Development and validation of AI/ML derived splice-switching oligonucleotides.

Splice-switching oligonucleotides (SSOs) are antisense compounds that act directly on pre-mRNA to modulate alternative splicing (AS). This study demonstrates the value that artificial intelligence/machine learning (AI/ML) provides for the identification of functional, verifiable, and therapeutic SSOs. We trained XGboost tree models using splicing factor (SF) pre-mRNA binding profiles and spliceosome assembly information to identify modulatory SSO binding sites on pre-mRNA. Using Shapley and out-of-bag analyses we also predicted the identity of specific SFs whose binding to pre-mRNA is blocked by SSOs. This step adds considerable transparency to AI/ML-driven drug discovery and informs biological insights useful in further validation steps. We applied this approach to previously established functional SSOs to retrospectively identify the SFs likely to regulate those events. We then took a prospective validation approach using a novel target in triple negative breast cancer (TNBC), NEDD4L exon 13 (NEDD4Le13). Targeting NEDD4Le13 with an AI/ML-designed SSO decreased the proliferative and migratory behavior of TNBC cells via downregulation of the TGFß pathway. Overall, this study illustrates the ability of AI/ML to extract actionable insights from RNA-seq data.

Extended-Spectrum Beta-Lactamase Shigella sonnei Cluster Among Men Who Have Sex with Men in Chicago, Illinois-July-October 2022.

Drug-resistant shigellosis is increasing, particularly among men who have sex with men (MSM). During July-October 2022, an extended-spectrum beta-lactamase producing Shigella sonnei cluster of 9 patients was identified in Chicago, of whom 8 were MSM and 6 were festival attendees. The cluster also included 4 domestic travelers to Chicago. Sexual health care for MSM should include shigellosis diagnosis and prevention.

Investigation of an mpox outbreak affecting many vaccinated persons in Chicago, IL-March 2023-June 2023.

BACKGROUND: After months of few mpox cases, an increased number of cases were reported in Chicago during May 2023; predominantly among fully vaccinated patients. We investigated the outbreak scope, differences between vaccinated and unvaccinated patients, and hypotheses for monkeypox virus (MPXV) infection after vaccination. METHODS: We interviewed patients and reviewed medical records to assess demographic, behavioral, and clinical characteristics, mpox vaccine status, and vaccine administration routes. We evaluated serum antibody levels after infection and compared patient viral genomes with MPXV sequences in available databases. We discussed potential vaccine compromise with partners who manufactured, handled, and administered vaccine associated with breakthrough infections. RESULTS: During March 18-June 27, 2023, we identified 49 mpox cases; 57% of these mpox patients were fully vaccinated (FV). FV patients received both JYNNEOS doses subcutaneously (57%), intradermally (7%), or via heterologous administration (36%). FV patients had more median sex partners (3, IQR=1-4) versus not fully vaccinated (NFV) patients (1, IQR=1-2). Thirty-six of 37 sequenced specimens belonged to lineage B.1.20 of clade IIb MPXV, which did not demonstrate any amino acid changes relative to B.1, the predominant lineage from May 2022. Vaccinated patients demonstrated expected humoral antibody responses; none were hospitalized. No vaccine storage excursions were identified. Approximately 63% of people at risk for mpox in Chicago were FV during this period. CONCLUSIONS: Our investigation indicated cases were likely due to frequent behaviors associated with mpox transmission, even with relatively high vaccine effectiveness and vaccine coverage. Cases after vaccination might occur in similar populations.

Measles Outbreak Associated with a Migrant Shelter - Chicago, Illinois, February-May 2024.

