The economic costs and cost-effectiveness of HIV self-testing among truck drivers in Kenya

HIV status awareness is critical for ending the HIV epidemic but remains low in high-HIV-risk and hard-to-reach sub-populations. Targeted, efficient interventions are needed to improve HIV test-uptake. We examined the incremental cost-effectiveness of offering the choice of self-administered oral HIV-testing (HIVST-Choice) compared with provider-administered testing only [standard-of-care (SOC)] among long-distance truck drivers. Effectiveness data came from a randomized-controlled trial conducted at two roadside wellness clinics in Kenya (HIVST-Choice arm, n = 150; SOC arm, n = 155). Economic cost data came from the literature, reflected a societal perspective and were reported in 2020 international dollars (I$), a hypothetical currency with equivalent purchasing power as the US dollar. Generalized Poisson and linear gamma regression models were used to estimate effectiveness and incremental costs, respectively; incremental effectiveness was reported as the number of long-distance truck drivers needing to receive HIVST-Choice for an additional HIV test-uptake. We calculated the incremental cost-effectiveness ratio (ICER) of HIVST-Choice compared with SOC and estimated 95% confidence intervals (CIs) using non-parametric bootstrapping. Uncertainty was assessed using deterministic sensitivity analysis and the cost-effectiveness acceptability curve. HIV test-uptake was 23% more likely for HIVST-Choice, with six individuals needing to be offered HIVST-Choice for an additional HIV test-uptake. The mean per-patient cost was nearly 4-fold higher in HIVST-Choice (I$39.28) versus SOC (I$10.80), with an ICER of I$174.51, 95% CI [165.72, 194.59] for each additional test-uptake. HIV self-test kit and cell phone service costs were the main drivers of the ICER, although findings were robust even at highest possible costs. The probability of cost-effectiveness approached 1 at a willingness-to-pay of I$200 for each additional HIV test-uptake. HIVST-Choice improves HIV-test-uptake among truck drivers at low willingness-to-pay thresholds, suggesting that HIV self-testing is an efficient use of resources. Policies supporting HIV self-testing in similar high risk, hard-to-reach sub-populations may expedite achievement of international targets.

Identification of the Thermal Activation Network in Human 15-Lipoxygenase-2: Divergence from Plant Orthologs and Its Relationship to Hydrogen Tunneling Activation Barriers

The oxidation of polyunsaturated fatty acids by lipoxygenases (LOXs) is initiated by a C-H cleavage step in which the hydrogen atom is transferred quantum mechanically (i.e., via tunneling). In these reactions, protein thermal motions facilitate the conversion of ground-state enzyme-substrate complexes to tunneling-ready configurations and are thus important for transferring energy from the solvent to the active site for the activation of catalysis. In this report, we employed temperature-dependent hydrogen-deuterium exchange mass spectrometry (TDHDX-MS) to identify catalytically linked, thermally activated peptides in a representative animal LOX, human epithelial 15-LOX-2. TDHDX-MS of wild-type 15-LOX-2 was compared to two active site mutations that retain structural stability but have increased activation energies (Ea) of catalysis. The Ea value of one variant, V427L, is implicated to arise from suboptimal substrate positioning by increased active-site side chain rotamer dynamics, as determined by X-ray crystallography and ensemble refinement. The resolved thermal network from the comparative Eas of TDHDX-MS between wild-type and V426A is localized along the front face of the 15-LOX-2 catalytic domain. The network contains a clustering of isoleucine, leucine, and valine side chains within the helical peptides. This thermal network of 15-LOX-2 is different in location, area, and backbone structure compared to a model plant lipoxygenase from soybean that exhibits a low Ea value of catalysis compared to the human ortholog. The presented data provide insights into the divergence of thermally activated protein motions in plant and animal LOXs and their relationships to the enthalpic barriers for facilitating hydrogen tunneling.

Mannosylated STING Agonist Drugamers for Dendritic Cell-Mediated Cancer Immunotherapy

The Stimulator of Interferon Genes (STING) pathway is a promising target for cancer immunotherapy. Despite recent advances, therapies targeting the STING pathway are often limited by routes of administration, suboptimal STING activation, or off-target toxicity. Here, we report a dendritic cell (DC)-targeted polymeric prodrug platform (polySTING) that is designed to optimize intracellular delivery of a diamidobenzimidazole (diABZI) small-molecule STING agonist while minimizing off-target toxicity after parenteral administration. PolySTING incorporates mannose targeting ligands as a comonomer, which facilitates its uptake in CD206+/mannose receptor+ professional antigen-presenting cells (APCs) in the tumor microenvironment (TME). The STING agonist is conjugated through a cathepsin B-cleavable valine-alanine (VA) linker for selective intracellular drug release after receptor-mediated endocytosis. When administered intravenously in tumor-bearing mice, polySTING selectively targeted CD206+/mannose receptor+ APCs in the TME, resulting in increased cross-presenting CD8+ DCs, infiltrating CD8+ T cells in the TME as well as maturation across multiple DC subtypes in the tumor-draining lymph node (TDLN). Systemic administration of polySTING slowed tumor growth in a B16-F10 murine melanoma model as well as a 4T1 murine breast cancer model with an acceptable safety profile. Thus, we demonstrate that polySTING delivers STING agonists to professional APCs after systemic administration, generating efficacious DC-driven antitumor immunity with minimal side effects. This new polymeric prodrug platform may offer new opportunities for combining efficient targeted STING agonist delivery with other selective tumor therapeutic strategies.

A natural bacterial pathogen of C. elegans uses a small RNA to induce transgenerational inheritance of learned avoidance

C. elegans can learn to avoid pathogenic bacteria through several mechanisms, including bacterial small RNA-induced learned avoidance behavior, which can be inherited transgenerationally. Previously, we discovered that a small RNA from a clinical isolate of Pseudomonas aeruginosa, PA14, induces learned avoidance and transgenerational inheritance of that avoidance in C. elegans. Pseudomonas aeruginosa is an important human pathogen, and there are other Pseudomonads in C. elegans' natural habitat, but it is unclear whether C. elegans ever encounters PA14-like bacteria in the wild. Thus, it is not known if small RNAs from bacteria found in C. elegans' natural habitat can also regulate host behavior and produce heritable behavioral effects. Here we screened a set of wild habitat bacteria, and found that a pathogenic Pseudomonas vranovensis strain isolated from the C. elegans microbiota, GRb0427, regulates worm behavior: worms learn to avoid this pathogenic bacterium following exposure, and this learned avoidance is inherited for four generations. The learned response is entirely mediated by bacterially-produced small RNAs, which induce avoidance and transgenerational inheritance, providing further support that such mechanisms of learning and inheritance exist in the wild. We identified Pv1, a small RNA expressed in P. vranovensis, that has a 16-nucleotide match to an exon of the C. elegans gene maco-1. Pv1 is both necessary and sufficient to induce learned avoidance of Grb0427. However, Pv1 also results in avoidance of a beneficial microbiome strain, P. mendocina. Our findings suggest that bacterial small RNA-mediated regulation of host behavior and its transgenerational inheritance may be functional in C. elegans' natural environment, and that this potentially maladaptive response may favor reversal of the transgenerational memory after a few generations. Our data also suggest that different bacterial small RNA-mediated regulation systems evolved independently, but define shared molecular features of bacterial small RNAs that produce transgenerationally-inherited effects.

Pretreatment and Acquired Drug Resistance in Children With Human Immunodeficiency Virus Type 1 in Jos, Nigeria

We determined pretreatment and acquired human immunodeficiency virus (HIV) drug resistance among children with HIV type 1 (HIV-1) in Jos, Nigeria. The majority (71%) of those who failed first-line antiretroviral therapy were on a nevirapine-containing regimen. The prevalence of pretreatment (48%) and acquired (76%) HIV drug resistance mutations was high in our study. Wider access to HIV drug resistance testing after treatment failure is necessary to optimize second-line treatment options among children with HIV in Nigeria.

