Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis [scRNA-seq 2]

Molecular and cellular characterization of tumors has become essential due to the complex and heterogeneous nature of cancer disease. In recent decades, many bioinformatic tools and experimental techniques have been developed to achieve personalized characterization of tumors. However, sample handling continues to be a major challenge as limitations such as prior treatments before sample acquisition, the amount of tissue obtained, transportation, or the inability to process fresh samples pose a challenge for experimental strategies that require viable cell suspensions. Here, we present an optimized protocol that allows recovery of highly viable cell suspensions from breast cancer biopsies. Using these cell suspensions we successfully characterized genome architecture through Hi-C. Also, we evaluated single-cell gene expression and the tumor cellular microenvironment through single cell RNAseq. Both technologies are key in the detailed and personalized molecular characterization of tumor samples. The protocol described here opens the possibility to obtain viable cell suspensions from biopsies in a simple and efficient manner The cell suspension was derived from a Tru-Cut biopsy specimen obtained from adjacent tissue from a Mexican female patient diagnosed with untreated triple-negative breast cancer. The adjacent tissue was collected at least 1 cm away from the tumor-affected area and presented a macroscopically healthy appearance.