TY  - JOUR
AU  - Li, Teng-Feng
AU  - Rothhaar, Paul
AU  - Lang, Arthur
AU  - Grünvogel, Oliver
AU  - Colasanti, Ombretta
AU  - Ugarte, Santa Mariela Olivera
AU  - Traut, Jannik
AU  - Piras, Antonio
AU  - Acosta-Rivero, Nelson
AU  - Gonçalves Magalhães, Vladimir
AU  - Springer, Emely
AU  - Betz, Andreas
AU  - Huang, Hao-En
AU  - Park, Jeongbin
AU  - Qiu, Ruiyue
AU  - Gnouamozi, Gnimah Eva
AU  - Mehnert, Ann-Kathrin
AU  - Thi, Viet Loan Dao
AU  - Urban, Stephan
AU  - Muckenthaler, Martina
AU  - Schlesner, Matthias
AU  - Wohlleber, Dirk
AU  - Binder, Marco
AU  - Bartenschlager, Ralf
AU  - Pichlmair, Andreas
AU  - Lohmann, Volker
TI  - RBM39 shapes innate immunity by controlling the expression of key factors of the interferon response.
JO  - Frontiers in immunology
VL  - 16
SN  - 1664-3224
CY  - Lausanne
PB  - Frontiers Media
M1  - DKFZ-2025-00941
SP  - 1568056
PY  - 2025
AB  - The contribution of innate immunity to clearance of viral infections of the liver, in particular sensing via Toll-like receptor 3 (TLR3), is incompletely understood. We aimed to identify the factors contributing to the TLR3 response in hepatocytes via CRISPR/Cas9 screening.A genome-wide CRISPR/Cas9 screen on the TLR3 pathway was performed in two liver-derived cell lines, followed by siRNA knockdown validation. SiRNA knockdown and indisulam treatment were used to study the role of RNA-binding motif protein 39 (RBM39) in innate immunity upon poly(I:C) or cytokine treatment and viral infections. Transcriptome, proteome, and alternative splicing were studied via RNA sequencing and mass spectrometry upon depletion of RBM39.Our CRISPR/Cas9 screen identified RBM39, which is highly expressed in hepatocytes, as an important regulator of the TLR3 pathway. Knockdown of RBM39 or treatment with indisulam, an aryl sulfonamide drug targeting RBM39 for proteasomal degradation, strongly reduced the induction of interferon-stimulated genes (ISGs) in response to double-stranded RNA (dsRNA) or viral infections. RNA sequencing (seq) and mass spectrometry identified that transcription and/or splicing of the key pathway components IRF3, RIG-I, and MDA5 were affected by RBM39 depletion, along with multiple other cellular processes identified previously. RBM39 knockdown further restrained type I and type III IFN pathways by reducing the expression of individual receptor subunits and STAT1/2. The function of RBM39 was furthermore not restricted to hepatocytes.We identified RBM39 as a regulatory factor of cell intrinsic innate immune signaling. Depletion of RBM39 impaired TLR3, RIG-I/MDA5, and IFN responses by affecting the basal expression of key pathway components.
KW  - RNA-Binding Proteins: genetics
KW  - RNA-Binding Proteins: metabolism
KW  - RNA-Binding Proteins: immunology
KW  - Immunity, Innate: genetics
KW  - Humans
KW  - Toll-Like Receptor 3: metabolism
KW  - Toll-Like Receptor 3: genetics
KW  - Toll-Like Receptor 3: immunology
KW  - Hepatocytes: immunology
KW  - Hepatocytes: metabolism
KW  - Signal Transduction
KW  - Interferons: immunology
KW  - Interferons: metabolism
KW  - Gene Expression Regulation
KW  - CRISPR-Cas Systems
KW  - Cell Line
KW  - IFNs (Other)
KW  - IRF3 (Other)
KW  - RBM39 (Other)
KW  - STAT1 (Other)
KW  - STAT2 (Other)
KW  - splicing (Other)
KW  - RNA-Binding Proteins (NLM Chemicals)
KW  - Toll-Like Receptor 3 (NLM Chemicals)
KW  - Interferons (NLM Chemicals)
KW  - TLR3 protein, human (NLM Chemicals)
LB  - PUB:(DE-HGF)16
C6  - pmid:40330464
C2  - pmc:PMC12054253
DO  - DOI:10.3389/fimmu.2025.1568056
UR  - https://inrepo02.dkfz.de/record/300827
ER  -