Upregulation of RNA Processing Factors in Poorly Differentiated Lung Cancer Cells

Abstract

Intratumoral heterogeneity in non–small cell lung cancer (NSCLC) has been appreciated at the histological and cellular levels, but the association of less differentiated pathology with poor clinical outcome is not understood at the molecular level. Gene expression profiling of intact human tumors fails to reveal the molecular nature of functionally distinct epithelial cell subpopulations, in particular the tumor cells that fuel tumor growth, metastasis, and disease relapse. We generated primary serum-free cultures of NSCLC and then exposed them to conditions known to promote differentiation: the air-liquid interface (ALI) and serum. The transcriptional network of the primary cultures was associated with stem cells, indicating a poorly differentiated state, and worse overall survival of NSCLC patients. Strikingly, the overexpression of RNA splicing and processing factors was a prominent feature of the poorly differentiated cells and was also observed in clinical datasets. A genome-wide analysis of splice isoform expression revealed many alternative splicing events that were specific to the differentiation state of the cells, including an unexpectedly high frequency of events on chromosome 19. The poorly differentiated cells exhibited alternative splicing in many genes associated with tumor progression, as exemplified by the preferential expression of the short isoform of telomeric repeat-binding factor 1 (TERF1), also known as Pin2. Our findings demonstrate the utility of the ALI method for probing the molecular mechanisms that underlie NSCLC pathogenesis and provide novel insight into posttranscriptional mechanisms in poorly differentiated lung cancer cells.

Cancer-associated fibroblasts suppress SOX2-induced dysplasia in a lung squamous cancer coculture

“…Specifically, primary human NSCLC cell cultures were embedded as single cells (≤6,500 cells per 100 μL) in growth factor-reduced Matrigel and cultured with serum-free (SF) medium. The four primary cell cultures (TUM622, TUM426, TUM449, and TUM110) were previously established directly from either human NSCLC tumors or the corresponding PDX (28–30) (see also SI Appendix , Fig. S1 A ).…”

Integrated Analysis of the Functions and Prognostic Values of RNA Binding Proteins in Lung Squamous Cell Carcinoma

“…In recent years, a large number of studies, have reported the role of aberrant RNA metabolism and RNA processing in various diseases (Li et al, 2017(Li et al, , 2018Li S. et al, 2019;. RNA processing factors were shown to have increased expression in poorly differentiated non-small-cell lung cancer cells (Geles et al, 2016). The TGF-beta signaling pathway is a classical tumorigenesis-related pathway; it exerts dual and opposing roles in oncogenesis, inhibiting cell proliferation in early tumors and inducing tumor progression and metastasis in advanced cancer (Seoane and Gomis, 2017;Batlle and Massague, 2019).…”

RNA processing genes characterize RNA splicing and further stratify lower-grade glioma

“…A dysregulated RNA expression profile is an important hallmark of tumors (19). RNA processing factors, such as RNA-binding proteins and RNA methylation regulators, are the main factors controlling the life cycle of RNA in cells and thus play vital roles in numerous diseases and cancers by determining the final content and isoforms of mature RNA transcripts (6,(20)(21)(22)(23)(24). However, studies on RNA processing factors in gliomas have mainly focused on GBM, and the roles of RNA processing factors in stem cell maintenance, cell adhesion, cell migration, cell growth, colony formation, and invasiveness have been demonstrated in GBM (6,20,(25)(26)(27)(28)(29).…”