CRISPR  pooled screen and QuantSeq 3' mRNA sequencing to identify  microRNAs (miRNAs) important for Breast Cancer 3D growth [RNA-seq]
Breast cancer (BC) is a heterogeneous malignancy with distinct molecular subtypes and clinical characteristics. Tumor-initiating cells (TICs) constitute a small subset of cancer cells responsible for tumor initiation and progression. MicroRNAs (miRNAs), small non-coding RNA molecules, play a pivotal role in regulating gene expression and have been implicated in cancer development and progression. In this study, we conducted genome-wide CRISPR-Cas9 screens within 3D tumorspheres of two BC cell lines, MCF7 (ER+) and HCC1395 (TNBC). Our objective was to identify miRNAs that govern TIC viability, employing CRISPR/Cas9 pooled screens that targeted a total of 19,052 genes and 1,864 miRNAs. By suppressing relevant miRNAs following QuantSeq 3' mRNA sequencing we identify the genes regulated by those miRNAs Overall design: We inhibited the top 6 miRNAs  (using anti-miRNA inhibitors) detected by the CRISPR screen and clinically relevant following QuantSeq 3' mRNA sequencing