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  Functional genomics reveals an off-target dependency of drug synergy in gastric cancer therapy [preprint]

  Leylek, Ozen; Honeywell, Megan E; Lee, Michael J; Hemann, Michael T; Ozcan, Gulnihal (2023-11-19)

  The rational combination of anticancer agents is critical to improving patient outcomes in cancer. Nonetheless, most combination regimens in the clinic result from empirical methodologies disregarding insight into the mechanism of action and missing the opportunity to improve therapy outcomes incrementally. Deciphering the genetic dependencies and vulnerabilities responsible for synergistic interactions is crucial for rationally developing effective anticancer drug combinations. Hence, we screened pairwise pharmacological interactions between molecular-targeted agents and conventional chemotherapeutics and examined the genome-scale genetic dependencies in gastric adenocarcinoma cell models. Since this type of cancer is mainly chemoresistant and incurable, clinical situations demand effective combination strategies. Our pairwise combination screen revealed SN38/erlotinib as the drug pair with the most robust synergism. Genome-wide CRISPR screening and a shRNA-based signature assay indicated that the genetic dependency/vulnerability signature of SN38/erlotinib is the same as SN38 alone. Additional investigation revealed that the enhanced cell death with improved death kinetics caused by the SN38/erlotinib combination is surprisingly due to erlotinib's off-target effect that inhibits ABCG2 but not its on-target effect on EGFR. Our results confirm that a genetic dependency signature different from the single-drug application may not be necessary for the synergistic interaction of molecular-targeted agents with conventional chemotherapeutics in gastric adenocarcinoma. The findings also demonstrated the efficacy of functional genomics approaches in unveiling biologically validated mechanisms of pharmacological interactions.
• Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors

  Boby, Melissa L; Fearon, Daren; Ferla, Matteo; Filep, Mihajlo; Koekemoer, Lizbé; Robinson, Matthew C; Chodera, John D; Lee, Alpha A; London, Nir; von Delft, Annette; et al. (2023-11-10)

  We report the results of the COVID Moonshot, a fully open-science, crowdsourced, and structure-enabled drug discovery campaign targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease. We discovered a noncovalent, nonpeptidic inhibitor scaffold with lead-like properties that is differentiated from current main protease inhibitors. Our approach leveraged crowdsourcing, machine learning, exascale molecular simulations, and high-throughput structural biology and chemistry. We generated a detailed map of the structural plasticity of the SARS-CoV-2 main protease, extensive structure-activity relationships for multiple chemotypes, and a wealth of biochemical activity data. All compound designs (>18,000 designs), crystallographic data (>490 ligand-bound x-ray structures), assay data (>10,000 measurements), and synthesized molecules (>2400 compounds) for this campaign were shared rapidly and openly, creating a rich, open, and intellectual property-free knowledge base for future anticoronavirus drug discovery.
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  Trends in COVID-19 vaccine administration across visit types in a safety net pediatric practice during the first year of authorization

  Ryan, Grace W; Goulding, Melissa; Beeler, Angela L; Nazarian, Beverly L; Pbert, Lori; Rosal, Milagros C; Lemon, Stephenie C (2023-11-06)

  We explored patterns of COVID-19 vaccination across pediatric visit types using electronic health record data from 7/1/2021 through 7/25/2022 in a pediatric safety-net clinic. We generated frequencies and descriptive statistics for patient demographic and vaccine administration variables. Analyses were stratified into age subgroups of 5-to-11-year-olds and 12- to-17-year-olds. 1,409 children received at least one dose of the COVID-19 vaccine and 2,197 doses were administered in this first year of vaccine delivery. Most vaccines given were first doses in the series (45%), followed by second doses (38%), and then booster doses (17%). First doses tended to be given at well-child (42%) or nurse visits (48%), while second doses were almost entirely given at nurse visits (87%) and booster doses at well-child visits (58%). Efforts to optimize COVID-19 vaccination could leverage clinic workflow systems to provide reminder prompts for vaccination for scheduling future doses and identify strategies to facilitate vaccination at non-well child visits, particularly for booster doses.
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  Distinct members of the C. elegans CeMbio reference microbiota exert cryptic virulence and infection protection [preprint]

