Cancer Ecology : TME (CRC & PDAC)

Question 1

How does IMC work?

Answer 1

uses Abs that is tagged with a heavy metal to identify different cell types based on the proteins they express and can measure dozens of markers at once

Question 2

What is the workflow of spatial transcriptomic profiling?

Answer 2

1. Selection regions of interest → each of these slides hasspatially arranged spotsor grids that are coated withcapture probes—these probes are essential for capturing the RNA from the tissue.
   
   • Vimentin → identifes anything in the stroma
   • PanCK+ → epithelium
2. Segmentation

Question 3

Explain the tumorigenesis of CRC

Answer 3

Normal epithelium → 5q loss APC → early adenoma (DNA hypomethylation happens) →12p activation + KRAS → intermediate adenoma → 18q loss + DCC → late adenoma → 17p loss + p53 → carcinoma → other alterations → metastasis

Question 4

What molecule is upregulated in CRC?

Answer 4

Upregulation of macrophage checkpoints; SIRPa. Cancer cells often exploit this system by overexpressing CD47, tricking the immune system into leaving them alone. It sends this “don’t eat me” signal by binding to SIRPα on macrophages.

Question 5

Function of vimentin and PanCK in spatial transcriptomics profiling?

Answer 5

• Vimentin → hallmark of mesenchymal cells (fibroblasts, endothelial cells, and certain immune cells). Basically identifes anything in the stroma
• PanCK → structural proteins found inepithelial cells → identifies **epithelial cells aka cancer cells

Question 6

Characteristics of PDAC

Answer 6

Bad prognosis and symptoms appear quite late