Genome profiles of pathologist-defined cell clusters by multiregional LCM and G&T-seq in one triple-negative breast cancer patient.
Cell Rep Med, 2021/10/19;2(10):100404.
Zhu Z[1, 2], Wang W[3, 4], Lin F[1], Jordan T[3], Li G[1], Silverman S[5], Qiu S[1], Joy AA[6], Chen C[1], Hockley DL[6], Zhang X[1], Zhou Q[1], Postovit LM[7], Zhang X[1], Hou Y[1], Mackey JR[6], Li B[1], Wong GK[1, 3, 8]
Affiliations
PMID: 34755126DOI: 10.1016/j.xcrm.2021.100404
Impact factor: 16.988
Abstract
Pathological examination is the gold standard for cancer diagnosis, and breast tumor cells are often found in clusters. We report a case study on one triple-negative breast cancer (TNBC) patient, analyzing tumor development, metastasis, and prognosis with simultaneous DNA and RNA sequencing of pathologist-defined cell clusters from multiregional frozen sections. The cell clusters are isolated by laser capture microdissection (LCM) from primary tumor tissue, lymphatic vessels, and axillary lymph nodes. Data are reported for a total of 97 cell clusters. A combination of tumor cell-cluster clonality and phylogeny reveals 3 evolutionarily distinct pathways for this patient, each associated with a unique mRNA signature, and each correlated with disparate survival outcomes. Hub gene analysis indicates that extensive downregulation of ribosomal protein mRNA is a potential marker of poor prognosis in breast cancer.
Keywords: G&T-seq; LCM; lymphovascular invasion; metastasis; triple-negative breast cancer
MeSH terms
Cell Aggregation; Cell Lineage; Clone Cells; DNA, Neoplasm; Disease Progression; Epithelial Cells; Fatal Outcome; Female; Gene Expression Regulation, Neoplastic; Genome, Human; High-Throughput Nucleotide Sequencing; Humans; Lymph Nodes; Lymphatic Metastasis; Lymphatic Vessels; Lymphocytes; Phylogeny; Prognosis; RNA, Neoplasm; Ribosomal Proteins; Triple Negative Breast Neoplasms; Young Adult
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