  Gonzalez, Xavier; Irazoqui, Javier E (2023-11-05)

  Microbiotas are complex microbial communities that colonize specific niches in the host and provide essential organismal functions that are important in health and disease. A key aspect is the ability of each distinct community member to promote or impair host health, alone or in the context of the community, in hosts with varied levels of immune competence. Understanding such interactions is limited by the complexity and experimental accessibility of current systems and models. Recently, a reference twelve-member microbiota for the model organism C. elegans, known as CeMbio, was defined to aid the dissection of conserved host-microbiota interactions. Understanding the physiological impact of the CeMbio bacteria on C. elegans is in its infancy. Here, we show the differential ability of each CeMbio bacterial species to activate innate immunity through the conserved PMK-1/p38 MAPK, ACh/WNT, and HLH-30/TFEB pathways. Using immunodeficient animals, we uncovered several examples of bacterial 'cryptic' virulence, or virulence that was masked by the host defense response. The ability to activate the PMK-1/p38 pathway did not correlate with bacterial virulence in wild type or immunodeficient animals. In contrast, ten out of twelve species activated HLH-30/TFEB, and most showed virulence towards hlh-30-deficient animals. In addition, we identified Pseudomonas lurida as a pathogen in wild type animals, and Acinetobacter guillouiae as avirulent despite activating all three pathways. Moreover, short pre-exposure to A. guillouiae promoted host survival of infection with P. lurida, which was dependent on PMK-1/p38 MAPK and HLH-30/TFEB. These results suggest that the microbiota of C. elegans is rife with "opportunistic" pathogens, and that HLH-30/TFEB is a fundamental and key host protective factor. Furthermore, they support the idea that bacteria like A. guillouiae evolved the ability to induce host innate immunity to improve host fitness when confronted with pathogens, providing new insights into how colonization order impacts host health.
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  Lipofuscin-like autofluorescence within microglia and its impact on studying microglial engulfment

  Stillman, Jacob M; Mendes Lopes, Francisco; Lin, Jing-Ping; Hu, Kevin; Reich, Daniel S; Schafer, Dorothy P (2023-11-03)

  Engulfment of cellular material and proteins is a key function for microglia, a resident macrophage of the central nervous system (CNS). Among the techniques used to measure microglial engulfment, confocal light microscopy has been used the most extensively. Here, we show that autofluorescence (AF) likely due to lipofuscin (lipo-AF) and typically associated with aging, can also be detected within microglial lysosomes in the young mouse brain by light microscopy. This lipo-AF signal accumulates first within microglia and it occurs earliest in white versus gray matter. Importantly, in gray matter, lipo-AF signal can confound the interpretation of antibody-labeled synaptic material within microglia in young adult mice. We further show that there is an age-dependent accumulation of lipo-AF inside and outside of microglia, which is not affected by amyloid plaques. We finally implement a robust and cost-effective strategy to quench AF in mouse, marmoset, and human brain tissue.
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  Non-canonical amino acid incorporation into AAV5 capsid enhances lung transduction in mice

  Chang, Hao; Du, Ailing; Jiang, Jun; Ren, Lingzhi; Liu, Nan; Zhou, Xuntao; Liang, Jialing; Gao, Guangping; Wang, Dan (2023-10-07)