Advancing Global Health Surveillance of Mycotoxin Exposures using Minimally Invasive Sampling Techniques: A State-of-the-Science Review

Mycotoxins are a heterogeneous group of toxins produced by fungi that can grow in staple crops (e.g., maize, cereals), resulting in health risks due to widespread exposure from human consumption and inhalation. Dried blood spot (DBS), dried serum spot (DSS), and volumetric tip microsampling (VTS) assays were developed and validated for several important mycotoxins. This review summarizes studies that have developed these assays to monitor mycotoxin exposures in human biological samples and highlights future directions to facilitate minimally invasive sampling techniques as global public health tools. A systematic search of PubMed (MEDLINE), Embase (Elsevier), and CINAHL (EBSCO) was conducted. Key assay performance metrics were extracted to provide a critical review of the available methods. This search identified 11 published reports related to measuring mycotoxins (ochratoxins, aflatoxins, and fumonisins) using DBS/DSS and VTS assays. Multimycotoxin assays adapted for DBS/DSS and VTS have undergone sufficient laboratory validation for applications in large-scale population health and human biomonitoring studies. Future work should expand the number of mycotoxins that can be measured in multimycotoxin assays, continue to improve multimycotoxin assay sensitivities of several biomarkers with low detection rates, and validate multimycotoxin assays across diverse populations with varying exposure levels. Validated low-cost and ultrasensitive minimally invasive sampling methods should be deployed in human biomonitoring and public health surveillance studies to guide policy interventions to reduce inequities in global mycotoxin exposures.

A Tandem-Affinity Purification Method for Identification of Primary Intracellular Drug-Binding Proteins

In the field of drug discovery, understanding how small molecule drugs interact with cellular components is crucial. Our study introduces a novel methodology to uncover primary drug targets using Tandem Affinity Purification for identification of Drug-Binding Proteins (TAP-DBP). Central to our approach is the generation of a FLAG-hemagglutinin (HA)-tagged chimeric protein featuring the FKBP12(F36V) adaptor protein and the TurboID enzyme. Conjugation of drug molecules with the FKBP12(F36V) ligand allows for the coordinated recruitment of drug-binding partners effectively enabling in-cell TurboID-mediated biotinylation. By employing a tandem affinity purification protocol based on FLAG-immunoprecipitation and streptavidin pulldown, alongside mass spectrometry analysis, TAP-DBP allows for the precise identification of drug-primary binding partners. Overall, this study introduces a systematic, unbiased method for identification of drug-protein interactions, contributing a clear understanding of target engagement and drug selectivity to advance the mode of action of a drug in cells.

Correlating Conformational Equilibria with Catalysis in the Electron Bifurcating EtfABCX of Thermotoga maritima

Electron bifurcation (BF) is an evolutionarily ancient energy coupling mechanism in anaerobes, whose associated enzymatic machinery remains enigmatic. In BF-flavoenzymes, a chemically high-potential electron forms in a thermodynamically favorable fashion by simultaneously dropping the potential of a second electron before its donation to physiological acceptors. The cryo-EM and spectroscopic analyses of the BF-enzyme Fix/EtfABCX from Thermotoga maritima suggest that the BF-site contains a special flavin-adenine dinucleotide and, upon its reduction with NADH, a low-potential electron transfers to ferredoxin and a high-potential electron reduces menaquinone. The transfer of energy from high-energy intermediates must be carefully orchestrated conformationally to avoid equilibration. Herein, anaerobic size exclusion-coupled small-angle X-ray scattering (SEC-SAXS) shows that the Fix/EtfAB heterodimer subcomplex, which houses BF- and electron transfer (ET)-flavins, exists in a conformational equilibrium of compacted and extended states between flavin-binding domains, the abundance of which is impacted by reduction and NAD(H) binding. The conformations identify dynamics associated with the T. maritima enzyme and also recapitulate states identified in static structures of homologous BF-flavoenzymes. Reduction of Fix/EtfABCX's flavins alone is insufficient to elicit domain movements conducive to ET but requires a structural "trigger" induced by NAD(H) binding. Models show that Fix/EtfABCX's superdimer exists in a combination of states with respect to its BF-subcomplexes, suggesting a cooperative mechanism between supermonomers for optimizing catalysis. The correlation of conformational states with pathway steps suggests a structural means with which Fix/EtfABCX may progress through its catalytic cycle. Collectively, these observations provide a structural framework for tracing Fix/EtfABCX's catalysis.

Standardization of zebrafish drug testing parameters for muscle diseases

Skeletal muscular diseases predominantly affect skeletal and cardiac muscle, resulting in muscle weakness, impaired respiratory function and decreased lifespan. These harmful outcomes lead to poor health-related quality of life and carry a high healthcare economic burden. The absence of promising treatments and new therapies for muscular disorders requires new methods for candidate drug identification and advancement in animal models. Consequently, the rapid screening of drug compounds in an animal model that mimics features of human muscle disease is warranted. Zebrafish are a versatile model in preclinical studies that support developmental biology and drug discovery programs for novel chemical entities and repurposing of established drugs. Due to several advantages, there is an increasing number of applications of the zebrafish model for high-throughput drug screening for human disorders and developmental studies. Consequently, standardization of key drug screening parameters, such as animal husbandry protocols, drug compound administration and outcome measures, is paramount for the continued advancement of the model and field. Here, we seek to summarize and explore critical drug treatment and drug screening parameters in the zebrafish-based modeling of human muscle diseases. Through improved standardization and harmonization of drug screening parameters and protocols, we aim to promote more effective drug discovery programs.

Using viral sequence diversity to estimate time of HIV infection in infants

Age at HIV acquisition may influence viral pathogenesis in infants, and yet infection timing (i.e. date of infection) is not always known. Adult studies have estimated infection timing using rates of HIV RNA diversification, however, it is unknown whether adult-trained models can provide accurate predictions when used for infants due to possible differences in viral dynamics. While rates of viral diversification have been well defined for adults, there are limited data characterizing these dynamics for infants. Here, we performed Illumina sequencing of gag and pol using longitudinal plasma samples from 22 Kenyan infants with well-characterized infection timing. We used these data to characterize viral diversity changes over time by designing an infant-trained Bayesian hierarchical regression model that predicts time since infection using viral diversity. We show that diversity accumulates with time for most infants (median rate within pol = 0.00079 diversity/month), and diversity accumulates much faster than in adults (compare previously-reported adult rate within pol = 0.00024 diversity/month [1]). We find that the infant rate of viral diversification varies by individual, gene region, and relative timing of infection, but not by set-point viral load or rate of CD4+ T cell decline. We compare the predictive performance of this infant-trained Bayesian hierarchical regression model with simple linear regression models trained using the same infant data, as well as existing adult-trained models [1]. Using an independent dataset from an additional 15 infants with frequent HIV testing to define infection timing, we demonstrate that infant-trained models more accurately estimate time since infection than existing adult-trained models. This work will be useful for timing HIV acquisition for infants with unknown infection timing and for refining our understanding of how viral diversity accumulates in infants, both of which may have broad implications for the future development of infant-specific therapeutic and preventive interventions.

Prime editing-mediated correction of the CFTR W1282X mutation in iPSCs and derived airway epithelial cells

A major unmet need in the cystic fibrosis (CF) therapeutic landscape is the lack of effective treatments for nonsense CFTR mutations, which affect approximately 10% of CF patients. Correction of nonsense CFTR mutations via genomic editing represents a promising therapeutic approach. In this study, we tested whether prime editing, a novel CRISPR-based genomic editing method, can be a potential therapeutic modality to correct nonsense CFTR mutations. We generated iPSCs from a CF patient homozygous for the CFTR W1282X mutation. We demonstrated that prime editing corrected one mutant allele in iPSCs, which effectively restored CFTR function in iPSC-derived airway epithelial cells and organoids. We further demonstrated that prime editing may directly repair mutations in iPSC-derived airway epithelial cells when the prime editing machinery is efficiently delivered by helper-dependent adenovirus (HDAd). Together, our data demonstrated that prime editing may potentially be applied to correct CFTR mutations such as W1282X.

