The HNRNPF/H RNA binding proteins and disease

hnRNPs in antiviral innate immunity

During virus infection, many host proteins are redirected from their normal cellular roles to restrict and terminate infection. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are cellular RNA-binding proteins critical to host nucleic acid homeostasis, but can also be involved in the viral infection process, affecting virus replication, assembly and propagation. It has become evident that hnRNPs play important roles in modulation of host innate immunity, which provides critical initial protection against infection. These novel findings can potentially lead to the leveraging of hnRNPs in antiviral therapies. We review hnRNP involvement in antiviral innate immunity, in humans, mice and other animals, and discuss hnRNP targeting as a potential novel antiviral therapeutic.

hnRNP H controls alternative splicing of human papillomavirus type 16 E1, E6, E7, and E6^E7 mRNAs via GGG motifs

The mRNAs encoding the human papillomavirus type 16 (HPV16) E6 and E7 oncogene mRNAs are subjected to extensive alternative RNA splicing at multiple regulated splice sites. One of the most extensively used 5'-splice sites in the HPV16 genome is named SD880 and is located immediately downstream of the E7 open reading frame. Here, we show that a cluster of three GGG-motifs adjacent to HPV16 SD880 interacts with heterogeneous nuclear ribonucleoprotein (hnRNP) H that cooperates with SD880 to stimulate splicing to the upstream HPV16 3'-splice site SA742. This splice site is located in the E7 coding region and is required for the production of the HPV16 226^742 mRNA that encodes the E6^E7 fusion protein. Enhancement of HPV16 E6^E7 mRNA production by hnRNP H occurred at the expense of the intron-retained E6 mRNAs and the spliced E7 mRNAs, demonstrating that hnRNP H controls the relative levels of E6, E7, and E6^E7 proteins. Unexpectedly, overexpression of hnRNP H also promoted retention of the downstream E1 encoding intron and enhanced E1 protein production. We concluded that hnRNP H plays an important role in the HPV16 gene expression program.IMPORTANCEHere, we show that hnRNP H binds to multiple GGG-motifs downstream of human papillomavirus type 16 (HPV16) splice site SD880 and acts in concert with SD880 to promote expression of the HPV16 E6^E7 mRNA. The E6^E7 protein has been shown previously to stabilize the HPV16 E6 and E7 oncoproteins and may as such contribute to the carcinogenic properties of HPV16. In its capacity of major regulator of HPV16 oncogene expression, hnRNP H may be exploited as a target for antiviral drugs to HPV16.

The MTR4/hnRNPK complex surveils aberrant polyadenylated RNAs with multiple exons

RNA surveillance systems degrade aberrant RNAs that result from defective transcriptional termination, splicing, and polyadenylation. Defective RNAs in the nucleus are recognized by RNA-binding proteins and MTR4, and are degraded by the RNA exosome complex. Here, we detect aberrant RNAs in MTR4-depleted cells using long-read direct RNA sequencing and 3' sequencing. MTR4 destabilizes intronic polyadenylated transcripts generated by transcriptional read-through over one or more exons, termed 3' eXtended Transcripts (3XTs). MTR4 also associates with hnRNPK, which recognizes 3XTs with multiple exons. Moreover, the aberrant protein translated from KCTD13 3XT is a target of the hnRNPK-MTR4-RNA exosome pathway and forms aberrant condensates, which we name KCTD13 3eXtended Transcript-derived protein (KeXT) bodies. Our results suggest that RNA surveillance in human cells inhibits the formation of condensates of a defective polyadenylated transcript-derived protein.

miR-19-3p/GRSF1/COX1 axis attenuates early brain injury via maintaining mitochondrial function after subarachnoid haemorrhage

BACKGROUND

Guanine-rich RNA sequence binding factor 1 (GRSF1) is an RNA-binding protein, which is eventually localised to mitochondria and promotes the translation of cytochrome C oxidase 1 (COX1) mRNA. However, the role of the miR-19-3p/GRSF1/COX1 axis has not been investigated in an experimental subarachnoid haemorrhage (SAH) model. Thus, we investigated the role of the miR-19-3p/GRSF1/COX1 axis in a SAH-induced early brain injury (EBI) course.

