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Biology subjects

Adam, A.

Publications and source records attributed to Adam, A..

At least 19 recordsLinked to original sources

A human-derived two-antibody cocktail confers prophylactic and therapeutic protection against authentic Mpox virus.

With sustained human-to-human transmission worldwide, Mpox virus remains a significant global health burden. However, there are no licensed therapeutics against Mpox, with clinical management limited to supportive care and pain management. Given the virus complex life cycles, effective treatments require the inhibition of both mature intracellular virions (MV) and extracellular virions (EV). Here, we describe the isolation of human monoclonal antibodies (mAbs) from antigen specific memory B cell using flow cytometry-based cell sorting. We also characterize the therapeutic potential of 2-mAb cocktails targeting both MV and EV using an in vitro neutralization assay and a mouse challenge model. Several developed human 2-mAb cocktails neutralized authentic Mpox in vitro. When administered 24 hours before or after Mpox challenge, the lead 2-mAb cocktail inhibited viral loads in mouse tissues, with the exception of the testes. Overall, our study identifies several human 2-mAb cocktails with therapeutic potential for controlling Mpox disease.

microbiology↗

Synthetic circRNAs employ IRES activity for translation in cells and in cell-free translation systems

Gene regulation through translation is critical for spatiotemporal protein expression. Internal ribosomal entry sites (IRESes) mediate mRNA-specific translation by recruiting ribosomes to 5' untranslated regions. Circular RNAs (circRNAs), naturally occurring and stable RNAs, are increasingly used as synthetic tools for sustained therapeutic protein translation by IRES-driven initiation. However, the functionality of different IRESes in synthetic circRNAs remains sparsely characterized. We systematically examine circRNA reporter translation by viral and cellular IRESes in human cells and in diverse in vitro translation systems. Improved circRNA purification by urea-PAGE and RNase R-treatment removes contaminants that induce RNA sensing. Viral CVB3 and HCV, as well as cellular Hoxa9, Chrdl1, Cofilin and c-Myc IRESes, effectively drive circRNA translation. We also establish circRNA translation in a recently developed human cell-free extract that recapitulates IRES-dependent regulation, and allows for precise engineering of HCV IRES-mediated translation. These findings inform IRES selection for synthetic circRNA translation relevant for circRNA-based medicine. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/715045v2_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1a60d08org.highwire.dtl.DTLVardef@a1a7d6org.highwire.dtl.DTLVardef@112042aorg.highwire.dtl.DTLVardef@1cf6c34_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

VSA-2, a novel plant-derived adjuvant for SARS-CoV-2 subunit vaccine

QS-21, a key component of several licensed vaccines is facing limited supply, dose-limiting toxicity and other drawbacks which together limit its broader usage. Development of saponin alternatives to QS-21 that retain its desirable adjuvant activity without its drawbacks is in high need. Incorporating an amide side chain into the more sustainable Momordica saponins (MS) I and II led to the recent discovery of two semisynthetic immunostimulatory adjuvants VSA-1 and VSA-2. Here, we showed that the receptor-binding protein (RBD) of ancestral SARS-CoV-2 adjuvanted with VSA-2 (VSA-2-RBD) induced high titers of SARS-CoV-2-specific humoral and T helper-1 prone immune responses in mice comparable to that triggered by QS-21-RBD. Vaccination with VSA-2-RBD provided strong protection against SARS-COV-2, Delta and Omicron variants infection and the virus-induced lung inflammation and pathology similarly as QS-21-RBD vaccination. Overall, our results suggest that VSA-2 adjuvant can potentially complement the clinically proven saponin adjuvant QS-21 in vaccines against infectious diseases.

microbiology↗

Respiratory syncytial virus infection confers heterologous protection against SARS-CoV-2 via induction of γδ T cell-mediated trained immunity and SARS-CoV-2 reactive mucosal T cells