Measles, a highly contagious respiratory virus with the potential to cause severe complications, hospitalization, and death, was declared eliminated from the United States in 2000; however, with ongoing global transmission, infections in the United States still occur. On March 7, 2024, the Chicago Department of Public Health (CDPH) confirmed a case of measles in a male aged 1 year residing in a temporary shelter for migrants in Chicago. Given the congregate nature of the setting, high transmissibility of measles, and low measles vaccination coverage among shelter residents, measles virus had the potential to spread rapidly among approximately 2,100 presumed exposed shelter residents. CDPH immediately instituted outbreak investigation and response activities in collaboration with state and local health departments, health care facilities, city agencies, and shelters. On March 8, CDPH implemented active case-finding and coordinated a mass vaccination campaign at the affected shelter (shelter A), including vaccinating 882 residents and verifying previous vaccination for 784 residents over 3 days. These activities resulted in 93% measles vaccination coverage (defined as receipt of ≥1 recorded measles vaccine dose) by March 11. By May 13, a total of 57 confirmed measles cases associated with residing in or having contact with persons from shelter A had been reported. Most cases (41; 72%) were among persons who did not have documentation of measles vaccination and were considered unvaccinated. In addition, 16 cases of measles occurred among persons who had received ≥1 measles vaccine dose ≥21 days before first known exposure. This outbreak underscores the need to ensure high vaccination coverage among communities residing in congregate settings.

Fibroblast Growth Factor 19: Potential modulation of hepatic metabolism for the treatment of non-alcoholic fatty liver disease.

Non-alcoholic fatty liver disease (NAFLD) is a spectrum of liver disease that is becoming more prevalent in concert with obesity and poor lifestyle habits. Although NAFLD is treatable via lifestyle modification in early stages, more advanced liver pathologies (eg non-alcoholic steatohepatitis [NASH]) are harder to reverse. There is no Food and Drug Administration approved pharmacological treatment for NAFLD, and little research has been done to identify compounds that target key NAFLD mechanisms. Bile acids and bile acid receptors have been implicated in NAFLD pathogenesis and modulating bile acids and bile acid receptors has recently been targeted as a therapeutic treatment option for NAFLD. Fibroblast growth factor 19 (FGF19), a nutritionally regulated post-prandial hormone, is a chief regulator of bile acid metabolism and an important player in lipid and carbohydrate metabolism, including key mechanisms of NAFLD pathogenesis. In this review, we discuss recent findings related to FGF19-regulated processes involved in the pathogenesis of NAFLD. We summarize known and conjectural frameworks and limitations for the clinical application of FGF19-targeted therapies as they relate to NAFLD.

Exercise and intestinal permeability: another form of exercise-induced hormesis?

Regular aerobic exercise has numerous benefits on human physiology, arguably by serving as a hormetic stressor resulting in positive adaptations over time. It has long been known that aerobic exercise at a variety of intensities and durations induces intestinal permeability, which is a feature of many pathologies of the gastrointestinal tract and metabolic diseases. Given the health benefits of exercise, it seems unlikely that intestinal permeability induced by exercise outweighs the positive adaptations. In fact, a growing body of evidence suggests adoption of exercise regimens lasting weeks to months improves indicators of intestinal permeability. In this brief review, we summarize factors contributing to acute exercise-induced intestinal permeability and what is known about chronic exercise and the gut barrier. Additionally, we outline known and theoretical adaptations of the gut to chronic exercise that may explain emerging reports that exercise improves markers of gut integrity.

Beyond the MHC: A canine model of dermatomyositis shows a complex pattern of genetic risk involving novel loci.

Juvenile dermatomyositis (JDM) is a chronic inflammatory myopathy and vasculopathy driven by genetic and environmental influences. Here, we investigated the genetic underpinnings of an analogous, spontaneous disease of dogs also termed dermatomyositis (DMS). As in JDM, we observed a significant association with a haplotype of the major histocompatibility complex (MHC) (DLA-DRB1*002:01/-DQA1*009:01/-DQB1*001:01), particularly in homozygosity (P-val = 0.0001). However, the high incidence of the haplotype among healthy dogs indicated that additional genetic risk factors are likely involved in disease progression. We conducted genome-wide association studies in two modern breeds having common ancestry and detected strong associations with novel loci on canine chromosomes 10 (P-val = 2.3X10-12) and 31 (P-val = 3.95X10-8). Through whole genome resequencing, we identified primary candidate polymorphisms in conserved regions of PAN2 (encoding p.Arg492Cys) and MAP3K7CL (c.383_392ACTCCACAAA>GACT) on chromosomes 10 and 31, respectively. Analyses of these polymorphisms and the MHC haplotypes revealed that nine of 27 genotypic combinations confer high or moderate probability of disease and explain 93% of cases studied. The pattern of disease risk across PAN2 and MAP3K7CL genotypes provided clear evidence for a significant epistatic foundation for this disease, a risk further impacted by MHC haplotypes. We also observed a genotype-phenotype correlation wherein an earlier age of onset is correlated with an increased number of risk alleles at PAN2 and MAP3K7CL. High frequencies of multiple genetic risk factors are unique to affected breeds and likely arose coincident with artificial selection for desirable phenotypes. Described herein is the first three-locus association with a complex canine disease and two novel loci that provide targets for exploration in JDM and related immunological dysfunction.

