Infectious disease
Bcl6 reactivity is associated with a distinct immune landscape and spatial transcriptome in COVID-19
Abstract
The regulation of follicular (F) and germinal center (GC) immune reactivity in human lymph nodes (LNs), particularly during the acute stages of viral infection, remains poorly understood: We have analyzed lung-draining lymph nodes (LD-LNs) from COVID-19 autopsies using multiplex imaging and spatial transcriptomics to examine the immune landscape with respect to follicular immune reactivity. We identified three groups of donors based on the Bcl6 prevalence of their Reactive Follicles (RFs): RF-Bcl6no/low, RF-Bcl6int, and RF-Bcl6high. A distinct B/TFH immune landscape, associated with increased prevalence of proliferating B-cell and TFH-cell subsets, was found in RF-Bcl6high LD-LNs. The comparison between LD-LNs and subdiaphragmatic (SD) LNs from the same donor revealed a divergent Bcl6 expression between the two anatomical sites. LD-LN Bcl6 expression was also associated with a distinct spatial transcriptomic profile. TH1-associated genes/pathways (e.g., CXCR3, STAT5, TNF-signaling) were significantly up-regulated in RF-Bcl6no/low tissues, while the RF-Bcl6high tissues exhibited significant up-regulation of GC-promoting genes/pathways (e.g., CXCL13, B-cell receptor signaling). Our findings reveal a heterogeneous F/GC landscape in COVID-19 LD-LNs, highlighting specific molecular targets and pathways that could regulate human F/GC immune dynamics during acute viral infections.
Authors
Cloé Brenna, Bernat Bramon Mora, Kalliopi Ioannidou, Julien Bodelet, Mia L. Siebmanns, Simon Burgermeister, Spiros Georgakis, Michail Orfanakis, Yannick D. Muller, Nazanin Sédille, Matthew J. Feinstein, Jon W. Lomasney, Oliver Y. Chén, Giuseppe Pantaleo, Sabina Berezowska, Laurence de Leval, Raphael Gottardo, Constantinos Petrovas
Abstract
BACKGROUND. Understanding age-associated differences in acute and memory adaptive immunity to SARS-CoV-2 and how this contributes to more favorable outcomes in children is critically important. METHODS. We evaluated SARS-CoV-2–specific T cell, B cell, and antibody responses in 329 peripheral blood samples collected from non-hospitalized children, adolescents, and adults at three timepoints, including acute and memory timepoints. RESULTS. Most children produced robust CD4+ T cell responses during infection and developed memory CD4+ T cells; however, young children <4 years old often had undetectable CD4+ T cell responses compared to older children and adults. Young children also generated reduced frequencies of memory B cells; despite this, they mounted substantial and durable neutralizing antibody responses. CD4+ T cell responses in children were biased towards non-spike epitopes, especially in asymptomatic cases. Memory B cells in children were preferentially classical memory or, paradoxically, CXCR3+. CONCLUSION. These findings support the concept that the kinetics and composition of T and B cell responses shift across age groups and may be associated with milder COVID-19 outcomes in children.
Authors
L. Benjamin Hills, Numana Bhat, Jillian H. Hurst, Amber Myers, Thomas W. Burke, Micah T. McClain, Elizabeth Petzold, Alexandre T. Rotta, Nicholas A. Turner, Alba Grifoni, Daniela Weiskopf, Yvonne Dogariu, Genevieve G. Fouda, Sallie R. Permar, Alessandro Sette, Christopher W. Woods, Matthew S. Kelly, Shane Crotty
Abstract
To radically diminish TB incidence and mortality by 2035, as set out by the WHO End TB Strategy, there is a desperate need for improved TB therapies and a more effective vaccine against the deadly pathogen Mycobacterium tuberculosis (Mtb). Aerosol vaccination with the MtbΔsigH mutant protects two different species of NHPs against lethal TB challenge by invoking vastly superior T and B cell responses in the lungs through superior antigen-presentation and interferon-conditioning. Since the Geneva consensus on essential steps towards the development of live mycobacterial vaccines recommends that live TB vaccines must incorporate at least two independent gene knock outs, we have now generated several rationally designed, double (DKO)- and triple (TKO) knock-out mutants in Mtb, each containing the ΔsigH deletion. Here, we report preclinical studies in the rhesus macaque model of aerosol infection and SIV/HIV co-infection, aimed at assessing the safety of these MtbΔsigH - based DKOs and TKOs. We found that most of these mutant strains are attenuated in both immunocompetent and SIV-co-infected macaques and combinatorial infection with these generated strong cellular immune responses in the lung, akin to MtbΔsigH. Aerosol infection with these KO strains elicited inducible Bronchus Associated Lymphoid Tissue (iBALT), which is a correlate of protection from TB.
