The rockefeller university

The application of machine learning to longitudinal gene-expression profiles has demonstrated potential to decrease the assessment gap, between biochemical determination and clinical manifestation, of a patient's response to treatment. Although psoriasis is a proven testing ground for treatment-response prediction using transcriptomic data from clinically accessible skin biopsies, these biopsies are expensive, invasive, and challenging to obtain from certain body areas. Response prediction from blood biochemical measurements could be a cheaper, less invasive predictive platform. Longitudinal profiles for 92 inflammatory and 65 cardiovascular disease proteins were measured from the blood of psoriasis patients at baseline, and 4-weeks, following tofacitinib (janus kinase-signal transducer and activator of transcription-inhibitor) or etanercept (tumor necrosis factor-inhibitor) treatment, and predictive models were developed by applying machine-learning techniques such as bagging and ensembles. This data driven approach developed predictive models able to accurately predict the 12-week clinical endpoint for psoriasis following tofacitinib (area under the receiver operating characteristic curve [auROC] = 78%), or etanercept (auROC = 71%) treatment in a validation dataset, revealing a robust predictive protein signature including well-established psoriasis markers such as IL-17A and IL-17C, highlighting potential for biologically meaningful and clinically useful response predictions using blood protein data. Although most blood classifiers were outperformed by simple models trained using Psoriasis Area Severity Index scores, performance might be enhanced in future studies by measuring a wider variety of proteins.

The discovery of specific microbiota metabolite mechanisms has begun to motivate new therapeutic approaches. Inspired by our mechanistic studies of microbiota-derived short chain fatty acid (SCFA) acylation of bacterial virulence factors, here we explored covalent protein acylation therapeutics as potential anti-infectives. For these studies, we focused on acetyl-salicylic acid, aspirin, and discovered that SCFA analogues such as butyryl-salicylic acid showed significantly improved anti-infective activity against Salmonella Typhimurium. Structure-activity studies showed that the ester functionality of butyryl-salicylic acid was crucial and associated with the acylation of key bacterial virulence factors and metabolic enzymes, which are important for Salmonella infection of host cells and bacterial growth. Beyond the Gram-negative bacterial pathogens, butyryl-salicylic acid also showed better antibacterial activity compared to aspirin against Clostridioides difficile, a clinically challenging Gram-positive bacterial pathogen. Notably, coadministration of butyryl-salicylic acid, but not aspirin, effectively attenuated Salmonella pathogenesis in vivo. This study highlights how the analysis of microbiota metabolite mechanisms may inspire the repurposing and development of new anti-infective agents.

This paper presents a high-throughput reverse transcription quantitative PCR (RT-qPCR) assay for Caenorhabditis elegans that is fast, robust, and highly sensitive. This protocol obtains precise measurements of gene expression from single worms or from bulk samples. The protocol presented here provides a novel adaptation of existing methods for complementary DNA (cDNA) preparation coupled to a nanofluidic RT-qPCR platform. The first part of this protocol, named 'Worm-to-CT', allows cDNA production directly from nematodes without the need for prior mRNA isolation. It increases experimental throughput by allowing the preparation of cDNA from 96 worms in 3.5 h. The second part of the protocol uses existing nanofluidic technology to run high-throughput RT-qPCR on the cDNA. This paper evaluates two different nanofluidic chips: the first runs 96 samples and 96 targets, resulting in 9,216 reactions in approximately 1.5 days of benchwork. The second chip type consists of six 12 x 12 arrays, resulting in 864 reactions. Here, the Worm-to-CT method is demonstrated by quantifying mRNA levels of genes encoding heat shock proteins from single worms and from bulk samples. Provided is an extensive list of primers designed to amplify processed RNA for the majority of coding genes within the C. elegans genome.

Interferon-induced transmembrane protein 3 (IFITM3) is a key interferon effector that broadly prevents infection by diverse viruses. However, the cellular factors that control IFITM3 homeostasis and antiviral activity have not been fully elucidated. Using site-specific photo-crosslinking and quantitative proteomic analysis, here we present the identification and functional characterization of VCP/p97 AAA-ATPase as a primary interaction partner of IFITM3. We show that IFITM3 ubiquitination at lysine 24 is crucial for VCP binding, trafficking, turnover, and engagement with incoming virus particles. Consistently, pharmacological inhibition of VCP/p97 ATPase activity leads to defective IFITM3 lysosomal sorting, turnover, and co-trafficking with virus particles. Our results showcase the utility of site-specific protein photo-crosslinking in mammalian cells and reveal VCP/p97 as a key cellular factor involved in IFITM3 trafficking and homeostasis.

Age-dependent cognitive and behavioral deterioration may arise from defects in different components of the nervous system, including those of neurons, synapses, glial cells, or a combination of them. We find that AFD, the primary thermosensory neuron of Caenorhabditis elegans, in aged animals is characterized by loss of sensory ending integrity, including reduced actin-based microvilli abundance and aggregation of thermosensory guanylyl cyclases. At the functional level, AFD neurons in aged animals are hypersensitive to high temperatures and show sustained sensory-evoked calcium dynamics, resulting in a prolonged operating range. At the behavioral level, senescent animals display cryophilic behaviors that remain plastic to acute temperature changes. Excessive cyclase activity of the AFD-specific guanylyl cyclase, GCY-8, is associated with developmental defects in AFD sensory ending and cryophilic behavior. Surprisingly, loss of the GCY-8 cyclase domain reduces these age-dependent morphological and behavioral changes, while a prolonged AFD operating range still exists in gcy-8 animals. The lack of apparent correlation between age-dependent changes in the morphology or stimuli-evoked response properties of primary sensory neurons and those in related behaviors highlights the importance of quantitative analyses of aging features when interpreting age-related changes at structural and functional levels. Our work identifies aging hallmarks in AFD receptive ending, temperature-evoked AFD responses, and experience-based thermotaxis behavior, which serve as a foundation to further elucidate the neural basis of cognitive aging.