  Gene therapy using recombinant adeno-associated virus (rAAV) relies on safe, efficient, and precise in vivo gene delivery that is largely dependent on the AAV capsid. The proteinaceous capsid is highly amenable to engineering using a variety of approaches, and most resulting capsids carry substitutions or insertions comprised of natural amino acids. Here, we incorporated a non-canonical amino acid (ncAA), Nε-2-azideoethyloxycarbonyl-L-lysine (also known as NAEK), into the AAV5 capsid using genetic code expansion, and serendipitously found that several NAEK-AAV5 vectors transduced various cell lines more efficiently than the parental rAAV5. Furthermore, one NAEK-AAV5 vector showed lung-specific transduction enhancement following systemic or intranasal delivery in mice. Structural modeling suggests that the long side chain of NAEK may impact on the 3-fold protrusion on the capsid surface that plays a key role in tropism, thereby modulating vector transduction. Recent advances in genetic code expansion have generated synthetic proteins carrying an increasing number of ncAAs that possess diverse biological properties. Our study suggests that ncAA incorporation into the AAV capsid may confer novel vector properties, opening a new and complementary avenue to gene therapy vector discovery.
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  Integrating Equity Into Bicycle Infrastructure, Planning, and Programming: A Mixed Methods Exploration of Implementation Among Participants in the Bicycle Friendly Community Program

  Lemon, Stephenie C; Neptune, Amelia; Goulding, Melissa; Pendharkar, Jyothi Ananth; Dugger, Roddrick; Chriqui, Jamie F (2023-10-05)

  Introduction: Integrating equity considerations into bicycle infrastructure, planning, and programming is essential to increase bicycling and reduce physical inactivity-related health disparities. However, little is known about communities' experiences with activities that promote equity considerations in bicycle infrastructure, planning, and programming or about barriers and facilitators to such considerations. The objective of this project was to gain in-depth understanding of the experiences, barriers, and facilitators that communities encounter with integrating equity considerations into bicycle infrastructure, planning, and programming. Methods: We administered a web-based survey in 2022 to assess communities' experiences with 31 equity-focused activities in 3 areas: 1) community engagement, education, events, and programming (community engagement); 2) data collection, evaluation, and goal setting (data); and 3) infrastructure, facilities, and physical amenities (infrastructure). Respondents were people who represented communities in the US that participated in the League of American Bicyclists' Bicycle Friendly Community (BFC) Program. We then conducted 6 focus groups with a subset of survey respondents to explore barriers and facilitators to implementing equity-focused activities. Results: Survey respondents (N = 194) had experience with a mean (SD) of 5.9 (5.7) equity-focused activities. Focus group participants (N = 30) identified themes related to community engagement (outreach to and engagement of underrepresented communities, cultural perceptions of bicycling, and funding and support for community rides and programs); data (locally relevant data); and infrastructure (political will, community design, and infrastructure). They described barriers and facilitators for each. Conclusion: Communities are challenged with integrating equity into bicycle infrastructure, planning, and programming. Multicomponent strategies with support from entities such as the BFC program will be required to make progress.
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  PAM-flexible genome editing with an engineered chimeric Cas9

  Zhao, Lin; Koseki, Sabrina R T; Silverstein, Rachel A; Amrani, Nadia; Peng, Christina; Kramme, Christian; Savic, Natasha; Pacesa, Martin; Rodríguez, Tomás C; Stan, Teodora; et al. (2023-10-04)

  CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a broad-targeting Cas9 possessing an NRN > NYN (R = A or G, Y = C or T) PAM preference, with the N-terminus of Sc + +, a Cas9 with simultaneously broad, efficient, and accurate NNG editing capabilities, to generate a chimeric enzyme with highly flexible PAM preference: SpRYc. We demonstrate that SpRYc leverages properties of both enzymes to specifically edit diverse PAMs and disease-related loci for potential therapeutic applications. In total, the approaches to generate SpRYc, coupled with its robust flexibility, highlight the power of integrative protein design for Cas9 engineering and motivate downstream editing applications that require precise genomic positioning.
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  Measuring The Enduring Imprint Of Structural Racism On American Neighborhoods

  Dyer, Zachary; Alcusky, Matthew J; Galea, Sandro; Ash, Arlene S. (2023-10-03)

