Early RNA Research Articles

SRSF1 acts as an IFN-I-regulated cellular dependency factor decisively affecting HIV-1 post-integration steps.

Efficient HIV-1 replication depends on balanced levels of host cell components including cellular splicing factors as the family of serine/arginine-rich splicing factors (SRSF, 1-10). Type I interferons (IFN-I) play a crucial role in the innate immunity against HIV-1 by inducing the expression of IFN-stimulated genes (ISGs) including potent host restriction factors. The less well known IFN-repressed genes (IRepGs) might additionally affect viral replication by downregulating host dependency factors that are essential for the viral life cycle; however, so far, the knowledge about IRepGs involved in HIV-1 infection is very limited. In this work, we could demonstrate that HIV-1 infection and the associated ISG induction correlated with low SRSF1 levels in intestinal lamina propria mononuclear cells (LPMCs) and peripheral blood mononuclear cells (PBMCs) during acute and chronic HIV-1 infection. In HIV-1-susceptible cell lines as well as primary monocyte-derived macrophages (MDMs), expression levels of SRSF1 were transiently repressed upon treatment with specific IFNα subtypes in vitro. Mechanically, 4sU labeling of newly transcribed mRNAs revealed that IFN-mediated SRSF1 repression is regulated on early RNA level. SRSF1 knockdown led to an increase in total viral RNA levels, but the relative proportion of the HIV-1 viral infectivity factor (Vif) coding transcripts, which is essential to counteract APOBEC3G-mediated host restriction, was significantly reduced. In the presence of high APOBEC3G levels, however, increased LTR activity upon SRSF1 knockdown facilitated the overall replication, despite decreased vif mRNA levels. In contrast, SRSF1 overexpression significantly impaired HIV-1 post-integration steps including LTR transcription, alternative splice site usage, and virus particle production. Since balanced SRSF1 levels are crucial for efficient viral replication, our data highlight the so far undescribed role of SRSF1 acting as an IFN-modulated cellular dependency factor decisively regulating HIV-1 post-integration steps.

S3317 Acute Hepatitis C Infection Accounts for Suspected Isoniazid Hepatitis in a Patient With Controlled HIV Infection on Antiretroviral Therapy

Introduction: Acute hepatitis C (HCV) infection is rising in intravenous drug users/non-monogamy. Isoniazid (INH), commonly used for tuberculosis, may cause idiosyncratic drug-induced liver injury (DILI). Acute HCV infection was reported in 1.5% of suspected DILI. We here report a case of acute HCV infection for suspicious INH hepatitis in a patient with controlled human immunodeficiency virus (HIV) infection on antiretroviral therapy (ART). Case Description/Methods: A 54 years-old Caucasian male was admitted for several days of fatigue/nausea/abdominal pain with elevated ALT/AST at 179/93. He has a history of controlled HIV infection on dolutegravir/tenofovir/emtricitabine, non-monogamy (men having sex with men), marijuana/herbal use, and latent tuberculosis (with a normal liver test/negative HCV antibody) treated with INH for 3 months. Serology for acute hepatitis A, B, C infection, other work-ups, and abdominal ultrasound/CT were negative. INH rather than ART/herbals was suspected as the possible culprit for hepatotoxicity and was continued due to ALT < 5 times upper normal limit. Patient was discharged after a negative esophagogastroduodenoscopy and symptomatic improvement. He presented again 2 days later with ALT/AST of 287/153 then to 984/388 on the 9th day after INH cessation. Total bilirubin and INR had remained normal with minimally elevated ALP. HCV RNA was detected at 16.5 million IU/ml. A liver biopsy was performed for rising liver enzymes and excluding autoimmune hepatitis. Moderate portal/lobular inflammation with abundant hepatocyte apoptosis and mild intra-canalicular cholestasis without autoimmune hepatitis was reported, suggesting possible DILI with viral hepatitis per pathologist. However, with a strong competing diagnosis of acute HCV hepatitis, persistently rising ALT/AST despite cessation of INH, and only possible causality score for INH-DILI, the suspected INH hepatitis was adjudicated as acute HCV infection. Sofosbuvir-velpatasvir treatment was initiated with rapid normalization of ALT/AST and decreasing HCV RNA. Discussion: This is the first reported case of acute HCV infection for suspected INH hepatitis in a patient with controlled HIV infection on ART. The case emphasizes the importance of early HCV RNA testing for diagnosing/excluding acute HCV infection in suspicious DILI due to delayed seroconversion of HCV antibody. Prompt treatment with highly potent antiviral agents leads to eradication of HCV with potential public health benefit.

A Rapid Translational Immune Response Program in CD8 Memory T Lymphocytes.

