The rockefeller university

Current methods for variant effect prediction do not differentiate between pathogenic variants resulting in different disease outcomes and are restricted in application due to a focus on variants with a single molecular consequence. We have developed Variant-to-Phenotype (V2P), a multi-task, multi-output machine learning model to predict variant pathogenicity conditioned on top-level Human Phenotype Ontology disease phenotypes (n = 23) for single nucleotide variants and insertions/deletions throughout the human genome. V2P leverages a unique approach for the modeling of variant effect that incorporates resultant disease phenotypes as output and during training to improve the quality of variant disease phenotype and effect predictions, simultaneously. We describe the architecture, training strategy, and biological features contributing to V2P's output, revealing initial characteristics underlying the relationship between disease genotype and phenotype. Moreover, we demonstrate the benefit of incorporating disease phenotypes for variant effect predictions by comparing V2P with several variant effect predictors across various high-quality evaluation datasets from manually curated databases and functional assays. Finally, we examine how V2P's predictions result in the successful identification of pathogenic variants in real and simulated patient sequencing data, outperforming other tested methods in initial comparisons. V2P offers a complete mapping of human genetic variants to disease-phenotypes, offering a uniquely conditioned set of variant effect characterizations.

Generation of in vitro human induced pluripotent cell (hiPSC)-derived skeletal muscle progenitor cells (SMPCs) holds great promise for regenerative medicine for skeletal muscle wasting diseases, for example Duchenne muscular dystrophy (DMD). While multiple approaches have been described to obtain SMPCs in vitro, hiPSC-derived SMPCs generated using transgene-free protocols are usually obtained in a low amount and resemble a more embryonal/fetal stage of differentiation. Here, we demonstrate that modulation of the JAK2/STAT3 signaling pathway during an in vitro skeletal muscle differentiation protocol increases the yield of PAX7+and CD54+human SMPCs (hSMPCs) and drives them to a higher maturation stage, in both human embryonic stem (ES) and patient-derived induced pluripotent cells (iPSCs). Importantly, the obtained SMPCs are able to differentiate into multinucleated myotubes in vitro and engraft in vivo. These findings reveal that modulation of the JAK2/STAT3 signaling pathway is a potential therapeutic avenue to generate SMPCs in vitro with potential for cell therapy approaches.

Although adenosine was identified in the brain many decades ago, our understanding of when, where, and how it functions has expanded rapidly in recent years, driven in part by innovative technological advances. Adenosine is now increasingly recognized as a key neuromodulator that dynamically regulates brain circuits important for sleep/wakefulness, movement, cognition, and homeostasis. In addition, growing attention has been directed toward the molecular mechanisms governing adenosine production and its downstream signaling pathways, both of which hold great promise as therapeutic targets for neuropsychiatric disorders and neurodegenerative diseases. This review highlights recent progress in detecting adenosine, unraveling its signaling pathways in vitro and in vivo, and understanding how it regulates brain function under physiological and pathological conditions.

Bacterial immune systems exhibit remarkable diversity and modularity, as a consequence of the continuous selective pressures imposed by phage predation. Despite recent mechanistic advances, the evolutionary origins of many antiphage immune systems remain elusive, especially for those that encode homologs of the structural maintenance of chromosomes (SMC) superfamily, which are essential for chromosome maintenance and DNA repair across domains of life. Here, we elucidate the structural basis and evolutionary emergence of Lamassu, a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor. Using cryo-EM, we determined structures of the Vibrio cholerae Lamassu complex in both apo-and dsDNA-bound states, revealing unexpected stoichiometry and topological architectures. We further demonstrate how Lamassu specifically senses dsDNA ends in vitro and phage replication origins in vivo, thereby triggering the formation of LmuA tetramers that activate its Cap4 nuclease domain. Our findings reveal that Lamassu evolved via exaptation of the bacterial Rad50-Mre11 DNA repair system to form a compact, modular sensor for viral replication, exemplifying how cellular machinery can be co-opted for novel immune functions.

Background: Brodalumab, an anti-interleukin-17 receptor A antibody, is effective in psoriasis via action on the IL-17 pathway. Objective: This analysis of an exploratory intervention study (ESPRIT) in Japanese patients with moderate to severe plaque psoriasis examined the brodalumab efficacy by clinical changes, and modulation of skin inflammation via changes in skin gene expression and blood sample protein expression. Methods: Primary clinical endpoints were changes in PASI score and PASI score 0 achievement rate at Week 12. For molecular endpoints, biopsies of lesional, non-lesional and healthy volunteer skin were examined by RNA sequencing and RT-PCR. Blood sample serum was analyzed by Olink high-throughput proteomics. Results: Twenty healthy volunteers and 40 patients were enrolled; 37 underwent molecular profiling. Clinical assessment showed that the median baseline PASI score (19.0) significantly decreased to 0.4 at Week 12 (P < 0.0001), with more rapid decline in higher PASI responders. Molecular assessment demonstrated that differential expressed genes in lesional skin were suppressed equivalently to non-lesional skin, establishing the molecular improvement with brodalumab. The transcriptomes of Japanese and Western patients were similar, and top-upregulated genes included IL-17-inducible and cardiovascular disease-related genes, which were suppressed by brodalumab. Serum protein analysis identified 22 proteins elevated by psoriasis. Several inflammatory and cardiovascular risk proteins correlated with psoriasis severity and BMI, but at lower rates than in Western patients. Conclusions: In summary, the transcriptome and the proteome characteristics of Japanese and Western psoriasis patients were similar. Brodalumab rapidly improved skin and serum molecular levels and reduced cardiovascular disease risk factor expression.

