Matthias W. Hentze

Pyruvate kinase M2 (PKM2) is a glycolytic enzyme that coordinates energy production with biosynthetic demands in physiologically proliferating and cancer cells. PKM2 has also emerged as a non-canonical RNA-binding protein. Here, we combine targeted PKM2 mutagenesis with RNA-protein interaction assays, biochemical and biophysical analyses to define how RNA binding relates to PKM2 allosteric control and oligomeric state. We show that the allosteric activator fructose-1,6-bisphosphate (FBP) strongly reduces PKM2 binding to RNA. Mutants with impaired oligomerization show reduced RNA binding, and RNA association is favored by the tetrameric state. A positively charged surface patch in the FBP-binding region is essential for RNA binding and displays emergent properties. Single-residue variants further link RNA association to FBP-responsive tetrameric conformations. Our data integrate RNA binding with PKM2 allosteric regulation.

Crosslinking and immunoprecipitation followed by sequencing (CLIP-seq) is widely used to identify the RNA targets of RNA-binding proteins (RBPs). However, its application to non-canonical RBPs lacking canonical RNA-binding domains and frequently displaying low or transient RNA occupancy, is limited by low signal-to-noise ratios, high input requirements and error-prone ligation steps during library preparation. To overcome these limitations, we developed soniCLIP, a streamlined CLIP-seq workflow that replaces RNase-mediated RNA fragmentation with sonication and uses a ligation-free strategy for library construction. soniCLIP is optimized for reproducible identification of enriched RBP-associated RNA regions from limited starting material. We benchmarked soniCLIP against the widespread eCLIP approach and observed reproducible recovery of known RBP-associated regions and target recovery comparable to ENCODE eCLIP, while requiring only 10% (500 ug) of protein input. We further applied soniCLIP to the glycolytic enzyme and non-canonical RBP pyruvate kinase M2 (PKM2). We identified 197 significantly enriched RNA regions and validated selected targets by RIP-qRT-PCR and in vitro binding assays. By combining reduced input requirements, high reproducibility, a shortened 3.5-day workflow and the elimination of gel-based purification, soniCLIP provides an efficient and robust approach for the identification of RNA targets of canonical and non canonical RBPs.

Custom oligonucleotides (oligos) play a crucial role in molecular biology applications, including sequencing, polymerase chain reaction (PCR), and library construction. For highly sensitive techniques such as next-generation sequencing (NGS) library preparation, oligos must exhibit exceptional purity and accuracy. Here, we provide a perspective on the presence of unrelated, contaminating sequences in custom-made oligos using a case study of an RNA–protein crosslinked immunoprecipitation (CLIP-seq) experiment. These contaminants led to artefactual results in NGS data, rendering their results uninterpretable. Systematic investigation identified a contaminating human immunodeficiency virus (HIV) gag sequence embedded between Illumina-compatible adapter sequences, forming a functional ‘library-structured’ molecule capable of amplification and sequencing. Additionally, other nonspecific sequences, including fragments from unrelated oligos, were detected. By sharing our analysis strategy and outcomes, we aim to raise awareness within the research community and emphasize the need for more stringent quality controls in oligo synthesis and validation by commercial suppliers, safeguarding academic experimenters’ time and resources. Furthermore, this perspective provides a systematic approach for the identification of the source of contaminating sequences in custom-made oligos designed for NGS library preparations.

Liver sinusoidal endothelial cells (LSECs) separate the blood from the hepatic parenchyma and thus are at the frontline as scavengers of blood-borne waste, pathogens and metabolic stimuli. LSECs are also critical for sensing systemic iron availability by controlling the synthesis of bone morphogenetic protein (BMP) 6, which is essential for hepcidin expression in hepatocytes. Hepcidin maintains systemic iron homeostasis by inhibiting dietary iron uptake and iron release from iron recycling macrophages. Hepcidin is also an acute-phase protein and its activation by inflammation requires active BMP signaling. It is incompletely understood how signals derived from inflammation, cellular damage and iron are integrated by the liver to assure adequate hepcidin expression. Here, we show that Bmp6 expression is activated in primary LSEC cultures upon their exposure to damage-associated molecular patterns (DAMPs), such as heme and myoglobin, pathogen-associated molecular patterns (PAMPs), such as lipopolysaccharide (LPS) and Fibroblast-Stimulating Lipopeptide-1 (FSL1), or oxidative stress inducers (H ₂ O ₂ ). All regulatory cues converge at the MAPK signaling pathway, although the specific signaling branches involved are stimulus-specific. Notably, Bmp6 upregulation in LSECs in response to all signals tested is strongly enhanced by the hepatocyte secretome. As hepatocytes critically depend on active BMP/SMAD signaling to control hepcidin activation, our results reveal that multiple sources of signaling input activating Bmp6 in LSECs and hepcidin in hepatocytes serve to determine BMP/SMAD signaling strength. Furthermore, our findings identify hypoferremia, the result of high hepcidin levels due to elevated Bmp6 , as a convergent response in conditions of inflammation, oxidative stress and cellular damage. Highlights: DAMPs (heme and myoglobin), PAMPs (LPS) and oxidative stress activate Bmp6 mRNA expression via the MAPK signaling pathway The TLR/MAPK/BMP6 regulatory axis integrates inflammatory and iron signals Our work uncovers a novel connection between innate immune sensing, oxidative stress and hepatic iron homeostasis