The respiratory viruses can concurrently or sequentially infect a host and influence the trajectory of each other. The underlying immune mechanisms are not well understood. Here, we investigated whether respiratory syncytial virus (RSV) infection affects host vulnerability to subsequent SARS-CoV-2 infection in two murine models of SARS-CoV-2 infection. We found that prior RSV infection-induced heterologous protection against subsequent SARS-CoV-2 infection was dose and time dependent. RNA-seq and immunological analyses revealed that RSV triggered the activation of lung antigen presenting cells (APC)s and SARS-CoV-2 reactive mucosal T cells at day 9, which declined at 1 month. RSV also induced the expansion of lung {gamma}{delta} T cells and the upregulation of their cellular metabolic pathways. Furthermore, RSV infection in TCR{delta}-/- mice, which are deficient of {gamma}{delta} T cells, resulted in a reduced SARS-CoV-2 reactive mucosal T cell response and subsequent increased viral loads and higher levels of virus-induced inflammatory responses in the lung upon SARS-CoV-2 challenge compared to the wild-type mice. In summary, our findings suggest that RSV infection provides heterologous protection against the subsequent SARS-CoV-2 infection via induction of {gamma}{delta} T cell-mediated trained immunity in the lung and SARS-CoV-2 reactive mucosal T cell responses.

microbiology↗

Serum albumin coated stellate mesoporous silica nanocomposites inhibit metastatic outgrowth in zebrafish embryos

Mesoporous silica-based nanoparticles (NPs) are promising tools for developing targeted therapeutic interventions in cancer. Endowed with a large pore silica shell suitable for drug encapsulation and with a responsive magnetic core, iron oxide stellate mesoporous silica (IO STMS) NPs stand out. Yet, their impact and potential toxicity on relevant in vivo models has not been carefully tested yet. Herein, we assessed the impact of these IO STMS nanocomposites in a syngeneic metastasis assay in zebrafish. NPs were surface-modified with human serum albumin (HSA) and loaded or not with the chemotherapeutic doxorubicin (DOX). In vitro, DOX-loaded NPs were expectedly more toxic to zebrafish melanoma (Zmel) cells than no-DOX NPs. In zebrafish embryos, the NPs were rapidly distributed through blood circulation and were found to colocalize over time with the vascular endothelium and local macrophages. Suprisingly, the NPs efficiently reduced the outgrowth of Zmel tumoral masses in an experimental metastasis assay in zebrafish embryos regardless of their loading with DOX. The anti-metastatic effect of these NPs was further improved by increasing the amount of HSA coating, also resulting in higher embryo survival. Altogether, IO STMS NPs showed promising cytotoxic effects on a relevant zebrafish metastasis model, inhibiting metastatic outgrowth in vivo independently of the drug loading. This opens the door to further testing for better exploiting their targeting and drug delivery potentialities.

cancer biology↗

A lipid metabolism defect is an underlying contributor to Diamond Blackfan anemia syndrome

Analysis of neither Diamond Blackfan anemia syndrome (DBAS) cohorts nor animal models has revealed a potential mechanism for the variable anemia phenotype, a key feature of this disease. Here, we utilized an established Rpl5Skax23-Jus/+ murine DBAS model in order to study this dynamic erythropoiesis deficiency. These haploinsufficient mice exhibit variably penetrant craniofacial and cardiac defects mimicking the phenotypes of DBAS patients bearing RPL5 mutations. We additionally discovered that this specific heterozygous splicing mutation is pathogenic and leads to partial intron retention. By examining the transcriptome of fetal liver erythroid progenitors at E12.5, we demonstrate that the downregulation of erythroid differentiation pathways is consistent with the DBAS phenotype. We also identified dysregulated transcription of lipid metabolism genes with significant reduction in the abundance of Scd1 in a subset of E12.5 mutant embryos at risk for erythroid failure. SCD1, a key enzyme that converts saturated to monounsaturated fatty acids, has not been previously linked to erythropoiesis or DBAS. When anemia was induced in adult mice, pretreatment with an SCD1 inhibitor resulted in improved erythropoiesis. This analysis suggests a key role of lipid metabolism in the variable anemia penetrance in DBAS and highlights a previously unappreciated pathway that may serve as a potential target for drug development. Key PointsO_LIThe variable anemia in Rpl5Skax23-Jus/+mice is triggered by intrinsic/extrinsic stress C_LIO_LIRpl5 haploinsufficient murine and human erythroid progenitors exhibit a lipid metabolism signature with downregulation of Scd1/SCD. C_LI