Associations of SARS-CoV-2 antibodies with birth outcomes: Results from three urban birth cohorts in the NIH environmental influences on child health outcomes program

Studies suggest perinatal infection with SARS-CoV-2 can induce adverse birth outcomes, but studies published to date have substantial limitations. We therefore conducted an observational study of 211 births occurring between January 2020-September 2021 in three urban cohorts participating in the Environmental Influences on Child Health Outcomes Program. Serology was assessed for IgG, IgM and IgA antibodies to nucleocapsid, S1 spike, S2 spike, and receptor-binding domain. There were no differences in gestational age (GA), birth weight, preterm birth (PTB) or low birth weight (LBW) among seropositive mothers. However, the few (n = 9) IgM seropositive mothers had children with lower BW (434g, 95% CI: 116-752), BW Z score-for-GA (0.73 SD, 95% CI 0.10-1.36) and were more likely to deliver preterm (OR 8.75, 95% CI 1.22-62.4). Though there are limits to interpretation, the data support efforts to prevent SARS-CoV-2 infections in pregnancy.

Transcription dosage compensation does not occur in Down syndrome

BACKGROUND

The increase in DNA copy number in Down syndrome (DS; caused by trisomy 21) has led to the DNA dosage hypothesis, which posits that the level of gene expression is proportional to the gene's DNA copy number. Yet many reports have suggested that a proportion of chromosome 21 genes are dosage compensated back towards typical expression levels (1.0×). In contrast, other reports suggest that dosage compensation is not a common mechanism of gene regulation in trisomy 21, providing support to the DNA dosage hypothesis.

RESULTS

In our work, we use both simulated and real data to dissect the elements of differential expression analysis that can lead to the appearance of dosage compensation, even when compensation is demonstrably absent. Using lymphoblastoid cell lines derived from a family with an individual with Down syndrome, we demonstrate that dosage compensation is nearly absent at both nascent transcription (GRO-seq) and steady-state RNA (RNA-seq) levels. Furthermore, we link the limited apparent dosage compensation to expected allelic variation in transcription levels.

CONCLUSIONS

Transcription dosage compensation does not occur in Down syndrome. Simulated data containing no dosage compensation can appear to have dosage compensation when analyzed via standard methods. Moreover, some chromosome 21 genes that appear to be dosage compensated are consistent with allele specific expression.

Social and Leisure Activities Predict Transitions in Cognitive Functioning in Older Mexican Adults: A Latent Transition Analysis of the Mexican Health and Aging Study

OBJECTIVES

Mexico has a rapidly aging population at risk for cognitive impairment. Social and leisure activities may protect against cognitive decline in older adults. The benefits of these behaviors may vary by patterns of cognitive impairment. The objectives of this study were to identify latent states of cognitive functioning, model the incidence of transitions between these states, and investigate how social and leisure activities were associated with state transitions over a 6-year period in Mexican adults aged 60 and older.

METHODS

We performed latent transition analyses to identify distinct cognitive statuses in the 2012 and 2018 waves of the Mexican Health and Aging Study (N = 9,091). We examined the transition probabilities between these states and their associations with social and leisure activities.

RESULTS

We identified 4 cognitive statuses at baseline: normal cognition (43%), temporal disorientation (30%), perceptual-motor function impairment (7%), and learning and memory impairment (20%). Various social and leisure activities were associated with reduced odds of death and disadvantageous cognitive transitions, as well as increased odds of beneficial transitions.

DISCUSSION

Mapping the effects of popular social and leisure activities onto common patterns in cognitive functioning may inform the development of more enjoyable and effective health-protective behavioral interventions.

Microglial MHC-I induction with aging and Alzheimer's is conserved in mouse models and humans

Major histocompatibility complex I (MHC-I) CNS cellular localization and function is still being determined after previously being thought to be absent from the brain. MHC-I expression has been reported to increase with brain aging in mouse, rat, and human whole tissue analyses, but the cellular localization was undetermined. Neuronal MHC-I is proposed to regulate developmental synapse elimination and tau pathology in Alzheimer's disease (AD). Here, we report that across newly generated and publicly available ribosomal profiling, cell sorting, and single-cell data, microglia are the primary source of classical and non-classical MHC-I in mice and humans. Translating ribosome affinity purification-qPCR analysis of 3-6- and 18-22-month-old (m.o.) mice revealed significant age-related microglial induction of MHC-I pathway genes B2m, H2-D1, H2-K1, H2-M3, H2-Q6, and Tap1 but not in astrocytes and neurons. Across a timecourse (12-23 m.o.), microglial MHC-I gradually increased until 21 m.o. and then accelerated. MHC-I protein was enriched in microglia and increased with aging. Microglial expression, and absence in astrocytes and neurons, of MHC-I-binding leukocyte immunoglobulin-like (Lilrs) and paired immunoglobin-like type 2 (Pilrs) receptor families could enable cell -autonomous MHC-I signaling and increased with aging in mice and humans. Increased microglial MHC-I, Lilrs, and Pilrs were observed in multiple AD mouse models and human AD data across methods and studies. MHC-I expression correlated with p16INK4A, suggesting an association with cellular senescence. Conserved induction of MHC-I, Lilrs, and Pilrs with aging and AD opens the possibility of cell-autonomous MHC-I signaling to regulate microglial reactivation with aging and neurodegeneration.

Quantifying cell viability through organelle ratiometric probing

Detecting cell viability is crucial in research involving the precancerous discovery of abnormal cells, the evaluation of treatments, and drug toxicity testing. Although conventional methods afford cumulative results regarding cell viability based on a great number of cells, they do not permit investigating cell viability at the single-cell level. In response, we rationally designed and synthesized a fluorescent probe, PCV-1, to visualize cell viability under the super-resolution technology of structured illumination microscopy. Given its sensitivity to mitochondrial membrane potential and affinity to DNA, PCV-1's ability to stain mitochondria and nucleoli was observed in live and dead cells, respectively. During cell injury induced by drug treatment, PCV-1's migration from mitochondria to the nucleolus was dynamically visualized at the single-cell level. By extension, harnessing PCV-1's excellent photostability and signal-to-noise ratio and by comparing the fluorescence intensity of the two organelles, mitochondria and nucleoli, we developed a powerful analytical assay named organelle ratiometric probing (ORP) that we applied to quantitatively analyze and efficiently assess the viability of individual cells, thereby enabling deeper insights into the potential mechanisms of cell death. In ORP analysis with PCV-1, we identified 0.3 as the cutoff point for assessing whether adding a given drug will cause apparent cytotoxicity, which greatly expands the probe's applicability. To the best of our knowledge, PCV-1 is the first probe to allow visualizing cell death and cell injury under super-resolution imaging, and our proposed analytical assay using it paves the way for quantifying cell viability at the single-cell level.

Cellular Validation of a Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2

Ubiquitin thioesterase OTUB2, a cysteine protease from the ovarian tumor (OTU) deubiquitinase superfamily, is often overexpressed during tumor progression and metastasis. Development of OTUB2 inhibitors is therefore believed to be therapeutically important, yet potent and selective small-molecule inhibitors targeting OTUB2 are scarce. Here, we describe the development of an improved OTUB2 inhibitor, LN5P45, comprising a chloroacethydrazide moiety that covalently reacts to the active-site cysteine residue. LN5P45 shows outstanding target engagement and proteome-wide selectivity in living cells. Importantly, LN5P45 as well as other OTUB2 inhibitors strongly induce monoubiquitination of OTUB2 on lysine 31. We present a route to future OTUB2-related therapeutics and have shown that the OTUB2 inhibitor developed in this study can help to uncover new aspects of the related biology and open new questions regarding the understanding of OTUB2 regulation at the post-translational modification level.