Authors
Garima Arora, Caden W. Munson, Mushtaq Ahmed, Vinay Shivanna, Annu Devi, Venkata S.R. Devireddy, Basil Antony, Shannan Hall-Ursone, Olga D. Gonzalez, Edward Dick Jr., Chinnaswamy Jagannath, Xavier Alvarez, Smriti Mehra, Shabaana A. Khader, Dhiraj K. Singh, Deepak Kaushal
Abstract
Exposure to Bacillus Calmette-Guérin (BCG) or Canarypox ALVAC/Alum vaccine elicits pro- or antiinflammatory innate responses, respectively. We tested whether prior exposure of macaques to these immunogens protected against SARS-CoV-2 replication in lungs and found more efficient replication control after the pro-inflammatory immunity elicited by BCG. The decreased virus level in lungs was linked to early infiltrates of classical monocytes producing IL-8 with systemic neutrophils, Th2 cells, and Ki67+CD95+CD4+ T cells producing CCR7. At the time of SARS-CoV-2 exposure, BCG-treated animals had higher frequencies of lung infiltrating neutrophils and higher CD14+ cells expressing efferocytosis marker MERTK, responses correlating with decreased SARS-CoV-2 replication in lung. At the same time point, plasma IL-18, TNF-α, TNFSF-10, and VEGFA levels were also higher in the BCG group and correlated with decreased virus replication. Finally, after SARS-CoV-2 exposure, decreased virus replication correlated with neutrophils producing IL-10 and CCR7 preferentially recruited to the lungs of BCG-vaccinated animals. These data point to the importance of the spatiotemporal distribution of functional monocytes and neutrophils in controlling SARS-CoV-2 levels and suggest a central role of monocyte efferocytosis in curbing replication.
Authors
Mohammad Arif Rahman, Katherine C. Goldfarbmuren, Sarkis Sarkis, Massimiliano Bissa, Anna Gutowska, Luca Schifanella, Ramona Moles, Melvin N. Doster, Hanne Andersen, Yogita Jethmalani, Leonid Serebryannyy, Timothy Cardozo, Mark G. Lewis, Genoveffa Franchini
Abstract
Infections with non-tuberculous mycobacterium (NTM) are on the rise. Here, we investigated an uncommon NTM infection, by M. haemophilum (Mh, n = 3), from a shared geographic location in the USA. All patients had underlying immunosuppressive conditions or treatments. We identified that all these individuals had a non-synonymous mutation in GATA2 gene, which was absent in Healthy controls (HCs, n = 4) from the same geographic area (Missouri, USA). Whole blood from these individuals had attenuated cytokine responses to Mh stimulation for IL1β, IL-6, IL-8, MIP-1α and β, but not to Phytohemagglutinin (PHA) or another NTM, M. abscessus. Impaired whole blood transcriptional responses in individuals with GATA2 mutation, included heightened Ras-homolog (Rho) guanosine triphosphate hydrolases (GTPase) and lowered Transforming growth factor (TGF)-β responses among others. Our results highlight that comparatively, M. abscessus and Mh elicit differential immune responses in humans, and we identify a 23-gene signature that distinguishes host response to Mh and M. abscessus and show that in vitro GATA2 siRNA knockdown indeed attenuates cytokine responses to Mh. Thus, we provide new evidence that links GATA2 mutation and immune dysfunction in individuals with compromised immunity to Mh infection in humans and outline host factors associated with the immune response of this clinically relevant NTM.
