Identification of histology-correlated intra-tumor genomic heterogeneity through stimulated Raman scattering micro-dissection sequencing

Morphologic and genetic alterations play crucial roles in tumorigenesis, and lay the foundation of diagnosis and cancer research. However, preservation of morphology with staining compromises the genetic materials. Here we propose SMD-Seq, a new approach to achieve consecutive label-free histological images construction and in situ laser micro-dissection of cancer samples for location-specific transcriptome and genome analysis. We applied SMD-Seq to unstained cryosections of human oral squamous cell carcinoma (OSCC) samples. The high quality and purity of genetic materials enabled the discovery of inter- and intra-tumor heterogeneities in both morphology and genetics. The correlative morphologic and molecular analysis of SMD-Seq is capable of dissecting the genetic variation and its effect on gene expression under shape, and provides complementary insights in cancer study.