Figure 1.

Preparation of whole-organ maps for multi-platform genomic profiling

(A) Top view of the mapping grid for whole-organ sampling.

(B) Diagram showing open cystectomy mounted on a paraffin block.

(C) Diagram showing the details of the mapping grid preserving the surface urothelium for histologic mapping and facilitating simultaneous DNA/RNA extraction as well as its quality assessment of cytologic preparations. The four preparation steps are described in the material and methods section.

(D) Top view of the mapping grid superimposed over bladder mucosa.

(E) Impression of the mapping grid on the bladder surface.

(F) A whole-organ histologic map prepared by sampling the entire bladder mucosa in a luminal map (map 24).

(G) A whole-organ histologic map prepared by sampling the entire bladder mucosa in a basal map (map 19). The histologic map code is as follows: NU, normal urothelium; MD, mild dysplasia; MdD, moderate dysplasia; SD, severe dysplasia; CIS, carcinoma in situ; UC, urothelial carcinoma. For analytical purposes, samples of MD and MdD were combined and referred to as LGIN. Samples of SD and CIS were combined and referred to as HGIN.

(H) Expression patterns for luminal and basal markers and BLT scores for mucosal and tumor samples obtained from a cystectomy specimen with luminal bladder cancer in map 24.

(I) Expression patterns for luminal and basal markers and BLT scores for mucosal and tumor samples obtained from a cystectomy specimen with basal bladder cancer in map 19.