The Impact of Tides on Microbial Water Quality at an Inland River Beach.

Most coastal freshwater ecosystems in the United States have semi-tidal movements during the day. Routine monitoring of these environments is conducted once during the day when tides can be at either ebb or flood conditions, causing a variability in bacterial concentrations and misinterpretation of the illness risk associated with human activities. The occurrence and levels of enterococci (enterococci 23S rDNA [Ent23S]) and human- (HF183) and avian- (GFD) associated microbial source tracking (MST) markers were investigated using quantitative polymerase chain reaction (qPCR) along with detection of culturable enterococci and environmental parameters. Samples were collected during flood and ebb tide conditions (May-September) from a tidal river used for recreational activities. Culturable enterococci [(420) = 2.093, = 0.040] and Ent23S [(420) = 2.243, = 0.028] controlled for tide type were significantly different; higher enterococci concentrations were detected during the flood tide. Among all samples, 6% were positive for HF183, and GFD was positively correlated with Ent23S ( = 0.92, = 0.029) and conductivity ( = 0.93, = 0.023) during flood tide. Unlike the general assumption that ebb tide flow in a river would likely carry runoff from the land, the microbial contaminants in this case were transported from upstream via ocean water to the river during the flood tide. These results suggest that hydrology and land use patterns must be considered in sampling design when conducting future microbial water quality monitoring programs to better characterize recreational water safety in tidal rivers.

Using wastewater surveillance for mpox as a complement to traditional case-based reporting - Chicago, March-June 2023.

The Chicago Department of Public Health tested wastewater samples for the presence of Monkeypox Virus (MPXV) from March 13 through June 26, 2023. There were persistent detections prior to reported cases. This indicated the baseline levels of MPXV prevalence might warrant routine monitoring. Detections in areas without corresponding reported clinical cases might highlight areas where cases are being under-reported by traditional surveillance.

Body composition and chemotherapy toxicity among women treated for breast cancer: a systematic review.

PURPOSE: Toxicity is a significant problem among women receiving systemic chemotherapy for breast cancer, with up to 60% experiencing hematologic and 14% experiencing non-hematologic toxicity. Chemotherapy is dosed using body surface area, which does not account for heterogeneity in lean body mass (LBM) and adipose tissue (AT). This systematic review, registered with the PROSPERO International Prospective Register of Systematic Reviews (#CRD42021279874), evaluates associations between body composition and chemotherapy-related toxicity during breast cancer treatment. METHODS: Scientific literature databases (PubMed, Scopus, CINAHL, and CENTRAL) were systematically searched in November 2021 for studies evaluating associations between body composition (assessed using computed tomography or dual x-ray absorptiometry) and chemotherapy-related toxicity among women receiving breast cancer treatment. Eligibility was not limited by year or country of publication. Article screening and data abstraction was conducted using the Covidence Systematic Review Management System. Predetermined criteria were used to evaluate rigor of participant recruitment, representativeness of the population, and use of validated measures of body composition and toxicity. RESULTS: An inverse association between LBM and toxicity was reported in seven of the eight included studies, although definitions of low LBM differed across studies. Three studies evaluated the association between AT and chemotherapy toxicity with inconsistent findings. Heterogeneity in body composition measures/definitions and treatment regimens precluded the ability to perform meta-analyses. CONCLUSION: Low LBM appears to be a risk factor for chemotherapy toxicity, but the role of AT is unclear. IMPLICATIONS FOR CANCER SURVIVORS: Further research that accounts for guideline concordance in chemotherapy prescriptions and the use of supportive care medications is needed.

U.S. Montmorency Tart Cherry Juice Decreases Bone Resorption in Women Aged 65-80 Years.

