Most lncRNA genes are expressed during spermatogenesis and are localized to many different subcellular locations.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein is essential for viral replication, making it a promising target for antiviral drug and vaccine development. SARS-CoV-2 infected patients exhibit an uncoordinated immune response; however, the underlying mechanistic details of this imbalance remain obscure. Here, starting from a functional proteomics workflow, we catalogued the protein-protein interactions of SARS-CoV-2 proteins, including an evolutionarily conserved specific interaction of N with the stress granule resident proteins G3BP1 and G3BP2. N localizes to stress granules and sequesters G3BPs away from their typical interaction partners, thus attenuating stress granule formation. We found that N binds directly to host mRNAs in cells, with a preference for 3´ UTRs, and modulates target mRNA stability. We show that the N protein rewires the G3BP1 mRNA-binding profile and suppresses the physiological stress response of host cells, which may explain the imbalanced immune response observed in SARS-CoV-2 infected patients.

A novel mass spectrometry (MS)-based lipidomics strategy that exposes glycerophospholipids to an ethereal solution of diazomethane and acid, derivatizing them to contain a net fixed, permanent positive charge, is described. The sensitivity of modified lipids to MS detection is enhanced via improved ionization characteristics as well as consolidation of ion dissociation to form one or two strong, characteristic polar headgroup fragments. Our strategy has been optimized to enable a priori prediction of ion fragmentation patterns for four subclasses of modified glycerophospholipid species. Our method enables analyte ionization regardless of proton affinity, thereby decreasing ion suppression and permitting predictable precursor ion-based quantitation with improved sensitivity in comparison to MS-based methods that are currently used on unmodified lipid precursors.

The COVID-19 pandemic has caused over one million deaths thus far. There is an urgent need for the development of specific viral therapeutics and a vaccine. SARS-CoV-2 nucleocapsid (N) protein is highly expressed upon infection and is essential for viral replication, making it a promising target for both antiviral drug and vaccine development. Here, starting from a functional proteomics workflow, we initially catalogued the protein-protein interactions of 21 SARS-CoV-2 proteins in HEK293 cells, finding that the stress granule resident proteins G3BP1 and G3BP2 co-purify with N with high specificity. We demonstrate that N protein expression of in human cells sequesters G3BP1 and G3BP2 through its physical interaction with these proteins, attenuating stress granule (SG) formation. The ectopic expression of G3BP1 in N-expressing cells was sufficient to reverse this phenotype. Since N is an RNA-binding protein, we performed iCLIP- sequencing experiments in cells, with or without exposure to oxidative stress, to identify the host RNAs targeted by N. Our results indicate that SARS-CoV-2 N protein binds directly to thousands of host mRNAs under both conditions. Like the G3BPs stress granule proteins, N was found to predominantly bind its target mRNAs in their 3UTRs. RNA sequencing experiments indicated that expression of N results in wide-spread gene expression changes in both unstressed and oxidatively stressed cells. We suggest that N regulates host gene expression by both attenuating stress granules and binding directly to target mRNAs.

Objectives: This study aimed to investigate the efficacy of simultaneous steroid and hyperbaric oxygen therapy (HBOT) in patients with severe to profound idiopathic sudden sensorineural hearing loss (ISSNHL), which has a poor prognosis. Methods: Sixty patients diagnosed with severe to profound ISSNHL (≥70 dB HL) were randomly divided into two groups in a prospective controlled trial: an oral steroid + intratympanic steroid injection (ITSI) group (control group) and an oral steroid + ITSI + HBOT group (study group). Pure-tone audiometry (PTA) results and word discrimination scores (WDS) were compared between the two groups before treatment and 10 days and 1, 2, and 3 months after treatment. Hearing improvement was assessed using the modified American Academy of Otolaryngology-Head and Neck Surgery criteria. Analyses were by both intention to treat and per protocol. Results: A total of 58 patients completed the 3-month follow-up, and 2 patients in the study group were excluded due to follow-up loss in the per-protocol analysis. In the intention-to-treat and per-protocol analyses, the study group showed significantly better hearing levels than did the control group at 500 Hz (p < 0.05) 1 month after treatment and at 1 kHz (p < 0.05) 3 months after treatment. However, the average PTA values and PTA at 2, 4, and 8 kHz showed no significant difference. WDS improvement was significantly higher in the study group compared to the control group 3 months after treatment by both per-protocol (66.4 ± 13.3 and 56.7 ± 19.1%, respectively; p = 0.029) and intention-to-treat analyses (65.9 ± 14.1 and 56.7 ± 19.1%, respectively; p = 0.035). The sum of complete and partial hearing recovery for the study group was significantly higher than that for the control group by per-protocol analysis (60.7 vs. 33.3%; p = 0.037) and intention-to-treat analysis (60.0 vs. 33.3%; p = 0.038). Conclusion: These results demonstrate that the addition of HBOT to steroid combination therapy does not improve the average PTA values in severe to profound ISSNHL; however, it was associated with a better outcome at 500 Hz 1 month after treatment and, at 1 kHz, WDS 3 months after treatment. The sum of complete and partial hearing recovery was significantly higher for the study group than for the control group.