Now showing items 41-60 of 5203

    • 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.
    • The homeodomain transcriptional regulator DVE-1 directs a program for synapse elimination during circuit remodeling

      Alexander, Kellianne D; Ramachandran, Shankar; Biswas, Kasturi; Lambert, Christopher M; Russell, Julia; Oliver, Devyn B; Armstrong, William; Rettler, Monika; Liu, Samuel; Doitsidou, Maria; et al. (2023-11-18)
      The elimination of synapses during circuit remodeling is critical for brain maturation; however, the molecular mechanisms directing synapse elimination and its timing remain elusive. We show that the transcriptional regulator DVE-1, which shares homology with special AT-rich sequence-binding (SATB) family members previously implicated in human neurodevelopmental disorders, directs the elimination of juvenile synaptic inputs onto remodeling C. elegans GABAergic neurons. Juvenile acetylcholine receptor clusters and apposing presynaptic sites are eliminated during the maturation of wild-type GABAergic neurons but persist into adulthood in dve-1 mutants, producing heightened motor connectivity. DVE-1 localization to GABAergic nuclei is required for synapse elimination, consistent with DVE-1 regulation of transcription. Pathway analysis of putative DVE-1 target genes, proteasome inhibitor, and genetic experiments implicate the ubiquitin-proteasome system in synapse elimination. Together, our findings define a previously unappreciated role for a SATB family member in directing synapse elimination during circuit remodeling, likely through transcriptional regulation of protein degradation processes.
    • Association between microbiome and the development of adverse posttraumatic neuropsychiatric sequelae after traumatic stress exposure

      Zeamer, Abigail L; Salive, Marie-Claire; An, Xinming; Beaudoin, Francesca L; House, Stacey L; Stevens, Jennifer S; Zeng, Donglin; Neylan, Thomas C; Clifford, Gari D; Linnstaedt, Sarah D; et al. (2023-11-18)
      Patients exposed to trauma often experience high rates of adverse post-traumatic neuropsychiatric sequelae (APNS). The biological mechanisms promoting APNS are currently unknown, but the microbiota-gut-brain axis offers an avenue to understanding mechanisms as well as possibilities for intervention. Microbiome composition after trauma exposure has been poorly examined regarding neuropsychiatric outcomes. We aimed to determine whether the gut microbiomes of trauma-exposed emergency department patients who develop APNS have dysfunctional gut microbiome profiles and discover potential associated mechanisms. We performed metagenomic analysis on stool samples (n = 51) from a subset of adults enrolled in the Advancing Understanding of RecOvery afteR traumA (AURORA) study. Two-, eight- and twelve-week post-trauma outcomes for post-traumatic stress disorder (PTSD) (PTSD checklist for DSM-5), normalized depression scores (PROMIS Depression Short Form 8b) and somatic symptom counts were collected. Generalized linear models were created for each outcome using microbial abundances and relevant demographics. Mixed-effect random forest machine learning models were used to identify associations between APNS outcomes and microbial features and encoded metabolic pathways from stool metagenomics. Microbial species, including Flavonifractor plautii, Ruminococcus gnavus and, Bifidobacterium species, which are prevalent commensal gut microbes, were found to be important in predicting worse APNS outcomes from microbial abundance data. Notably, through APNS outcome modeling using microbial metabolic pathways, worse APNS outcomes were highly predicted by decreased L-arginine related pathway genes and increased citrulline and ornithine pathways. Common commensal microbial species are enriched in individuals who develop APNS. More notably, we identified a biological mechanism through which the gut microbiome reduces global arginine bioavailability, a metabolic change that has also been demonstrated in the plasma of patients with PTSD.
    • Dendritic amphiphilic siRNA: Selective albumin binding, efficacy, and low toxicity

      Fakih, Hassan H; Tang, Qi; Summers, Ashley; Shin, Minwook; Buchwald, Julianna E; Gagnon, Rosemary; Hariharan, Vignesh N; Echeverria, Dimas; Cooper, David A; Watts, Jonathan K; et al. (2023-11-17)
      Although an increasing number of small interfering RNA (siRNA) therapies are reaching the market, the challenge of efficient extra-hepatic delivery continues to limit their full therapeutic potential. Drug delivery vehicles and hydrophobic conjugates are being used to overcome the delivery bottleneck. Previously, we reported a novel dendritic conjugate that can be appended efficiently to oligonucleotides, allowing them to bind albumin with nanomolar affinity. Here, we explore the ability of this novel albumin-binding conjugate to improve the delivery of siRNA in vivo. We demonstrate that the conjugate binds albumin exclusively in circulation and extravasates to various organs, enabling effective gene silencing. Notably, we show that the conjugate achieves a balance between hydrophobicity and safety, as it significantly reduces the side effects associated with siRNA interactions with blood components, which are commonly observed in some hydrophobically conjugated siRNAs. In addition, it reduces siRNA monocyte uptake, which may lead to cytokine/inflammatory responses. This work showcases the potential of using this dendritic conjugate as a selective albumin binding handle for the effective and safe delivery of nucleic acid therapeutics. We envision that these properties may pave the way for new opportunities to overcome delivery hurdles of oligonucleotides in future applications.
    • Differential Viral Dynamics by Sex and Body Mass Index During Acute SARS-CoV-2 Infection: Results from a Longitudinal Cohort Study

