Identification of disease-promoting stromal components by comparative proteomic and transcriptomic profiling of canine mammary tumors using laser-capture microdissected FFPE tissue

Abstract

Cancer-associated stroma (CAS) profoundly influences progression of tumors including mammary carcinoma (mCA). Canine simple mCA represent relevant models of human mCA, notably also with respect to CAS. While transcriptomic changes in CAS of mCA are well described, it remains unclear to what extent these translate to the protein level. Therefore, we sought to gain insight into the proteomic changes in CAS and compare them with transcriptomic changes in the same tissue. To this end, we analyzed CAS and matched normal stroma using laser-capture microdissection (LCM) and LC-MS/MS in a cohort of 14 formalin-fixed paraffin embedded (FFPE) canine mCAs that we had previously characterized using LCM-RNAseq. Our results reveal clear differences in protein abundance between CAS and normal stroma, which are characterized by changes in the extracellular matrix, the cytoskeleton, and cytokines such as TNF. The proteomics- and RNAseq-based analyses of LCM-FFPE show a substantial degree of correlation, especially for the most deregulated targets and a comparable activation of pathways. Finally, we validate transcriptomic upregulation of LTBP2, IGFBP2, COL6A5, POSTN, FN1, COL4A1, COL12A1, PLOD2, COL4A2, and IGFBP7 in CAS on the protein level and demonstrate their adverse prognostic value for human breast cancer. Given the relevance of canine mCA as a model for the human disease, our analysis substantiates these targets as disease-promoting stromal components with implications for breast cancer in both species.

Single-cell transcriptomic analysis suggests two molecularly distinct subtypes of intrahepatic cholangiocarcinoma

“…ID3 + cells located opposite to ALB + cells in the trajectory and were enriched for pathways in the collagen-containing extracellular matrix and negative regulation of cell adhesion. For example, the expression of COL12A1 , which encodes the alpha chain of type XII collagen and is overexpressed in several cancer types 38 , 39 , decreased gradually along the transition from ALB- cells to ALB + cells (Fig. 5e ).…”

Cancer-Associated Stromal Fibroblast-Derived Transcriptomes Predict Poor Clinical Outcomes and Immunosuppression in Colon Cancer

“…Numerous evidence indicated that immunohistochemistry is a highly effective substantial tool to predict survival prognosis in patients with various cancer types [ 78 ]. Since laser-capture micro-dissected stromal FFPE tissue can be utilized to identify molecular proteomic and transcriptomic profiling [ 79 ], measuring the key genes with immunohistochemistry in the laser micro-dissected CAFs may lead the clinicians to taking decisions in diagnosis and specific gene-oriented targeted therapy of colon cancer patients. However, for using these findings in clinical and therapeutic applications, further experimental and clinical verification would be necessary.…”

Single-Cell Transcriptomic Analysis Reveals Two Molecularly and Clinically Distinct Subtypes of Intrahepatic Cholangiocarcinoma

“…ID3+ cells located opposite to ALB+ cells in the trajectory and were enriched for pathways in collagen containing extracellular matrix and negative regulation of cell adhesion. For example, the expression of COL12A1, which encodes the alpha chain of type XII collagen and is overexpressed in several cancer types 34,35 , decreased gradually along transition from ALB-cells to ALB+ cells (Fig. 5e).…”