A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer (cohort 2)

Ayse Bassez, Hanne Vos, Laurien Van Dyck, Giuseppe Floris, Ingrid Arijs, Christine Desmedt, Bram Boeckx, Marlies Vanden Bempt, Ines Nevelsteen, Kathleen Lambein, Kevin Punie, Patrick Neven, Abhishek D. Garg, Hans Wildiers, Junbin Qian, Ann Smeets, Diether Lambrechts

Study ID

ayse_et_al_2021_cohort2_all

Total cells

50,693

Abtract
Immune-checkpoint blockade (ICB) combined with neoadjuvant chemotherapy improves pathological complete response in breast cancer. To understand why only a subset of tumors respond to ICB, patients with hormone receptor-positive or triple-negative breast cancer were treated with anti-PD1 before surgery. Paired pre- versus on-treatment biopsies from treatment-naive patients receiving anti-PD1 (nā€‰=ā€‰29) or patients receiving neoadjuvant chemotherapy before anti-PD1 (nā€‰=ā€‰11) were subjected to single-cell transcriptome, T cell receptor and proteome profiling. One-third of tumors contained PD1-expressing T cells, which clonally expanded upon anti-PD1 treatment, irrespective of tumor subtype. Expansion mainly involved CD8+ T cells with pronounced expression of cytotoxic-activity (PRF1, GZMB), immune-cell homing (CXCL13) and exhaustion markers (HAVCR2, LAG3), and CD4+ T cells characterized by expression of T-helper-1 (IFNG) and follicular-helper (BCL6, CXCR5) markers. In pre-treatment biopsies, the relative frequency of immunoregulatory dendritic cells (PD-L1+), specific macrophage phenotypes (CCR2+ or MMP9+) and cancer cells exhibiting major histocompatibility complex class I/II expression correlated positively with T cell expansion. Conversely, undifferentiated pre-effector/memory T cells (TCF7+, GZMK+) or inhibitory macrophages (CX3CR1+, C3+) were inversely correlated with T cell expansion. Collectively, our data identify various immunophenotypes and associated gene sets that are positively or negatively correlated with T cell expansion following anti-PD1 treatment. We shed light on the heterogeneity in treatment response to anti-PD1 in breast cancer.

Author's cell type

T cell
14655 cells
Fibroblast
11640 cells
Cancer cell
10453 cells
Myeloid cell
6661 cells
Endothelial cell
5411 cells
B cell
1620 cells
pDC
194 cells
Mast cell
59 cells

Breast cancer type

Triple negative breast cancer
36721 cells
ER+ breast cancer
10679 cells
HER2+ breast cancer
3293 cells

Clonotype expansion

Patients with clonotype expansion (E)
25471 cells
Patients with no/limited clonotype expansion (NE)
25222 cells

Cohort

neoadjuvant chemo
50693 cells

Condition

triple-negative breast cancer
36721 cells
ER-positive breast cancer
10679 cells
HER2-positive breast cancer
3293 cells

Developmental stage

young adult
26129 cells
middle-age adult
13334 cells
old adult
11230 cells

Gender

female
50693 cells

Louvain clustering

Cluster 2
7492 cells
Cluster 3
6229 cells
Cluster 13
5140 cells
Cluster 1
4836 cells
Cluster 11
4590 cells
Cluster 9
4585 cells
Cluster 14
3481 cells
Cluster 16
2332 cells
Cluster 8
2085 cells
Cluster 10
2043 cells
Cluster 17
1808 cells
Cluster 18
1719 cells
Cluster 5
1665 cells
Cluster 12
907 cells
Cluster 6
760 cells
Cluster 4
548 cells
Cluster 7
420 cells
Cluster 15
53 cells

Quantification

CellRanger 2.1.1
21539 cells
CellRanger 2.2.0
12782 cells
CellRanger 3.1.0
8324 cells
CellRanger 3.0.2
8048 cells

Sample ID

Patient 34
12005 cells
Patient 35
7225 cells
Patient 32
6241 cells
Patient 36
5557 cells
Patient 39
3962 cells
Patient 40
3367 cells
Patient 33
3293 cells
Patient 38
2712 cells
Patient 42
2631 cells
Patient 41
2326 cells
Patient 37
1374 cells

Sampling technique

surgical resection
30325 cells
core needle biopsy
20368 cells

Sequencing platform

Chromium 5' v1
50693 cells

Storage technique

fresh
50693 cells

Subject ID

Patient 34
12005 cells
Patient 35
7225 cells
Patient 32
6241 cells
Patient 36
5557 cells
Patient 39
3962 cells
Patient 40
3367 cells
Patient 33
3293 cells
Patient 38
2712 cells
Patient 42
2631 cells
Patient 41
2326 cells
Patient 37
1374 cells

Timepoint

On-treatment
30325 cells
Pre-treatment
20368 cells

Tissue

breast
50693 cells

Treatment

neoadjuvant pembrolizumab combination
30325 cells
anthracycline-taxane based chemotherapy
20368 cells

Tumor biopsy

primary tumor
50693 cells