Anti-schistosomal immunity to core xylose/fucose in N-glycans

Schistosomiasis is a globally prevalent, debilitating disease that is poorly controlled by chemotherapy and for which no vaccine exists. While partial resistance in people may develop over time with repeated infections and treatments, some animals, including the brown rat (Rattus norvegicus), are only semi-permissive and have natural protection. To understand the basis of this protection, we explored the nature of the immune response in the brown rat to infection by Schistosoma mansoni. Infection leads to production of IgG to Infection leads to production of IgG to parasite glycoproteins parasite glycoproteins with complex-type N-glycans that contain a non-mammalian-type modification by core α2-Xylose and core α3-Fucose (core Xyl/Fuc). These epitopes are expressed on the surfaces of schistosomula and adult worms. Importantly, IgG to these epitopes can kill schistosomula by a complement-dependent process in vitro. Additionally, sera from both infected rhesus monkey and infected brown rat were capable of killing schistosomula in a manner inhibited by glycopeptides containing core Xyl/Fuc. These results demonstrate that protective antibodies to schistosome infections in brown rats and rhesus monkeys include IgG responses to the core Xyl/Fuc epitopes in surface-expressed N-glycans, and raise the potential of novel glyco-based vaccines that might be developed to combat this disease

Genomic and serologic characterization of enterovirus A71 brainstem encephalitis

OBJECTIVE: In 2016, Catalonia experienced a pediatric brainstem encephalitis outbreak caused by enterovirus A71 (EV-A71). Conventional testing identified EV in the periphery but rarely in CSF. Metagenomic next-generation sequencing (mNGS) and CSF pan-viral serology (VirScan) were deployed to enhance viral detection and characterization. METHODS: RNA was extracted from the CSF (n = 20), plasma (n = 9), stool (n = 15), and nasopharyngeal samples (n = 16) from 10 children with brainstem encephalitis and 10 children with meningitis or encephalitis. Pathogens were identified using mNGS. Available CSF from cases (n = 12) and pediatric other neurologic disease controls (n = 54) were analyzed with VirScan with a subset (n = 9 and n = 50) validated by ELISA. RESULTS: mNGS detected EV in all samples positive by quantitative reverse transcription polymerase chain reaction (qRT-PCR) (n = 25). In qRT-PCR-negative samples (n = 35), mNGS found virus in 23% (n = 8, 3 CSF samples). Overall, mNGS enhanced EV detection from 42% (25/60) to 57% (33/60) (p-value = 0.013). VirScan and ELISA increased detection to 92% (11/12) compared with 46% (4/12) for CSF mNGS and qRT-PCR (p-value = 0.023). Phylogenetic analysis confirmed the EV-A71 strain clustered with a neurovirulent German EV-A71. A single amino acid substitution (S241P) in the EVA71 VP1 protein was exclusive to the CNS in one subject. CONCLUSION: mNGS with VirScan significantly increased the CNS detection of EVs relative to qRT-PCR, and the latter generated an antigenic profile of the acute EV-A71 immune response. Genomic analysis confirmed the close relation of the outbreak EV-A71 and neuroinvasive German EV-A71. A S241P substitution in VP1 was found exclusively in the CSF.Grants supporting this project include the National Multiple Sclerosis Society and the American Academy of Neurology award FAN-1608-25607 (R.D.S.), Clinical Research Training Scholarship P0534134 (P.S.R.), Sandler and William K. Bowes Jr Foundations (M.R.W., J.L.D., L.M.K., H.A.S., K.C.Z.), Rachleff Family Foundation (M.R.W.), and NINDS of the NIH under award K08NS096117 (M.R.W.) and F31NS113432 (K.E.L.). This study was partially supported by a grant from the Spanish National Health Institute [grant number PI15CIII-00020] and the European Regional Development Fund (FEDER funds). UCSF Biomedical Sciences Program (I.A.H., K.E.L.), UCSF Medical Scientist Training Program (K.E.L.), and the Chan Zuckerberg Biohub (J.E.P., W.W., C.K.C., J.L.D., E.D.C.) also supported this project.S