Pre-clinical studies have demonstrated that tart cherries, rich in hydroxycinnamic acids and anthocyanins, protect against age-related and inflammation-induced bone loss. This study examined how daily consumption of Montmorency tart cherry juice (TC) alters biomarkers of bone metabolism in older women. Healthy women, aged 65-80 years (n = 27), were randomly assigned to consume ~240 mL (8 fl. oz.) of juice once (TC1X) or twice (TC2X) per day for 90 d. Dual-energy x-ray absorptiometry (DXA) scans were performed to determine bone density at baseline, and pre- and post-treatment serum biomarkers of bone formation and resorption, vitamin D, inflammation, and oxidative stress were assessed. Irrespective of osteoporosis risk, the bone resorption marker, tartrate resistant acid phosphatase type 5b, was significantly reduced with the TC2X dose compared to baseline, but not with the TC1X dose. In terms of indicators of bone formation and turnover, neither serum bone-specific alkaline phosphatase nor osteocalcin were altered. No changes in thiobarbituric acid reactive substances or high sensitivity C-reactive protein were observed in response to either TC1X or TC2X. We conclude that short-term supplementation with the higher dose of tart cherry juice decreased bone resorption from baseline without altering bone formation and turnover biomarkers in this cohort.

Pinto beans modulate the gut microbiome, augment MHC II protein, and antimicrobial peptide gene expression in mice fed a normal or western-style diet.

The onset of type 2 diabetes in obesity is associated with gut dysbiosis and a failure to confine commensal bacteria and toxins to the gut lumen while prebiotics may prevent these effects. This study evaluated the effects of pinto beans (PB) supplementation on cecal bacteria, short-chain fatty acids (SCFAs), distal ileal antigen presentation marker (major histocompatibility complex [MHC] II) and antimicrobial peptide genes during short-term high-fat, high sucrose (HFS) feeding. Six-week-old, male C57BL/6J mice were randomly assigned to four groups (n=12/group), and fed a control (C) or HFS diet with or without cooked PB (10%, wt/wt) for 30 days. Supplemental PB in both the C and HFS diets decreased the abundance of Tenericutes and the sulfate-reducing bacteria Bilophila. In contrast, PB raised the abundance of taxa within the SCFAs-producing family, Lachnospiraceae, compared to groups without PB. Consequently, fecal butyric acid was significantly higher in PB-supplemented groups compared to C and HFS groups. PB reversed the HFS-induced ablation of the distal ileal STAT3 phosphorylation, and up-regulated antimicrobial peptide genes (Reg3γ and Reg3ß). Furthermore, the expression of MHC II protein was elevated in the PB supplemented groups compared to C and HFS. Tenericutes and Bilophilia negatively correlated with activated STAT3 and MHC II proteins. Finally, supplemental PB improved fasting blood glucose, glucose tolerance and suppressed TNFα and inducible nitric oxide synthase mRNA in the visceral adipose tissue. Put together, the beneficial impact of PB supplementation on the gut may be central to its potential to protect against diet-induced inflammation and impaired glucose tolerance.

Solar Powered Microplasma-Generated Ozone: Assessment of a Novel Point-of-Use Drinking Water Treatment Method.

Ozonation is widely used in high-income countries for water disinfection in centralized treatment facilities. New microplasma technology has reduced the energy requirements for ozone generation dramatically, such that a 15-watt solar panel is sufficient to produce small quantities of ozone. This technology has not been used previously for point-of-use drinking water treatment. We conducted a series of assessments of this technology, both in the laboratory and in homes of residents of a village in western Kenya, to estimate system efficacy and to determine if the solar-powered point-of-use water ozonation system appears safe and acceptable to end-users. In the laboratory, two hours of point-of-use ozonation reduced E. coli in 120 L of wastewater by a mean (standard deviation) of 2.3 (0.84) log-orders of magnitude and F+ coliphage by 1.54 (0.72). Based on laboratory efficacy, 10 families in Western Kenya used the system to treat 20 L of household stored water for two hours on a daily basis for eight weeks. Household stored water E. coli concentrations of >1000 most probable number (MPN)/100 mL were reduced by 1.56 (0.96) log removal value (LRV). No participants experienced symptoms of respiratory or mucous membrane irritation. Focus group research indicated that families who used the system for eight weeks had very favorable perceptions of the system, in part because it allowed them to charge mobile phones. Drinking water ozonation using microplasma technology may be a sustainable point-of-use treatment method, although system optimization and evaluations in other settings would be needed.

