The rockefeller university

Common variable immunodeficiency (CVID) is one of the most common groups of human inborn errors of immunity. In addition to infections resulting from insufficient levels of immunoglobulins and antibodies, a signifi cant proportion of patients develop autoimmune cytopenias, especially immune thrombocytopenia, hemolytic anemia, or neutropenia. They may be the initial manifestation of CVID in a patient who has not had significant infections, and similar episodes may recur at intervals over time. Treatment of these hematologic complications includes the use of corticosteroids or other medications, often including rituximab; splenectomy is discouraged. Here we outline the overall occurrence of these blood cytopenias in a cohort of 408 patients, as well as the clinical and genetic associations noted in these individuals.

It has been shown that excitotoxicity and tau-mediated toxicities are major contributing factors to neuronal death in Alzheimer's disease (AD). The excitatory amino acid transporter 2 (EAAT2 or GLT-1), the major glutamate transporter in the brain that regulates glutamate levels synaptically and extrasynaptically, has been shown to be deficient in AD brains, leading to excitotoxicity and subsequent cell death. Similarly, buildup of neurofibrillary tangles, which consist of hyperphosphorylated tau protein, correlates with cognitive decline and neuronal atrophy in AD. However, common genes and pathways that are critical in the aforementioned toxicities have not been well elucidated. To investigate the impact of glutamate dyshomeostasis and tau accumulation on translational profiles of affected hippocampal neurons, we used mouse models of excitotoxicity and tau-mediated toxicities (GLT-1(-/-) and P301S, respectively) in conjunction with BAC-TRAP technology. Our data show that GLT-1 deficiency in CA3 pyramidal neurons leads to translational signatures characterized by dysregulation of pathways associated with synaptic plasticity and neuronal survival, while the P301S mutation induces changes in endocytic pathways and mitochondrial dysfunction. Finally, the commonly dysregulated pathways include impaired ion homeostasis and metabolic pathways. These common pathways may shed light on potential therapeutic targets for ameliorating glutamate and tau-mediated toxicities in AD.

Folded RNAs contain tertiary contact motifs whose structures and energetics are conserved across different RNAs. The transferable properties of RNA motifs simplify the RNA folding problem, but measuring energetic and conformational properties of many motifs remains a challenge. Here, we use a high-throughput thermodynamic approach to investigate how sequence changes alter the binding properties of naturally occurring motifs, the GAAA tetraloop center dot tetraloop receptor (TLR) interactions. We measured the binding energies and conformational preferences of TLR sequences that span mutational pathways from the canonical 11ntR to two other natural TLRs, the IC3R and Vc2R. While the IC3R and Vc2R share highly similar energetic and conformational properties, the landscapes that map the sequence changes for their conversion from the 11ntR to changes in these properties differ dramatically. Differences in the energetic landscapes stem from the mutations needed to convert the 11ntR to the IC3R and Vc2R rather than a difference in the intrinsic energetic architectures of these TLRs. The conformational landscapes feature several nonnative TLR variants with conformational preferences that differ from both the initial and final TLRs; these species represent potential branching points along the multidimensional sequence space to sequences with greater fitness in other RNA contexts with alternative conformational preferences. Our high-throughput, quantitative approach reveals the complex nature of sequence-fitness landscapes and leads to models for their molecular origins. Systematic and quantitative molecular approaches provide critical insights into understanding the evolution of natural RNAs as they traverse complex landscapes in response to selective pressures.

