Tumor immunological phenotype signature-based high-throughput screening for the discovery of combination immunotherapy compounds

Abstract

Combination immunotherapy is promising to overcome the limited objective response rates of immune checkpoint blockade (ICB) therapy. Here, a tumor immunological phenotype (TIP) gene signature and high-throughput sequencing–based high-throughput screening (HTS2) were combined to identify combination immunotherapy compounds. We firstly defined a TIP gene signature distinguishing “cold” tumors from “hot” tumors. After screening thousands of compounds, we identified that aurora kinase inhibitors (AKIs) could reprogram the expression pattern of TIP genes in triple-negative breast cancer (TNBC) cells. AKIs treatments up-regulate expression of chemokine genes CXCL10 and CXCL11 through inhibiting aurora kinase A (AURKA)–signal transducer and activator of transcription 3 (STAT3) signaling pathway, which promotes effective T cells infiltrating into tumor microenvironment and improves anti-programmed cell death 1 (PD-1) efficacy in preclinical models. Our study established a novel strategy to discover combination immunotherapy compounds and suggested the therapeutic potential of combining AKIs with ICB for the treatment of TNBC.

ZetaSuite, A Computational Method for Analyzing Multi-dimensional High-throughput Data, Reveals Genes with Opposite Roles in Cancer Dependency

“…The increasing power and decreasing cost with deep sequencing technologies have enabled multi-dimensional analyses of gene expression. By coupling high throughput screening with high throughput sequencing (HTS 2 ), it is possible to utilize a specific set of genes as a surrogate for specific cellular activities in chemical and genomic screens 8,9 . By monitoring hundred or even thousand functional readouts, such “ultrahigh-content” screens offer numerous advantages over traditional one-dimensional screens, among which include the ability to deduce gene networks directly from the primary screen results and the feasibility to perform a drug screen without relying on a pre-defined druggable target 8,9 .…”

“…By coupling high throughput screening with high throughput sequencing (HTS 2 ), it is possible to utilize a specific set of genes as a surrogate for specific cellular activities in chemical and genomic screens 8,9 . By monitoring hundred or even thousand functional readouts, such “ultrahigh-content” screens offer numerous advantages over traditional one-dimensional screens, among which include the ability to deduce gene networks directly from the primary screen results and the feasibility to perform a drug screen without relying on a pre-defined druggable target 8,9 . More recently, we have extended the HTS 2 approach to a genome-wide screen by scoring hundreds of alternative splicing events to identify global splicing regulators 23 , illustrating a two-dimensional screen strategy that can be adapted to study many different paradigms in regulated gene expression.…”

“…The array-based strategy has been extended to examine multiple functional parameters in response to each treatment, known as multi-content (many-to-a few) screen 1,7 . In the deep sequencing era, the array-based strategy has further evolved toward two-dimensional high throughput (many-to-many) screen because of the feasibility to perform functional perturbations and monitor functional consequences, both in a high throughput fashion, as exemplified by the HTS 2 screen platform to monitor a gene signature comprising a set of specific genes, rather than a single gene 8,9 . Pooled shRNA or sgRNA libraries have also been used to treat hundreds of cell lines to deduce cancer dependencies [10][11][12][13] , representing another format of two-dimensional screen.…”

High-Throughput Strategies for the Discovery of Anticancer Drugs by Targeting Transcriptional Reprogramming

“…Combined with this gene signature, HTS 2 technology was applied for the identification of immunotherapy combination agents in TNBC. The results showed that aurora kinase inhibitors reprogram the expression of TIP gene signature and thus promote effective Tcell infiltration into the tumor microenvironment, significantly improving anti-programmed cell death 1 (PD-1) efficacy in preclinical models (51).…”

A Complex Metabolic Network Confers Immunosuppressive Functions to Myeloid-Derived Suppressor Cells (MDSCs) within the Tumour Microenvironment

“…Recently, a conserved stroma-immune relationship has been identified in 20 different cancers, and this relationship is capable of playing a prognostic role in response to ICI-based immunotherapy [23]. Additionally, alterations in both the adhesion molecules in endothelial cells and the chemokine-based axis can strongly influence T cell homing into the tumour [24][25][26]. The lack of expression of costimulatory receptors and the downregulation of major histocompatibility complex (MHC) molecules on the surface of tumour cells can affect TIL activation [27].…”