Bulk RNA-seq analysis of gene expression characteristics induced by Adamts7 over-expression in B2905-M4 subcutaneous implanted tumors

Secreted proteins are central mediators of intercellular communications and can serve as therapeutic targets in diverse diseases. The ~1903 human genes encoding secreted proteins are difficult to study through common genetic approaches. To address this hurdle and, more generally, to discover cancer therapeutics, we developed the Cancer Immunology Data Engine (CIDE, https://cide.ccr.cancer.gov), which incorporates 90 omics datasets spanning 8575 tumor profiles with immunotherapy outcomes from 17 solid tumor types. CIDE systematically identifies all genes associated with immunotherapy outcomes. Then, we focused on secreted proteins prioritized by CIDE without known cancer roles and validated regulatory effects on immune checkpoint blockade for AOAH, CR1L, COLQ, and ADAMTS7 in mouse models. The top hit, AOAH (Acyloxyacyl Hydrolase), potentiates immunotherapies in multiple tumor models by sensitizing T-cell receptors to weak antigens and protecting dendritic cells through depleting immunosuppressive arachidonoyl phosphatidylcholines and oxidized derivatives. For subcutaneous tumor models, 3E6 B2905-M4 cells were injected subcutaneously into 7-8-week-old female C57BL/6J. Tumor volume was measured based on the formula: (Length×Width^2)/2. Mice were euthanized according to a pre-determined survival endpoint defined as tumor volume ≥ 2000 mm^3 or the tumor length (longer diameter) ≥ 20 mm. We aim to harvest tumors on the same day for RNA-seq analysis. However, as tumors with Adamts7 over-expression (OE) grew much faster than tumors with vector OE, vector-OE tumors were too small for analysis when Adamts7-OE tumors reached endpoints. Thus, first, we harvested two Adamts7-OE tumors at day 35 post-tumor inoculation when they reached endpoints. Three tumors from the Adamts7 and vector OE groups were collected together at day 45 post-tumor inoculation. Finally, two vector tumors reached a reasonable size (shortest edge > 5mm) at day 50 post-tumor inoculation and were harvested for analysis.