  A long history of discriminatory policies in the United States has created disparities in neighborhood resources that shape ethnoracial health inequities today. To quantify these differences, we organized publicly available data on forty-two variables at the census tract level within nine domains affected by structural racism: built environment, criminal justice, education, employment, housing, income and poverty, social cohesion, transportation, and wealth. Using data from multiple sources at several levels of geography, we developed scores in each domain, as well as a summary score that we call the Structural Racism Effect Index. We examined correlations with life expectancy and other measures of health for this index and other commonly used area-based indices. The Structural Racism Effect Index was more strongly associated with each health outcome than were the other indices. Its domain and summary scores can be used to describe differences in social risk factors, and they provide powerful new tools to guide policies and investments to advance health equity.
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  Beyond genome-wide association studies: Investigating the role of noncoding regulatory elements in primary sclerosing cholangitis

  Pratt, Henry E; Wu, Tong; Elhajjajy, Shaimae I; Zhou, Jeffrey Y.; Fitzgerald, Kate; Fazzio, Tom; Weng, Zhiping; Pratt, Daniel S (2023-09-27)

  Background: Genome-wide association studies (GWAS) have identified 30 risk loci for primary sclerosing cholangitis (PSC). Variants within these loci are found predominantly in noncoding regions of DNA making their mechanisms of conferring risk hard to define. Epigenomic studies have shown noncoding variants broadly impact regulatory element activity. The possible association of noncoding PSC variants with regulatory element activity has not been studied. We aimed to (1) determine if the noncoding risk variants in PSC impact regulatory element function and (2) if so, assess the role these regulatory elements have in explaining the genetic risk for PSC. Methods: Available epigenomic datasets were integrated to build a comprehensive atlas of cell type-specific regulatory elements, emphasizing PSC-relevant cell types. RNA-seq and ATAC-seq were performed on peripheral CD4+ T cells from 10 PSC patients and 11 healthy controls. Computational techniques were used to (1) study the enrichment of PSC-risk variants within regulatory elements, (2) correlate risk genotype with differences in regulatory element activity, and (3) identify regulatory elements differentially active and genes differentially expressed between PSC patients and controls. Results: Noncoding PSC-risk variants are strongly enriched within immune-specific enhancers, particularly ones involved in T-cell response to antigenic stimulation. In total, 250 genes and >10,000 regulatory elements were identified that are differentially active between patients and controls. Conclusions: Mechanistic effects are proposed for variants at 6 PSC-risk loci where genotype was linked with differential T-cell regulatory element activity. Regulatory elements are shown to play a key role in PSC pathophysiology.
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  Identifying new players in structural synaptic plasticity through dArc1 interrogation

  Xiao, Cong; M'Angale, P Githure; Wang, Shuhao; Lemieux, Adrienne; Thomson, Travis (2023-09-27)

  The formation, expansion, and pruning of synapses, known as structural synaptic plasticity, is needed for learning and memory, and perturbation of plasticity is associated with many neurological disorders and diseases. Previously, we observed that the Drosophila homolog of Activity-regulated cytoskeleton-associated protein (dArc1), forms a capsid-like structure, associates with its own mRNA, and is transported across synapses. We demonstrated that this transfer is needed for structural synaptic plasticity. To identify mRNAs that are modified by dArc1 in presynaptic neuron and postsynaptic muscle, we disrupted the expression of dArc1 and performed genomic analysis with deep sequencing. We found that dArc1 affects the expression of genes involved in metabolism, phagocytosis, and RNA-splicing. Through immunoprecipitation we also identified potential mRNA cargos of dArc1 capsids. This study suggests that dArc1 acts as a master regulator of plasticity by affecting several distinct and highly conserved cellular processes.
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  Awake intracerebroventricular delivery and safety assessment of oligonucleotides in a large animal model

  Benatti, Hector Ribeiro; Prestigiacomo, Rachel D; Taghian, Toloo; Miller, Rachael; King, Robert; Gounis, Matthew J; Celik, Ugur; Bertrand, Stephanie; Tuominen, Susan; Bierfeldt, Lindsey; et al. (2023-09-26)