Hidradenitis Suppurativa (HS) is a chronic inflammatory dermatosis in which B cells play a prominent but unclear role. Our understanding of the role of B cells in innate and adaptive immunity (including antibody production, antigen presentation and effector functions) is rapidly evolving; and these novel findings require integration into the pathophysiologic model of HS. B cells are transiently present in normal human skin and have functions in the maintenance of innate cutaneous immunity. Recruitment and trafficking of B cells in significant numbers to skin is mediated via B cell-specific chemokines as well as shared signalling with T-cells. The evidence suggests that the presence of antibody-secreting B cells is not sufficient to induce clinical disease and T-cell interaction is required to induce clinical disease. Such interactions can occur in secondary lymphoid organs adjacent to involved tissue or in tertiary lymphoid organs which develop in response to the HS inflammatory milieu. This milieu directly mediates the types of antibodies produced by B cells, given the role of cytokines in B-cell class switching. Identified antibodies in HS (IgG, IgM, ASCA, ACPA) currently demonstrate no evidence of pathogenicity, but may be novel biomarkers for disease severity. B cells also have anti-inflammatory properties through production of IL-10 and IL-35 which require experimental validation. Overall, B cells in HS are likely to be involved in amplification of a pre-existing inflammatory response; but it remains unclear whether they may be directly pathogenic.

Emerging urinary biomarkers continue to show promise in evaluating lupus nephritis (LN). Here, we screen urine from active LN patients for 1129 proteins using an aptamer-based platform, followed by ELISA validation in two independent cohorts comprised of 127 inactive lupus, 107 active LN, 67 active non-renal lupus patients and 74 healthy controls, of three different ethnicities. Urine proteins that best distinguish active LN from inactive disease are ALCAM, PF-4, properdin, and VCAM-1 among African-Americans, sE-selectin, VCAM-1, BFL-1 and Hemopexin among Caucasians, and ALCAM, VCAM-1, TFPI and PF-4 among Asians. Most of these correlate significantly with disease activity indices in the respective ethnic groups, and surpass conventional metrics in identifying active LN, with better sensitivity, and negative/positive predictive values. Several elevated urinary molecules are also expressed within the kidneys in LN, based on single-cell RNAseq analysis. Longitudinal studies are warranted to assess the utility of these biomarkers in tracking lupus nephritis. Developing noninvasive diagnostic biomarkers for lupus nephritis (LN) diagnosis is an important clinical goal. Here the authors identify urinary proteins correlated with active LN and disease severity, which differ across ethnicities but collectively outperform the current clinical method.

Follicular lymphomas (FLs) are slow-growing, indolent tumors containing extensive follicular dendritic cell (FDC) networks and recurrent EZH2 gain-of-function mutations. Paradoxically, FLs originate from highly proliferative germinal center (GC) B cells with proliferation strictly dependent on interactions with T follicular helper cells. Herein, we show that EZH2 mutations initiate FL by attenuating GC B cell requirement for T cell help and driving slow expansion of GC centrocytes that become enmeshed with and dependent on FDCs. By impairing T cell help, mutant EZH2 prevents induction of proliferative MYC programs. Thus, EZH2 mutation fosters malignant transformation by epigenetically reprograming B cells to form an aberrant immunological niche that reflects characteristic features of human FLs, explaining how indolent tumors arise from GC B cells.

Increasing evidence suggests that tRNA levels are dynamically and specifically regulated in response to internal and external cues to modulate the cellular translational program. However, the molecular players and the mechanisms regulating the gene-specific expression of tRNAs are still unknown. Using an inducible auxin-degron system to rapidly deplete RPB1 (the largest subunit of RNA Pol II) in living cells, we identified Pol II as a direct gene-specific regulator of tRNA transcription. Our data suggest that Pol II transcription robustly interferes with Pol III function at specific tRNA genes. This activity was further found to be essential for MAF1-mediated repression of a large set of tRNA genes during serum starvation, indicating that repression of tRNA genes by Pol II is dynamically regulated. Hence, Pol II plays a direct and central role in the gene-specific regulation of tRNA expression.

Aims: Explore potential of 31 tear biomarkers involved in screening for diabetic peripheral neuropathy (DPN). Assess the utility of aesthesiometry for measuring corneal damage in DPN and determine optimal cutoff point for detecting DPN. Methods: Screening test pilot study recruited 90 participants from a tertiary hospital in Lima, Peru. Participants were grouped by diabetes and neuropathy status. Tears collected on Schirmer strips, and proteins measured by both ELISA and multiplex-bead assay. Corneal sensitivity was measured by aesthesiometry, and DPN by vibration perception threshold testing. Results: There were 89 participants included in the analysis. The mean age was 55.7 +/- 1.46, and 58.4% were female. MMP-9 and TGF-alpha concentrations were higher in participants with DPN versus diabetes alone, though not significant. Aesthesiometry was decreased in individuals with DPN when compared to participants with diabetes alone (p < 0.01) and normal controls (p < 0.01). Optimal cutoff point for aesthesiometry was found to be 5.8 cm, with 79% sensitivity and 75% specificity. Conclusions: Tears are an insufficient standalone tool for detecting DPN based on the biomarkers analyzed. Aesthesiometry is a simple, inexpensive, and accurate method to assess corneal damage associated with moderate-severe DPN, and its integration into screening practices has potential to improve detection of DPN in poor-resource settings. (C) 2020 Elsevier B.V. All rights reserved.