Epithelial miR-149-5p up-regulation is associated with immune evasion in progressive bronchial premalignant lesions

Ning, B.; Chiu, D. J.; Pfefferkorn, R. M.; Kefella, Y.; Kane, E.; Reyes-Ortiz, V.; Liu, G.; Zhang, S.; Liu, H.; Sultan, L.; Green, E.; Constant, M.; Spira, A. E.; Campbell, J. D.; Reid, M. E.; Varelas, X.; Burks, E. J.; Lenburg, M. E.; Mazzilli, S. A.; Beane, J. E.

doi:10.1101/2025.02.03.636307

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bioRxiv · 10.1101/2025.02.03.636307

Epithelial miR-149-5p up-regulation is associated with immune evasion in progressive bronchial premalignant lesions

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Abstract

The molecular drivers bronchial premalignant lesion progression to invasive lung squamous cell carcinoma are not well defined. Prior work profiling longitudinally collected bronchial premalignant lesion biopsies by RNA sequencing defined a proliferative subtype, enriched with bronchial dysplasia. We found that a gene co-expression module associated with interferon gamma signaling and antigen processing/presentation was down-regulated in progressive/persistent versus regressive lesions within the proliferative subtype, suggesting a functional impact of these genes on immune evasion. RNA from these same premalignant lesions was profiled by microRNA (miRNA) sequencing and a miRNA-gene network analysis identified hsa-miR-149-5p as a potential regulator of this antigen presentation gene co-expression module associated with lesion progression. hsa-miR-149-5p was found to be predominantly expressed in the epithelium and up-regulated in progressive/persistent versus regressive proliferative lesions while targets of this miRNA, the transcriptional coactivator of MHC-I gene expression, NLRC5, and the genes it regulates were down-regulated. MicroRNA in situ hybridization of hsa-miR-149-5p in tissue from adjacent fixed biopsies showed that hsa-miR-149-5p was increased in areas of bronchial dysplasia in progressive/persistent versus regressive lesions. Imaging mass cytometry showed that NLRC5 protein expression was decreased in progressive/persistent versus regressive lesions within areas of hyperplasia, metaplasia, and dysplasia. Additionally, basal cells with high versus low levels of NLRC5 were found to be in close spatial proximity to CD8 T cells, suggesting that these cells exhibit increased functional MHC-I gene expression in lesions with low hsa-miR-149-5p expression. Collectively, our data suggests a functional role for hsa-miR-149-5p in bronchial premalignant lesions and may serve as a therapeutic target for PML immunomodulation. STATEMENT OF SIGNIFICANCEIntegrative analysis across bronchial premalignant lesions has identified and localized a potential regulator of immune evasion in progressive/persistent lesions that could be a novel therapeutic target.

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Ning, B., Chiu, D. J., Pfefferkorn, R. M., Kefella, Y., Kane, E., Reyes-Ortiz, V., Liu, G., Zhang, S., Liu, H., Sultan, L., Green, E., Constant, M., Spira, A. E., Campbell, J. D., Reid, M. E., Varelas, X., Burks, E. J., Lenburg, M. E., Mazzilli, S. A., Beane, J. E.. 2025-02-05. Epithelial miR-149-5p up-regulation is associated with immune evasion in progressive bronchial premalignant lesions. https://doi.org/10.1101/2025.02.03.636307

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