developmental biology↗

A rapidly closing window for coral persistence under global warming

Summary paragraphCoral reefs around the world are threatened by recurrent marine heatwaves causing mass coral bleaching and mortality1. Mitigating future warming impacts requires strategic management2 that adopts a long-term lens. Global analyses of projected heatwaves3,4 are critical for decision-making but how disturbance refugia, coral life-histories and adaptation interact with warming is unknown. Here, we simulate coral eco-evolutionary dynamics across >3,800 individual reefs of Australias iconic Great Barrier Reef under the current suite of climate projections5. We forecast a rapid coral decline before mid-century regardless of emissions scenario. Under the most likely warming6, corals may continue to decline throughout the century. However, corals may recover after mid-century provided that warming is sufficiently slow, allowing thermal adaptation to keep pace with temperature changes - as projected if warming does not exceed 2{degrees}C. Higher emission scenarios would drive most reefs to a near collapse. Future resilient reefs were mostly found in bleaching refugia, which also possessed a greater diversity of thermal phenotypes. Although cool-adapted corals disperse to thermal hotspots, there was no evidence of gene swamping undermining thermal adaptation. While opportunities exist to build management strategies that promote adaptation in thermal refugia and warm spots, curbing the rate of warming by 2050 is crucial for coral persistence.

ecology↗

Longitudinal cellular and humoral immune responses following Covid-19 BNT162b2-mRNA-based booster vaccination of craft and manual workers in Qatar.

IntroductionIn March 2020, the rapid spread of SARS-CoV-2 prompted global vaccination campaigns to mitigate COVID-19 disease severity and mortality. The 2-dose BNT162b2- mRNA vaccine effectively reduced infection and mortality rates, however, waning vaccine effectiveness necessitated the introduction of a third vaccine dose or booster. To assess the magnitude and longevity of booster-induced immunity, we conducted a longitudinal study of SARS-CoV-2 specific cellular and humoral immune responses among Qatars vulnerable craft and manual worker community. We also investigated the impact of prior naturally acquired immunity on booster vaccination efficacy. MethodsSeventy healthy participants were enrolled in the study, of whom half had prior SARS-CoV-2 infection. Blood samples were collected before and after booster vaccination to evaluate immune responses through SARS- CoV-2 specific ELISpots, IgG ELISA, neutralization assays, and flow cytometric immunophenotyping ResultsT cell analysis revealed increased Th1 cellular responses, marked by enhanced IFN-{gamma} release, in recently infected participants, which was further enhanced by booster vaccination for up to 6-months. Furthermore, booster vaccination stimulated cytotoxic T cell responses in infection-naive participants, characterized by granzyme B production. Both natural SARS-CoV-2 infection and booster vaccination induced robust and durable SARS-CoV-2 specific humoral immune responses, with high neutralizing antibody levels. Prior natural infection was also linked to an increased number of class- switched B cells prior to booster vaccination. ConclusionThese findings underscore the importance of booster vaccination in enhancing anti-viral immunity across both infection-naive and previously infected individuals, enhancing distinct arms of the anti-viral immune response and prolonging naturally acquired immunity.

immunology↗

A safe insect-based Chikungunya fever vaccine affords rapid and durable protection in cynomolgus macaques

Chikungunya virus (CHIKV), which induces chikungunya fever and chronic arthralgia, is an emerging public health concern. Safe and efficient vaccination strategies are needed to prevent or mitigate virus-associated acute and chronic morbidities for preparation of future outbreaks. Eilat (EILV)/CHIKV, a chimeric alphavirus which contains the structural proteins of CHIKV and the non-structural proteins of EILV, does not replicate in vertebrate cells. The chimeric virus was previously reported to induce protective adaptive immunity in mice. Here, we assessed the capacity of the virus to induce quick and durable protection in cynomolgus macaques. EILV/CHIKV protected macaques from wild-type (WT) CHIKV infection one year after a single dose vaccination. Transcriptome and in vitro functional analyses reveal that the chimeric virus triggered toll-like receptor signaling and T cell, memory B cell and antibody responses in a dose-dependent manner. Notably, EILV/CHIKV preferentially induced more durable, robust, and broader repertoire of CHIKV-specific T cell responses, compared to a live attenuated CHIKV 181/25 vaccine strain. The insect-based chimeric virus did not cause skin hypersensitivity reactions in guinea pigs sensitized to mosquito bites. Furthermore, EILV/CHIKV induced strong neutralization antibodies and protected cynomolgus macaques from WT CHIKV infection within six days post vaccination. Transcriptome analysis also suggest that the chimeric virus induction of multiple innate immune pathways, including Toll-like receptor signaling, type I IFN and IL-12 signaling, antigen presenting cell activation, and NK receptor signaling. Our findings suggest that EILV/CHIKV is a safe, highly efficacious vaccine, and provides both rapid and long-lasting protection in cynomolgus macaques.