  Oligonucleotide therapeutics offer great promise in the treatment of previously untreatable neurodegenerative disorders; however, there are some challenges to overcome in pre-clinical studies. (1) They carry a well-established dose-related acute neurotoxicity at the time of administration. (2) Repeated administration into the cerebrospinal fluid may be required for long-term therapeutic effect. Modifying oligonucleotide formulation has been postulated to prevent acute toxicity, but a sensitive and quantitative way to track seizure activity in pre-clinical studies is lacking. The use of intracerebroventricular (i.c.v.) catheters offers a solution for repeated dosing; however, fixation techniques in large animal models are not standardized and are not reliable. Here we describe a novel surgical technique in a sheep model for i.c.v. delivery of neurotherapeutics based on the fixation of the i.c.v. catheter with a 3D-printed anchorage system composed of plastic and ceramic parts, compatible with magnetic resonance imaging, computed tomography, and electroencephalography (EEG). Our technique allowed tracking electrical brain activity in awake animals via EEG and video recording during and for the 24-h period after administration of a novel oligonucleotide in sheep. Its anchoring efficiency was demonstrated for at least 2 months and will be tested for up to a year in ongoing studies.
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  Association of neighborhood-level sociodemographic factors with Direct-to-Consumer (DTC) distribution of COVID-19 rapid antigen tests in 5 US communities

  Herbert, Carly; Shi, Qiming; Baek, Jonggyu; Wang, Biqi; Kheterpal, Vik; Nowak, Christopher; Suvarna, Thejas; Singh, Aditi; Hartin, Paul; Durnam, Basyl; et al. (2023-09-22)

  Background: Many interventions for widescale distribution of rapid antigen tests for COVID-19 have utilized online, direct-to-consumer (DTC) ordering systems; however, little is known about the sociodemographic characteristics of home-test users. We aimed to characterize the patterns of online orders for rapid antigen tests and determine geospatial and temporal associations with neighborhood characteristics and community incidence of COVID-19, respectively. Methods: This observational study analyzed online, DTC orders for rapid antigen test kits from beneficiaries of the Say Yes! Covid Test program from March to November 2021 in five communities: Louisville, Kentucky; Indianapolis, Indiana; Fulton County, Georgia; O'ahu, Hawaii; and Ann Arbor/Ypsilanti, Michigan. Using spatial autoregressive models, we assessed the geospatial associations of test kit distribution with Census block-level education, income, age, population density, and racial distribution and Census tract-level Social Vulnerability Index. Lag association analyses were used to measure the association between online rapid antigen kit orders and community-level COVID-19 incidence. Results: In total, 164,402 DTC test kits were ordered during the intervention. Distribution of tests at all sites were significantly geospatially clustered at the block-group level (Moran's I: p < 0.001); however, education, income, age, population density, race, and social vulnerability index were inconsistently associated with test orders across sites. In Michigan, Georgia, and Kentucky, there were strong associations between same-day COVID-19 incidence and test kit orders (Michigan: r = 0.89, Georgia: r = 0.85, Kentucky: r = 0.75). The incidence of COVID-19 during the current day and the previous 6-days increased current DTC orders by 9.0 (95% CI = 1.7, 16.3), 3.0 (95% CI = 1.3, 4.6), and 6.8 (95% CI = 3.4, 10.2) in Michigan, Georgia, and Kentucky, respectively. There was no same-day or 6-day lagged correlation between test kit orders and COVID-19 incidence in Indiana. Conclusions: Our findings suggest that online ordering is not associated with geospatial clustering based on sociodemographic characteristics. Observed temporal preferences for DTC ordering can guide public health messaging around DTC testing programs.
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  Nanoparticle delivery of innate immune agonists combines with senescence-inducing agents to mediate T cell control of pancreatic cancer [preprint]