METHODS

Primary neurons were treated with oxyhaemoglobin (OxyHb) to simulate in vitro SAH. The rat SAH model was established by injecting autologous arterial blood into the optic chiasma cisterna. The GRSF1 level was downregulated or upregulated by treating the rats and neurons with lentivirus-GRSF1 shRNA (Lenti-GRSF1 shRNA) or lentivirus-GRSF1 (Lenti-GRSF1).

RESULTS

The miR-19-3p level was upregulated and the protein levels of GRSF1 and COX1 were both downregulated in SAH brain tissue. GRSF1 silence decreased and GRSF1 overexpression increased the protein levels of GRSF1 and COX1 in primary neurons and brain tissue, respectively. Lenti-GRSF1 shRNA aggravated, but Lenti-GRSF1 alleviated, the indicators of neuronal injury and neurological impairment in both in vitro and in vivo SAH conditions. In addition, miR-19-3p mimic reduced the protein levels of GRSF1 and COX1 in cultured neurons while miR-19-3p inhibitor increased them. More importantly, Lenti-GRSF1 significantly relieved mitochondrial damage of neurons exposed to OxyHb or induced by SAH and was beneficial to maintaining mitochondrial integrity. Lenti-GRSF1 shRNA treatment, conversely, aggravated mitochondrial damage in neurons.

CONCLUSION

The miR-19-3p/GRSF1/COX1 axis may serve as an underlying target for inhibiting SAH-induced EBI by maintaining mitochondrial integrity.

Viral hijacking of hnRNPH1 unveils a G-quadruplex-driven mechanism of stress control

Viral genomes are enriched with G-quadruplexes (G4s), non-canonical structures formed in DNA or RNA upon assembly of four guanine stretches into stacked quartets. Because of their critical roles, G4s are potential antiviral targets, yet their function remains largely unknown. Here, we characterize the formation and functions of a conserved G4 within the polymerase coding region of orthoflaviviruses of the Flaviviridae family. Using yellow fever virus, we determine that this G4 promotes viral replication and suppresses host stress responses via interactions with hnRNPH1, a host nuclear protein involved in RNA processing. G4 binding to hnRNPH1 causes its cytoplasmic retention with subsequent impacts on G4-containing tRNA fragments (tiRNAs) involved in stress-mediated reductions in translation. As a result, these host stress responses and associated antiviral effects are impaired. These data reveal that the interplay between hnRNPH1 and both host and viral G4 targets controls the integrated stress response and viral replication.

Differences between human male and female neutrophils in mRNA, translation efficiency, protein, and phosphoprotein profiles

Background

Human males and females show differences in the incidence of neutrophil-associated diseases such as systemic lupus erythematosus, rheumatoid arthritis, and reactive arthritis, and differences in neutrophil physiological responses such as a faster response to the chemorepellent SLIGKV. Little is known about the basis of sex-based differences in human neutrophils.

Methods

Starting with human neutrophils from healthy donors, we used RNA-seq to examine total mRNA profiles, mRNAs not associated with ribosomes and thus not being translated, mRNAs in monosomes, and mRNAs in polysomes and thus heavily translated. We used mass spectrometry systems to identify proteins and phosphoproteins.

Results

There were sex-based differences in the translation of 24 mRNAs. There were 132 proteins with higher levels in male neutrophils; these tended to be associated with RNA regulation, ribosome, and phosphoinositide signaling pathways, whereas 30 proteins with higher levels in female neutrophils were associated with metabolic processes, proteosomes, and phosphatase regulatory proteins. Male neutrophils had increased phosphorylation of 32 proteins. After exposure to SLIGKV, male neutrophils showed a faster response in terms of protein phosphorylation compared to female neutrophils.

Conclusions

Male neutrophils have higher levels of proteins and higher phosphorylation of proteins associated with RNA processing and signaling pathways, while female neutrophils have higher levels of proteins associated with metabolism and proteolytic pathways. This suggests that male neutrophils might be more ready to adapt to a new environment, and female neutrophils might be more effective at responding to pathogens. This may contribute to the observed sex-based differences in neutrophil behavior and neutrophil-associated disease incidence and severity.

