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Table S1 to S4; Figures S1 to S12

Numerous studies have implicated changes in the Y chromosome in male cancers, yet few have investigated the biological importance of Y chromosome noncoding RNA. Here we identify a group of Y chromosome–expressed long noncoding RNA (lncRNA) that are involved in male non–small cell lung cancer (NSCLC) radiation sensitivity. Radiosensitive male NSCLC cell lines demonstrated a dose-dependent induction of linc-SPRY3-2/3/4 following irradiation, which was not observed in radioresistant male NSCLC cell lines. Cytogenetics revealed the loss of chromosome Y (LOY) in the radioresistant male NSCLC cell lines. Gain- and loss-of-function experiments indicated that linc-SPRY3-2/3/4 transcripts affect cell viability and apoptosis. Computational prediction of RNA binding proteins (RBP) motifs and UV-cross-linking and immunoprecipitation (CLIP) assays identified IGF2BP3, an RBP involved in mRNA stability, as a binding partner for linc-SPRY3-2/3/4 RNA. The presence of linc-SPRY3-2/3/4 reduced the half-life of known IGF2BP3 binding mRNA, such as the antiapoptotic HMGA2 mRNA, as well as the oncogenic c-MYC mRNA. Assessment of Y chromosome in NSCLC tissue microarrays and expression of linc-SPRY3-2/3/4 in NSCLC RNA-seq and microarray data revealed a negative correlation between the loss of the Y chromosome or linc-SPRY3-2/3/4 and overall survival. Thus, linc-SPRY3-2/3/4 expression and LOY could represent an important marker of radiotherapy in NSCLC.Significance:This study describes previously unknown Y chromosome–expressed lncRNA regulators of radiation response in male NSCLC and show a correlation between loss of chromosome Y and radioresistance.

SARS-CoV-2 infection results in wide-ranging disease manifestation from asymptomatic to potentially lethal. Infection poses an increased threat of severity to at-risk populations including those with hypertension, diabetes, and obesity. Type 2 Diabetes (T2DM), is characterized, in part, by insulin insensitivity and impaired glucose regulation. T2DM patients have increased disease severity and poorer outcomes with COVID-19. We utilized the diet-induced obesity (DIO) model of Type 2 Diabetes in SARS-CoV-2-susceptible K18-hACE2 transgenic mice to better understand the obesity co-morbidity. Female DIO, but not male DIO mice challenged with SARS-CoV-2 were observed to have shortened time to morbidity compared to normal diet mice. Increase in susceptibility to SARS-CoV2 in female DIO was associated with increased total viral RNA burden compared to male mice. RNAseq analysis was performed on the lungs of non-challenged, challenged, females, males, of either normal diet or DIO cohorts to determine the disease specific transcriptional profiles. DIO female mice had more total activated genes than normal diet mice after challenge; however, male mice experienced a decrease. GO term analysis revealed the DIO condition increased interferon response signatures and interferon gamma production following challenge. Male challenged mice had robust expression of antibody-related genes suggesting antibody producing cell localization in the lung. DIO reduced antibody gene expression in challenged males. Collectively this study establishes a preclinical T2DM/obesity co-morbidity model of COVID-19 in mice where we observed sex and diet specific responses that begin to explain the effects of obesity and diabetes on COVID-19 disease.

SARS-CoV-2 variants of concern (VoC) are impacting responses to the COVID-19 pandemic. Here, we utilized passive immunization using human convalescent plasma (HCP) obtained from a critically ill COVID-19 patient in the early pandemic to study the efficacy of polyclonal antibodies generated to ancestral SARS-CoV-2 against the Alpha, Beta, and Delta VoC in the K18 human angiotensin converting enzyme 2 (hACE2) transgenic mouse model. HCP protected mice from challenge with the original WA-1 SARS-CoV-2 strain; however, only partially protected mice challenged with the Alpha VoC (60% survival) and failed to save Beta challenged mice from succumbing to disease. HCP treatment groups had elevated receptor binding domain (RBD) and nucleocapsid IgG titers in the serum; however, Beta VoC viral RNA burden in the lung and brain was not decreased due to HCP treatment. While mice could be protected from WA-1 or Alpha challenge with a single dose of HCP, six doses of HCP could not decrease mortality of Delta challenged mice. Overall, these data demonstrate that VoC have enhanced immune evasion and this work underscores the need for