Fermi-Level Engineering of Nitrogen Core-Doped Armchair Graphene Nanoribbons

Substitutional heteroatom doping of bottom-up engineered 1D graphene nanoribbons (GNRs) is a versatile tool for realizing low-dimensional functional materials for nanoelectronics and sensing. Previous efforts have largely relied on replacing C-H groups lining the edges of GNRs with trigonal planar N atoms. This type of atomically precise doping, however, only results in a modest realignment of the valence band (VB) and conduction band (CB) energies. Here, we report the design, bottom-up synthesis, and spectroscopic characterization of nitrogen core-doped 5-atom-wide armchair GNRs (N2-5-AGNRs) that yield much greater energy-level shifting of the GNR electronic structure. Here, the substitution of C atoms with N atoms along the backbone of the GNR introduces a single surplus π-electron per dopant that populates the electronic states associated with previously unoccupied bands. First-principles DFT-LDA calculations confirm that a sizable shift in Fermi energy (∼1.0 eV) is accompanied by a broad reconfiguration of the band structure, including the opening of a new band gap and the transition from a direct to an indirect semiconducting band gap. Scanning tunneling spectroscopy (STS) lift-off charge transport experiments corroborate the theoretical results and reveal the relationship among substitutional heteroatom doping, Fermi-level shifting, electronic band structure, and topological engineering for this new N-doped GNR.

Prioritized polycystic kidney disease drug targets and repurposing candidates from pre-cystic and cystic mouse Pkd2 model gene expression reversion

BACKGROUND

Autosomal dominant polycystic kidney disease (ADPKD) is one of the most prevalent monogenic human diseases. It is mostly caused by pathogenic variants in PKD1 or PKD2 genes that encode interacting transmembrane proteins polycystin-1 (PC1) and polycystin-2 (PC2). Among many pathogenic processes described in ADPKD, those associated with cAMP signaling, inflammation, and metabolic reprogramming appear to regulate the disease manifestations. Tolvaptan, a vasopressin receptor-2 antagonist that regulates cAMP pathway, is the only FDA-approved ADPKD therapeutic. Tolvaptan reduces renal cyst growth and kidney function loss, but it is not tolerated by many patients and is associated with idiosyncratic liver toxicity. Therefore, additional therapeutic options for ADPKD treatment are needed.

METHODS

As drug repurposing of FDA-approved drug candidates can significantly decrease the time and cost associated with traditional drug discovery, we used the computational approach signature reversion to detect inversely related drug response gene expression signatures from the Library of Integrated Network-Based Cellular Signatures (LINCS) database and identified compounds predicted to reverse disease-associated transcriptomic signatures in three publicly available Pkd2 kidney transcriptomic data sets of mouse ADPKD models. We focused on a pre-cystic model for signature reversion, as it was less impacted by confounding secondary disease mechanisms in ADPKD, and then compared the resulting candidates' target differential expression in the two cystic mouse models. We further prioritized these drug candidates based on their known mechanism of action, FDA status, targets, and by functional enrichment analysis.

RESULTS

With this in-silico approach, we prioritized 29 unique drug targets differentially expressed in Pkd2 ADPKD cystic models and 16 prioritized drug repurposing candidates that target them, including bromocriptine and mirtazapine, which can be further tested in-vitro and in-vivo.

CONCLUSION

Collectively, these results indicate drug targets and repurposing candidates that may effectively treat pre-cystic as well as cystic ADPKD.

Facing financial barriers to healthcare: patient-informed adaptation of a conceptual framework for adults with a history of cancer

Background

Cancer-related financial hardship is associated with negative clinical outcomes, which may be partially explained by cost-related delayed or forgone care in response to financial barriers. We sought to understand patient experiences facing financial barriers to medical care following a cancer diagnosis.

Methods

We conducted virtual, semi-structured interviews in Fall 2022 with 20 adults with a history of cancer who had experienced cancer-related financial hardship in the prior year. We used template analysis within a pragmatic paradigm, combining constructivist and critical realist theoretical perspectives, to analyze interview transcripts and adapt an existing conceptual framework of financial barriers to care.

Results

The majority of interviewees identified as women (70%), non-Hispanic white (60%), and reported an annual household income of <$48,000 (60%). As interviewees sought to overcome financial barriers, they described substantial frustration at the limitations and complexities of United States health and social care systems, resulting in a reliance on a fragmented, uncertain resource landscape. The administrative burden resulting from bureaucratic systems and the advocacy responsibilities required to navigate them ultimately fell on interviewees and their caregivers. Thus, participants described their ability to overcome financial barriers as being influenced by individual and interpersonal factors, such as social support, comfort asking for help, time, prior experience navigating resources, and physical and mental health. However, participants noted health system organizational factors, such as whether all new patients proactively met with a social worker or financial navigator, as having the potential to lessen the administrative and financial burden experienced.

Conclusion

We present an adapted conceptual framework outlining multi-level factors influencing patient experiences coping with financial barriers to medical care. In addition to influencing whether a patient ultimately delays or forgoes care due to cost, financial barriers also have the potential to independently affect patient mental, physical, and financial health.

Gender, Personality, and Cognitive Resilience Against Early-Life Disadvantage

OBJECTIVES

Early-life disadvantage (ELD) relates to lower late-life cognition. However, personality factors, including having an internal locus of control (LOC) or a conscientious personality, relate to resilience and effective stress coping. We explore whether personality factors convey resilience against the negative effects of ELD on cognition, by gender, in Mexico.

METHODS

Using the 2015 Mexican Health and Aging Study, we estimated expected cognition using multiple ELD markers to identify a subsample in the lowest quartile of expected cognition given ELD (n = 2,086). In this subsample, we estimated cross-sectional associations between personality and having above-median observed cognitive ability (n = 522) using logistic regression.

RESULTS

Among those in the lowest quartile of expected cognition, a more internal LOC (β = 0.32 [men] and β = 0.44 [women]) and conscientious personality (β = 0.39 [men] and β = 0.17 [women]) were significantly associated with having above-median cognitive ability in models adjusted for demographic confounders. Larger benefits of conscientiousness were observed for men than women. Associations between personality and having above-median cognitive ability remained statistically significant after further adjustment for health, stress, and cognitive stimulation variables, regardless of gender.

DISCUSSION

Personality factors may convey resilience among individuals who experienced ELD, potentially breaking the link between ELD and worse late-life cognition. Structural factors and gender roles may affect how much women benefit from personality factors.

Association of Longitudinal Activity Measures and Diabetes Risk: An Analysis From the National Institutes of Health All of Us Research Program

CONTEXT

Prior studies of the relationship between physical activity and incident type 2 diabetes mellitus (T2DM) relied primarily on questionnaires at a single time point.

OBJECTIVE

We sought to investigate the relationship between physical activity and incident T2DM with an innovative approach using data from commercial wearable devices linked to electronic health records in a real-world population.

METHODS

Using All of Us participants' accelerometer data from their personal Fitbit devices, we used a time-varying Cox proportional hazards models with repeated measures of physical activity for the outcome of incident T2DM. We evaluated for effect modification with age, sex, body mass index (BMI), and sedentary time using multiplicative interaction terms.

RESULTS

From 5677 participants in the All of Us Research Program (median age 51 years; 74% female; 89% White), there were 97 (2%) cases of incident T2DM over a median follow-up period of 3.8 years between 2010 to 2021. In models adjusted for age, sex, and race, the hazard of incident diabetes was reduced by 44% (95% CI, 15%-63%; P = 0.01) when comparing those with an average daily step count of 10 700 to those with 6000. Similar benefits were seen comparing groups based on average duration of various intensities of activity (eg, lightly active, fairly active, very active). There was no evidence for effect modification by age, sex, BMI, or sedentary time.

CONCLUSION

Greater time in any type of physical activity intensity was associated with lower risk of T2DM irrespective of age, sex, BMI, or sedentary time.

Chd5 Regulates the Transcription Factor Six3 to Promote Neuronal Differentiation

Chromodomain helicase DNA-binding protein 5 (Chd5) is an ATP-dependent chromatin remodeler that promotes neuronal differentiation. However, the mechanism behind the action of Chd5 during neurogenesis is not clearly understood. Here we use transcriptional profiling of cells obtained from Chd5 deficient mice at early and late stages of neuronal differentiation to show that Chd5 regulates neurogenesis by directing stepwise transcriptional changes. During early stages of neurogenesis, Chd5 promotes expression of the proneural transcription factor Six3 to repress Wnt5a, a non-canonical Wnt ligand essential for the maturation of neurons. This previously unappreciated ability of Chd5 to transcriptionally repress neuronal maturation factors is critical for both lineage specification and maturation. Thus, Chd5 facilitates early transcriptional changes in neural stem cells, thereby initiating transcriptional programs essential for neuronal fate specification.

