Understanding racial differences in financial hardship among older adults surviving cancer.

BACKGROUND: Despite Medicare coverage, financial hardship is a prevalent issue among those diagnosed with cancer at age 65 years and older, particularly among those belonging to a racial or ethnic minority group. Sociodemographic, clinical, and area-level factors may mediate this relationship; however, no studies have assessed the extent to which these factors contribute to the racial/ethnic disparities in financial hardship. METHODS: Surveys assessing financial hardship were completed by 721 White (84%) or Black (16%) patients (aged 65 years and older) who were diagnosed with breast (34%), prostate (27%), lung (17%), or colorectal (14%) cancer or lymphoma (9%) at the University of Alabama at Birmingham between 2000 and 2019. Financial hardship included material, psychological, and behavioral domains. Nonlinear Blinder-Oaxaca effect decomposition methods were used to evaluate the extent to which individual and area-level factors contribute to racial disparities in financial hardship. RESULTS: Black patients reported lower income (65% vs. 34% earning <$50,000) and greater scores on the Area Deprivation Index (median, 93.0 vs. 55.0). Black patients reported significantly higher rates of overall (39% vs. 18%), material (29% vs. 11%), and psychological (27% vs. 11%) hardship compared with White patients. Overall, the observed characteristics explained 51% of racial differences in financial hardship among cancer survivors, primarily because of differences in income (23%) and area deprivation (11%). CONCLUSIONS: The current results identify primary contributors to racial disparities in financial hardship among older cancer survivors, which can be used to develop targeted interventions and allocate resources to those at greatest risk for financial hardship.

Testing a Brief Quitline Intervention for Tobacco Cannabis Co-Users: A Randomized Controlled Pilot Study.

Background: Tobacco cannabis co-use is common and becoming more prevalent. Frequent and heavy users of cannabis may struggle to quit smoking. Quitlines offer free cessation treatment in the United States and 25% of quitline callers may also be cannabis users. The present paper describes a randomized pilot study of a tailored intervention for cannabis and cigarette co-users. The intervention combines the quitline smoking cessation treatment with a motivational enhancement therapy-based cannabis intervention. Methods: The randomized pilot study was conducted within four state-funded quitlines with quitline coaches as interventionists. 102 quitline callers who were cannabis and cigarette co-users were randomized to receive treatment as usual (TAU) or the new Quitline Check-Up (QLCU) intervention. Outcomes were collected 90 days post-randomization. Primary outcomes included feasibility and acceptability of delivering the QLCU in the quitline setting. Secondary outcomes included 7-day point prevalence tobacco abstinence, past 30-day cannabis use, and Cannabis Use Disorder Identification Test scores. Results: Study participants were heavy cannabis users, averaging 25 days of use in the past 30; nearly 70% used at a level considered hazardous. Fidelity ratings indicated coaches were successful at delivering the intervention. Treatment engagement was high for both groups (TAU m = 3.4 calls; QLCU m = 3.6 calls) as was treatment satisfaction. Intent-to-treat quit rates (with survey non-responders classified as smokers) were 28.6% for the TAU control group and 24.5% for the QLCU group (P = .45). Discussion: Hazardous cannabis use rates were high in this sample of tobacco cannabis co-users calling quitlines to quit smoking. The intervention for co-users was acceptable and feasible to deliver. No improvements in tobacco cessation outcomes were observed. Pragmatic intervention development within a real-world clinical setting can streamline the intervention development process. More research is needed on tobacco cannabis co-users and who can benefit from a tailored intervention. Registered: ClinicalTrials.gov NCT04737772, February 4, 2021.

Reconstitution of the alternative pathway of the complement system enables rapid delineation of the mechanism of action of novel inhibitors.