The activation of memory T cells is a very rapid and concerted cellular response that requires coordination between cellular processes in different compartments and on different time scales. In this study, we use ribosome profiling and deep RNA sequencing to define the acute mRNA translation changes in CD8 memory T cells following initial activation events. We find that initial translation enables subsequent events of human and mouse T cell activation and expansion. Briefly, early events in the activation of Ag-experienced CD8 T cells are insensitive to transcriptional blockade with actinomycin D, and instead depend on the translation of pre-existing mRNAs and are blocked by cycloheximide. Ribosome profiling identifies ∼92 mRNAs that are recruited into ribosomes following CD8 T cell stimulation. These mRNAs typically have structured GC and pyrimidine-rich 5' untranslated regions and they encode key regulators of T cell activation and proliferation such as Notch1, Ifngr1, Il2rb, and serine metabolism enzymes Psat1 and Shmt2 (serine hydroxymethyltransferase 2), as well as translation factors eEF1a1 (eukaryotic elongation factor α1) and eEF2 (eukaryotic elongation factor 2). The increased production of receptors of IL-2 and IFN-γ precedes the activation of gene expression and augments cellular signals and T cell activation. Taken together, we identify an early RNA translation program that acts in a feed-forward manner to enable the rapid and dramatic process of CD8 memory T cell expansion and activation.

Novel viral splicing events and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts.

Adenovirus is a common human pathogen that relies on host cell processes for transcription and processing of viral RNA and protein production. Although adenoviral promoters, splice junctions, and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and RNA cleavage and polyadenylation sites across the adenovirus genome. In addition to confirming the known canonical viral early and late RNA cassettes, our analysis of splice junctions within long RNA reads revealed an additional 35 novel viral transcripts that meet stringent criteria for expression. These RNAs include fourteen new splice junctions which lead to expression of canonical open reading frames (ORFs), six novel ORF-containing transcripts, and 15 transcripts encoding for messages that could alter protein functions through truncation or fusion of canonical ORFs. In addition, we detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking distinct gene transcription units. Among these chimeric proteins we detected an evolutionarily conserved protein containing the N-terminus of E4orf6 fused to the downstream DBP/E2A ORF. Loss of this novel protein, E4orf6/DBP, was associated with aberrant viral replication center morphology and poor viral spread. Our work highlights how long-read sequencing technologies combined with mass spectrometry can reveal further complexity within viral transcriptomes and resulting proteomes.

Clinicopathological features of mature T/NK cell lymphoma with aberrant CD20 or CD79α expression

Objective: To investigate the clinicopathological characteristics and prognosis of mature T/NK cell lymphomas with aberrant CD20 or CD79α expression. Methods: A retrospective analysis of 641 cases of mature T/NK cell lymphoma diagnosed from January 2014 to December 2020 was performed, and 14 cases of CD20-positive and one case of CD79α-positive mature T/NK-cell lymphoma were identified. Histological examination, immunohistochemical characterization, in situ hybridization for Epstein-Barr virus encoded early RNA (EBER), and PCR testing for immunoglobulin and T cell receptor (TCR) gene rearrangements were performed. Clinicopathological characteristics of these lymphomas were analyzed. Results: There were 13 males and 2 females, with a median age of 56 years. There were 8 cases of peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS), 3 cases of extranodal NK/T-cell lymphoma, nasal type (ENKTCL), 2 cases of monomorphic epitheliotropic intestinal T-cell lymphoma (MEITL) and 2 cases of angioimmunoblastic T-cell lymphoma (AITL). Twelve cases were stage Ⅲ or Ⅳ lymphomas. The prognosis was overall poor. The histology, immunophenotype and TCR gene rearrangement were not significantly different from the corresponding types of lymphoma. Ki-67 proliferation index was over 70% in all cases. The expression of CD20 or CD79α was weak and heterogeneous. All 15 case of Ig gene rearrangement were polyclonal. Conclusions: Mature T/NK cell lymphoma with abnormal expression of CD20 or CD79α is rare, commonly found in advanced stage, and associated with poor prognosis. The expression of CD20 or CD79α in these cases is weaker than the corresponding mature T/NK cell lymphomas, while its proliferation index is higher. Histomorphology, extensive immunoprofiling and molecular detection are required for accurate diagnosis.

Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome.

Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of the new phyla "Taraviricota," a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.

Structure and mechanism of the methyltransferase ribozyme MTR1.

RNA-catalysed RNA methylation was recently shown to be part of the catalytic repertoire of ribozymes. The methyltransferase ribozyme MTR1 catalyses the site-specific synthesis of 1-methyladenosine (m1A) in RNA, using O6-methylguanine (m6G) as methyl group donor. Here we report the crystal structure of MTR1 at a resolution of 2.8 Å, which reveals a guanine binding site reminiscent of natural guanine riboswitches. The structure represents the postcatalytic state of a split ribozyme in complex with the m1A-containing RNA product and the demethylated cofactor guanine. The structural data suggest the mechanistic involvement of a protonated cytidine in the methyl transfer reaction. A synergistic effect of two 2'-O-methylated ribose residues in the active site results in accelerated methyl group transfer. Supported by these results, it seems plausible that modified nucleotides may have enhanced early RNA catalysis and that metabolite-binding riboswitches may resemble inactivated ribozymes that have lost their catalytic activity during evolution.