Methods for the identification and characterization of extracellular vesicles in cardiovascular studies: from exosomes to microvesicles

Extracellular vesicles (EVs) are nanosized vesicles with a lipid bilayer that are released from cells of the cardiovascular system, and are considered important mediators of intercellular and extracellular communications. Two types of EVs of particular interest are exosomes and microvesicles, which have been identified in all tissue and body fluids and carry a variety of molecules including RNAs, proteins, and lipids. EVs have potential for use in the diagnosis and prognosis of cardiovascular diseases and as new therapeutic agents, particularly in the setting of myocardial infarction and heart failure. Despite their promise, technical challenges related to their small size make it challenging to accurately identify and characterize them, and to study EV-mediated processes. Here, we aim to provide the reader with an overview of the techniques and technologies available for the separation and characterization of EVs from different sources. Methods for determining the protein, RNA, and lipid content of EVs are discussed. The aim of this document is to provide guidance on critical methodological issues and highlight key points for consideration for the investigation of EVs in cardiovascular studies.

Unique Profile of Inflammation and Immune Activation in Pregnant People With HIV in the United States

BACKGROUND

Little is known about inflammation/immune activation during pregnancy in people with HIV (PWH) and growth in their children who are HIV-exposed and uninfected (CHEU).

METHODS

Using data from the Pediatric HIV/AIDS Cohort Study and an HIV-seronegative comparison group, we assessed associations of (1) HIV status, mode of HIV acquisition (perinatally vs nonperinatally acquired), and type of antiretroviral therapy (ART) with inflammation/immune activation in pregnancy; and (2) inflammation/immune activation in pregnancy with growth of CHEU at 12 months. Interleukin 6 (IL-6), high-sensitivity C-reactive protein (hs-CRP), soluble(s) TNF-α receptor 1 and 2 (sTNFR1, sTNFR2), sCD14, and sCD163 were measured between 13 and 27 weeks' gestation. Linear regression models were fit to estimate differences between groups for each log-transformed biomarker, adjusted for confounders.

RESULTS

Pregnant PWH (188 total, 39 perinatally acquired, 149 nonperinatally acquired) and 76 HIV-seronegative persons were included. PWH had higher IL-6, sTNFR1, sCD14, and sCD163 and lower sTNFR2 compared to HIV-seronegative persons in adjusted models. Among PWH, sCD163 was higher in those with perinatally versus nonperinatally acquired HIV and on PI-based versus INSTI-based ART. Higher maternal concentrations of IL-6, sTNFR2, and hs-CRP were associated with poorer growth at 12 months.

CONCLUSIONS

Maternal HIV status is associated with a distinct profile of inflammation/immune activation during pregnancy, which may influence child growth.

Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work

The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception 20 years ago. Here we describe the general operation of the PSI, including its leadership, working groups, yearly workshops, and the document process by which proposals are thoroughly and publicly reviewed in order to be ratified as PSI standards. We briefly describe the current state of the many existing PSI standards, some of which remain the same as when originally developed, some of which have undergone subsequent revisions, and some of which have become obsolete. Then the set of proposals currently being developed are described, with an open call to the community for participation in the forging of the next generation of standards. Finally, we describe some synergies and collaborations with other organizations and look to the future in how the PSI will continue to promote the open sharing of data and thus accelerate the progress of the field of proteomics.

Photocatalytic Depolymerization of Native Lignin toward Chemically Recyclable Polymer Networks

As an inedible component of biomass, lignin features rich functional groups that are desired for chemical syntheses. How to effectively depolymerize lignin without compromising the more valuable cellulose and hemicellulose has been a significant challenge. Existing biomass processing procedures either induce extensive condensation in lignin that greatly hinders its chemical utilization or focus on fully depolymerizing lignin to produce monomers that are difficult to separate for subsequent chemical synthesis. Here, we report a new approach to selective partial depolymerization, which produces oligomers that can be readily converted to chemically recyclable polymer networks. The process takes advantage of the high selectivity of photocatalytic activation of the β-O-4 bond in lignin by tetrabutylammonium decatungstate (TBADT). The availability of exogenous electron mediators or scavengers promotes cleavage or oxidation of this bond, respectively, enabling high degrees of control over the depolymerization and the density of a key functional group, C=O, in the products. The resulting oligomers can then be readily utilized for the synthesis of polymer networks through reactions between C=O and branched -NH₂ as a dynamic covalent cross-linker. Importantly, the resulting polymer network can be recycled to enable a circular economy of materials directly derived from biomass.

Integrated Infectious Disease and Substance Use Disorder Care for the Treatment of Injection Drug Use-Associated Infections: A Prospective Cohort Study With Historical Control

Background

To address the infectious disease (ID) and substance use disorder (SUD) syndemic, we developed an integrated ID/SUD clinical team rooted in harm reduction at a county hospital in Miami, Florida. The Severe Injection-Related Infection (SIRI) team treats people who inject drugs (PWID) and provides medical care, SUD treatment, and patient navigation during hospitalization and after hospital discharge. We assessed the impact of the SIRI team on ID and SUD treatment and healthcare utilization outcomes.

Methods

We prospectively collected data on patients seen by the SIRI team. A diagnostic code algorithm confirmed by chart review was used to identify a historical control group of patients with SIRI hospitalizations in the year preceding implementation of the SIRI team. The primary outcome was death or readmission within 90 days post-hospital discharge. Secondary outcomes included initiation of medications for opioid use disorder (MOUD) and antibiotic course completion.

Results

There were 129 patients included in the study: 59 in the SIRI team intervention and 70 in the pre-SIRI team control group. SIRI team patients had a 45% risk reduction (aRR, 0.55 [95% confidence interval CI, .32-.95]; 24% vs 44%) of being readmitted in 90 days or dying compared to pre-SIRI historical controls. SIRI team patients were more likely to initiate MOUD in the hospital (93% vs 33%, P < .01), complete antibiotic treatment (90% vs 60%, P < .01), and less likely to have patient-directed discharge (17% vs 37%, P = .02).

Conclusions

An integrated ID/SUD team was associated with improvements in healthcare utilization, MOUD initiation, and antibiotic completion for PWID with infections.

Sexually Transmitted Infections in Pregnant People With Human Immunodeficiency Virus: Temporal Trends, Demographic Correlates, and Association With Preterm Birth

BACKGROUND

We describe trends in prevalence and identify factors associated with Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), syphilis, and Trichomonas vaginalis (TV) diagnosed in pregnancy among US people with human immunodeficiency virus (PWH) and evaluate associations of sexually transmitted infections (STIs) with preterm birth (PTB).

METHODS

We included pregnant PWH enrolled in the Surveillance Monitoring for ART Toxicities dynamic cohort of the Pediatric HIV/AIDS Cohort Study network who delivered between 2010 and 2019. Multivariable log-binomial or Poisson generalized estimating equation models were used to estimate the association of calendar year with each STI, controlling for confounders; the association of demographic and clinical factors with each STI; and the association of each STI with PTB.

RESULTS

The sample included 2241 pregnancies among 1821 PWH. Median age at delivery was 29.2 years; 71% of participants identified as Black or African American. STI prevalence was: CT 7.7%, NG 2.3%, syphilis 2.4%, and TV 14.5%; 30% had unknown TV status. There were no temporal changes in STI prevalence. Younger age and initial HIV viral load ≥400 copies/mL were associated with increased risk of CT, NG, and TV. Recreational substance use was a risk factor for NG, syphilis, and TV. No STI was associated with PTB.

CONCLUSIONS

Unlike nationwide trends, no changes in STI prevalence during the study period were observed. The large proportion with unknown TV status underscores the need for increased adherence to screening guidelines. STIs diagnosed during pregnancy in PWH were not associated with risk of PTB.