Central Nervous System Virus Infection in African Children with Cerebral Malaria

We aimed to identify the contribution of central nervous system (CNS) viral coinfection to illness in African children with retinopathy-negative or retinopathy-positive cerebral malaria (CM). We collected cerebrospinal fluid (CSF) from 272 children with retinopathy-negative or retinopathy-positive CM and selected CSF from 111 of these children (38 retinopathy positive, 71 retinopathy negative, 2 retinopathy unknown) for analysis by metagenomic next-generation sequencing. We found CSF viral coinfections in 7/38 (18.4%) retinopathy-positive children and in 18/71 (25.4%) retinopathy-negative children. Excluding HIV-1, human herpesviruses (HHV) represented 61% of viruses identified. Excluding HIV-1, CNS viral coinfection was equally likely in children who were retinopathy positive and retinopathy negative (P = 0.1431). Neither mortality nor neurological morbidity was associated with the presence of virus (odds ratio [OR] = 0.276, 95% CI: 0.056-1.363). Retinopathy-negative children with a higher temperature, lower white blood cell count, or being dehydrated were more likely to have viral coinfection. Level of consciousness at admission was not associated with CNS viral coinfection in retinopathy-negative children. Viral CNS coinfection is unlikely to contribute to coma in children with CM. The herpesviruses other than herpes simplex virus may represent incidental bystanders in CM, reactivating during acute malaria infection

Migraine polygenic risk score associates with efficacy of migraine-specific drugs

Objective To assess whether the polygenic risk score (PRS) for migraine is associated with acute and/or prophylactic migraine treatment response. Methods We interviewed 2,219 unrelated patients at the Danish Headache Center using a semistructured interview to diagnose migraine and assess acute and prophylactic drug response. All patients were genotyped. A PRS was calculated with the linkage disequilibrium pred algorithm using summary statistics from the most recent migraine genome-wide association study comprising ∼375,000 cases and controls. The PRS was scaled to a unit corresponding to a twofold increase in migraine risk, using 929 unrelated Danish controls as reference. The association of the PRS with treatment response was assessed by logistic regression, and the predictive power of the model by area under the curve using a case-control design with treatment response as outcome. Results A twofold increase in migraine risk associates with positive response to migraine-specific acute treatment (odds ratio [OR] = 1.25 [95% confidence interval (CI) = 1.05–1.49]). The association between migraine risk and migraine-specific acute treatment was replicated in an independent cohort consisting of 5,616 triptan users with prescription history (OR = 3.20 [95% CI = 1.26–8.14]). No association was found for acute treatment with non–migraine-specific weak analgesics and prophylactic treatment response. Conclusions The migraine PRS can significantly identify subgroups of patients with a higher-than-average likelihood of a positive response to triptans, which provides a first step toward genetics-based precision medicine in migraine

Zika Virus Disrupts the Nonsense-mediated mRNA Decay Pathway feat. A Clinical Application of Next Generation Sequencing

Zika virus (ZIKV) is a mosquito-borne illness responsible for an outbreak of microcephaly in Brazil in 2015. To better understand the molecular mechanisms behind the neurodevelopmental delay seen, we explored the pathways perturbed by ZIKV to establish an infection and cause the neurological sequelae seen in patients. We focused particularly on the Nonsense-mediated mRNA Decay (NMD) pathway: a cellular RNA quality control pathway responsible for degrading mRNAs with premature termination codons that also regulates a significant subset of normal mRNAs. To best study the impacts of ZIKV, we used neural progenitor cells (NPCs) derived from induced pluripotent stem cells. We found that during ZIKV infection, the viral Capsid protein interacted with and degraded UPF1, the master regulator of the NMD pathway, in the nucleus. UPF1 was a viral restriction factor, and removal of UPF1 from the cell leads to increased permissivity to ZIKV infection. We next found that ZIKV-mediated UPF1 degradation led to a loss of UPF1 occupancy on host transcripts, which caused a shift in cellular localization and trapped specific transcripts in the nucleus. An extracellular matrix protein involved in fetal development, FREM2, had mRNA retained in the nucleus, leading to decreased protein levels. Depletion of FREM2 in NPCs led to premature neuronal differentiation. Overall, it leads to a model system where ZIKV, using its capsid protein, causes destruction of UPF1 to promote a productive infection As we find UPF1 linked to many neurodevelopment pathways, we propose that the disruption of the NMD and the lack of host mRNA export contributes to virally induced neurodevelopmental disorders in ZIKV infection. Lastly, we show an example of how laboratory techniques used in the study of viral infections in vitro can be used in a clinical application. An outbreak of EV-A71 in Catalonia, Spain caused widespread brainstem encephalitis in a pediatric population. To better understand the outbreak, we compare metagenomic next generation sequencing (mNGS) to quantitative PCR (qPCR) as a diagnostic tool in the CSF of patients. We show that mNGS is capable of identifying virus in samples that qPCR can’t. Using mNGS data, we obtained several full-length genomes, allowing for phylogenetic analyses and the identification of a single mutation potentially responsible for the enhanced neuroinvasive characteristics. We then used VirScan, a phage display library expressing a wide variety of human viral protein peptides, to identify patients exposed to virus and characterize which viral epitopes were the most immunoreactive, complementing the mNGS data. Overall, we show that this standard laboratory technique can play an important role in patient care, especially for viral detection in typically hard-to-diagnose body sites. This also applies to surveillance of current and future viral outbreaks. Given the circumstances—writing a dissertation regarding the molecular pathogenesis of a virus responsible for an epidemic concurrent with the COVID-19 pandemic highlights the need for translation of cutting-edge laboratory techniques to improve virus detection and comprehension for more personalized therapeutics