microbiology↗

Modulation of Ideonella sakaiensis PETase active site flexibility and activity on morphologically distinct substrates by surface charge engineering

Enzymatic hydrolysis of polyethylene terephthalate (PET) waste is a compelling strategy for environmentally friendly recycling of a major pollutant. Here, we investigate the effects of surface charge point mutations both proximal and distal to the active site of the mesophilic PET-degrading enzyme from Ideonella sakaienses (IsPETase) and an engineered thermostable variant with superior activity, STAR PETase. The vicinal K95A mutation significantly inhibited IsPETase activity on mechanically processed PET powder. Conversely, this mutation significantly increased hydrolysis of PET powder in the STAR PETase background. Activity of both enzymes on PET film was inhibited by the K95A mutation, highlighting complex interplay between mutation context and substrate morphology. Further installing the distal R132N and R280A surface charge mutations potentiated activity of STAR on all substrates tested. This variant afforded 100% degradation of bottle-grade PET powder in 3 days at 40{degrees}C reaction temperature, a 3-fold improvement over IsPETase. Molecular dynamics simulations reveal modulation of active site flexibility in mutants, which differentially impacts both hydrolysis of morphologically distinct PET substrates and the concentration-dependent inhibition phenomenon observed for PETase.

bioengineering↗

Decoration of Burkholderia Hcp1 protein to virus-like particles as a vaccine delivery platform.

Virus-like particles (VLPs) are protein-based nanoparticles frequently used as carrier in conjugate vaccine platforms. VLPs have been used to display foreign antigens for vaccination and to deliver immunotherapeutic against diseases. Hemolysin-coregulated proteins 1 (Hcp1) is a protein component of the Burkholderia type 6 secretion system which participates in intracellular invasion and dissemination. This protein has been reported as a protective antigen and is used in multiple vaccine candidates with various platforms against melioidosis, a severe infectious disease caused by the intracellular pathogen B. pseudomallei. In this study, we used P22 VLPs as a surface platform for decoration with Hcp1 using chemical conjugation. C57BL/6 mice were intranasally immunized with three doses of either PBS, VLPs or conjugated Hcp1-VLPs. Immunization with Hcp1-VLPs formulation induced Hcp1-specific-IgG, IgG1, IgG2c and IgA antibody responses. Furthermore, the serum from Hcp1-VLPs immunized mice enhanced the bacterial uptake and opsonophagocytosis by macrophages in the presence of complement. This study demonstrated an alternative strategy to develop a VLPs-based vaccine platform against Burkholderia species.

microbiology↗

A Murine Model of Post-acute Neurological Sequelae Following SARS-CoV-2 Variant Infection

Viral variant is one known risk factor associated with post-acute sequelae of COVID-19 (PASC), yet the pathogenesis is largely unknown. Here, we studied SARS-CoV-2 Delta variant-induced PASC in K18-hACE2 mice. The virus replicated productively, induced robust inflammatory responses in lung and brain tissues, and caused weight loss and mortality during the acute infection. Longitudinal behavior studies in surviving mice up to 4 months post-acute infection revealed persistent abnormalities in neuropsychiatric state and motor behaviors, while reflex and sensory functions recovered over time. Surviving mice showed no detectable viral RNA in the brain and minimal neuroinflammation post-acute infection. Transcriptome analysis revealed persistent activation of immune pathways, including humoral responses, complement, and phagocytosis, and reduced levels of genes associated with ataxia telangiectasia, impaired cognitive function and memory recall, and neuronal dysfunction and degeneration. Furthermore, surviving mice maintained potent T helper 1 prone cellular immune responses and high neutralizing antibodies against Delta and Omicron variants in the periphery for months post-acute infection. Overall, infection in K18-hACE2 mice recapitulates the persistent clinical symptoms reported in long COVID patients and may be useful for future assessment of the efficacy of vaccines and therapeutics against SARS-CoV-2 variants.