HIV RNA Screening Reduces Integrase Strand Transfer Inhibitor Resistance Risk in Persons Receiving Long-Acting Cabotegravir for HIV Prevention

BACKGROUND

The HPTN 083 trial demonstrated that long-acting cabotegravir (CAB-LA) was superior to tenofovir-disoproxil fumarate/emtricitabine for human immunodeficiency virus (HIV) preexposure prophylaxis (PrEP). Integrase strand transfer inhibitor (INSTI) resistance-associated mutations (RAMs) were detected in some participants with HIV infection. We used a low viral load INSTI genotyping assay to evaluate the timing of emergence of INSTI RAMs and assessed whether HIV screening with a sensitive RNA assay would have detected HIV infection before INSTI resistance emerged.

METHODS

Single-genome sequencing to detect INSTI RAMs was performed for samples with viral loads <500 copies/mL from 5 participants with previously identified INSTI RAMs and 2 with no prior genotyping results.

RESULTS

Major INSTI RAMs were detected in all 7 cases. HIV RNA testing identified infection before major INSTI RAMs emerged in 4 cases and before additional major INSTI RAMs accumulated in 1 case. Most INSTI RAMs were detected early when the viral load was low and CAB concentration was high.

CONCLUSIONS

When using CAB-LA PrEP, earlier detection of HIV infection with a sensitive RNA assay may allow for earlier treatment initiation with the potential to reduce INSTI resistance risk. Further studies are needed to evaluate the value and feasibility of HIV RNA testing with CAB-LA PrEP.

Multiple Infection and Human Immunodeficiency Virus Superinfection Among Persons who Inject Drugs in Indonesia and Ukraine

BACKGROUND

The HIV Prevention Trials Network (HPTN) 074 study evaluated an integrated human immunodeficiency virus (HIV) treatment and prevention strategy among persons who inject drugs (PWID) in Indonesia, Ukraine, and Vietnam. We previously detected multiple HIV infection in 3 of 7 (43%) of seroconverters with 3-8 HIV strains per person. In this report, we analyzed multiple HIV infection and HIV superinfection (SI) in the HPTN 074 cohort.

METHODS

We analyzed samples from 70 participants in Indonesia and Ukraine who had viral load >400 copies/mL at enrollment and the final study visit (median follow-up, 2.5 years). HIV was characterized with Sanger sequencing, next-generation sequencing, and phylogenetic analysis. Additional methods were used to characterize a rare case of triple-variant SI.

RESULTS

At enrollment, multiple infection was detected in only 3 of 58 (5.2%) participants with env sequence data. SI was detected in only 1 of 70 participants over 172.3 person-years of follow-up (SI incidence, 0.58/100 person-years [95% confidence interval, .015-3.2]). The SI case involved acquisition of 3 HIV strains with rapid selection of a strain with a single pol region cluster.

CONCLUSIONS

These data from a large cohort of PWID suggest that intrahost viral selection and other factors may lead to underestimation of the frequency of multiple HIV infection and SI events.

Considerations for the Use of Long-Acting and Extended-Release Agents During Pregnancy and Lactation

Long-acting agents hold significant promise for treating and preventing common illnesses, including infections. Pharmacokinetic and safety data during pregnancy and lactation are often unavailable for new drugs; these data are vital to facilitate optimal drug use by pregnant and lactating women and women who may conceive. In this commentary, we summarize the circumstances in which pregnant and lactating women are likely to use and benefit from long-acting agents. We focus on long-acting formulations of small molecules (rather than biologics such as monoclonal antibodies) and on several infections of global importance (human immunodeficiency virus, tuberculosis, malaria, and hepatitis C). We discuss pregnancy pharmacokinetic/pharmacodynamic and potential safety and efficacy considerations pertaining to the use of long-acting agents in pregnancy and lactation. Finally, we summarize existing preclinical and pregnancy pharmacokinetic data that are available (or expected in the near future) for several agents that are under development or approved, and how key research gaps may be addressed.

Androgen-mediated Perturbation of the Hepatic Circadian System Through Epigenetic Modulation Promotes NAFLD in PCOS Mice

In women, excess androgen causes polycystic ovary syndrome (PCOS), a common fertility disorder with comorbid metabolic dysfunctions including diabetes, obesity, and nonalcoholic fatty liver disease. Using a PCOS mouse model, this study shows that chronic high androgen levels cause hepatic steatosis while hepatocyte-specific androgen receptor (AR)-knockout rescues this phenotype. Moreover, through RNA-sequencing and metabolomic studies, we have identified key metabolic genes and pathways affected by hyperandrogenism. Our studies reveal that a large number of metabolic genes are directly regulated by androgens through AR binding to androgen response element sequences on the promoter region of these genes. Interestingly, a number of circadian genes are also differentially regulated by androgens. In vivo and in vitro studies using a circadian reporter [Period2::Luciferase (Per2::LUC)] mouse model demonstrate that androgens can directly disrupt the hepatic timing system, which is a key regulator of liver metabolism. Consequently, studies show that androgens decrease H3K27me3, a gene silencing mark on the promoter of core clock genes, by inhibiting the expression of histone methyltransferase, Ezh2, while inducing the expression of the histone demethylase, JMJD3, which is responsible for adding and removing the H3K27me3 mark, respectively. Finally, we report that under hyperandrogenic conditions, some of the same circadian/metabolic genes that are upregulated in the mouse liver are also elevated in nonhuman primate livers. In summary, these studies not only provide an overall understanding of how hyperandrogenism associated with PCOS affects liver gene expression and metabolism but also offer insight into the underlying mechanisms leading to hepatic steatosis in PCOS.

The Effects of Combined Respiratory-Gated Auricular Vagal Afferent Nerve Stimulation and Mindfulness Meditation for Chronic Low Back Pain: A Pilot Study

OBJECTIVE

Respiratory-gated Auricular Vagal Afferent Nerve stimulation (RAVANS) is a safe nonpharmacological approach to managing chronic pain. The purpose of the current study was to examine (1) the feasibility and acceptability of RAVANS, combined with mindful meditation (MM) for chronic low back pain (CLBP), (2) the potential synergy of MM+RAVANS on improving pain, and (3) possible moderators of the influence of MM+RAVANS on pain.

DESIGN

Pilot feasibility and acceptability study.

SETTING

Pain management center at large academic medical center.

SUBJECTS

Nineteen adults with CLBP and previous MM training.

METHODS

Participants attended two sessions during which they completed quantitative sensory testing (QST), rated pain severity, and completed a MM+stimulation session. Participants received RAVANS during one visit and sham stimulation during the other, randomized in order. Following intervention, participants repeated QST.

RESULTS

MM+RAVANS was well tolerated, acceptable, and feasible to provide relief for CLBP. Both MM+stimulation sessions resulted in improved back pain severity, punctate pain ratings, and pressure pain threshold. Individuals with greater negative affect showed greater back pain improvement from MM+RAVANS while those with greater mindfulness showed greater back pain improvement from MM+sham.

CONCLUSIONS

Results suggest that for CLBP patients with prior MM training, the analgesic effects of MM may have overshadowed effects of RAVANS given the brief single session MM+RAVANS intervention. However, those with greater negative affect may benefit from combined MM+RAVANS.

Communities Helping the Hearing of Infants by Reaching Parents (CHHIRP) through patient navigation: a hybrid implementation effectiveness stepped wedge trial protocol

INTRODUCTION

As the most common neonatal sensory disorder in the USA, infant hearing loss has an incidence of 1.7 per 1000 births. The consequences of delayed diagnosis and failure to obtain timely intervention include significant communication impairment and negative socioeconomic effects. Early Hearing Detection and Intervention (EHDI) national standards dictate that all infants should be screened and diagnosed by 3 months of age and there is a need for interventions that promote adherence to timely diagnosis. Patient navigation (PN) has been shown to be efficacious to decrease non-adherence with infant hearing diagnostic care; however, PN has yet to be tested in diverse communities or implemented into real-world settings.

METHODS AND ANALYSIS

The proposed research is a community-engaged, type 1 hybrid effectiveness-implementation trial of a PN intervention aimed at decreasing infant hearing diagnosis non-adherence after failed newborn hearing screening, delivered in state-funded EHDI clinics. Guided by our community advisory board and partners, we aim to (1) test the effectiveness of PN to decrease non-adherence to receipt of infant hearing diagnosis within 3 months after birth using a stepped-wedge trial design, (2) investigate implementation outcomes and factors influencing implementation and (3) determine the cost-effectiveness of PN from the perspective of third-party payers. The study will be conducted from April 2019 until March 2024.

