Tumor Microenvironment Profiles Reveal Distinct Therapy-Oriented Proteogenomic Characteristics in Colorectal Cancer.

Nan Wang,Xia Li,Zhentao Song,Zhiyong Ding,Lingbo Xia,Li Zhang,Rongshui Wang,Jue Wang,Aiwen Wu

doi:10.3389/fbioe.2021.757378

Abstract

Advances in immunotherapy have made an unprecedented leap in treating colorectal cancer (CRC). However, more effective therapeutic regimes need a deeper understanding of molecular architectures for precise patient stratification and therapeutic improvement. We profiled patients receiving neoadjuvant chemotherapy alone or in combination with immunotherapy (PD-1 checkpoint inhibitor) using Digital Spatial Profiler (DSP), a high-plex spatial proteogenomic technology. Compartmentalization-based high-plex profiling of both proteins and mRNAs revealed pronounced immune infiltration at tumor regions associated with immunotherapy treatment. The protein and the corresponding mRNA levels within the same selected regions of those patient samples correlate, indicating an overall concordance between the transcriptional and translational levels. An elevated expression of PD-L1 at both protein and the mRNA levels was discovered in the tumor compartment of immunotherapy-treated patients compared with chemo-treated patients, indicating potential prognostic biomarkers are explorable in a spatial manner at the local tumor microenvironment (TME). An elevated expression of PD-L1 was verified by immunohistochemistry. Other compartment-specific biomarkers were also differentially expressed between the tumor and stromal regions, indicating a dynamic interplay that can potentiate novel biomarker discovery from the TME perspectives. Simultaneously, a high-plex spatial profiling of protein and mRNA in the tumor microenvironment of colorectal cancer was performed.

Highlights

This study proved that tertiary lymphoid structures (TLSs) defined by a high density of CD3/CD4 T cells, B cells, CD163 macrophage, and CD4/ CD45RO T cells are associated with better clinical outcomes for Crohn’s-like reaction (CLR) phenotype, whereas PD-1/CD4 expression T cells in granulocyte defined neighborhood positively correlated with survival in diffuse inflammatory infiltration (DII) subtype of colorectal cancer (CRC) (Schurch et al, 2020)
This study looked at the spatial-directed proteogenomic profiling on 4 Stage III CRC formalin-fixed paraffin-embedded (FFPE) patient samples to provide insights into the therapeutic mechanisms and biomarkers discovery, and compare the biological differences between mRNA and protein under the same experimental setting
The correlation matrix provided a distinct association between regions of interest (ROIs) and genes, respectively, with strong tumoral and stromal ROI clusters confirming the robustness of the technology

Summary

Introduction

As colorectal cancer is one of the leading causes of cancer deaths around the world, multiple clinical trials have proven the efficacy and rationale for immunotherapy in improving treatment outcomes for late-stage colorectal cancer (CRC), especially for those bearing genetic traits of mismatch-repair deficient (MMR-D) and/or microsatellite instability (MSI-H) (Golshani and Zhang, 2020; Siegel et al, 2018; Overman et al, 2017; PD-1 Inhibitor Bests Chemo for Colorectal Cancer, 2020).Spatial Proteomic and Transcriptomic ProfilingNotwithstanding the effort made toward MMR-D and/or MSI-H CRC, of more clinical importance, about 95% of CRC patients are MMR proficient (MMR-P) and/or microsatellite stable (MSS). Specific clusters of TH1-like (T-helper 1-like) T-cell co-expressing CXCL13 (Chemokine C-X-C motif ligand 13) and BHLHE40 (Class E basic helix-loop-helix protein 40) were associated with only microsatellite-instable tumors and shared an increased level of IGFLR1 (IGF-like family receptor 1) with CD8 exhausted T cells, indicating likely co-stimulatory mechanisms and biomarkers for MSI-H patients (Zhang et al, 2018). Focusing on myeloid cell populations in CRC, other groups discovered novel SPP1 (secreted phosphoprotein 1) expressing tumor association macrophage (TAM) that could play critical roles in CRC tumorigenesis. This subpopulation exhibits a tighter association with cancer-associated fibroblast stressing the dynamic cross-talk within the TME (Zhang et al, 2020)

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Conclusion