Zika Virus Disrupts the Nonsense-mediated mRNA Decay Pathway feat. A Clinical Application of Next Generation Sequencing

Zika virus (ZIKV) is a mosquito-borne illness responsible for an outbreak of microcephaly in Brazil in 2015. To better understand the molecular mechanisms behind the neurodevelopmental delay seen, we explored the pathways perturbed by ZIKV to establish an infection and cause the neurological sequelae seen in patients. We focused particularly on the Nonsense-mediated mRNA Decay (NMD) pathway: a cellular RNA quality control pathway responsible for degrading mRNAs with premature termination codons that also regulates a significant subset of normal mRNAs. To best study the impacts of ZIKV, we used neural progenitor cells (NPCs) derived from induced pluripotent stem cells. We found that during ZIKV infection, the viral Capsid protein interacted with and degraded UPF1, the master regulator of the NMD pathway, in the nucleus. UPF1 was a viral restriction factor, and removal of UPF1 from the cell leads to increased permissivity to ZIKV infection. We next found that ZIKV-mediated UPF1 degradation led to a loss of UPF1 occupancy on host transcripts, which caused a shift in cellular localization and trapped specific transcripts in the nucleus. An extracellular matrix protein involved in fetal development, FREM2, had mRNA retained in the nucleus, leading to decreased protein levels. Depletion of FREM2 in NPCs led to premature neuronal differentiation. Overall, it leads to a model system where ZIKV, using its capsid protein, causes destruction of UPF1 to promote a productive infection As we find UPF1 linked to many neurodevelopment pathways, we propose that the disruption of the NMD and the lack of host mRNA export contributes to virally induced neurodevelopmental disorders in ZIKV infection. Lastly, we show an example of how laboratory techniques used in the study of viral infections in vitro can be used in a clinical application. An outbreak of EV-A71 in Catalonia, Spain caused widespread brainstem encephalitis in a pediatric population. To better understand the outbreak, we compare metagenomic next generation sequencing (mNGS) to quantitative PCR (qPCR) as a diagnostic tool in the CSF of patients. We show that mNGS is capable of identifying virus in samples that qPCR can’t. Using mNGS data, we obtained several full-length genomes, allowing for phylogenetic analyses and the identification of a single mutation potentially responsible for the enhanced neuroinvasive characteristics. We then used VirScan, a phage display library expressing a wide variety of human viral protein peptides, to identify patients exposed to virus and characterize which viral epitopes were the most immunoreactive, complementing the mNGS data. Overall, we show that this standard laboratory technique can play an important role in patient care, especially for viral detection in typically hard-to-diagnose body sites. This also applies to surveillance of current and future viral outbreaks. Given the circumstances—writing a dissertation regarding the molecular pathogenesis of a virus responsible for an epidemic concurrent with the COVID-19 pandemic highlights the need for translation of cutting-edge laboratory techniques to improve virus detection and comprehension for more personalized therapeutics

An 'Arms Race' between the Nonsense-mediated mRNA Decay Pathway and Viral Infections.

The Nonsense-mediated mRNA Decay (NMD) pathway is an RNA quality control pathway conserved among eukaryotic cells. While historically thought to predominantly recognize transcripts with premature termination codons, it is now known that the NMD pathway plays a variety of roles, from homeostatic events to control of viral pathogens. In this review we highlight the reciprocal interactions between the host NMD pathway and viral pathogens, which have shaped both the host antiviral defense and viral pathogenesis