Purpose The pathogenesis of life-threatening coronavirus disease 2019 (COVID-19) pneumonia in ICU patients can involve pre-existing auto-antibodies (auto-Abs) neutralizing type I interferons (IFNs). The impact of these auto-Abs on SARS-CoV-2 clearance in the lower respiratory tract (LRT) is unclear. Methods We performed a retrospective study in 99 ICU patients with COVID-19 pneumonia between March and May 2020. LRT SARS-CoV-2 load (intensity and duration) was analyzed according to the presence or not of circulating auto-Abs neutralizing type I IFNs. Results Among the 99 included patients, 38 (38%) were positive for auto-Abs neutralizing type I IFNs, with 5 (5%) harboring auto-Abs neutralizing IFN-alpha 2 at any concentration, while 33 (33%) had auto-Abs neutralizing only IFN-omega at the lower concentration. SARS-CoV-2 load in the LRT and duration of viral shedding, were similar in patients with or without auto-Abs neutralizing type I IFNs. Patients with auto-Abs had the same mortality than those without auto-Abs, despite greater occurrence of renal failure and ECMO support, and longer duration of mechanical ventilation and ICU stay. Conclusion In summary, 5% of patients with critical COVID-19 pneumonia carried auto-Abs neutralizing IFN-alpha 2, while about 1/3 harbored auto-Abs neutralizing low concentrations of IFN-omega. The detection of either type of auto-Abs did not impact LRT viral clearance and mortality, although it was associated with greater morbidity and a longer hospitalization. These findings suggest that similar albeit hitherto unknown mechanisms of disease drive critical COVID-19 pneumonia in patients without auto-Abs against type I IFNs.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has emerged as a global pandemic pathogen with high mortality. While treatments have been developed to reduce morbidity and mortality of COVID-19, more antivirals with broad-spectrum activities are still needed. Here, we identified lonafarnib (LNF), a Food and Drug Administration-approved inhibitor of cellular farnesyltransferase (FTase), as an effective anti-SARS-CoV-2 agent. LNF inhibited SARS-CoV-2 infection and acted synergistically with known anti-SARS antivirals. LNF was equally active against diverse SARS-CoV-2 variants. Mechanistic studies suggested that LNF targeted multiple steps of the viral life cycle. Using other structurally diverse FTase inhibitors and a LNF-resistant FTase mutant, we demonstrated a key role of FTase in the SARS-CoV-2 life cycle. To demonstrate in vivo efficacy, we infected SARS-CoV-2-susceptible humanized mice expressing human angiotensin-converting enzyme 2 (ACE2) and treated them with LNF. LNF at a clinically relevant dose suppressed the viral titer in the respiratory tract and improved pulmonary pathology and clinical parameters. Our study demonstrated that LNF, an approved oral drug with excellent human safety data, is a promising antiviral against SARS-CoV-2 that warrants further clinical assessment for treatment of COVID-19 and potentially other viral infections.

A measurement is performed of Higgs bosons produced with high transverse momentum (p(T)) via vector boson or gluon fusion in proton-proton collisions. The result is based on a data set with a center-of-mass energy of 13 TeV collected in 2016-2018 with the CMS detector at the LHC and corresponds to an integrated luminosity of 138 fb(-1). The decay of a high-p(T) Higgs boson to a boosted bottom quark-antiquark pair is selected using large-radius jets and employing jet substructure and heavy-flavor taggers based on machine learning techniques. Independent regions targeting the vector boson and gluon fusion mechanisms are defined based on the topology of two quark-initiated jets with large pseudorapidity separation. The signal strengths for both processes are extracted simultaneously by performing a maximum likelihood fit to data in the large-radius jet mass distribution. The observed signal strengths relative to the standard model expectation are 4.9(-1.6)(+1.9) and 1.6(-1.5)(+1.7) for the vector boson and gluon fusion mechanisms, respectively. A differential cross section measurement is also reported in the simplified template cross section framework.

Cell biology and genetic studies have demonstrated that DNA double-strand break (DSB) repair can be performed using an RNA transcript that spans the site of the DNA break as a template for repair. This type of DSB repair requires a reverse transcriptase to convert an RNA sequence into DNA to facilitate repair of the break, rather than copying from a DNA template as in canonical DSB repair. Translesion synthesis (TLS) DNA polymerases (Pol) are often more promiscuous than DNA Pols, raising the notion that reverse transcription could be performed by a TLS Pol. Indeed, several studies have demonstrated that human Pol h has reverse transcriptase activity, while others have suggested that the yeast TLS Polz is involved. Here, we purify all seven known nuclear DNA Pols of Saccharomyces cerevisiae and compare their reverse transcriptase activities. The comparison shows that Polz far surpasses Pol h and all other DNA Pols in reverse transcriptase activity. We fi nd that Polz reverse transcriptase activity is not affected by RPA or RFC/PCNA and acts distributively to make DNA complementary to an RNA template strand. Consistent with prior S. cerevisiae studies performed in vivo, we propose that Polz is the major DNA Pol that functions in the RNAtemplated DSB repair pathway.