RNA self-splicing by engineered hairpin ribozyme variants.

Small RNAs capable of self-cleavage and ligation might have been the precursors for the much more complex self-splicing group I and II introns in an early RNA world. Here, we demonstrate the activity of engineered hairpin ribozyme variants, which as self-splicing introns are removed from their parent RNA. In the process, two cleavage reactions are supported at the two intron-exon junctions, followed by ligation of the two generated exon fragments. As a result, the hairpin ribozyme, here acting as the self-splicing intron, is cut out. Two self-splicing hairpin ribozyme variants were investigated, one designed by hand, the other by a computer-aided approach. Both variants perform self-splicing, generating a cut-out intron and ligated exons.

RNA Biomarkers as a Response Measure for Survival in Patients with Metastatic Castration-Resistant Prostate Cancer.

Simple SummaryDespite the increasing number of treatments for advanced prostate cancer, the evaluation of the added value of each line of treatment on survival outcome is challenging. Therefore, biomarkers to discriminate short-term survivors from long-term survivors shortly after start of treatment are urgently needed. We demonstrate that in 93 patients with mCRPC treated with first-line abiraterone acetate or enzalutamide the addition of KLK3 and miR-375 (at baseline and 1 month) to standard clinical parameters resulted in the best prediction model for survival assessment.Treatment evaluation in metastatic castration-resistant prostate cancer is challenging. There is an urgent need for biomarkers to discriminate short-term survivors from long-term survivors, shortly after treatment initiation. Thereto, the added value of early RNA biomarkers on predicting progression-free survival (PFS) and overall survival (OS) were explored. The RNA biomarkers: KLK3 mRNA, miR-375, miR-3687, and NAALADL2-AS2 were measured in 93 patients with mCRPC, before and 1 month after start of first-line abiraterone acetate or enzalutamide treatment, in two prospective clinical trials. The added value of the biomarkers to standard clinical parameters in predicting PFS and OS was tested by Harell’s C-index. To test whether the biomarkers were independent markers of PFS and OS, multivariate Cox regression was used. The best prediction model for PFS and OS was formed by adding miR-375 and KLK3 (at baseline and 1 month) to standard clinical parameters. Baseline miR-375 and detectable KLK3 after 1 month of therapy were independently related to shorter PFS, which was not observed for OS. In conclusion, the addition of KLK3 and miR-375 (at baseline and 1 month) to standard clinical parameters resulted in the best prediction model for survival assessment.

Identification and characterization of early Fusarium wilt responsive mRNAs and long non-coding RNAs in banana root using high-throughput sequencing

Fusarium wilt disease, caused by Fusarium oxysporum f.sp. cubense (Foc), has been recognized as the most devastating disease to banana. The regulatory role of long non-coding RNAs (lncRNAs) in plant defense has been verified in many plant species. However, the understanding of their role during early FocTR4 (Foc tropical race 4) infection stage is very limited. In this study, lncRNA sequencing was used to reveal banana root transcriptome profile changes during early FocTR4 infection stages. Quantitative real time PCR (qRT-PCR) was performed to confirm the expression of eight differentially expressed (DE) lncRNAs (DELs) and their predicted target genes (DETs), and three DE genes (DEGs). Totally, 12,109 lncRNAs, 36,519 mRNAs and 2642 novel genes were obtained, of which 1398 (including 78 DELs, 1220 DE known genes and 100 DE novel genes) were identified as FocTR4 responsive DE transcripts. Gene function analysis revealed that most DEGs were involved in biosynthesis of secondary metabolites, plant–pathogen interaction, plant hormone signal transduction, phenylalanine metabolism, phenylpropanoid biosynthesis, alpha-linolenic acid metabolism and so on. Coincidently, many DETs have been identified as DEGs in previous transcriptome studies. Moreover, many DETs were found to be involved in ribosome, oxidative phosphorylation, lipoic acid metabolism, ubiquitin mediated proteolysis, N-glycan biosynthesis, protein processing in endoplasmic reticulum and DNA damage response pathways. QRT-PCR result showed the expression patterns of the selected transcripts were mostly consistent with our lncRNA sequencing data. Our present study showed the regulatory role of lncRNAs on known biotic and abiotic stress responsive genes and some new-found FocTR4 responsive genes, which can provide new insights into FocTR4-induced changes in the banana root transcriptome during the early pathogen infection stage.