The complement system plays a critical role in the innate immune response, acting as a first line of defense against invading pathogens. However, dysregulation of the complement system is implicated in the pathogenesis of numerous diseases, ranging from Alzheimer's to age-related macular degeneration (AMD) and rare blood disorders. As such, complement inhibitors have enormous potential to alleviate disease burden. While a few complement inhibitors are in clinical use, there is still a significant unmet medical need for the discovery and development of novel inhibitors to treat patients suffering from disorders of the complement system. A key hurdle in the development of complement inhibitors has been the determination of their mechanism of action. Progression along the complement cascade involves the formation of numerous multimeric protein complexes, creating the potential for inhibitors to act at multiple nodes in the pathway. This is especially true for molecules that target the central component C3 and its fragment C3b, which serve a dual role as a substrate for the C3 convertases and as a scaffolding protein in both the C3 and C5 convertases. Here, we report a step-by-step in vitro reconstitution of the complement alternative pathway using bio-layer interferometry. By physically uncoupling each step in the pathway, we were able to determine the kinetic signature of inhibitors that act at single steps in the pathway and delineate the full mechanism of action of known and novel C3 inhibitors. The method could have utility in drug discovery and further elucidating the biochemistry of the complement system.

Fasting and postprandial plasma metabolite responses to a 12-week dietary intervention in tissue-specific insulin resistance: a secondary analysis of the PERSON randomized trial.

BACKGROUND: We previously showed that dietary intervention effects on cardiometabolic health were driven by tissue-specific insulin resistance (IR) phenotype: individuals with predominant muscle IR (MIR) benefitted more from a low-fat, high-protein, high-fiber diet (LFHP), while individuals with predominant liver IR (LIR) benefitted more from a diet rich in mono-unsaturated fat (HMUFA). OBJECTIVE: To further characterize the effects of LFHP and HMUFA diets and their interaction with tissue-specific IR, we investigated dietary intervention effects on fasting and postprandial plasma metabolite profile. METHODS: Adults with MIR or LIR (40-75 years, BMI 25-40 kg/m2) were randomized to a 12-week HMUFA or LFHP diet (n=242). After exclusion of statin use, 214 participants were included in this pre-specified secondary analysis. Plasma samples were collected before (T=0) and after (T=30, 60, 120, 240 min) a high-fat mixed meal for quantification of 247 metabolite measures using nuclear magnetic resonance spectroscopy. RESULTS: A larger reduction in fasting VLDL-TAG and VLDL particle size was observed in individuals with MIR following the LFHP diet and those with LIR following the HMUFA diet, although no longer statistically significant after false discovery rate (FDR) adjustment. No IR phenotype-diet interactions were found for postprandial plasma metabolites assessed as total area under the curve (tAUC). Irrespective of IR phenotype, the LFHP diet induced greater reductions in postprandial plasma tAUC of the larger VLDL particles and small HDL particles, and TAG content in most VLDL subclasses and the smaller LDL and HDL subclasses (e.g. VLDL-TAG tAUC standardized mean change [95% CI] LFHP = -0.29 [-0.43, -0.16] compared to HMUFA = -0.04 [-0.16, 0.09]; FDR-adjusted P for Diet x Time = 0.041). CONCLUSIONS: Diet effects on plasma metabolite profiles were more pronounced than phenotype-diet interactions. A LFHP diet may be more effective than a HMUFA diet for reducing cardiometabolic risk in individuals with tissue-specific IR, irrespective of IR phenotype. GOV REGISTRATION: NCT03708419, https://clinicaltrials.gov/study/NCT03708419?term=NCT03708419&rank=1 CCMO REGISTRATION: NL63768.068.17, https://www.toetsingonline.nl/to/ccmo_search.nsf/fABRpop?readform&unids=3969AABCD9BA27FEC12587F1001BCC65.

Educating Families on Urgent Maternal Warning Signs: Learning From a Pilot to Improve Training and Tools for Maternal and Child Home Visiting Programs.

Early recognition of the warning signs of pregnancy-related complications and provision of timely, quality care could prevent many maternal deaths. We piloted a maternal warning signs education intervention with five Maryland-based maternal, infant, and early childhood home visiting programs serving populations disproportionately affected by adverse maternal outcomes. The intervention included a 1.5-hr online training for home visitors, monthly collaborative calls with program managers, and a client education toolkit with a 3-min video, illustrated handout of 15 urgent maternal warning signs, magnet with the same, and discussion guide for home visitor-client interactions. A mixed-methods formative evaluation assessed the acceptability, feasibility, and utilization of different components of the intervention. Home visiting program staff reported that the materials were highly acceptable and easily understood by diverse client populations. They valued the illustrations, simple language, and translation of materials in multiple languages. Program managers found implementation a relatively simple process, feasible for in-person and remote visits. Despite positive reception, not all components of the toolkit were used consistently. Program managers and staff also identified the need for more guidance and tools to help clients communicate with health care providers and advocate for their health care needs. Feedback from pilot sites was used to adapt the training and tools, including adding content on patient self-advocacy. Home visiting programs have a unique ability to engage families during pregnancy and the postpartum period. This pilot offers lessons learned on strategies and tools that home visiting programs can use to improve early recognition and care-seeking for urgent maternal warning signs.