  Chibaya, Loretah; Lusi, Christina F; DeMarco, Kelly D; Kane, Griffin I; Brassil, Meghan L; Parikh, Chaitanya N; Murphy, Katherine C; Li, Junhui; Naylor, Tiana E; Cerrutti, Julia; et al. (2023-09-18)

  Pancreatic ductal adenocarcinoma has quickly risen to become the 3rd leading cause of cancer-related death. This is in part due to its fibrotic tumor microenvironment (TME) that contributes to poor vascularization and immune infiltration and subsequent chemo- and immunotherapy failure. Here we investigated an innovative immunotherapy approach combining local delivery of STING and TLR4 innate immune agonists via lipid-based nanoparticles (NPs) co-encapsulation with senescence-inducing RAS-targeted therapies that can remodel the immune suppressive PDAC TME through the senescence-associated secretory phenotype. Treatment of transplanted and autochthonous PDAC mouse models with these regimens led to enhanced uptake of NPs by multiple cell types in the PDAC TME, induction of type I interferon and other pro-inflammatory signaling, increased antigen presentation by tumor cells and antigen presenting cells, and subsequent activation of both innate and adaptive immune responses. This two-pronged approach produced potent T cell-driven and Type I interferon-dependent tumor regressions and long-term survival in preclinical PDAC models. STING and TLR4-mediated Type I interferon signaling were also associated with enhanced NK and CD8+ T cell immunity in human PDAC. Thus, combining localized immune agonist delivery with systemic tumor-targeted therapy can synergize to orchestrate a coordinated innate and adaptive immune assault to overcome immune suppression and activate durable anti-tumor T cell responses against PDAC.
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  A brown fat-enriched adipokine, ASRA, is a leptin receptor antagonist that stimulates appetite [preprint]

  Huang, Lei; Liu, Pengpeng; Du, Yong; Pan, Dongning; Lee, Alexandra; Wolfe, Scot A; Wang, Yong-Xu (2023-09-12)

  The endocrine control of food intake remains incompletely understood, and whether the leptin receptor-mediated anorexigenic pathway in the hypothalamus is negatively regulated by a humoral factor is unknown. Here we identify an appetite-stimulating factor - ASRA - that acts as a leptin receptor antagonist. ASRA encodes an 8 kD protein that is abundantly and selectively expressed in adipose tissue and to a lesser extent, in liver, and is upregulated during fasting and cold. ASRA protein associates with autophagosomes and its secretion is induced by energy deficiency. Overexpression of ASRA in mice attenuates leptin receptor signaling leading to elevated blood glucose and development of severe hyperphagic obesity, whereas either adipose- or liver-specific ASRA knockout mice display increased leptin sensitivity, improved glucose homeostasis, reduced food intake, and resistance to high fat diet-induced obesity. Furthermore, ASRA is indispensable for cold-evoked feeding response. Recombinant ASRA (rASRA) protein binds to leptin receptor and suppresses leptin receptor signaling in cultured cells. In vivo, rASRA promotes food intake and increases blood glucose in a leptin receptor signaling-dependent manner. Our studies collectively show that ASRA, acting as a peripheral signal of energy deficit, stimulates appetite and regulates glucose metabolism by antagonizing leptin receptor signaling, thus revealing a previously unknown endocrine mechanism that has important implications for our understanding of leptin resistance.
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  CD20 is a mammalian odorant receptor expressed in a subset of olfactory sensory neurons that mediates innate avoidance of predators [preprint]

  Jiang, Hao-Ching; Park, Sung Jin; Wang, I-Hao; Bear, Daniel M; Nowlan, Alexandra; Greer, Paul L (2023-09-12)