Impact of the Duration of Methotrexate Administration and the Specific HLA Alleles on the Regressive Methotrexate-Induced Lymphoproliferative Disorders

[Background]Methotrexate-induced lymphoproliferative disorders (MTX-LPDs) are categorized as iatrogenic diseases and belong to the group of other iatrogenic immunodeficiency-associated LPDs, as defined in the 4th edition of the WHO classification manual for immunodeficiency-associated LPD. The phenomenon of LPD regression after MTX withdrawal is a specific event, directly suggesting an MTX influence on LPD development. Although previous data suggests this regressive phenomenon might be related to Epstein-Barr virus (EBV) infection, the precise pathogenesis still remains to be discovered. To investigate the factors involved in this phenomenon, we analyzed patients with regressive LPD after MTX withdrawal in this study.[Methods]Data were collected from 43 patients with autoimmune diseases (ADs) who developed LPD and were treated at our institutions. All diagnoses were confirmed by immunohistochemistry performed on paraffin-embedded tissue sections, along with EBV early RNAs (EBERs). All pathological samples were classified and diagnosed according to the WHO 2016 revision of classification (5th edition). HLA analysis was performed by the PCR-luminex method. The frequency of each HLA allele was determined by referring to the database of an HLA laboratory that has studied HLA alleles. The statistical analyses such as t-tests and the Kaplan-Meier method were performed using EZR software.[Results]Of 43 patients with MTX-LPD, the median age of patients at the time of LPD diagnosis was 64.7 years old (range: 41-83). Sixteen men and 27 women were included. The basal ADs were RA (N = 40), psoriasis vulgaris (N = 1), systemic lupus erythematosus (N = 1), and dermatomyositis (N = 1). The median durations of the basal ADs and MTX treatment were 10.5 (0.5-17.8) and 5.1 (0.2-16.3) years, respectively. Histopathological analysis of the LPDs revealed 14 cases of EBV + DLBCL, 6 DLBCL-NOS, 9 Hodgkin lymphoma (HL), 9 LPD, 3 follicular lymphoma (FL), 2 peripheral T-cell lymphoma (PTCL)-NOS, 1 extranodal marginal zone lymphoma of mucosal-associated lymphoid tissue (MALT), 1 plasmablastic lymphoma, and 3 with other LPDs. Regarding the clinical outcome, 32 patients (74%) were alive. After the LPD regression, 19 patients (44%) relapsed or experienced regrowth. Although patients with HL, FL, and other LPDs showed high relapse rates (100%, 67%, and 100%, respectively), the DLBCL-EBV+ and LPD cases had lower relapse rates (11% and 11%, respectively). In addition, patients with the PTCL-NOS and MALT subtypes were disease-free at the time of writing. Five and 10-year OS were 76.4% and 53.2%, respectively.To investigate any EBV influence, we compared the clinical parameters such as age, sex, clinical stages, serum LDH, serum CRP, serum soluble interleukin-2, MTX dose at the time of LDP development, the disease duration, MTX administration duration, and OS between the EBV+ and EBV - groups. Of 42 patients who underwent an EBER test, 20 patients (48%) were positive. Although for all parameters except MTX duration, significant differences were not detected, a strong association between EBV infection and the median MTX duration was observed (treatment durations in EBV + and EBV- patients were 7.4 years and 4.4 years, respectively; p = 0.0016).On the basis of the higher frequency seen in Japan, 18 patients with regressive LPD underwent HLA analysis. Ten alleles (A*2402, A*3101, A*1101, B*5101, B*5201, C*0303, DRB1*0405, DRB1*1502, DQB1*0401, and DQB1*0601) were significantly positive compared with the general frequency of these alleles in Japan.[Summary]In this study, we analyzed 43 patients with regressive MTX-LPD. After LPD regression, 19 patients (44%) experienced relapsed/regrowth, and their 5 and 10-year OS were 76.4% and 53.2%, respectively. Of 42 patients tested with EBER, 20 patients (48%) were positive. Although the clinical parameters were not significantly influenced by EBV infection, the MTX duration was strongly affected by EBV infection. In addition, 10 specific alleles including A*2402 as seen in Japanese and DRB1*0405 as seen in ADs were significantly positive compared with the general frequency of these alleles in Japan in this study.[Conclusions]Our data suggest that a longer period of MTX administration might activate EBV infection dependent on the presence of specific HLA alleles. DisclosuresTokuhira:Ezai: Honoraria. Mori:Pfizer Japan: Research Funding; Pfizer Japan: Honoraria; Bristol-Myers K.K: Research Funding; Chugai Pharmaceutical Co: Research Funding; Novartis: Research Funding. Amano:Pfizer Japan Inc: Honoraria. Okamoto:Bristol-Myers K.K: Research Funding; Pfizer: Research Funding; Bristol-Myers K.K: Honoraria; Astellas: Honoraria; Pfizer Japan: Speakers Bureau; Chugai Pharmaceutical Co.: Research Funding; Novartis: Research Funding; Alexion Pharma G.K.: Honoraria. Takeuchi:Eisai Co., Ltd: Honoraria; Janssen Pharmaceutical K.K: Honoraria; Mitsubishi Tanabe Pharma Co.: Research Funding; Bristol-Myers K.K: Honoraria; Asahi Kasei Medical K.K: Honoraria; Chugai Pharmaceutical Co., Ltd.: Honoraria; Astellas Pharma Inc.: Research Funding; Bristol-Myers K.K: Research Funding; Abbivie GK,: Research Funding; Asahi Kasei Medical K.K: Research Funding; Mitsubishi Tanabe Pharma Co: Honoraria; Abbivie GK: Honoraria; Astellas Pharma Inc: Honoraria. Tamaru:Chugai Pharmaceutical Co., Ltd.: Honoraria; Takeda Pharmaceutical Co., Ltd.: Honoraria; Nichirei Biosciences Inc.: Research Funding.

