Background:
Immunotherapies targeting immune checkpoint proteins CTLA-4, PD-1, and PD-L1 have saved lives, but these therapies have only been effective in some patients. Patients positive for expression of immune checkpoint proteins in the tumor microenvironment show better response to immune checkpoint inhibitors. Consequently, knowledge of which genes are consistently expressed in lymphocytes within the tumor microenvironment can convey potentially effective and complementary new immunotherapy targets.
Results:
We identified 54 genes that have higher co-expression with the pan T-cell marker
CD3E
than
CTLA4
or
PDCD1
. In a dataset of 26 patients who received anti-PD-1 therapy, we observed that co-expression between
CD3E
and
PDCD1
was higher among responders than non-responders, supporting our correlation-based approach.
Conclusions:
The genes highlighted in these analyses, which include
CD6
,
TIGIT
,
CD96
, and
SLAMF6
, warrant further investigation of their therapeutic potential.
Methods:
We analyzed and ranked genes that were co-expressed with the pan T-cell marker
CD3E
in 9,601 human tumors, spanning 31 cancer types. To further identify targets that may be complementary to existing PD-1 therapy, we examined and ranked genes with high
CD3E
co-expression and relatively low
PDCD1
co-expression.