Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion.
Chris J FrangiehJohannes C MelmsPratiksha I ThakoreKathryn R Geiger-SchullerPatricia HoAdrienne M LuomaBrian ClearyLivnat JerbyShruti MaluMichael S CuocoMaryann ZhaoCasey R AgerMeri RogavaLila HoveyAsaf RotemChantale BernatchezKai W WucherpfennigBruce E JohnsonOrit Rozenblatt-RosenDirk SchadendorfAviv RegevBenjamin IzarPublished in: Nature genetics (2021)
Resistance to immune checkpoint inhibitors (ICIs) is a key challenge in cancer therapy. To elucidate underlying mechanisms, we developed Perturb-CITE-sequencing (Perturb-CITE-seq), enabling pooled clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 perturbations with single-cell transcriptome and protein readouts. In patient-derived melanoma cells and autologous tumor-infiltrating lymphocyte (TIL) co-cultures, we profiled transcriptomes and 20 proteins in ~218,000 cells under ~750 perturbations associated with cancer cell-intrinsic ICI resistance (ICR). We recover known mechanisms of resistance, including defects in the interferon-γ (IFN-γ)-JAK/STAT and antigen-presentation pathways in RNA, protein and perturbation space, and new ones, including loss/downregulation of CD58. Loss of CD58 conferred immune evasion in multiple co-culture models and was downregulated in tumors of melanoma patients with ICR. CD58 protein expression was not induced by IFN-γ signaling, and CD58 loss conferred immune evasion without compromising major histocompatibility complex (MHC) expression, suggesting that it acts orthogonally to known mechanisms of ICR. This work provides a framework for the deciphering of complex mechanisms by large-scale perturbation screens with multimodal, single-cell readouts, and discovers potentially clinically relevant mechanisms of immune evasion.
Keyphrases
- single cell
- rna seq
- high throughput
- genome wide
- crispr cas
- cancer therapy
- dendritic cells
- immune response
- case report
- stem cells
- poor prognosis
- randomized controlled trial
- induced apoptosis
- squamous cell carcinoma
- bone marrow
- mesenchymal stem cells
- papillary thyroid
- study protocol
- pain management
- nucleic acid
- peripheral blood