Bioinformatics analysis identifies potential chemoresistance-associated genes across multiple types of cancer

Post-Hypoxic Cells Promote Metastatic Recurrence after Chemotherapy Treatment in TNBC

Simple Summary

Intratumoral hypoxia is a negative prognostic factor in breast cancer progression and recurrence. By implementing a hypoxia fate-mapping system, we followed cells that experience intratumoral hypoxia in vivo and determined that these cells have an increased ability to metastasize compared to cells that were never exposed to hypoxia. In this work, we investigate whether cells that experienced intratumoral hypoxia are also resistant to chemotherapy. By utilizing both in vivo and ex vivo models, we conclude that metastatic cells found in the lung and liver, that were exposed to hypoxia in the primary tumor, are less sensitive to doxorubicin and paclitaxel and drive recurrence after treatment. Our studies also suggest that chemoresistance is associated with a cancer stem cell-like phenotype that is maintained in post-hypoxic cells.

Abstract

Hypoxia occurs in 90% of solid tumors and is associated with treatment failure, relapse, and mortality. HIF-1α signaling promotes resistance to chemotherapy in cancer cell lines and murine models via multiple mechanisms including the enrichment of breast cancer stem cells (BCSCs). In this work, we utilize a hypoxia fate-mapping system to determine whether triple-negative breast cancer (TNBC) cells that experience hypoxia in the primary tumor are resistant to chemotherapy at sites of metastasis. Using two orthotopic mouse models of TNBC, we demonstrate that cells that experience intratumoral hypoxia and metastasize to the lung and liver have decreased sensitivity to doxorubicin and paclitaxel but not cisplatin or 5-FU. Resistance to therapy leads to metastatic recurrence caused by post-hypoxic cells. We further determined that the post-hypoxic cells that metastasize are enriched in pathways related to cancer stem cell gene expression. Overall, our results show that even when hypoxic cancer cells are reoxygenated in the bloodstream they retain a hypoxia-induced cancer stem cell-like phenotype that persists and promotes resistance and eventually recurrence.

Identification of Key Gene Targets for Sensitizing Colorectal Cancer to Chemoradiation: an Integrative Network Analysis on Multiple Transcriptomics Data

PURPOSE

Colorectal cancer (CRC) is a main cause of morbidity and mortality in the world. Chemoradioresistance is a major problem in CRC treatment. Identification of novel therapeutic targets in order to overcome treatment resistance in CRC is necessary.

METHODS

In this study, gene expression omnibus (GEO) database was searched to find microarray datasets. Data normalization/analyzing was performed using ExAtlas. The gene ontology (GO) and pathway enrichment analysis was performed using g:Profiler. Protein-protein interaction network (PPIN) was constructed by Search Tool for the Retrieval of Interacting Genes (STRING) and analyzed using Cytoscape. Survival analysis was done using Kaplan-Meier curve method.

RESULTS

Forty-one eligible datasets were included in study. A total of 12,244 differentially expressed genes (DEGs) and 7337 unique DEGs were identified. Among them, 1187 DEGs were overlapped in ≥ 3 datasets. Fifty-five overlapped genes were considered as hub genes. Common hub genes in chemo/radiation/chemoradiation datasets were chosen as the essential candidate genes (n = 13). Forty-one hub gene and 7 essential candidate genes were contributed in the significant modules. The modules were mainly enriched in the signaling pathways of senescence, autophagy, NF-κB, HIF-1, stem cell pluripotency, notch, neovascularization, cell cycle, p53, chemokine, and PI3K-Akt. NGFR, FGF2, and PROM1 genes were significantly predictors of CRC patient's survival.

CONCLUSION

Our study revealed three-gene signatures as potential therapeutic targets and also candidate molecular markers in CRC chemoradioresistance.