ProjecTILs Case Studies

We will be posting here interesting/instructive case studies of single-cell data analysis using ProjecTILs:

1. MC38 TILs with clonotype analysis

In this case study, we build an integrated scRNA-seq analysis workflow to interpret the transcriptional (scRNA-seq) and clonal structure (scTCR-seq) of tumor-infiltrating T cells in MC38 colon adenocarcinoma.

2. Project human data on mouse TIL atlas

Exploiting the ortholog mapping functionality of ProjecTILs, we project scRNA-seq from melanoma patients (Sade-Feldman, 2018) onto a mouse reference atlas, to interpret T cell phenotype differences between responders and non-responders to checkpoint blockade therapy.

3. T cell diversity across multiple tissues

Apply ProjecTILs to investigate transcriptional profiles of CD8 T cells in chronic infection from six different tissues.

4. Exhausted CD8 T cells are associated with ICB responsiveness in breast cancer

Re-analysis of the dataset by Bassez et al. Nat Med (2020) of breast cancer patients treated with anti-PD-1 therapy

5. Memory phenotypes of CD4+ T cells after acute infection

A case study of projection of virus-specific CD4+ T cells in late acute infection.

6. Detecting novel/unrepresented cell states

Projection of tumor-specific T cells on a viral reference, illustrating how one can interpret subtypes not represented in the reference.

7. Effect of anti-PD-L1 therapy on CD4+ T cells

Analysing the transcriptional phenotype of CD4+ T cells in chronic infection after treatment with an anti-PD-L1 antibody.

8. Exploring dendritic cell diversity in human spleen

Projection of human DCs from spleen from the study of Brown et al. Cell (2019)