Single cell T cell landscape and T cell receptor repertoire profiling of AML in context of PD-1 blockade therapy

Abstract

In contrast to the curative effect of allogenic stem cell transplantation in acute myeloid leukemia via T cell activity, only modest responses are achieved with checkpoint-blockade therapy, which might be explained by T cell phenotypes and T cell receptor (TCR) repertoires. Here, we show by paired single-cell RNA analysis and TCR repertoire profiling of bone marrow cells in relapsed/refractory acute myeloid leukemia patients pre/post azacytidine+nivolumab treatment that the disease-related T cell subsets are highly heterogeneous, and their abundance changes following PD-1 blockade-based treatment. TCR repertoires expand and primarily emerge from CD8+ cells in patients responding to treatment or having a stable disease, while TCR repertoires contract in therapy-resistant patients. Trajectory analysis reveals a continuum of CD8+ T cell phenotypes, characterized by differential expression of granzyme B and a bone marrow-residing memory CD8+ T cell subset, in which a population with stem-like properties expressing granzyme K is enriched in responders. Chromosome 7/7q loss, on the other hand, is a cancer-intrinsic genomic marker of PD-1 blockade resistance in AML. In summary, our study reveals that adaptive T cell plasticity and genomic alterations determine responses to PD-1 blockade in acute myeloid leukemia.

Immune dysfunction signatures predict outcomes and define checkpoint blockade–unresponsive microenvironments in acute myeloid leukemia

“…As shown in Figure 9D , high IFN scores were associated with prolonged OS ( P = 0.01; optimal cut-point = 6.39). The analysis of scRNA-Seq data from 8 patients with relapsed/refractory AML treated with AZA + nivolumab ( 36 ) confirmed enrichment of IED68 scores on CD4 + and CD8 + T cells, NK cells, and NK/T cell precursors ( Supplemental Figure 25A ). In line with findings in the AZA+Pembro cohort, the IED68 score was significantly lower at baseline in responders to nivolumab-based immunotherapy; Supplemental Figure 25B ).…”

“…The semantic similarity between IED172 genes in the context of their chromosomal location is shown in Figure 3B . No genes in the IED172 signature were on chromosome 7, the loss of which has been associated with failure to respond to PD-1 blockade ( 36 ). Furthermore, IED172 genes were enriched in Kyoto Encyclopedia of Genes and Genomes pathways related to T helper differentiation, T cell receptor (TCR) signaling, and T and NK cell–mediated cytotoxicity ( Supplemental Table 5 ), as well as miRNAs implicated in cancer immune escape and immune metabolism ( 37 – 39 ) ( Supplemental Figure 8 , B and C).…”

Distinct molecular and immune hallmarks of inflammatory arthritis induced by immune checkpoint inhibitors for cancer therapy

“…Likely dying or apoptotic cells where >15% of transcripts derived from the mitochondrial genome were also excluded. Next, likely doublets or multiplets were detected and carefully removed through a multi-step approach as described in our recent studies 73 – 75 . Doublets and multiplets were identified by the following methods: (1) library complexity: cells with high complexity libraries (in which detected transcripts are aligned to >6500 genes) were removed; (2) Cluster distribution: doublets or multiplets likely form distinct clusters with hybrid expression features and exhibit an aberrantly high gene count; (3) cluster marker gene expression: cells of a cluster express markers from distinct lineages (e.g., cells in the T-cell cluster co-expressed myeloid cell markers and vice versa); (4) doublet detection algorithm: Scrublet 76 , an algorithm to predict doublets in scRNA-seq data, was applied to further identify and clean doublets that could have been missed by steps 1–3.…”

Plasmacytoid Dendritic Cells, a Novel Target in Myeloid Neoplasms

“…Current clinical trials targeting PD-1, PD-L1 and CTLA-4 are now predominant and, in combination with an hypomethylating agent, aim to enhance both activities [ 147 , 148 ]. Of note, pDCs could also persist in the BM microenvironment even after anti-PD-1 therapies [ 149 ]. In addition, the use of vaccination in AML may overcome the limitations of the immune checkpoint blockade by evoking a clonal T-cell response [ 150 ].…”