Barriers to resection following neoadjuvant chemotherapy for resectable pancreatic adenocarcinoma: A national and local perspective.

BACKGROUND: Neoadjuvant chemotherapy (NAC) use for pancreatic ductal adenocarcinoma (PDAC) has increased, but some patients never get resection following NAC. METHODS: Data from January 2012 to December 2019 for all clinically resectable patients across two health networks were utilized, as well as data from the ACS NCDB registry. Univariate testing, multivariable logistic regression, and survival analyses were employed to evaluate failure to resection after neo-adjuvant chemotherapy. RESULTS: Of the 10 007 registry patients eligible for resection, the resected group was younger (64.6 vs. 69.5 years; p < 0.001) and had a slightly lower mean comorbidity index (0.41 vs. 0.45; p < 0.001) than the nonsurgical group. The nonsurgical group was composed of a higher percentage of Black and Hispanic patients (17.5 vs. 13.1%; p < 0.001). After adjusting for age and comorbidities, the factors associated with decreased probability of resection after NAC were evaluation at a community hospital (OR 2.4), Black or Hispanic race (OR 1.6), areas of increased high school drop-out rates (OR 1.4), and lack of private health insurance (OR 1.3). The median overall survival for nonsurgery was markedly worse than the surgical cohort (10.6 vs. 26.6 months; p < 0.001). The most frequent reasons for a lack of definitive resection were operative upstaging to unresectable (39.6%), patient preference (14.5%), progression on NAC (13.2%), deconditioning or comorbidity severity (12.5%), and nonreferral to a surgeon (8.8%). CONCLUSIONS: Racial, economic, and educational disparities have a considerable influence on the successful completion of a neoadjuvant approach for resectable PDAC. A comprehensive closed or highly collaborative/communicative multidisciplinary neoadjuvant program is optimal for treatment success and completion.

GNN Codon Adjacency Tunes Protein Translation.

The central dogma treats the ribosome as a molecular machine that reads one mRNA codon at a time as it adds each amino acid to its growing peptide chain. However, this and previous studies suggest that ribosomes actually perceive pairs of adjacent codons as they take three-nucleotide steps along the mRNA. We examined GNN codons, which we find are surprisingly overrepresented in eukaryote protein-coding open reading frames (ORFs), especially immediately after NNU codons. Ribosome profiling experiments in yeast revealed that ribosomes with NNU at their aminoacyl (A) site have particularly elevated densities when NNU is immediately followed (3') by a GNN codon, indicating slower mRNA threading of the NNU codon from the ribosome's A to peptidyl (P) sites. Moreover, if the assessment was limited to ribosomes that have only recently arrived at the next codon, by examining 21-nucleotide ribosome footprints (21-nt RFPs), elevated densities were observed for multiple codon classes when followed by GNN. This striking translation slowdown at adjacent 5'-NNN GNN codon pairs is likely mediated, in part, by the ribosome's CAR surface, which acts as an extension of the A-site tRNA anticodon during ribosome translocation and interacts through hydrogen bonding and pi stacking with the GNN codon. The functional consequences of 5'-NNN GNN codon adjacency are expected to influence the evolution of protein coding sequences.

Recent Advancements in Bone Tissue Engineering: Integrating Smart Scaffold Technologies and Bio-Responsive Systems for Enhanced Regeneration.