microbiology↗

Pharmacologic inhibition of BAF chromatin remodeling complexes as a therapeutic approach to transcription factor-dependent cancers

The BRG/Brahma-associated factors (BAF or mSWI/SNF) family of chromatin remodeling complexes are critical regulators of gene expression and are major determinants of cancer and other diseases. Two paralog ATPases, SMARCA4 and SMARCA2 (BRG1 and BRM, respectively), provide the enzymatic activity required for chromatin remodeling. Here, we discover and characterize a novel series of compounds that potently and selectively inhibit SMARCA4/SMARCA2. Mutational and biochemical studies demonstrate that these inhibitors act through a unique mode of inhibition, distinct from reported SMARCA4/SMARCA2 inhibitors. Across a range of cancer cell lines, SMARCA4/SMARCA2 inhibition resulted in lineage-specific changes in chromatin accessibility at binding sites for key transcription factors (TFs). In uveal melanoma (UM), BAF inhibition resulted in loss of enhancer occupancy of SOX10 and MITF, two essential TFs, leading to down-regulation of the melanocytic gene expression program. In a mouse xenograft model of UM, SMARCA4/SMARCA2 inhibition was well tolerated and resulted in dose-dependent tumor regression correlating with pharmacodynamic modulation of BAF-target gene expression. These data provide the foundation for first-in-human studies of BAF ATPase inhibition as a novel therapeutic to treat TF-dependent cancers.

cancer biology↗

A single-dose of intranasal vaccination with a live-attenuated SARS-CoV-2 vaccine candidate promotes protective mucosal and systemic immunity

An attenuated SARS-CoV-2 virus with modified viral transcriptional regulatory sequences and deletion of open-reading frames 3, 6, 7 and 8 ({triangleup}3678) was previously reported to protect hamsters from SARS-CoV-2 infection and transmission. Here we report that a single-dose intranasal vaccination of {triangleup}3678 protects K18-hACE2 mice from wild-type or variant SARS-CoV-2 challenge. Compared with wild-type virus infection, the {triangleup}3678 vaccination induces equivalent or higher levels of lung and systemic T cell, B cell, IgA, and IgG responses. The results suggest {triangleup}3678 as an attractive mucosal vaccine candidate to boost pulmonary immunity against SARS-CoV-2.

microbiology↗

Humoral and T-cell-mediated responses to a pre-clinical Zika vaccine candidate that utilizes a unique insect-specific flavivirus platform

Vaccination is critical for the control and prevention of viral outbreaks, yet conventional vaccine platforms may involve trade-offs between immunogenicity and safety. Insect-specific viruses have emerged as a novel vaccine platform to overcome this challenge. Detailed studies of humoral and T-cell responses induced by new insect-specific flavivirus (ISFV)-based vaccine platforms are needed to better understand correlates of protection and improve vaccine efficacy. Previously, we used a novel ISFV called Aripo virus (ARPV) to create a Zika virus (ZIKV) vaccine candidate (designated ARPV/ZIKV). ARPV/ZIKV demonstrated exceptional safety and single-dose efficacy, completely protecting mice from a lethal ZIKV challenge. Here, we explore the development of immune responses induced by ARPV/ZIKV immunization and evaluate its correlates of protection. Passive transfer of ARPV/ZIKV-induced immune sera to naive mice prior to challenge emphasized the importance of neutralizing antibodies as a correlate of protection. Depletion of T-cells in vaccinated mice and adoptive transfer of ARPV/ZIKV-primed T-cells to naive mice prior to challenge indicated that ARPV/ZIKV-induced CD4+ and CD8+ T-cell responses contribute to the observed protection but may not be essential for protection during ZIKV challenge. However, vaccination of Rag1 KO, Tcra KO, and muMt- mice demonstrated the critical role for ARPV/ZIKV-induced T-cells in developing protective immune responses following vaccination. Overall, both humoral and T-cell-mediated responses induced by ISFV-based vaccines are important for comprehensive immunity, and ISFV platforms continue to be a promising method for future vaccine development.

