lncRNA 3222401L13Rik/ENSG00000272070 modulates microglial inflammatory programs in association with PU.1

Pradhan, R.; Sakib, M. S.; Kaurani, L.; Krueger, D. M.; Pena, T.; Burckhardt, S.; Schuetz, A.-L.; Kronenberg-Verstee, D.; Delalle, I.; Sananbenesi, F.; Fischer, A.

doi:10.1101/2025.10.31.685723

bioRxiv · 10.1101/2025.10.31.685723

lncRNA 3222401L13Rik/ENSG00000272070 modulates microglial inflammatory programs in association with PU.1

Pradhan, R.·Sakib, M. S.·Kaurani, L.·Krueger, D. M.·Pena, T.·Burckhardt, S.·Schuetz, A.-L.·Kronenberg-Verstee, D.·Delalle, I.·Sananbenesi, F.·Fischer, A.

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Abstract

Long non-coding RNAs (lncRNAs) are emerging as key regulators of brain function, but their contribution to microglial aging and neurodegenerative disease remains largely unknown. Because only 1.5% of the human genome encodes proteins, whereas the vast majority of transcripts belong to the largely unexplored non-coding RNAome, elucidating the functions of non-coding RNAs provides an unprecedented opportunity to expand the space for therapeutic discovery. We recently identified the glia-enriched lncRNA 3222401L13Rik as upregulated in the aging mouse hippocampus. Here, we investigated its function in microglia and its human homolog ENSG00000272070. We found that 3222401L13Rik is expressed in both astrocytes and microglia and increases with age. Knockdown of 3222401L13Rik in primary microglia led to enhanced expression of pro-inflammatory cytokines, including TNF, and increased phagocytic activity. RNA-sequencing revealed widespread transcriptional changes enriched for TNF and complement signaling pathways. The human homolog ENSG00000272070 showed conserved functions in iPSC-derived microglia, where its loss similarly promoted inflammatory gene expression and phagocytosis. Mechanistically, 3222401L13Rik interacts with the microglial transcription factor PU.1, and its depletion overlapped with PU.1-driven transcriptional programs. Consistent with these findings, ENSG00000272070 expression was significantly reduced in postmortem Alzheimers disease (AD) brains, and AD-associated genes were enriched among 3222401L13Rik-regulated targets. Together, our results identify 3222401L13Rik/ENSG00000272070 as a conserved, aging-associated lncRNA that modulates microglial inflammatory states through interaction with PU.1. This work links glial lncRNA regulation to AD-related neuroinflammation and suggests 3222401L13Rik as a potential molecular target to fine-tune microglial activity in neurodegenerative diseases. HighlightsO_LI3222401L13Rik is a glia-enriched long non-coding RNA regulating microglial state C_LIO_LIKnockdown of 3222401L13Rik increases TNF signaling C_LIO_LIThe human homolog ENSG00000272070 shows reduced expression in AD brains C_LIO_LI3222401L13Rik interacts with the AD-associated transcription factor PU.1 C_LIO_LIA conserved 3222401L13Rik-PU.1 axis modulates microglial inflammation in aging and disease C_LI

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Pradhan, R., Sakib, M. S., Kaurani, L., Krueger, D. M., Pena, T., Burckhardt, S., Schuetz, A.-L., Kronenberg-Verstee, D., Delalle, I., Sananbenesi, F., Fischer, A.. 2025-11-01. lncRNA 3222401L13Rik/ENSG00000272070 modulates microglial inflammatory programs in association with PU.1. https://doi.org/10.1101/2025.10.31.685723

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