In exploring the challenges of bone repair and regeneration, this review evaluates the potential of bone tissue engineering (BTE) as a viable alternative to traditional methods, such as autografts and allografts. Key developments in biomaterials and scaffold fabrication techniques, such as additive manufacturing and cell and bioactive molecule-laden scaffolds, are discussed, along with the integration of bio-responsive scaffolds, which can respond to physical and chemical stimuli. These advancements collectively aim to mimic the natural microenvironment of bone, thereby enhancing osteogenesis and facilitating the formation of new tissue. Through a comprehensive combination of in vitro and in vivo studies, we scrutinize the biocompatibility, osteoinductivity, and osteoconductivity of these engineered scaffolds, as well as their interactions with critical cellular players in bone healing processes. Findings from scaffold fabrication techniques and bio-responsive scaffolds indicate that incorporating nanostructured materials and bioactive compounds is particularly effective in promoting the recruitment and differentiation of osteoprogenitor cells. The therapeutic potential of these advanced biomaterials in clinical settings is widely recognized and the paper advocates continued research into multi-responsive scaffold systems.

Pharyngeal Mucosal Margin Vessel Counts Predict Pharyngocutaneous Fistula in Salvage Laryngectomy.

OBJECTIVE: We evaluated vessel counts in the pharyngeal mucosal margins of patients who underwent salvage laryngectomy to establish whether mucosal vascularity might predict fistula risk. STUDY DESIGN: Retrospective cohort. SETTING: Tertiary Medical Center. METHODS: Patients who underwent salvage total laryngectomy at our institution between 1999 and 2015 were identified. Pharyngeal mucosal margins from laryngectomy specimens were evaluated histologically for each patient, and vessel counts were performed on 5 ×10 images. The primary outcome measure was fistula within 30 days of surgery and mean vessel counts were assessed as the principle explanatory variable. RESULTS: Seventy patients were included and 40% developed a postoperative fistula. There was a large difference in the mean vessel count in patients who did develop fistula (48.6 vessels/×10 field) compared to those who did not (34.7 vessels/×10 field). A receiver operative characteristic curve found that a cutoff value of 33.9 vessels/×10 field provided a sensitivity of 75% and specificity of 62% to predict the likelihood of fistula occurrence (area under the curve = 0.71, 95% confidence interval [CI]: 0.59-0.83). In a binary logistic regression, patients with vessel counts greater than 33.9 had a 5-fold increased risk of developing fistula (95% CI: 1.8-16.45). Histologically, vessels in the pharyngeal mucosa of patients who developed fistulas were more disorganized. CONCLUSION: After salvage laryngectomy, patients with higher mean mucosal margin vessel counts are at increased risk of fistula. The mechanism is unknown, but the disorganization of the vasculature may contribute to poor wound healing. Vessel counting may allow for fistula risk stratification and guide postoperative care.

Commentary: Engagement for Research and Quality Improvement - More Than Just Words.

We reflect on the paper from Hahn-Goldberg et al. (2024) who shared key learnings from a pan-Canadian quality improvement (QI) and patient engagement care transition initiative called Bridge-to-Home. In considering the approach and outcomes presented in their paper, we have generated reflections and practical suggestions on how to amplify engagement work even further: (1) patient engagement and QI are about relationships; (2) seamlessly implementing complex interventions across siloed organizations continues to be a challenge, which engagement alone cannot solve; (3) it is time for a paradigm shift; (4) QI is about human behaviour change and is inherently messy; and (5) embedding fulsome evaluation of engagement is essential.

Growth of Staphylococcus aureus in the presence of oleic acid shifts the glycolipid fatty acid profile and increases resistance to antimicrobial peptides.

Staphylococcus aureus readily adapts to various environments and quickly develops antibiotic resistance, which has led to an increase in multidrug-resistant infections. Hence, S. aureus presents a significant global health issue and its adaptations to the host environment are crucial for understanding pathogenesis and antibiotic susceptibility. When S. aureus is grown conventionally, its membrane lipids contain a mix of branched-chain and straight-chain saturated fatty acids. However, when unsaturated fatty acids are present in the growth medium, they become a major part of the total fatty acid composition. This study explores the biophysical effects of incorporating straight-chain unsaturated fatty acids into S. aureus membrane lipids. Membrane preparations from cultures supplemented with oleic acid showed more complex differential scanning calorimetry scans than those grown in tryptic soy broth alone. When grown in the presence of oleic acid, the cultures exhibited a transition significantly above the growth temperature, attributed to the presence of glycolipids with long-chain fatty acids causing acyl chain packing frustration within the bilayer. Functional aspects of the membrane were assessed by studying the kinetics of dye release from unilamellar vesicles induced by the antimicrobial peptide mastoparan X. Dye release was slower from liposomes prepared from cells grown in oleic acid-supplemented cultures, suggesting that changes in membrane lipid composition and biophysics protect the cell membrane against peptide-induced lysis. These findings underscore the intricate relationship between the growth environment, membrane lipid composition, and the physical properties of the bacterial membrane, which should be considered when developing new strategies against S. aureus infections.