ETHICS AND DISSEMINATION

This protocol was approved by the University of Kentucky Institutional Review Board. Although all research involving human subjects contains some risk, there are no known serious risks anticipated from participating in this study. We will seek to disseminate our results in a systematic fashion to patients, key stakeholder, policymakers and the scientific community. Our results will impact the field by partnering with communities to inform the scale-up of this innovative patient supportive intervention to create efficient and effective EHDI programmes and maximise public health impact.

TRIAL REGISTRATION NUMBER

Clinicaltrials.gov (Pre-results phase): NCT03875339.

Human Immunodeficiency Virus/AIDS in the Era of Coronavirus Disease 2019: A Juxtaposition of 2 Pandemics

The coronavirus disease 2019 (COVID-19) pandemic has significantly impacted persons with human immunodeficiency virus (HIV), interfering with critical health services for HIV prevention, treatment, and care. While there are multiple profiles of persons living with HIV and the impact of COVID-19 may differ for each, the severity of COVID-19 in persons with HIV is related strongly to the presence of comorbidities that increase the risk of severe disease in COVID-19 patients in the absence of HIV. An effective response to the juxtaposition of the HIV and COVID-19 pandemics requires a novel coordinated and collaborative global effort of scientists, industry, and community partners to accelerate basic and clinical research, as well as implementation science to operationalize evidence-based interventions expeditiously in real-world settings. Accelerated development and clinical evaluation of prevention and treatment countermeasures are urgently needed to mitigate the juxtaposition of the HIV and COVID-19 pandemics.

Deconvoluting Mechanisms of Acquired Resistance to RAF Inhibitors in BRAFV600E-Mutant Human Glioma

PURPOSE

Selective RAF-targeted therapy is effective in some patients with BRAFV600E-mutated glioma, though emergent and adaptive resistance occurs through ill-defined mechanisms.

EXPERIMENTAL DESIGN

Paired pre-/post- RAF inhibitor (RAFi)-treated glioma samples (N = 15) were obtained and queried for treatment-emergent genomic alterations using DNA and RNA sequencing (RNA-seq). Functional validation of putative resistance mechanisms was performed using established and patient-derived BRAFV600E-mutant glioma cell lines.

RESULTS

Analysis of 15 tissue sample pairs identified 13 alterations conferring putative resistance were identified among nine paired samples (including mutations involving ERRFI1, BAP1, ANKHD1, and MAP2K1). We performed functional validation of mechanisms of resistance, including loss of NF1, PTEN, or CBL, in BRAFV600E-mutant glioma lines, and demonstrate they are capable of conferring resistance in vitro. Knockdown of CBL resulted in increased EGFR expression and phosphorylation, a possible mechanism for maintaining ERK signaling within the cell. Combination therapy with a MEKi or EGFR inhibitor was able to overcome resistance to BRAFi, in NF1 knockdown and CBL knockdown, respectively. Restoration of wild-type PTEN in B76 cells (PTEN-/-) restored sensitivity to BRAFi. We identified and validated CRAF upregulation as a mechanism of resistance in one resistant sample. RNA-seq analysis identified two emergent expression patterns in resistant samples, consistent with expression patterns of known glioma subtypes.

CONCLUSIONS

Resistance mechanisms to BRAFi in glioma are varied and may predict effective precision combinations of targeted therapy, highlighting the importance of a personalized approach.

SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection causes Coronavirus Disease 2019 (COVID-19), a pandemic that seriously threatens global health. SARS-CoV-2 propagates by packaging its RNA genome into membrane enclosures in host cells. The packaging of the viral genome into the nascent virion is mediated by the nucleocapsid (N) protein, but the underlying mechanism remains unclear. Here, we show that the N protein forms biomolecular condensates with viral genomic RNA both in vitro and in mammalian cells. While the N protein forms spherical assemblies with homopolymeric RNA substrates that do not form base pairing interactions, it forms asymmetric condensates with viral RNA strands. Cross-linking mass spectrometry (CLMS) identified a region that drives interactions between N proteins in condensates, and deletion of this region disrupts phase separation. We also identified small molecules that alter the size and shape of N protein condensates and inhibit the proliferation of SARS-CoV-2 in infected cells. These results suggest that the N protein may utilize biomolecular condensation to package the SARS-CoV-2 RNA genome into a viral particle.

Temperature Dependence of Charge and Spin Transfer in Azurin

The steady-state charge and spin transfer yields were measured for three different Ru-modified azurin derivatives in protein films on silver electrodes. While the charge-transfer yields exhibit weak temperature dependences, consistent with operation of a near activation-less mechanism, the spin selectivity of the electron transfer improves as temperature increases. This enhancement of spin selectivity with temperature is explained by a vibrationally induced spin exchange interaction between the Cu(II) and its chiral ligands. These results indicate that distinct mechanisms control charge and spin transfer within proteins. As with electron charge transfer, proteins deliver polarized electron spins with a yield that depends on the protein's structure. This finding suggests a new role for protein structure in biochemical redox processes.

Explaining Why Farmers Grow Tobacco: Evidence From Malawi, Kenya, and Zambia

INTRODUCTION

Tobacco production continues to increase in low- and middle-income countries creating complications for tobacco control efforts. There is the need to understand and address the global tobacco leaf supply as a means of decreasing tobacco consumption and improving farmers livelihoods in line with Article 17 of the WHO Framework Convention on Tobacco Control. This study aims to understand the reasons why farmers grow tobacco and identify factors that influence these reasons.

METHODS

Primary survey data (N = 1770) collected in Kenya, Malawi, and Zambia in the 2013-2014 farming season. Data analysis uses both descriptive and multinomial logistical regression methods.

RESULTS

Majority of farmers started and are currently growing tobacco because they believed it was the only economically viable crop. Compared with Malawi, farmers in Kenya and Zambia have a 0.2 and 0.4 lower probability of growing tobacco, respectively because they perceive it as the only economically viable crop, but a 0.04 and 0.2 higher probability of growing tobacco, respectively because they believe it is highly lucrative. There are district/county differences in the reasons provided with some districts having a majority of the farmers citing the existence of a ready market or incentives from the tobacco industry. Statistically significant factors influencing these reasons are the educational level and age of the household head, land allocated to tobacco and debts.

CONCLUSION

There is the need to address the unique features of each district to increase successful uptake of alternative livelihoods. One consistent finding is that farmers' perceived economic viability contributes to tobacco growing.

IMPLICATIONS

This study finds that perceived economic viability of tobacco is the dominant factor in the decisions to grow tobacco by smallholder farmers in Malawi, Kenya, and Zambia. There is the need to more deeply understand what contributes to farmers' perceived viability of a crop. Understanding and addressing these factors may increase the successful uptake of alternative livelihoods to tobacco. Furthermore, this study demonstrates that a one-size fits all alternative livelihood intervention is less likely to be effective as each district has unique features affecting farmers' decisions on growing tobacco.

Cadherin preserves cohesion across involuting tissues during C. elegans neurulation

The internalization of the central nervous system, termed neurulation in vertebrates, is a critical step in embryogenesis. Open questions remain regarding how force propels coordinated tissue movement during the process, and little is known as to how internalization happens in invertebrates. We show that in C. elegans morphogenesis, apical constriction in the retracting pharynx drives involution of the adjacent neuroectoderm. HMR-1/cadherin mediates this process via inter-tissue attachment, as well as cohesion within the neuroectoderm. Our results demonstrate that HMR-1 is capable of mediating embryo-wide reorganization driven by a centrally located force generator, and indicate a non-canonical use of cadherin on the basal side of an epithelium that may apply to vertebrate neurulation. Additionally, we highlight shared morphology and gene expression in tissues driving involution, which suggests that neuroectoderm involution in C. elegans is potentially homologous with vertebrate neurulation and thus may help elucidate the evolutionary origin of the brain.

