G C A T T A C G G C A T genes Article Blockade of PD-1, PD-L1, and TIM-3 Altered Distinct Immune- and Cancer-Related Signaling Pathways in the Transcriptome of Human Breast Cancer Explants 1, 1, 2 1 1, Reem Saleh y, Salman M. Toor y, Dana Al-Ali , Varun Sasidharan Nair and Eyad Elkord * 1 Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha 34110, Qatar;
[email protected] (R.S.);
[email protected] (S.M.T.);
[email protected] (V.S.N.) 2 Department of Medicine, Weil Cornell Medicine-Qatar, Doha 24144, Qatar;
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[email protected]; Tel.: +974-4454-2367 Authors contributed equally to this work. y Received: 21 May 2020; Accepted: 21 June 2020; Published: 25 June 2020 Abstract: Immune checkpoint inhibitors (ICIs) are yet to have a major advantage over conventional therapies, as only a fraction of patients benefit from the currently approved ICIs and their response rates remain low. We investigated the effects of different ICIs—anti-programmed cell death protein 1 (PD-1), anti-programmed death ligand-1 (PD-L1), and anti-T cell immunoglobulin and mucin-domain containing-3 (TIM-3)—on human primary breast cancer explant cultures using RNA-Seq. Transcriptomic data revealed that PD-1, PD-L1, and TIM-3 blockade follow unique mechanisms by upregulating or downregulating distinct pathways, but they collectively enhance immune responses and suppress cancer-related pathways to exert anti-tumorigenic effects.