SARS-CoV-2 is a viral respiratory pathogen responsible for the current global pandemic and the disease that causes COVID-19. All current WHO approved COVID-19 vaccines are administered through the muscular route. We have developed a prototype two-dose vaccine (BReC-CoV-2) by combining the Receptor Binding Domain (RBD) antigen, via conjugation to Diphtheria toxoid (EcoCRM®). The vaccine is adjuvanted with Bacterial Enzymatic Combinatorial Chemistry (BECC), BECC470. Intranasal (IN) administration of BreC-CoV-2 in K18-hACE2 mice induced a strong systemic and localized immune response in the respiratory tissues which provided protection against the Washington strain of SARS-CoV-2. Protection provided after IN administration of BReC-CoV-2 was associated with decreased viral RNA copies in the lung, robust RBD IgA titers in the lung and nasal wash, and induction of broadly neutralizing antibodies in the serum. We also observed that BReC-CoV-2 vaccination administered using an intramuscular (IM) prime and IN boost protected mice from a lethal challenge dose of the Delta variant of SARS-CoV-2. IN administration of BReC-CoV-2 provided better protection than IM only administration to mice against lethal challenge dose of SARS-CoV-2. These data suggest that the IN route of vaccination induces localized immune responses that can better protect against SARS-CoV-2 than the IM route in the upper respiratory tract.

Risk stratification of COVID‐19 patients is essential for pandemic management. Changes in the cell fitness marker, hFwe‐Lose, can precede the host immune response to infection, potentially making such a biomarker an earlier triage tool. Here, we evaluate whether hFwe‐Lose gene expression can outperform conventional methods in predicting outcomes (e.g., death and hospitalization) in COVID‐19 patients. We performed a post‐mortem examination of infected lung tissue in deceased COVID‐19 patients to determine hFwe‐Lose’s biological role in acute lung injury. We then performed an observational study (n = 283) to evaluate whether hFwe‐Lose expression (in nasopharyngeal samples) could accurately predict hospitalization or death in COVID‐19 patients. In COVID‐19 patients with acute lung injury, hFwe‐Lose is highly expressed in the lower respiratory tract and is co‐localized to areas of cell death. In patients presenting in the early phase of COVID‐19 illness, hFwe‐Lose expression accurately predicts subsequent hospitalization or death with positive predictive values of 87.8–100% and a negative predictive value of 64.1–93.2%. hFwe‐Lose outperforms conventional inflammatory biomarkers and patient age and comorbidities, with an area under the receiver operating characteristic curve (AUROC) 0.93–0.97 in predicting hospitalization/death. Specifically, this is significantly higher than the prognostic value of combining biomarkers (serum ferritin, D‐dimer, C‐reactive protein, and neutrophil–lymphocyte ratio), patient age and comorbidities (AUROC of 0.67–0.92). The cell fitness marker, hFwe‐Lose, accurately predicts outcomes in COVID‐19 patients. This finding demonstrates how tissue fitness pathways dictate the response to infection and disease and their utility in managing the current COVID‐19 pandemic., A post‐mortem examination of COVID‐19 infected lung tissues and an observational study were performed in order to evaluate whether expression of cell fitness marker hFwe‐Lose in patient's nasopharyngeal swabs could predict hospitalization or death from COVID‐19.

SUMMARYSARS-CoV-2 variants of concern (VoCs) are impacting responses to the COVID-19 pandemic. Here we present a comparison of the SARS-CoV-2 USA-WA1/2020 (WA-1) strain with B.1.1.7 and B.1.351 VoCs and identify significant differences in viral propagationin vitroand pathogenicityin vivousing K18-hACE2 transgenic mice. Passive immunization with plasma from an early pandemic SARS-CoV-2 patient resulted in significant differences in the outcome of VoC-infected mice. WA-1-infected mice were protected by plasma, B.1.1.7-infected mice were partially protected, and B.1.351-infected mice were not protected. Serological correlates of disease were different between VoC-infected mice, with B.1.351 triggering significantly altered cytokine profiles than other strains. In this study, we defined infectivity and immune responses triggered by VoCs and observed that early 2020 SARS-CoV-2 human immune plasma was insufficient to protect against challenge with B.1.1.7 and B.1.351 in the mouse model.