  The mammalian olfactory system detects and discriminates between millions of odorants to elicit appropriate behavioral responses. While much has been learned about how olfactory sensory neurons detect odorants and signal their presence, how specific innate, unlearned behaviors are initiated in response to ethologically relevant odors remains poorly understood. Here, we show that the 4-transmembrane protein CD20, also known as MS4A1, is expressed in a previously uncharacterized subpopulation of olfactory sensory neurons in the main olfactory epithelium of the murine nasal cavity and functions as a mammalian odorant receptor that recognizes compounds produced by mouse predators. While wild-type mice avoid these predator odorants, mice genetically deleted of CD20 do not appropriately respond. Together, this work reveals a novel CD20-mediated odor-sensing mechanism in the mammalian olfactory system that triggers innate behaviors critical for organismal survival.
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  Paying for Medical and Social Complexity in Massachusetts Medicaid

  Alcusky, Matthew J; Mick, Eric O.; Allison, Jeroan J.; Kiefe, Catarina I; Sabatino, Meagan J; Eanet, Frances E; Ash, Arlene S. (2023-09-05)

  Importance: The first MassHealth Social Determinants of Health payment model boosted payments for groups with unstable housing and those living in socioeconomically stressed neighborhoods. Improvements were designed to address previously mispriced subgroups and promote equitable payments to MassHealth accountable care organizations (ACOs). Objective: To develop a model that ensures payments largely follow observed costs for members with complex health and/or social risks. Design, setting, and participants: This cross sectional study used administrative data for members of the Massachusetts Medicaid program MassHealth in 2016 or 2017. Participants included members who were eligible for MassHealth's managed care, aged 0 to 64 years, and enrolled for at least 183 days in 2017. A new total cost of care model was developed and its performance compared with 2 earlier models. All models were fit to 2017 data (most recent available) and validated on 2016 data. Analyses were begun in February 2019 and completed in January 2023. Exposures: Model 1 used age-sex categories, a diagnosis-based morbidity relative risk score (RRS), disability, serious mental illness, substance use disorder, housing problems, and neighborhood stress. Model 2 added an interaction for unstable housing with RRS. Model 3 added rurality and updated diagnosis-based RRS, medication-based RRS, and interactions between sociodemographic characteristics and morbidity. Main outcome and measures: Total 2017 annual cost was modeled and overall model performance (R2) and fair pricing of subgroups evaluated using observed-to-expected (O:E) ratios. Results: Among 1 323 424 members, mean (SD) age was 26.4 (17.9) years, 53.4% were female (46.6% male), and mean (SD) 2017 cost was $5862 ($15 417). The R2 for models 1, 2, and 3 was 52.1%, 51.5%, and 60.3%, respectively. Earlier models overestimated costs for members without behavioral health conditions (O:E ratios 0.94 and 0.93 for models 1 and 2, respectively) and underestimated costs for those with behavioral health conditions (O:E ratio >1.10); model 3 O:E ratios were near 1.00. Model 3 was better calibrated for members with housing problems, those with children, and those with high morbidity scores. It reduced underpayments to ACOs whose members had high medical and social complexity. Absolute and relative model performance were similar in 2016 data. Conclusions and relevance: In this cross-sectional study of data from Massachusetts Medicaid, careful modeling of social and medical risk improved model performance and mitigated underpayments to safety-net systems.
• COVID-19 in the intensive care unit: Unmasking the critical factors impacting patient survival

  Srichawla, Bahadar S; Quast, Jared; Pacut, Peter; Sivakumar, Shravan; Garcia-Dominguez, Maria A; Belgrad, Jillian; Panda, Ashwin; Carbone, Sara; Sanders, Delia T; Min, Eli; et al. (2023-08-31)