Racial and Socioeconomic Disparities Exist in Patients Pursuing Peanut Oral Immunotherapy.

BACKGROUND: Oral immunotherapy (OIT) is a promising treatment for food allergy. Prior studies demonstrate significant differences among food-allergic individuals across race, ethnicity, and socioeconomic groups. Disparities in OIT have not been evaluated. OBJECTIVE: We assessed disparities in the use of OIT in patients with peanut allergy based on race, ethnicity, and socioeconomic status at a single academic medical center. METHODS: We identified 1028 peanut-allergic patients younger than 18 years receiving care in the University of Michigan food allergy clinics. Of these, 148 patients who underwent peanut OIT (treatment group) were compared with the 880 patients who avoided peanut (control group). Pertinent demographic and socioeconomic characteristics were compared. RESULTS: There were no differences in gender or ethnicity between the OIT and control groups. However, Black patients comprised 18% of the control group but only 4.1% of the OIT treatment group (P < .0001). The proportion of patients with private insurance was significantly higher in the treatment group compared with the control group (93.2% vs 82.2%, P = .0004). Finally, the neighborhood affluence index, a census-based measure of the relative socioeconomic prosperity of a neighborhood, was significantly higher in the OIT group than the control group (0.51 ± 0.18 vs 0.47 ± 0.19, P = .015), whereas the neighborhood disadvantage index, a census-based measure of the relative socioeconomic disadvantage of a neighborhood, was significantly lower (0.082 ± 0.062 vs 0.10 ± 0.093, P = .020). CONCLUSIONS: Significant racial and economic disparities exist at our institution between peanut-allergic individuals who receive OIT and those who do not. Efforts to understand the basis for these disparities are important to ensure that patients have equitable access to OIT.

Timed up and go demonstrates strong interrater agreement and criterion validity as a functional test in geriatric dogs.

OBJECTIVE: To measure interobserver agreement for 4 functional tasks and their summed geriatric functional score (GFS) and correlate tasks and GFS with client-specific outcome measurements (CSOMs): Canine Brief Pain Inventory (CBPI) pain severity, CBPI pain interference, and Liverpool Osteoarthritis in Dogs. ANIMALS: 89 geriatric dogs were recruited between April and September 2023 from staff, friends, and clients of the Cornell University College of Veterinary Medicine with a median age of 11.0 years and weight of 26.4 kg. METHODS: Dogs underwent 4 sequential functional tests: timed up and go (TUG), cavallettis, figure 8s, and down to stands. Two observers independently scored each dog. The GFS was calculated based on the summed scores of the individual tests. Additional information collected included signalment, weight, measurements reflecting the comorbidities of aging (body condition score and muscle condition score), and CSOMs. RESULTS: Strong interrater agreement was found for all functional tests. The TUG in seconds (sTUG) and figure 8s demonstrated significant (P < .05) moderate to strong correlations to all CSOMs. The GFS showed similar significant correlations with all CSOMs except CBPI pain severity; however, when correlating individual tests to CSOMs, only figure 8s and TUG were significantly contributing to GFS results. Receiver operating characteristic curve analysis defined highly functional dogs as those completing the sTUG in under 3.83 seconds. The sTUG represented the best test for geriatric function given it was objective, reliable, correlated well to CSOMs, and could help identify highly functioning dogs. CLINICAL RELEVANCE: The sTUG appears to be the first practical and reliable functional test of canine geriatric mobility.

The CD8+ T cell tolerance checkpoint triggers a distinct differentiation state defined by protein translation defects.