A multi-layered and dynamic apical extracellular matrix shapes the vulva lumen in Caenorhabditis elegans

Biological tubes must develop and maintain their proper diameter to transport materials efficiently. These tubes are molded and protected in part by apical extracellular matrices (aECMs) that line their lumens. Despite their importance, aECMs are difficult to image in vivo and therefore poorly understood. The Caenorhabditis elegans vulva has been a paradigm for understanding many aspects of organogenesis. Here we describe the vulva luminal matrix, which contains chondroitin proteoglycans, Zona Pellucida (ZP) domain proteins, and other glycoproteins and lipid transporters related to those in mammals. Confocal and transmission electron microscopy revealed, with unprecedented detail, a complex and dynamic aECM. Different matrix factors assemble on the apical surfaces of each vulva cell type, with clear distinctions seen between Ras-dependent (1°) and Notch-dependent (2°) cell types. Genetic perturbations suggest that chondroitin and other aECM factors together generate a structured scaffold that both expands and constricts lumen shape.

Shifting from tobacco growing to alternatives in Malawi? A qualitative analysis of policy and perspectives

Tobacco is the primary export commodity in Malawi and an important contributor to foreign earnings. The entrenchment of tobacco interests within government has partly explained why Malawi has lagged in its efforts to address the health consequences of tobacco and has been a vocal opponent of global tobacco control. Despite the extensive historical and entrenched relationship between the economy of Malawi and tobacco production, there have been important shifts at the highest policy levels towards the need to explore diversification in the agricultural sector. There is explicit recognition that alternatives to tobacco production must be pursued. This study provides an analysis of the policies and perspectives that characterize contemporary government approaches to tobacco and alternatives in Malawi by interviewing key government officials working on tobacco policy and reviewing recent policy documents. This research finds that there is openness and movement towards reducing tobacco growing in Malaw, including efforts to reduce tobacco dependency. Rather than a singular tobacco policy discourse in the country, there is a somewhat conflictual set of policies and perspectives on the future of tobacco in Malawi. Informing these policies and perspectives is the interplay between the economics of agricultural production (tobacco vs other crops), global markets (ranging from the ability to generate export earnings to the inability to compete with wealthier countries' non-tobacco crop subsidies) and the lack of developed supply and value chains other than those created by the transnational tobacco industry. The implications for government policy supporting a move away from tobacco dependence are not straightforward: there is a need to fill the supply chain gap for alternative crops, which requires not only strong intersectoral support within the country (and some challenge to the residual pro-tobacco narratives) but also international support.

Systematic Profiling of Full-Length Ig and TCR Repertoire Diversity in Rhesus Macaque through Long Read Transcriptome Sequencing

The diversity of Ig and TCR repertoires is a focal point of immunological studies. Rhesus macaques (Macaca mulatta) are key for modeling human immune responses, placing critical importance on the accurate annotation and quantification of their Ig and TCR repertoires. However, because of incomplete reference resources, the coverage and accuracy of the traditional targeted amplification strategies for profiling rhesus Ig and TCR repertoires are largely unknown. In this study, using long read sequencing, we sequenced four Indian-origin rhesus macaque tissues and obtained high-quality, full-length sequences for over 6000 unique Ig and TCR transcripts, without the need for sequence assembly. We constructed, to our knowledge, the first complete reference set for the constant regions of all known isotypes and chain types of rhesus Ig and TCR repertoires. We show that sequence diversity exists across the entire variable regions of rhesus Ig and TCR transcripts. Consequently, existing strategies using targeted amplification of rearranged variable regions comprised of V(D)J gene segments miss a significant fraction (27-53% and 42-49%) of rhesus Ig/TCR diversity. To overcome these limitations, we designed new rhesus-specific assays that remove the need for primers conventionally targeting variable regions and allow single cell level Ig and TCR repertoire analysis. Our improved approach will enable future studies to fully capture rhesus Ig and TCR repertoire diversity and is applicable for improving annotations in any model organism.

Characterization of gene expression changes over healthy term pregnancies

During pregnancy, women experience numerous physiological changes but, to date, there is limited published data that characterize accompanying changes in gene expression over pregnancy. This study sought to characterize the complexity of the transcriptome over the course of pregnancy among women with healthy pregnancies. Subjects provided a venous blood sample during early (6-15 weeks) and late (22-33 weeks) pregnancy, which was used to isolate peripheral blood mononuclear cells prior to RNA extraction. Gene expression was examined for 63 women with uncomplicated, term deliveries. We evaluated the association between weeks gestation at sample collection and expression of each transcript. Of the 16,311 transcripts evaluated, 439 changed over pregnancy after a Bonferroni correction to account for multiple comparisons. Genes whose expression increased over pregnancy were associated with oxygen transport, the immune system, and host response to bacteria. Characterization of changes in the transcriptome over the course of healthy term pregnancies may enable the identification of genes whose expression predicts complications or adverse outcomes of pregnancy.

Liver macrophage-associated inflammation correlates with SIV burden and is substantially reduced following cART

Liver disease is a leading contributor to morbidity and mortality during HIV infection, despite the use of combination antiretroviral therapy (cART). The precise mechanisms of liver disease during HIV infection are poorly understood partially due to the difficulty in obtaining human liver samples as well as the presence of confounding factors (e.g. hepatitis co-infection, alcohol use). Utilizing the simian immunodeficiency virus (SIV) macaque model, a controlled study was conducted to evaluate the factors associated with liver inflammation and the impact of cART. We observed an increase in hepatic macrophages during untreated SIV infection that was associated with a number of inflammatory and fibrosis mediators (TNFα, CCL3, TGFβ). Moreover, an upregulation in the macrophage chemoattractant factor CCL2 was detected in the livers of SIV-infected macaques that coincided with an increase in the number of activated CD16+ monocyte/macrophages and T cells expressing the cognate receptor CCR2. Expression of Mac387 on monocyte/macrophages further indicated that these cells recently migrated to the liver. The hepatic macrophage and T cell levels strongly correlated with liver SIV DNA levels, and were not associated with the levels of 16S bacterial DNA. Utilizing in situ hybridization, SIV-infected cells were found primarily within portal triads, and were identified as T cells. Microarray analysis identified a strong antiviral transcriptomic signature in the liver during SIV infection. In contrast, macaques treated with cART exhibited lower levels of liver macrophages and had a substantial, but not complete, reduction in their inflammatory profile. In addition, residual SIV DNA and bacteria 16S DNA were detected in the livers during cART, implicating the liver as a site on-going immune activation during antiretroviral therapy. These findings provide mechanistic insights regarding how SIV infection promotes liver inflammation through macrophage recruitment, with implications for in HIV-infected individuals.

Evolutionary divergence of the vertebrate TNFAIP8 gene family: Applying the spotted gar orthology bridge to understand ohnolog loss in teleosts

Comparative functional genomic studies require the proper identification of gene orthologs to properly exploit animal biomedical research models. To identify gene orthologs, comprehensive, conserved gene synteny analyses are necessary to unwind gene histories that are convoluted by two rounds of early vertebrate genome duplication, and in the case of the teleosts, a third round, the teleost genome duplication (TGD). Recently, the genome of the spotted gar, a holostean outgroup to the teleosts that did not undergo this third genome duplication, was sequenced and applied as an orthology bridge to facilitate the identification of teleost orthologs to human genes and to enhance the power of teleosts as biomedical models. In this study, we apply the spotted gar orthology bridge to help describe the gene history of the vertebrate TNFAIP8 family. Members of the TNFAIP8 gene family have been linked to regulation of immune function and homeostasis and the development of multiple cancer types. Through a conserved gene synteny analysis, we identified zebrafish orthologs to human TNFAIP8L1 and TNFAIP8L3 genes and two co-orthologs to human TNFAIP8L2, but failed to identify an ortholog to human TNFAIP8. Through the application of the orthology bridge, we determined that teleost orthologs to human TNFAIP8 genes were likely lost in a genome inversion event after their divergence from their common ancestor with spotted gar. These findings demonstrate the value of this enhanced approach to gene history analysis and support the development of teleost models to study complex questions related to an array of biomedical issues, including immunity and cancer.