Mining of RNA Methylation-Related Genes and Elucidation of Their Molecular Biology in Gallbladder Carcinoma.

Gallbladder carcinoma (GBC), which has high invasion and metastasis risks, remains the most common biliary tract malignancy. Surgical resection for GBC is the only effective treatment, but most patients miss the opportunity for curative surgery because of a lack of timely diagnosis. The aim of this study was to identify and verify early candidate diagnostic and prognostic RNA methylation related genes for GBC via integrated transcriptome bioinformatics analysis. Lists of GBC-related genes and methylation-related genes were collected from public databases to screen differentially expressed genes (DEGs) by using the limma package and the RobustRankAggreg (RRA) package. The core genes were collected with batch effects corrected by the RRA algorithm through protein interaction network analysis, signaling pathway enrichment analysis and gene ranking. Four modules obtained from four public microarray datasets were found to be related to GBC, and FGA, F2, HAO1, CFH, PIPOX, ITIH4, GNMT, MAT1A, MTHFD1, HPX, CTH, EPHX2, HSD17B6, AKR1C4, CFHR3, ENNP1, and NAT2 were revealed to be potential hub genes involved in methylation-related pathways and bile metabolism-related pathways. Among these, FGA, CFH, F2, HPX, and PIPOX were predicted to be methylated genes in GBC, but POPIX had no modification sites for RNA methylation. Furthermore, survival analysis of TCGA (the Cancer Genome Atlas) database showed that six genes among the hub genes, FGA, CFH, ENPP1, CFHR3, ITIH4, and NAT2, were highly expressed and significantly correlated with worse prognosis. Gene correlation analysis revealed that the FGA was positively correlated with the ENPP1, NAT2, and CFHR3, while CFH was positively correlated with the NAT2, CFHR3, and FGA. In addition, the results of immunohistochemistry (IHC) showed that the expressions of FGA, F2, CFH, PIPOX, ITIH4, GNMT, MAT1A, MTHFD1, HPX, CFHR3, NAT2, and ENPP1 were higher in GBC tissues than that in control tissues. In conclusion, two genes, FGA and CFH, were identified as RNA methylation-related genes also involved in bile metabolism in GBC, which may be novel biomarkers to early diagnose and evaluate prognosis for GBC.

In vitro selections with RNAs of variable length converge on a robust catalytic core.

In vitro selection is a powerful tool that can be used to understand basic principles of molecular evolution. We used in vitro selection to understand how changes in length and the accumulation of point mutations enable the evolution of functional RNAs. Using RNA populations of various lengths, we performed a series of in vitro experiments to select for ribozymes with RNA ligase activity. We identified a core ribozyme structure that was robust to changes in RNA length, high levels of mutagenesis, and increased selection pressure. Elaboration on this core structure resulted in improved activity which we show is consistent with a larger trend among functional RNAs in which increasing motif size can lead to an exponential improvement in fitness. We conclude that elaboration on conserved core structures is a preferred mechanism in RNA evolution. This conclusion, drawn from selections of RNAs from random sequences, is consistent with proposed evolutionary histories of specific biological RNAs. More generally, our results indicate that modern RNA structures can be used to infer ancestral structures. Our observations also suggest a mechanism by which structural outcomes of early RNA evolution would be largely reproducible even though RNA fitness landscapes consist of disconnected clusters of functional sequences.

HCV testing and treatment initiation in an Italian prison setting: A step-by-step model to micro-eliminate hepatitis C