Authors
Ananya Gupta, Shail B. Mehta, Abhimanyu A, Bruce A. Rosa, John Martin, Mushtaq Ahmed, Shyamala Thirunavukkarasu, Farheen Fatma, Gaya Amarsinghe, Makedonka Mitreva, Thomas C. Bailey, David B. Clifford, Shabaana A. Khader
Abstract
Multidrug-resistant (MDR) bacterial pneumonias pose a critical threat to global public health. The opportunistic Gram-negative pathogen Pseudomonas aeruginosa is a leading cause of nosocomial-associated pneumonia, and an effective vaccine could protect vulnerable populations, including the elderly, immunocompromised, and those with chronic respiratory diseases. Highly heterogeneous outer membrane vesicles (OMVs), shed from Gram-negative bacteria, are studded with immunogenic lipids, proteins, and virulence factors. To overcome limitations in OMV stability and consistency, we described a believed to be novel vaccine platform that combines immunogenic OMVs with precision nanotechnology—creating a bacterial cellular nanoparticle vaccine candidate (CNP), termed Pa-STING-CNP, which incorporates an adjuvanted core that activates the STING (stimulator of interferon genes) pathway. In this design, OMVs are coated onto the surface of self-adjuvanted STING nanocores. Pa-STING CNP vaccination induced substantial antigen presenting cell recruitment and activation in draining lymph nodes, robust anti-Pseudomonas antibody responses, and provided protection against lethal challenge with the hypervirulent clinical P. aeruginosa isolate PA14. Antibody responses mediated this protection and provided passive immunity against the heterologous P. aeruginosa strain PA01. These findings provided evidence that nanotechnology can be used to create a highly efficacious vaccine platform against high priority MDR pathogens such as P. aeruginosa.
Authors
Elisabet Bjånes, Nishta Krishnan, Truman Koh, Anh T.P. Ngo, Jason Cole, Joshua Olson, Ingrid Cornax, Chih-Ho Chen, Natalie Chavarria, Samira Dahesh, Shawn M. Hannah, Alexandra Stream, Jiaqi Amber Zhang, Hervé Besançon, Daniel Sun, Siri Yendluri, Sydney Morrill, Jiarong Zhou, Animesh Mohapatra, Ronnie H. Fang, Victor Nizet
Abstract
X-linked Lymphoproliferative Syndromes (XLP), arising from mutations in SH2D1A or XIAP genes, are characterized by fulminant Epstein-Barr Virus (EBV) infection. Lymphomas occur frequently in XLP-1 and in other congenital conditions with heightened EBV susceptibility, but not in XLP-2. Why XLP-2 patients are apparently protected from EBV-driven lymphomagenesis remains a key open question. To gain insights, newly EBV-infected versus receptor-stimulated primary B-cells from XLP-2 patients or with XIAP CRISPR editing were compared to healthy controls. XIAP perturbation impeded outgrowth of newly EBV-infected B-cells, but not that of CD40 ligand and interleukin-21 stimulated B-cells. XLP-2 deficient B-cells showed significantly lower EBV transformation efficiency than healthy controls. Interestingly, EBV-immortalized lymphoblastoid cell proliferation was not impaired by XIAP knockout, implicating an XIAP role in early EBV B-cell transformation. Mechanistically, nascent EBV infection activated p53-mediated apoptosis signaling, which was counteracted by XIAP in control cells. With XIAP deficiency, EBV markedly elevated apoptosis rates over the first two weeks of infection. Interferon-gamma, whose levels are increased with severe XLP2 EBV infection, markedly increased newly EBV-infected B-cell apoptosis. These findings underscored XIAP's crucial role in support of the earliest stages of EBV-mediated B-cell immortalization and provide insights into the curious absence of EBV+ lymphoma in XLP-2 patients.
Authors
Yizhe Sun, Janet Chou, Kevin D. Dong, Steven P. Gygi, Benjamin E. Gewurz
Abstract
Yellow Fever virus (YFV) infection is fatal in 5–10% of the 200,000 yearly cases. There is currently no available antiviral treatment. We showed previously that administration of 50 mg/kg of a YFV-specific neutralizing monoclonal antibody (nmAb) at 2 days post-infection (dpi), prior to the onset of severe disease, protected YFV-infected rhesus macaques from death. To further explore the clinical applicability of our nmAb MBL-YFV-01, we treated rhesus macaques with a lower dose (10 mg/kg) of this nmAb prophylactically or therapeutically at 3.5 dpi. We show that a single prophylactic or therapeutic intravenous dose of our nmAb protects rhesus macaques from death following challenge. A comprehensive analysis of 167 inflammatory cytokine and chemokines revealed that protection was associated with significantly reduced expression of 125 of these markers, including type I interferons, IL6, and CCL2. This study further expands the potential clinical use of our YFV-specific nmAb, which could be used during an outbreak for immediate prophylactic immunity or for patients with measurable serum viremia.