microbiology↗

The Resolvin D2-GPR18 Axis Enhances Bone Marrow Function and Limits Hepatic Fibrosis in Aging

Aging is associated with non-resolving inflammation and tissue dysfunction. Resolvin D2 (RvD2) is a pro-resolving ligand that acts through the G-protein coupled receptor (GPCR) called GRP18. Using an unbiased screen, we report increased Gpr18 expression in macrophages from old mice and in livers from elderly humans that is associated with increased steatosis and fibrosis in middle-aged (MA) and old mice. MA mice that lack GPR18 on myeloid cells had exacerbated steatosis and hepatic fibrosis, which was associated with a decline in Mac2+ macrophages. Treatment of MA mice with RvD2 reduced steatosis and decreased hepatic fibrosis, correlating with increased Mac2+ macrophages, monocyte-derived macrophages and elevated numbers of monocytes in the liver, blood, and bone marrow. RvD2 acted directly upon the bone marrow to increase monocyte-macrophage progenitors. Using a transplantation assay we further demonstrated that bone marrow from old mice facilitated hepatic collagen accumulation in young mice, and transient RvD2 treatment to mice transplanted with bone marrow from old mice prevented hepatic collagen accumulation. Together, our study demonstrates that RvD2-GPR18 signaling controls steatosis and fibrosis and provides a mechanistic-based therapy for promoting liver repair in aging.

physiology↗

The common oral parasitic protozoan Entamoeba gingivalis forms cysts in response to antibiotic treatment

The eukaryotic protozoan Entamoeba gingivalis (E.g.) is strongly associated with inflamed periodontal pockets. Unlike other obligate anaerobic Entamoeba species, it is considered to not have a life cycle of actively dividing trophozoites and dormant cysts. Accordingly, it has been regarded as non-infectious. To investigate if E.g is capable of encystation in response to adverse environmental conditions, we cultivated clinical isolates of E.g. collected from inflamed periodontal pockets in antibiotics for 8 days. The cytomorphological and ultrastructure forms of the amoeba were investigated by transmission and scanning electron microscopy to reveal cyst formation. We observed exocysts and the encapsulated trophozoids separated by an intra-cystic space, a dense poorly vesiculated cytoplasma and polygonal surface areas of cysts. The cysts walls were composed of chitin. Cysts were conspicuously smaller compared to trophozoids and lacked pseudo- and filipodia. We did not observe multi-nucleated trophozoids after antibiotic induces encystation. Cyst formation in E.g may explain why established treatment approaches often do not stop periodontal tissue destruction during periodontitis and periimplantitis.

microbiology↗

Deep learning in human neurons predicts mechanistic subtypes of Parkinson's

Parkinsons disease (PD) is a common, devastating, and incurable neurodegenerative disorder. Several molecular mechanisms have been proposed to drive PD, with genetic and pathological evidence pointing towards aberrant protein homeostasis and mitochondrial dysfunction. PD is clinically highly heterogeneous, it is likely that different mechanisms underlie the pathology in different individuals, each requiring a specific targeted treatment. Recent advances in stem cell technology and fluorescent live-cell imaging have enabled the generation of patient-derived neurons with different mechanistic subtypes of PD. Here, we performed multi-dimensional fluorescent labelling of organelles in iPSC-derived neurons, in healthy control cells, and in four different disease subclasses. We generated a machine learning-based model that can simultaneously predict the presence of disease, and its primary mechanistic subtype. We independently trained a series of classifiers using both quantitative single-cell fluorescence variables and images to build deep neural networks. Quantitative cellular profile-based classifiers achieve an accuracy of 82%, whilst image based deep neural networks predict control, and four distinct disease subtypes with an accuracy of 95%. The classifiers achieve their accuracy across all subtypes primarily utilizing the organellar features of the mitochondria, with additional contribution of the lysosomes, confirming their biological importance in PD. Taken together, we show that machine learning approaches applied to patient-derived cells are able to predict disease subtypes, demonstrating that this approach may be used to guide personalized treatment approaches in the future.

cell biology↗