Peripheral CD8+ T cell tolerance is a checkpoint in both autoimmune disease and anti-cancer immunity. Despite its importance, the relationship between tolerance-induced states and other CD8+ T cell differentiation states remains unclear. Using flow cytometric phenotyping, single-cell RNA sequencing (scRNA-seq), and chromatin accessibility profiling, we demonstrated that in vivo peripheral tolerance to a self-antigen triggered a fundamentally distinct differentiation state separate from exhaustion, memory, and functional effector cells but analogous to cells defectively primed against tumors. Tolerant cells diverged early and progressively from effector cells, adopting a transcriptionally and epigenetically distinct state within 60 h of antigen encounter. Breaching tolerance required the synergistic actions of strong T cell receptor (TCR) signaling and inflammation, which cooperatively induced gene modules that enhanced protein translation. Weak TCR signaling during bystander infection failed to breach tolerance due to the uncoupling of effector gene expression from protein translation. Thus, tolerance engages a distinct differentiation trajectory enforced by protein translation defects.

Spatial and Temporal Resolution of Cyanobacterial Bloom Chemistry Reveals an Open-Ocean Trichodesmium thiebautii as a Talented Producer of Specialized Metabolites.

While the ecological role that Trichodesmium sp. play in nitrogen fixation has been widely studied, little information is available on potential specialized metabolites that are associated with blooms and standing stock Trichodesmium colonies. While a collection of biological material from a T. thiebautii bloom event from North Padre Island, Texas, in 2014 indicated that this species was a prolific producer of chlorinated specialized metabolites, additional spatial and temporal resolution was needed. We have completed these metabolite comparison studies, detailed in the current report, utilizing LC-MS/MS-based molecular networking to visualize and annotate the specialized metabolite composition of these Trichodesmium blooms and colonies in the Gulf of Mexico (GoM) and other waters. Our results showed that T. thiebautii blooms and colonies found in the GoM have a remarkably consistent specialized metabolome. Additionally, we isolated and characterized one new macrocyclic compound from T. thiebautii, trichothilone A (1), which was also detected in three independent cultures of T. erythraeum. Genome mining identified genes predicted to synthesize certain functional groups in the T. thiebautii metabolites. These results provoke intriguing questions of how these specialized metabolites affect Trichodesmium ecophysiology, symbioses with marine invertebrates, and niche development in the global oligotrophic ocean.

Food insecurity in high-risk rural communities before and during the COVID-19 pandemic.

Objective: To perform a geospatial analysis of food insecurity in a rural county known to have poor health outcomes and assess the effect of the COVID-19 pandemic. Methods: In 2020, we mailed a comprehensive cross-sectional survey to all households in Sullivan County, a rural county with the second-worst health outcomes among all counties in New York State. Surveys of households included validated food insecurity screening questions. Questions were asked in reference to 2019, prior to the pandemic, and for 2020, in the first year of the pandemic. Respondents also responded to demographic questions. Raking adjustments were performed using age, sex, race/ethnicity, and health insurance strata to mitigate non-response bias. To identify significant hotspots of food insecurity within the county, we also performed geospatial analysis. Findings: From the 28,284 households surveyed, 20% of households responded. Of 4725 survey respondents, 26% of households reported experiencing food insecurity in 2019, and in 2020, this proportion increased to 35%. In 2020, 58% of Black and Hispanic households reported experiencing food insecurity. Food insecurity in 2020 was also present in 58% of unmarried households with children and in 64% of households insured by Medicaid. The geospatial analyses revealed that hotspots of food insecurity were primarily located in or near more urban areas of the rural county. Conclusions: Our countywide health survey in a high-risk rural county identified significant increases of food insecurity in the first year of the COVID-19 pandemic, despite national statistics reporting a stable rate. Responses to future crises should include targeted interventions to bolster food security among vulnerable rural populations.

Survey of Pharmaceutical Industry's Best Practices around In Vitro Transporter Assessment and Implications for Drug Development: Considerations from the International Consortium for Innovation and Quality for Pharmaceutical Development Transporter Working Group.