Anemia of inflammation is a prevalent comorbidity in patients with chronic inflammatory disorders. Inflammation causes hypoferremia and iron-restricted erythropoiesis by limiting ferroportin (FPN)–mediated iron export from macrophages that recycle senescent erythrocytes. Macrophage cell surface expression of FPN is reduced by hepcidin-induced degradation and/or by repression of FPN (Slc40a1) transcription via cytokine and Toll-like receptor (TLR) stimulation. Although the mechanisms underlying hepcidin-mediated control of FPN have been extensively studied, those inhibiting Slc40a1 messenger RNA (mRNA) expression remain unknown. We applied targeted RNA interference and pharmacological screens in macrophages stimulated with the TLR2/6 ligand FSL1 and identified critical signaling regulators of Slc40a1 mRNA repression downstream of TLRs and NF-κB signaling. Interestingly, the NF-κB regulatory hub is equally relevant for Slc40a1 mRNA repression driven by the TLR4 ligand lipopolysaccharide, the cytokine tumor necrosis factor β/lymphotoxin-alpha (LTA), and heat-killed bacteria. Mechanistically, macrophage stimulation with heat-killed Staphylococcus aureus recruits the histone deacetylases (HDACs) HDAC1 and HDAC3 to the antioxidant response element (ARE) located in the Slc40a1 promoter. Accordingly, pretreatment with a pan-HDAC inhibitor abrogates Slc40a1 mRNA repression in response to inflammatory cues, suggesting that HDACs act downstream of NF-κB to repress Slc40a1 transcription. Consistently, recruitment of HDAC1 and HDAC3 to the Slc40a1 ARE after stimulation with heat-killed S aureus is dependent on NF-κB signaling. These results support a model in which the ARE integrates the transcriptional responses of Slc40a1 triggered by signals from redox, metabolic, and inflammatory pathways. This work identifies the long-sought mechanism of Slc40a1 transcriptional downregulation upon inflammation, paving the way for therapeutic interventions at this critical juncture.

TRIM25 is an RNA-binding ubiquitin E3 ligase with central but poorly understood roles in the innate immune response to RNA viruses. The link between TRIM25’s RNA binding and its role in innate immunity has not been established. Thus, we utilized a multitude of biophysical techniques to identify key RNA-binding residues of TRIM25 and developed an RNA-binding deficient mutant (TRIM25-m9). Using iCLIP2 in virus-infected and uninfected cells, we identified TRIM25’s RNA sequence and structure specificity, that it binds specifically to viral RNA, and that the interaction with RNA is critical for its antiviral activity.

Most mitochondrial proteins are encoded by the nuclear genome, translated as precursor proteins in the cytosol and matured during directed import into the mitochondria ¹ . For many mitochondrial proteins this process is carefully regulated to meet demand and to avoid mitochondrial stress ^2,3,4 . Recently, mitochondrial F1-ATP synthase subunits have been found to interact with RNA across various eukaryotes. This includes genome wide RNA-interactome studies from yeast ^5–7 , fruit flies ^8,9 , plants ^10–12 , mice ^13–17 and humans ^18–24 . To shed light on this unexpected observation, we determined the interacting cellular RNAs of ATP5A1 and the subcellular sites of interaction. Using RNA binding-deficient mutants of ATP5A1 and functional assays, we show that specific cytosolic RNAs bind ATP5A1 precursor proteins at the outer surface of mitochondria and promote their mitochondrial import both in vitro and in cellulo. These findings add an unexpected twist to understanding mitochondrial protein import and expand the growing list of riboregulated cellular processes.

ALK-positive NSCLC patients demonstrate initial responses to ALK tyrosine kinase inhibitor (TKI) treatments, but eventually develop resistance, causing rapid tumor relapse and poor survival rates. Growing evidence suggests that the combination of drug and immune therapies greatly improves patient survival; however, due to the low immunogenicity of the tumors, ALK-positive patients do not respond to currently available immunotherapies. Tumor-associated macrophages (TAMs) play a crucial role in facilitating lung cancer growth by suppressing tumoricidal immune activation and absorbing chemotherapeutics. However, they can also be programmed toward a pro-inflammatory tumor suppressive phenotype, which represents a highly active area of therapy development. Iron loading of TAMs can achieve such reprogramming correlating with an improved prognosis in lung cancer patients. We previously showed that superparamagnetic iron oxide nanoparticles containing core-cross-linked polymer micelles (SPION-CCPMs) target macrophages and stimulate pro-inflammatory activation. Here, we show that SPION-CCPMs stimulate TAMs to secrete reactive nitrogen species and cytokines that exert tumoricidal activity. We further show that SPION-CCPMs reshape the immunosuppressive Eml4-Alk lung tumor microenvironment (TME) toward a cytotoxic profile hallmarked by the recruitment of CD8⁺ T cells, suggesting a multifactorial benefit of SPION-CCPM application. When intratracheally instilled into lung cancer-bearing mice, SPION-CCPMs delay tumor growth and, after first line therapy with a TKI, halt the regrowth of relapsing tumors. These findings identify SPIONs-CCPMs as an adjuvant therapy, which remodels the TME, resulting in a delay in the appearance of resistant tumors.