Congenital myasthenic syndrome in Golden Retrievers is associated with a novel COLQ mutation.

BACKGROUND: Congenital myasthenic syndromes (CMSs) are a group of inherited disorders of neuromuscular transmission that may be presynaptic, synaptic, or postsynaptic. Causative mutations have been identified in 4 breeds including the Labrador Retriever, Jack Russell Terrier, Heideterrier, and Danish Pointing Dog. HYPOTHESIS/OBJECTIVE: Clinical and genetic characterization of a neuromuscular disorder in Golden Retriever (GR) puppies. ANIMALS: Four GR puppies from California were evaluated for generalized muscle weakness beginning at weaning. Biological specimens were collected from the affected puppies, and familial information was obtained. Blood or buccal swabs were obtained from 63 unaffected GRs. METHODS: Complete physical, neurological, electrodiagnostic, and histological evaluations and biochemical quantification of muscle acetylcholine receptors were performed. Polymerase chain reaction was used to amplify the 17 exons of COLQ, and sequences were obtained by Sanger sequencing. Variant frequency was assessed in unrelated GRs and a public database. RESULTS: Clinical, neurological, and electrodiagnostic evaluations confirmed a disorder of neuromuscular transmission in a GR family. Sequencing of all exons and splice sites of a primary candidate gene, COLQ, identified a point mutation that predicts an amino acid substitution (G294R). The primary COLQ transcript was absent from affected muscle samples. All affected puppies were homozygous for the mutation, which was not detected outside this GR family or in other breeds. CONCLUSIONS AND CLINICAL IMPORTANCE: We confirmed the diagnosis of a CMS in GR puppies and identified a novel COLQ mutation. The COLQ gene encodes the collagenous tail of acetylcholinesterase, the enzyme responsible for termination of skeletal muscle contraction by clearing acetylcholine at the neuromuscular junction. Clinicians and breeders should be aware of this CMS in GR puppies with an early onset of weakness.

YAP inhibition enhances the differentiation of functional stem cell-derived insulin-producing ß cells.

Stem cell-derived insulin-producing beta cells (SC-ß) offer an inexhaustible supply of functional ß cells for cell replacement therapies and disease modeling for diabetes. While successful directed differentiation protocols for this cell type have been described, the mechanisms controlling its differentiation and function are not fully understood. Here we report that the Hippo pathway controls the proliferation and specification of pancreatic progenitors into the endocrine lineage. Downregulation of YAP, an effector of the pathway, enhances endocrine progenitor differentiation and the generation of SC-ß cells with improved insulin secretion. A chemical inhibitor of YAP acts as an inducer of endocrine differentiation and reduces the presence of proliferative progenitor cells. Conversely, sustained activation of YAP results in impaired differentiation, blunted glucose-stimulated insulin secretion, and increased proliferation of SC-ß cells. Together these results support a role for YAP in controlling the self-renewal and differentiation balance of pancreatic progenitors and limiting endocrine differentiation in vitro.

A Comparative Study of Modern and Heirloom Wheat on Indicators of Gastrointestinal Health.

Wheat consumption has declined amid growing concerns about gluten-sensitivity. To determine if genetic manipulation of wheat contributes to systemic and localized gut inflammation, we compared the effects of the modern variety Gallagher and a blend of two heirloom varieties, Turkey and Kharkof, on measures of gut inflammation, structural characteristics, and barrier integrity under normal and Western diet (WD) conditions in C57BL/6 mice. Indicators of gut inflammation, including lymphocyte infiltration and cytokine expression, were largely unaffected by WD or wheat, although WD elevated interferon-γ (Ifng) and heirloom varieties modestly reduced interleukin-17 (Il17) in the context of WD. WD negatively affected jejunal villi structure, while the modern variety improved villi structure in the ileum. Relative mRNA and tight junction proteins and serum lipopolysaccharide binding protein were unaltered by WD or wheat. These findings indicate that the modern variety did not compromise barrier function or contribute to gut inflammation compared to its heirloom predecessor.