The International Consortium for Innovation and Quality in Pharmaceutical Development Transporter Working Group had a rare opportunity to analyze a crosspharma collation of in vitro data and assay methods for the evaluation of drug transporter substrate and inhibitor potential. Experiments were generally performed in accordance with regulatory guidelines. Discrepancies, such as not considering the impact of preincubation for inhibition and free or measured in vitro drug concentrations, may be due to the retrospective nature of the dataset and analysis. Lipophilicity was a frequent indicator of crosstransport inhibition (P-gp, BCRP, OATP1B, and OCT1), with high molecular weight (MW ≥500 Da) also common for OATP1B and BCRP inhibitors. A high level of overlap in in vitro inhibition across transporters was identified for BCRP, OATP1B1, and MATE1, suggesting that prediction of DDIs for these transporters will be common. In contrast, inhibition of OAT1 did not coincide with inhibition of any other transporter. Neutrals, bases, and compounds with intermediate-high lipophilicity tended to be P-gp and/or BCRP substrates, whereas compounds with MW <500 Da tended to be OAT3 substrates. Interestingly, the majority of in vitro inhibitors were not reported to be followed up with a clinical study by the submitting company, whereas those compounds identified as substrates generally were. Approaches to metabolite testing were generally found to be similar to parent testing, with metabolites generally being equally or less potent than parent compounds. However, examples where metabolites inhibited transporters in vitro were identified, supporting the regulatory requirement for in vitro testing of metabolites to enable integrated clinical DDI risk assessment. SIGNIFICANCE STATEMENT: A diverse dataset showed that transporter inhibition often correlated with lipophilicity and molecular weight (>500 Da). Overlapping transporter inhibition was identified, particularly that inhibition of BCRP, OATP1B1, and MATE1 was frequent if the compound inhibited other transporters. In contrast, inhibition of OAT1 did not correlate with the other drug transporters tested.

The complete sequence and comparative analysis of ape sex chromosomes.

Apes possess two sex chromosomes-the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked to infertility1. The X chromosome is vital for reproduction and cognition2. Variation in mating patterns and brain function among apes suggests corresponding differences in their sex chromosomes. However, owing to their repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (bonobo (Pan paniscus), chimpanzee (Pan troglodytes), western lowland gorilla (Gorilla gorilla gorilla), Bornean orangutan (Pongo pygmaeus) and Sumatran orangutan (Pongo abelii)) and a lesser ape (the siamang gibbon (Symphalangus syndactylus)), and untangled the intricacies of their evolution. Compared with the X chromosomes, the ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements-owing to the accumulation of lineage-specific ampliconic regions, palindromes, transposable elements and satellites. Many Y chromosome genes expand in multi-copy families and some evolve under purifying selection. Thus, the Y chromosome exhibits dynamic evolution, whereas the X chromosome is more stable. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of more than 100 individual great apes. These reference assemblies are expected to inform human evolution and conservation genetics of non-human apes, all of which are endangered species.

Placental and Immune Cell DNA Methylation Reference Panel for Bulk Tissue Cell Composition Estimation in Epidemiological Studies.

To distinguish DNA methylation (DNAm) from cell proportion changes in whole placental tissue research, we developed a robust cell type-specific DNAm reference to estimate cell composition. We collated newly collected and existing cell type DNAm profiles quantified via Illumina EPIC or 450k microarrays. To estimate cell composition, we deconvoluted whole placental samples (n=36) with robust partial correlation based on the top 50 hyper- and hypomethylated sites per cell type. To test deconvolution performance, we evaluated RMSE in predicting principal component one of DNAm variation in 204 external placental samples. We analyzed DNAm profiles (n=368,435 sites) from 12 cell types: cytotrophoblasts (n=18), endothelial cells (n=19), Hofbauer cells (n=26), stromal cells (n=21), syncytiotrophoblasts (n=4), six lymphocyte types (n=36), and nucleated red blood cells (n=11). Median cell composition was consistent with placental biology: 60.4% syncytiotrophoblast, 17.1% stromal, 8.8% endothelial, 4.5% cytotrophoblast, 3.9% Hofbauer, 1.7% nucleated red blood cells, and 1.2% neutrophils. Our expanded reference outperformed an existing reference in predicting DNAm variation (15.4% variance explained, IQR=21.61) with cell composition estimates (RMSE:10.51 vs. 11.43, p-value<0.001). This cell type reference can robustly estimate cell composition from whole placental DNAm data to detect important cell types, reveal biological mechanisms, and improve casual inference.