BackgroundHCV infection among vulnerable populations is currently a major issue for HCV elimination program. Incarcerated people and people who inject drugs (PWIDs) are key population groups potentially at high risk for HCV infection. Our aim was to evaluate an extended program of screening, staging and treatment in Italian prison settings. MethodsPatients from eight prisons in five different Italian Regions were enrolled. HCV saliva test (QuickOral Test®) was offered. Data on infection awareness and illicit drug use were also collected. Positive patients underwent early HCV RNA evaluation, staging and prescription on DAAs treatment.The definition of PWID was based on self-reported injecting drug use extracted from medical records (injecting drug use during the previous six months). ResultsA total of 2,376 out of 2,687 individuals (88%) was tested. The median (IQR) age was 42 (32–50) years. PWIDs were 537out of 2,376 (23%). Prevalence of HCV antibodies was 10.4% (248/2,376). PWIDs had a lower awareness of their HCV-Ab positivity than non-PWIDs (p-value <0.001). Furthermore, PWIDs were less likely to be previously treated than non-PWIDs (78% vs 96%, p-value= 0.017). Active infection was found in 41% of patients (101/248). Overall, 61% HCV-positive were PWIDs, with 44% HCV RNA positive. HCV therapy was prescribed to 83% (84/101) of patients with active HCV infection and 67% of these (56/84) were PWIDs. Prescription for HCV treatment in PWIDs accounted for 84% (56/67) (while for non-PWIDs was 82% (28/34) p-value: 0.88. Seventeen patients were referred to a Specialist in other prisons because they were going to be transferred soon to another prison. EOT, as well as SVR12 were achieved in 98% (82/84) treated patients. ConclusionsAmong patients, PWIDs had a lower awareness of their HCV-Ab positivity and had previously received less treatments. Saliva test allowed to achieve a more rapid result, stage, and treatment approach. More than 80% of patients underwent treatment, without differences between PWIDs and non-PWIDs. Linkage to care during prison transfer allowed to avoid unplanned interruptions and offered more chances to reach the end of treatment.

Corticosteroid, oseltamivir and delayed admission are independent risk factors for prolonged viral shedding in patients with Coronavirus Disease 2019.

IntroductionCoronavirus Disease 2019 (COVID‐19) has spread worldwide, and it has reached to more than 14.5 million cases. Although Hubei province is the epicenter of China, little is known about epidemiological and clinical features of COVID‐19 in other areas in Hubei province around Wuhan. In addition, the virological data, particularly the factors associated with viral shedding of COVID‐19 has not been well described.ObjectiveTo describe the epidemiological and clinical features of patients with COVID‐19 in Tianmen city, and identify risk factors associated with prolonged viral shedding of COVID‐19.MethodsInpatients with COVID‐19 admitted before February 9, 2020 were included. Characteristics were compared between patients with early and late viral RNA shedding. Multivariate cox regression model was used to investigate variables associated with prolonged viral shedding.ResultsOne hundred and eighty‐three patients were included. About 8.2% patients were categorized as critical degree of severity. All patients received antiviral therapy, with arbidol and interferon being the commonest. About 38.3% and 16.9% patients were treated with corticosteroid and immunoglobulin, respectively. Time from onset to admission (HR = 0.829, P < 0.001), and administration of corticosteroid (HR = 0.496, P = 0.002), arbidol (HR = 2.605, P = 0.008) and oseltamivir (HR = 0.416, P < 0.001) were independently associated with duration of viral shedding.ConclusionSymptoms of patients from Tianmen are relatively mild. Treatment should be started as early as possible, but corticosteroid and oseltamivir should be initiated with caution. In addition, clinical trials on arbidol should be conducted to demonstrate its effectiveness.

Factors Associated With Prolonged Viral RNA Shedding in Patients with Coronavirus Disease 2019 (COVID-19).

BackgroundAn outbreak of coronavirus disease 2019 (COVID-19) is becoming a public health emergency. Data are limited on the duration and host factors related to viral shedding.MethodsIn this retrospective study, risk factors associated with severe acute respiratory coronavirus 2 (SARS-CoV-2) RNA shedding were evaluated in a cohort of 113 symptomatic patients from two hospitals outside Wuhan.ResultsThe median duration of SARS-CoV-2 RNA detection was 17 days (Interquartile Range [IQR], 13–22 days) as measured from illness onset. When comparing patients with early (<15 days) and late viral RNA clearance (≥15 days after illness onset), prolonged SARS-CoV-2 RNA shedding was associated with male sex (p=0.009), old age (p=0.033), concomitated with hypertension (p=0.009), delayed admission to hospital after illness onset (p=0.001), severe illness at admission (p=0.049), invasive mechanical ventilation (p=0.006), and corticosteroid treatment (p=0.025). Patients with longer SARS-CoV-2 RNA shedding duration had slower recovery of body temperature (p<0.001) and focal absorption on radiograph images (p<0.001) than patients with early SARS-CoV-2 RNA clearance. Male sex (odds ratio [OR], 3.24 [95% CI, 1.31–8.02]), delayed hospital admission (OR, 1.30 [95% CI, 1.10–1.54]), and invasive mechanical ventilation (OR, 9.88 [95% CI, 1.11–88.02]) were independent risk factors for prolonged SARS-CoV-2 RNA shedding.ConclusionsMale sex, delayed admission to hospital after illness onset, and invasive mechanical ventilation were associated with prolonged SARS-CoV-2 RNA shedding. Hospital admission and general treatments should be started as soon as possible in symptomatic COVID-19 patients, especially male patients.