Authors
Lauren N. Rust, Michael J. Ricciardi, Savannah S. Lutz, Sofiya Yusova, Johan J. Louw, Aaron Yrizarry-Medina, Sreya Biswas, Miranda Fischer, Aaron Barber-Axthelm, Gavin Zilverberg, Lauren Bailey, Tonya Swanson, Rachael Tonelli, G.W. McElfresh, Brandon C. Rosen, Thomas B. Voigt, Christakis Panayiotou, Jack T. Mauter, Noor Ghosh, Jenna Meanor, Giovana Godoy, Michael Axthelm, Jeremy Smedley, Mark K. Slifka, Esper G. Kallas, Gabriela Webb, Robert Zweig, Caralyn S. Labriola, Benjamin N. Bimber, Jonah B. Sacha, David I. Watkins, Benjamin J. Burwitz
Abstract
Bacteriophages, viruses that parasitize bacteria, are abundant in the human microbiome and may influence human health, in part, through their interactions with bacterial hosts. Whether endogenous bacteriophages or their products are vertically transmitted from mother to fetus during human pregnancy is not known. Here, we searched for bacteriophage sequences from five bacteriophage databases (474,031 total sequences) in cell-free DNA (cfDNA) of paired maternal and umbilical cord blood samples from two independent cohorts. First, we sequenced cfDNA from 10 pairs of maternal and cord blood samples, including four pairs affected by preeclampsia. We validated our findings in a previously published dataset of 62 paired maternal and cord blood samples, including 43 pairs from preterm or chorioamnionitis-affected deliveries. We identified 94 and 596 bacteriophage sequences in maternal and cord blood cfDNA samples from the first and second cohort, respectively. We identified 58 phage sequences across maternal-infant dyads and 581 phage sequences that were unique to a single sample. We did not identify any phage sequences consistently associated with preeclampsia, preterm, or chorioamnionitis-affected samples. This study demonstrated the presence of bacteriophage DNA in human cord blood at birth, providing evidence that the human fetus is exposed to bacteriophage DNA in utero.
Authors
Jennifer A. Sequoia, Naomi L. Haddock, Paw Mar Gay, Layla J. Barkal, Purnima Narasimhan, Nadine Martinez, Virginia D. Winn, Paul L. Bollyky
Abstract
Prion diseases are fatal, infectious and incurable neurodegenerative conditions affecting humans and animals, caused by the misfolding of the cellular prion protein (PrPC) into its pathogenic isoform, PrPSc. In humans, sporadic Creutzfeldt-Jakob disease (sCJD) is the most prevalent form. Recently, we demonstrated that treatment with the FDA-approved anti-HIV drug Efavirenz (EFV) significantly reduced PrPSc and extended survival of scrapie prion-infected mice. Among other effects, EFV activates the brain cholesterol metabolizing enzyme, CYP46A1, which converts cholesterol into 24S-hydroxycholesterol (24S-HC). However, drugs effective against scrapie prions often fail in human prion diseases, and a relation of the anti-prion effects of EFV to CYP46A1 activation is not established. Thus, we evaluated EFV treatment in mice overexpressing human PrPC infected with human sCJD prions. Oral, low-dose EFV treatment starting at 30- or 130-days post-infection significantly slowed disease progression and extended their survival. At early clinical stage, we observed reduced PrPSc accumulation, decreased cholesterol and lipid droplet content, and elevated CYP46A1 and 24S-HC levels in EFV-treated mice. Overexpression of CYP46A1 in prion-infected neuronal cells reduced PrPSc levels and increased 24S-HC, indicating that anti-prion effects of EFV correlate with CYP46A1 activation. These findings highlight EFV as a safe and efficacious therapeutic candidate for human prion diseases.
Authors
Tahir Ali, Jessica Cashion, Samia Hannaoui, Hanaa Ahmed-Hassan, Hermann M. Schatzl, Sabine Gilch
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