METTL3-Mediated LINC00475 Alternative Splicing Promotes Glioma Progression by Inducing Mitochondrial Fission

Mitochondrial fission promotes glioma progression. The function and regulation mechanisms of lncRNAs in glioma mitochondrial fission are unclear. The expression of LINC00475 and its correlation with clinical parameters in glioma were analyzed using bioinformatics. Then, in vitro and in vivo assays were performed to explore the function of spliced variant LINC00475 (LINC00475-S) in gliomas. To explore the mechanisms, RNA-seq, MeRIP, RIP, pulldown-IP, dCas9-ALKBH5 editing system, LC/MS, and Western blotting were utilized. LINC00475 was confirmed to be overexpressed and with higher frequencies of AS events in gliomas compared to normal brain tissue and was associated with worse prognosis. In vitro and animal tumor formation experiments demonstrated that the effect of LINC00475-S on proliferation, metastasis, autophagy, and mitochondrial fission of glioma cells was significantly stronger than that of LINC00475. Mechanistically, METTL3 induced the generation of LINC00475-S by splicing LINC00475 through m6A modification and subsequently promotes mitochondrial fission in glioma cells by inhibiting the expression of MIF. Pull-down combined LC/MS and RIP assays identified that the m6A recognition protein HNRNPH1 bound to LINC00475 within GYR and GY domains and promoted LINC00475 splicing. METTL3 facilitated HNRNPH1 binding to LINC00475 in an m6A-dependent manner, thereby inducing generation of LINC00475-S. METTL3 facilitated HNRNPH1-mediated AS of LINC00475, which promoted glioma progression by inducing mitochondrial fission. Targeting AS of LINC00475 and m6A editing could serve as a therapeutic strategy against gliomas.

Mendelian Randomization Validates the Immune Landscape Mediated by Aggrephagy in Esophageal Squamous Cell Carcinoma Patients from the Perspectives of Multi-omics

Objective: To delineate the immune landscape of ESCC patients mediated by aggrephagy through bioinformatics and identify prognostic cell cluster genes with causal attributes to esophageal cancer through Mendelian randomization. Methods: Quality control, dimension reduction, and annotation were performed on the ESCC single-cell dataset. NMF clustering of various cell subgroups was carried out based on the expression of AGG-related genes, and AGG-related genes in each cluster were identified. Pseudo-temporal analysis was used to observe changes in the expression of AGG-related genes in each cluster. Cell communication analysis was employed to observe interactions between cell subgroups. Changes in classification, metabolism, or KEGG pathways in related subgroups were observed based on different cell characteristics. The AGG cluster attributes of TCGA and GEO samples were assessed based on GSVA, and the prognosis of each cluster was observed. The immune treatment situation and the relationship between mutation level and prognosis of AGG cluster-related samples were observed through the TIDE database and microsatellite instability. Finally, the eQTL of genes in each prognostic AGG cluster was used as an instrumental variable, with esophageal cancer as the outcome factor. Through Mendelian randomization analysis, AGG cluster-related genes with a causal relationship to esophageal cancer were established. Results: Dimension reduction clustering of single-cell transcriptome data identified 19 different cell subgroups. After re-annotation of the 19 cell subgroups, it was found that the CAF cells, B cells, T cells, NK cells, etc., of ESCA patients were all elevated compared to the control group. CAF cells had a high degree of communication with most cells. There were significant differences in macrophage metabolism and B-cell-mediated signal transduction pathways in different AGG clusters. The TUBA1B+Mac-C0 cluster, along with other clusters, exhibits predictive prognostic and immunotherapeutic potential at the transcriptional level. Mendelian randomization analysis revealed a causal relationship between genes such as CTSZ, CTSC, DAD, COLEC12, ATOX1, within the AGG cluster, and the onset of esophageal cancer. Conclusion: Aggrephagy mediates and influences the alterations and interactions of various immune cells in patients with ESCC. We elucidate the roles of AGG-related clusters, such as TUBA1B+Mac-C0, VIM+CD8+T_cells-C0, UBB+Mac-C2, in mediating prognosis and immune therapy in ESCC patients. Genes causally associated with the occurrence of esophageal cancer are identified within the AGG cluster, including CTSZ, CTSC, DAD, COLEC12, ATOX1, etc., offering new evidence for clinical immune therapy. These findings underscore the significance of these gene clusters in influencing both prognosis and immune responses in the context of esophageal cancer, shedding light on potential therapeutic targets and prognostic markers.