Modified nucleotides may have enhanced early RNA catalysis

The modern version of the RNA World Hypothesis begins with activated ribonucleotides condensing (nonenzymatically) to make RNA molecules, some of which possess (perhaps slight) catalytic activity. We propose that noncanonical ribonucleotides, which would have been inevitable under prebiotic conditions, might decrease the RNA length required to have useful catalytic function by allowing short RNAs to possess a more versatile collection of folded motifs. We argue that modified versions of the standard bases, some with features that resemble cofactors, could have facilitated that first moment in which early RNA molecules with catalytic capability began their evolutionary path toward self-replication.

Abstract 50: RNA Expression for Diagnosis of Stroke Etiology Differentiating Large Artery and Cardioembolic Stroke: Analytical Validation of Testing From the BASE Clinical Trial

Background: An accurate test to differentiate large artery stroke (LAS) patients from those with cardioembolic stroke (CES) would be of significant clinical utility. Using the Biomarkers of Acute Stroke Etiology (BASE) trial (NCT02014896) dataset, our purpose was to utilize blood gene expression signatures for accurately differentiating LAS from CES acute stroke etiologies. Methods: The BASE trial enrolled suspected stroke patients presenting to 20 hospitals within 24 hrs of symptom onset. Final gold standard diagnosis and stroke etiology were determined by an adjudication committee using all hospital data but blinded to RNA test results. Whole blood, obtained in PAX tubes, was frozen at -20C within 72 hrs and analyzed at a core lab (Ischemia Care, Dayton, OH) using Affymetrix HTA microarrays. Genes on the HTA microarray were filtered to eliminate genes with low expression or high CV (&gt; 10%) when run on replicate samples leaving 9,513 potential signature genes. A two-way random forest classifier was built through cross validation of the training data resulting in a 45 gene diagnostic signature. Results: This is a planned interim cohort study of the 1700 patients enrolled in the BASE trial that does not include lacunar strokes, TIA, or stroke mimics. Overall, 222 patients were enrolled with NIHSS&gt;5, 70 (32%) with LAS and 152 (68%) with CES; 59% were male, and median (IQR) age was 70.7 yrs (62.0, 80.2). Median (IQR) time from symptom onset to blood collection was 1200 (448, 1568) minutes. Coexistent pathology at presentation included atrial fibrillation 90 (48%), hypertension 153 (82%), hyperlipidemia 87 (47%), diabetes 60 (32%), and coronary artery disease 70 (37%). Patients were randomly divided into training (148), early symptom onset (&lt;18hrs) validation (39) and a late symptom onset (&gt;18 hrs) validation (35). The diagnostic gene signature results in the early validation cohort distinguished LAS from CES; C-statistic 0.78 (0.50-1.0, 95% CI), sensitivity 0.90 (0.55-1.0, 95% CI) and specificity of 0.70 (0.43-1.0, 95% CI). Conclusion: Early RNA expression differentiates large artery stroke patients from those with cardioembolic stroke, and may have therapeutic and secondary prevention implications.

Epstein-Barr virus associated gastric carcinoma at the United States-Mexico border: A single institution study.

440 Background: Globally, gastric cancer (GC) is the fourth most prevalent cancer, and the second leading cause of cancer related deaths. Epstein-Barr virus is implicated in the pathogenesis of 5-10% of gastric cancers. Based upon the results obtained from of the cancer genome atlas, EBV related GC is characterized by promoter hypermethylation, PIK3CA mutations (80%) and increased expression of PD-1 and PD-L1, making it an attractive target for molecularly targeted therapy and immunotherapeutic options. As such, a case can be made for routine testing for EBV in all GC patients. University medical center, El Paso is a tax payer funded safety net health system in El Paso country, TX. We conducted a pilot study to characterize the prevalence of EBV associated gastric cancer seen at this facility. Methods: After obtaining institutional review board (IRB) approval, we identified cases of GC that were diagnosed between January 1, 2008- and December 31-2017. A total of 104 cases were identified of which 17 samples were randomly selected. Pathology specimens were reviewed to identify grade, subtype (intestinal vs diffuse), degree of lymphocytic infiltration and presence/absence of H. pylori. Representative sections from archived tumors were used to perform in-situ hybridization to look for the presence of Epstein-Barr virus. Samples were analyzed using the Rembrandt In situ Hybridization and Detection Universal RISH&amp; HRP Detection Kit for Epstein-Barr early RNA. Results: The median age of the 17 patients is 63 years with 59% being males. 95% self identified as Hispanic. 41% were smokers, 18% used alcohol. The mean BMI was 27.3. Forty one percent of gastric cancer cases were found in the body, 29% in the antrum, 12% in the cardia, and 6% in the fundus. Forty one percent of cases were Stage IV, 24% stage II, 17% Stage III and 17% Stage I. 95% of cases were high grade, 53% of them had signet ring features. 18% of samples were H. pylori positive. None of the seventeen samples tested positive for EBV. Conclusions: EBV does not seem to contribute significantly to the pathogenesis of gastric cancer in our local population. As such routine testing for EBV in all gastric cancer patients may not be a cost effective utilization of resources at our hospital.