Background: The pathogenesis of type 2 diabetes mellitus is known to alter cardiac mitochondrial bioenergetics, but the role of non-coding RNAs (ncRNAs) in regulating this process remains poorly understood, specifically within the mitochondrion. Here we characterized the mitochondrial localization of nuclear-encoded lncRNAs in the heart in an effort to understand how import of lncRNAs can modify mitochondrial function during diabetes mellitus.Methods: Human patient and FVB/NJ mouse cardiac tissues were collected from type 2 diabetics and non-diabetics. Immunoblotting was used to validate purity of mitochondrial fractionation. NcRNA from subcellular compartments (cytoplasmic and mitochondrial) were sequenced through the Illumina 2500 HiSeq. LncRNA mitochondrial targeting sequences were acquired through crosslinking immunoprecipitation (CLIP) with Polynucleotide Phosphorylase (PNPase) and secondary structures were analyzed using supervised and unsupervised machine learning algorithms. Fluorescence in situ hybridization (FISH) allowed for visualization of Malat1 localization. Mitochondrial function was assessed through oxygen consumption rate.Results: 2448 LncRNAs were discovered in human cardiac mitochondria. Malat1 and microRNA-23b abundance were significantly reduced in human and mouse diabetic mitochondria. Modification of the import protein PNPase in HL-1 cells decreased binding affinity (~80%) of transcript variant 4 of Malat1 (Malat1-204), with machine learning (AUC 0.75) identifying stem-loops as shared secondary structures of lncRNAs bound to PNPase. Knockdown of Malat1-204 and microRNA-23b in mitochondria decreased protein expression of mt-Nd4 (~55%), though showed little/no binding homology to the mt-Nd4 mRNA transcript. Malat1-204 and microRNA-23b were identified bound to mt-Rnr1 rRNA, which could influence translation of mt-Nd4 through the mitochondrial 12S rRNA pathway.Conclusions: Malat1-204 and microRNA-23b, decreased in cardiac diabetic mitochondria, likely stabilize the mitochondrial ribosomal complexes through binding of mt-Rnr1. The significant decrease in total abundance of lncRNAs in diabetic mitochondria could suggest maladaptation for regulating bioenergetics and managing future insults.

Lyme disease is the most wide-spread vector-borne disease in the eastern United States. Lyme disease is caused by a bacterium, Borrelia burgdorferi, that is transmitted by a tick vector, most commonly Ixodes scapularus. In this study, 400 ticks were collected from around Upshur county, West Virginia, and tested by PCR for the presence of B. burgdorferi DNA. Tick specimen belong to Ixodes scapularus, Rhipicephalus sanguineus, or are unidentified. One unidentified sample, which tested positive for B. burgdorferi, has been tentatively identified as the new invasive Haemaphysalis longicorni. This is the first report of the Asian Longhorned Tick carrying B. burgdorferi in West Virginia. In the future, this ongoing project will expand its sampling techniques, as well as expand testing for the presence of other possible tick-borne diseases in collected samples.

Pseudomonas aeruginosa (Pa) is an opportunistic Gram-negative pathogen that can lead to life-threatening pulmonary infections. Several promising vaccine candidates against Pa evaluated in clinical trials. However, there is still no commercial vaccine available against this pathogen, in part due to a lack of clarity of protective correlates of vaccine–induced immunity. To elucidate correlates of protection against Pa, we used an intranasal whole–cell Pa vaccine adjuvanted with curdlan WCV in a murine vaccination and challenge model. Immunization with WCV significantly decreased the bacterial burden and lung edema after Pa challenge. We found that WCV immunization leads to a significant increase in Th17 cellular immune response and Pa–specific serum IgG and IgA titers compared to naive animals. To identify mechanistic correlates of protection, we performed anti–CD4, – CD8, and –CD20 antibody mediated depletions prior to vaccination and challenge. Depletion of these populations did not affect the response to challenge in naive animals. Interestingly, we observed that depletion of B cells but not CD8+ or CD4+ T cells during WCV priming resulted in loss of protection against Pa. Furthermore, passive immunization of WCV sera was sufficient to protect naive mice against Pa. Taken together, vaccine-mediated humoral immune response was the critical component of immunity against Pa in acute lung pneumonia model. This study suggests that adjuvants stimulating humoral immune response may be used to enhance the efficacy of vaccine candidates against Pa.