  In the midst of the coronavirus disease 2019 (COVID-19) pandemic, intensive care units (ICUs) around the world have been pushed to their limits as they grapple with the effects of the severe acute respiratory syndrome coronavirus 2 virus. Identifying prognostic factors that influence mortality in COVID-19 patients admitted to the ICU could offer valuable insights for clinicians seeking to prevent disease progression. A retrospective analysis was conducted on COVID-19 patients admitted to the ICU between January and September 2020. The analysis considered patient demographics, comorbidities, neurological and non-neurological symptoms, as well as laboratory markers. The multivariate logistic regression analysis aims to uncover associations between these factors and patient outcomes. Of the 387 patients included in this study, nearly half (48.5%) of the ICU patients succumbed to COVID-19. Factors that contributed to increased mortality included being 60 years of age or older, impaired consciousness, lung disease, elevated international normalized ratio (INR), and elevated blood urea nitrogen (BUN) levels. Surprisingly, symptoms such as dizziness/lightheadedness, myalgia, and headache were associated with a higher likelihood of survival. In addition, elevated D-dimer and aspartate aminotransferase (AST) levels, as well as lymphopenia, were more commonly observed in deceased patients. The study concluded that those who died in the ICU tended to be older, white, and burdened with more comorbidities and impaired consciousness. With the intriguing link between specific symptoms and survival, further research is essential to uncover the underlying pathophysiological mechanisms that influence ICU patient outcomes in the context of COVID-19.
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  Anxiety and Depression Among US Nursing Home Residents with Chronic Obstructive Pulmonary Disease

  Osundolire, Seun; Goldberg, Robert J; Lapane, Kate L (2023-08-28)

  Background: Chronic obstructive pulmonary disease (COPD) is highly prevalent among nursing home residents; however, few studies have focused on the psychological impact of this clinically significant condition on nursing home residents. Objective: We examine the prevalence of, and factors associated with, anxiety and depression in nursing home residents with COPD. Methods: Using the US 2018 Minimum Dataset (MDS), we conducted a cross-sectional study among 239,615 residents aged ≥50 years old in US Medicare/Medicaid certified nursing homes with COPD. Anxiety and depression were diagnosed based on clinical diagnoses, physical examination findings, and treatment orders. Multivariable adjusted Poisson models with a generalized estimating equations approach account for the clustering among residents within nursing homes. Results: The average age of the study population was 79 years (SD: 10.6), 62.0% were women, and 43.7% had five or more comorbid conditions. In this population, 37.2% had anxiety, 57.6% had depression, and 27.5% had both mental health conditions. Women, current tobacco users, persons 50-64 years old, those who reported having moderate or severe pain, and nursing home residents with multimorbidity were more likely to have anxiety or depression than respective comparison groups. Conclusion: Anxiety and depression are common among US nursing home residents with COPD. Women, medically complex patients, and those who report having moderate-to-severe pain appear to be more likely to have anxiety and depression. Clinical teams should be aware of these findings when managing nursing home residents with COPD and use various nonpharmacological and medical interventions for the effective management of anxiety and depression. Longitudinal studies evaluating how anxiety and depression affect the management of COPD and related outcomes, and how best to improve the quality of life of nursing home residents with COPD, are warranted.
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  A comparative analysis of microglial inducible Cre lines

  Faust, Travis E; Feinberg, Philip A; O'Connor, Ciara; Kawaguchi, Riki; Chan, Andrew; Strasburger, Hayley; Frosch, Maximilian; Boyle, Margaret A; Masuda, Takahiro; Amann, Lukas; et al. (2023-08-26)

  Cre/loxP technology has revolutionized genetic studies and allowed for spatial and temporal control of gene expression in specific cell types. Microglial biology has particularly benefited because microglia historically have been difficult to transduce with virus or electroporation methods for gene delivery. Here, we investigate five of the most widely available microglial inducible Cre lines. We demonstrate varying degrees of recombination efficiency, cell-type specificity, and spontaneous recombination, depending on the Cre line and inter-loxP distance. We also establish best practice guidelines and protocols to measure recombination efficiency, particularly in microglia. There is increasing evidence that microglia are key regulators of neural circuits and major drivers of a broad range of neurological diseases. Reliable manipulation of their function in vivo is of utmost importance. Identifying caveats and benefits of all tools and implementing the most rigorous protocols are crucial to the growth of the field and the development of microglia-based therapeutics.

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