Mouse Erythroid Cells Originate from a Megakaryocyte Precursor in Common Myeloid Progenitors

The hierarchical model of hematopoiesis posits that hematopoietic stem and progenitor cells produce common myeloid progenitors (CMP). CMP can become granulocyte/monocyte progenitors (GMP) or bipotential megakaryocyte/erythroid progenitors (MEP). MEP can produce megakaryocytic (Mk) or erythroid (Ery) cells. However, we and others have shown that early mouse and human progenitor populations express many Mk genes (Heuston, Epig. Chrom., 2016), while single cell studies have identified lineage-specific colony forming cells in progenitor populations thought to be multipotent (Psaila, Genome Biol., 2016). To identify the earliest mouse Ery and Mk cells, we performed single cell RNASeq on 10000 stem and progenitor cells (Lin-Sca1+Kit+), 12000 CMP (Lin-Sca1-Kit+CD16/32-CD34+), 6000 MEP (Lin-Sca1-Kit+CD16/32-CD34-) and 8000 GMP (Lin-Sca1-Kit+CD16/32+CD34+). TSNE analysis of expression in the 4 populations identified 33 clusters, which were correlated to biological functions using gene set enrichment analysis. In LSK, no cells with an Ery RNA profile were found, while 56% of cells co-expressed Mk-associated (e.g., Meis1, Fli1) and lymphoid genes. In CMP, 12% of the cells co-expressed Ery (e.g., Gata1, Fog1) and Mk (e.g., Pf4, Cd41) genes, while 23% had an Mk-specific profile (e.g., Fli1, Cd41) enriched for platelet biology processes (p&amp;lt; 3E-18). Unlike traditional models, over 94% of MEP had Ery RNA profiles enriched for ribosome synthesis and heme-biology processes (p&amp;lt; 4E-10). To establish developmental relationships, we performed pseudotime analysis using the Monocle and Scanpy software packages. These programs model differentiation by mapping similar transcriptomes together. Map nodes indicate lineage commitment points and cells further from a node are more differentiated. Combined analysis of LSK, CMP, and MEP generated a model with a single node and 2 trajectories. LSK with Mk and lymphoid RNA profiles diverged at the node, as did 14% of CMP. 31% of CMP with an Mk RNA profile were downstream of the node. Further downstream were cells with mixed Ery/Mk profiles, and furthest from the node were MEP with Ery profiles. A separate pseudotime analysis of CMP only 2 trajectories: one with decreasing Mk- and increasing Ery RNA profiles, and a second with an early Mk endomitotic RNA profile. Pseudotime analysis of MEP only identified a linear trajectory: cells at one end expressed early Ery RNA profiles, and cells at the other end had RNA profiles similar to those of burst-forming unit-erythroid (BFU-E). We generated a predictive set of RNAs for each TSNE cluster. We used index-sorting with 11 markers (Kit, Sca1, CD34, CD16/32, CD36, CD41, CD48, CD123, CD150, CD9, Flk2) to isolate single cells for custom high-throughput multiplex qPCR. This allowed confirmation of cell frequency within TSNE clusters while identifying surface markers for prospective isolation of cell subsets. We focused on 2 populations: CMP-E, which had an Ery RNA profile (10% of clustered CMP and 12% of CMP in the qPCR assay), and CMP-MkE, which had Mk and Ery RNA profiles (12% of clustered CMP and 13% of CMP in the qPCR assay). We prospectively isolated CMP-E and CMP-MkE to compare RNASeq profiles, ATACSeq profiles, and colony forming ability against those of bulk CMP, Ery, and Mk. In CMP-E, 54% of RNAs were expressed in both CMP and ERY, while 41% were expressed only in CMP (p &amp;lt; 6E-72). In contrast, 41% of CMP-E ATACSeq peaks were present in CMP and ERY, while 57% of CMP-E peaks were present only in CMP (p &amp;lt; 1E-3). We conclude that in CMP-E, the RNASeq profile is more erythroid than the ATACSeq profile. In CMP-MkE, 89% of RNAs were expressed in both CMP and Mk, while 7% were expressed only in CMP (p &amp;lt; 8E-190). Likewise, 88% of CMP-MkE ATACSeq peaks were present in both CMP and Mk, while 3% were present only in CMP (p &amp;lt; 1E-3). We conclude that in CMP-MkE, the RNASeq and ATACSeq profiles are equivalent. In soft agar assays, 21% of CMP-E and 3% of CMP-MkE colonies contained BFU-E, compared to 9% of control colonies. We conclude that the CMP-E and CMP-MkE populations are skewed towards the ERY and MK lineages, but are not erythro-megakaryocyte restricted. Our data support a model in which there are two megakaryocyte precursor populations and no erythroid populations in LSK. A third megakaryocyte population in CMP gives rise to erythroid cells. Finally, our data show that transcriptional changes precede chromatin accessibility changes in the earliest erythroid cells. Disclosures No relevant conflicts of interest to declare.