Identification of clinically relevant T cell receptors for personalized T cell therapy using combinatorial algorithms.

A central challenge in developing personalized cancer cell immunotherapy is the identification of tumor-reactive T cell receptors (TCRs). By exploiting the distinct transcriptomic profile of tumor-reactive T cells relative to bystander cells, we build and benchmark TRTpred, an antigen-agnostic in silico predictor of tumor-reactive TCRs. We integrate TRTpred with an avidity predictor to derive a combinatorial algorithm of clinically relevant TCRs for personalized T cell therapy and benchmark it in patient-derived xenografts.

Clonal expansion of intra-epithelial T cells in breast cancer revealed by spatial transcriptomics.

The spatial distribution of tumor-infiltrating lymphocytes (TIL) predicts breast cancer outcome and response to systemic therapy, highlighting the importance of an intact tissue structure for characterizing tumors. Here, we present ST-FFPE, a spatial transcriptomics method for the analysis of formalin-fixed paraffin-embedded samples, which opens the possibility of interrogating archival tissue. The method involves extraction, exome capture and sequencing of RNA from different tumor compartments microdissected by laser-capture, and can be used to study the cellular composition of tumor microenvironment. Focusing on triple-negative breast cancer (TNBC), we characterized T cells, B cells, dendritic cells, fibroblasts and endothelial cells in both stromal and intra-epithelial compartments. We found a highly variable spatial distribution of immune cell subsets among tumors. This analysis revealed that the immune repertoires of intra-epithelial T and B cells were consistently less diverse and more clonal than those of stromal T and B cells. T-cell receptor (TCR) sequencing confirmed a reduced diversity and higher clonality of intra-epithelial T cells relative to the corresponding stromal T cells. Analysis of the top 10 dominant clonotypes in the two compartments showed a majority of shared but also some unique clonotypes both in stromal and intra-epithelial T cells. Hyperexpanded clonotypes were more abundant among intra-epithelial than stromal T cells. These findings validate the ST-FFPE method and suggest an accumulation of antigen-specific T cells within tumor core. Because ST-FFPE is applicable for analysis of previously collected tissue samples, it could be useful for rapid assessment of intratumoral cellular heterogeneity in multiple disease and treatment settings.

In the era of the 24 h laboratory, does communicating Gram stain results from blood cultures flagging positive outside of conventional working hours alter patient management?

AIMS: As laboratories move towards 24 h a day working patterns, we aim to evaluate if expediting the availability of provisional blood culture results outside of normal working hours would derive clinical benefit. METHODS: 116 blood cultures flagging positive outside of conventional working hours (20:00-09:00) were studied. In each case, medical records were reviewed and cases discussed with clinicians to determine if earlier communication of results would have altered management and affected the outcome. RESULTS: Organisms were seen in 102/116 blood cultures. In total, 76/82 (92.7%) patients with cultures deemed to be significant were on an antibiotic. The isolate was sensitive to the prescribed antibiotic in 56/74 (76%) cases. Input from a microbiologist is likely to have altered management in 14 (13.7%) cases, but unlikely to have affected any outcomes. CONCLUSIONS: We found no compelling evidence that expediting the availability of Gram stain results from positive blood cultures alone improves patient outcome.