Although the etiological relevance of the detection of microsporidia in human stool samples remains uncertain, the immunological status of patients has been posited as an important determinant of potential clinical impact of these parasites. To further assess the interplay between the epidemiology of microsporidia and immunological markers, we conducted a study utilizing real-time PCR targeting Enterocytozoon bieneusi, Encephalitozoon cuniculi, Encephalitozoon hellem, and Encephalitozoon intestinalis, combined in a single fluorescence channel. The study involved a cohort of 595 clinically and immunologically well-characterized Ghanaian HIV patients, alongside 82 HIV-negative control individuals from Ghana. While microsporidial DNA was absent in HIV-negative controls, among people living with HIV, its prevalence was inversely correlated with CD4+ lymphocyte counts: 6.0% in those with >500 cells/mu L, 9.5% in those with 200-499 cells/mu L, 13.8% in those with 50-199 cells/mu L, and 27.5% in those with <50 cells/L, respectively. Correspondingly, microsporidia were more frequently detected in HIV patients who were not receiving antiretroviral therapy. There were no associations with clinical symptoms including gastroenteritis with the exception of a non-significant trend towards weight loss. HLA-DR+CD38+ on CD4+ T lymphocytes, a marker of immune activation, as well as Ki67, a marker of cell proliferation, were increased on CD4+ T lymphocytes in HIV patients with microsporidia, suggesting an immune response may be triggered. In conclusion, our assessment indicates a higher prevalence of microsporidia in the stool of Ghanaian HIV patients, which varies with their immunological status. However, given the lack of clear associations with clinical symptoms, the detection of microsporidia in the stool of HIV patients needs to be cautiously interpreted in clinical settings.

Glioblastoma is incurable and in urgent need of improved therapeutics(1). Here we identify a small compound, gliocidin, that kills glioblastoma cells while sparing non-tumour replicative cells. Gliocidin activity targets a de novo purine synthesis vulnerability in glioblastoma through indirect inhibition of inosine monophosphate dehydrogenase 2 (IMPDH2). IMPDH2 blockade reduces intracellular guanine nucleotide levels, causing nucleotide imbalance, replication stress and tumour cell death(2). Gliocidin is a prodrug that is anabolized into its tumoricidal metabolite, gliocidin-adenine dinucleotide (GAD), by the enzyme nicotinamide nucleotide adenylyltransferase 1 (NMNAT1) of the NAD(+) salvage pathway. The cryo-electron microscopy structure of GAD together with IMPDH2 demonstrates its entry, deformation and blockade of the NAD(+) pocket(3). In vivo, gliocidin penetrates the blood-brain barrier and extends the survival of mice with orthotopic glioblastoma. The DNA alkylating agent temozolomide induces Nmnat1 expression, causing synergistic tumour cell killing and additional survival benefit in orthotopic patient-derived xenograft models. This study brings gliocidin to light as a prodrug with the potential to improve the survival of patients with glioblastoma.

In view of changing climatic conditions and disappearing natural resources such as fertile soil and water, exploring alternatives to today's industrial monocrop farming becomes essential. One promising farming practice is intercropping (IC), in which two or more crop species are grown together. Many experiments have shown that, under certain circumstances, IC can decrease soil erosion and fertilizer use, improve soil health and land management, while preserving crop production levels. However, there have been no quantitative approaches to predict, design, and control appropriate IC implementation for given particular environmental and farming conditions, and to assess its robustness. Here, we develop such an approach, based on methods and concepts developed in data science and systems biology. Our dataset groups the results of 2258 IC experiments, involving 274 pairs of 69 different plants. The data include 4 soil characteristics and 5 environmental and farming conditions, together with 8 traits for each of the two intercropped plants. We performed a dimensional reduction of the resulting 25-dimensional variable space and showed that, from a few quantities, one can predict IC yield relative to sole cultivation with good accuracy. For given environmental conditions, our computational approach can help to choose a companion plant and appropriate farming practices. It also indicates how to estimate the robustness of IC to external perturbations. This approach, together with its results, can be viewed as an initial step toward "systems agriculture," which would ultimately develop systems of multiple plant grown together in appropriately designed and controlled settings.