In psoriatic lesions, interleukin (IL)-17C protein expression has been reported as high as 125 times that of IL-17A; as such, it is crucial to understand the role that IL-17C plays in psoriasis, inflammation, and treatment response. Overexpression or injection of IL-17C in mice results in increased epidermal thickening and inflammation, whereas psoriatic mice with IL-17C knockout have decreased disease severity compared with control littermates. In psoriasis, IL-17C likely acts as a critical inflammatory amplifier via a feed-forward mechanism, wherein IL-17-producing CD4+ helper T (TH17) cells and IL-17-producing CD8+ cytotoxic T (TC17) cells stimulate IL-17C expression in keratinocytes. Then, keratinocyte-derived IL-17C induces IL-17A expression in TH17 and TC17 cells. Additionally, keratinocyte-derived IL-17C propagates its own signaling in an autocrine manner. Furthermore, studies suggest that IL-17C acts as an early mediator of psoriasis. No approved therapies directly target IL-17C. Brodalumab is an IL-17 receptor (IL-17R) A antagonist that inhibits IL-17A, F, C, and E signaling and has a unique mechanism of action among biologic therapies for psoriasis. By way of IL-17RA blockade, brodalumab is the only approved therapy for psoriasis that inhibits IL-17C signaling. This unique mechanism of action is hypothesized to correlate with efficacy in patients with prior failures to anti-IL-17A therapies and relatively higher rates of early skin clearance compared with those of other biologic therapies. Clinical studies are needed to confirm these correlations. In summary, IL-17C is an inflammatory amplifier and early psoriatic mediator, and inhibition of IL-17C may be beneficial in psoriasis management.

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by antinuclear antibodies (ANAs). Epstein-Barr virus (EBV) infection has been epidemiologically associated with SLE, yet its role in pathogenesis remains incompletely defined. Here, we developed an EBV-specific single-cell RNA-sequencing platform and used it to demonstrate that EBV infection reprograms autoreactive antinuclear antigen B cells to drive autoimmunity in SLE. We demonstrated that, in SLE, EBV+ B cells are predominantly CD27+CD21low memory B cells that are present at increased frequencies and express ZEB2, TBX21 (T-bet), and antigen-presenting cell transcriptional pathways. Integrative analysis of chromatin immunoprecipitation sequencing (ChIP-seq), assay for transposase-accessible chromatin sequencing (ATAC-seq), and RNA polymerase II occupancy data revealed EBV nuclear antigen 2 (EBNA2) binding at the transcriptional start sites and regulatory regions of CD27, ZEB2, and TBX21, as well as the antigen-presenting cell genes demonstrated to be up-regulated in SLE EBV+ B cells. We expressed recombinant antibodies from SLE EBV+ B cells and demonstrated that they bind prototypical SLE nuclear autoantigens, whereas those from healthy individuals do not. We further found that SLE EBV+ B cells can serve as antigen-presenting cells to drive activation of T peripheral helper cells with concomitant activation of related EBV- antinuclear double-negative 2 B cells and plasmablasts. Our results provide a mechanistic basis for EBV being a driver of SLE through infecting and reprogramming nuclear antigen-reactive B cells to become activated antigen-presenting cells with the potential to promote systemic disease-driving autoimmune responses.

The clinical outcome of SARS-CoV-2 infection spans from asymptomatic viral elimination to lethal COVID-19 pneumonia, which is due to type I interferon (IFN) deficiency in at least 15-20% of cases. We report two unrelated male patients with critical COVID-19 who are heterozygous for rare deleterious variants in RB1CC1, encoding the autophagy-related FIP200 protein. Airway epithelial cells genetically deprived of FIP200 or cell lines expressing the RB1CC1/FIP200 patient variants exhibit elevated SARS-CoV-2 replication and impaired autophagic flux. The antiviral function of FIP200 is independent of canonical autophagy and type I IFN, but involves the selective autophagy receptor NDP52. We identify a non-canonical function of FIP200 in a novel lysosomal degradation pathway, in which SARS-CoV-2 virions are targeted to single-membrane compartments for degradation of viral RNA in LC3B-positive acidified vesicles. This pathway is impaired in FIP200-deficient cells and in cells expressing FIP200 patient haplotypes. Collectively, we describe a cell-autonomous anti-SARS-CoV-2 restriction pathway, dependent on FIP200 and NDP52, and independent of canonical autophagy and type I IFN, which can underlie critical COVID-19 pneumonia.