment on Pluto Bioinformatics