      Herbert, Carly; Manabe, Yukari C; Filippaios, Andreas; Lin, Honghuang; Wang, Biqi; Achenbach, Chad; Kheterpal, Vik; Hartin, Paul; Suvarna, Thejas; Harman, Emma; et al. (2023-11-16)
      Background: There is evidence of an association of severe COVID-19 outcomes with increased body mass index (BMI) and male sex. However, few studies have examined the interaction between sex and BMI on SARS-CoV-2 viral dynamics. Methods: Participants conducted RT-PCR testing every 24-48 hours over a 15-day period. Sex and BMI were self-reported, and Ct values from E-gene were used to quantify viral load. Three distinct outcomes were examined using mixed effects generalized linear models, linear models, and logistic models, respectively: all Ct values (Model 1); nadir Ct value (model 2); and strongly detectable infection (at least one Ct value ≤28 during their infection) (Model 3). An interaction term between BMI and sex was included, and inverse logit transformations were applied to quantify the differences by BMI and sex using marginal predictions. Results: In total, 7,988 participants enrolled in this study, and 439 participants (Model 1) and 309 (Model 2 and 3) were eligible for these analyses. Among males, increasing BMI was associated with lower Ct values in a dose-response fashion. For participants with BMIs greater than 29, males had significantly lower Ct values and nadir Ct values than females. In total, 67.8% of males and 55.3% of females recorded a strongly detectable infection; increasing proportions of men had Ct values <28 with BMIs of 35 and 40. Conclusions: We observed sex-based dimorphism in relation to BMI and COVID-19 viral load. Further investigation is needed to determine the cause, clinical impact, and transmission implications of this sex-differential effect of BMI on viral load.
    • Addressing Bottlenecks of Prime Editing Through Improved pegRNA Designs and Rationally Engineered Prime Editor Variants

      Ponnienselvan, Karthikeyan (2023-11-15)
      Prime editing systems have enabled the incorporation of precise edits within a genome without introducing double strand breaks. With the versatile ability to introduce point mutations, deletions and insertions, prime editors have the ability to correct around 89% of known genetic variants associated with human diseases. However, there are several bottlenecks currently restricting prime editing activity that need to be addressed to further their use as therapeutics. In the first half of this thesis, we address the auto-inhibitory interaction between the PBS and the spacer sequence that affects pegRNA binding efficiency and target recognition. We show that destabilizing this auto-inhibitory interaction by reducing the complementarity between the PBS-spacer region enhances prime editing efficiency. These design parameters were initially fueled by our goal to improve prime editor ribonucleoprotein activity where the auto-inhibitory interaction of the pegRNA is more prominent, but we show that they can be applied to multiple prime editing formats to increase editing rates. In the case of end-protected pegRNAs, we discover that a shorter PBS length with a PBS-target strand melting temperature near 37°C is optimal in mammalian cells. Additionally, we show that a transient cold shock treatment of the cells post PE-pegRNA delivery further increases prime editing outcomes for pegRNAs with optimized PBS lengths. In the first study, we noticed that the prime editor protein had the tendency to aggregate during purification procedures and that the editing rates were still modest in primary cells. MMLV-reverse transcriptase - the prime editor polymerase subunit - requires high intracellular dNTPs levels for efficient polymerization. Prior optimization of the system has been performed in rapidly dividing cell lines like HEK293Ts where dNTP concentration is not a limiting factor. Primary cells that are quiescent or slowly proliferating have tightly regulated intracellular dNTP levels that could limit the reverse transcription process. Therefore, in the second half of this thesis, we address two more bottlenecks of prime editing - solubility of the prime editor protein and the intracellular dNTP concentration. To address that, in the reverse transcriptase domain, we introduced the L435K mutation that improves the solubility of the protein. Additionally, we introduced a V223M mutation that changes the active site of the reverse transcriptase to resemble a lentiviral enzyme that is more efficient in non-dividing cells. We show that this rationally engineered prime editor variant with increased solubility and lower Km to dNTPs, increases editing rates across diverse cell types and in vivo. Finally, we show that targeted SAMHD1 degradation by co-delivery of VPX to increase dNTP concentration in the cell further increases prime editing rates. We believe that addressing these bottlenecks, with the recommendations we describe in this thesis, will contribute to the advancement of prime editor ribonucleoproteins and mRNA for in vivo and ex vivo therapeutics.
    • 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.
    • MassHealth Social Determinants of Health Risk Adjustment Model: Version 4.0

      Alcusky, Matthew J; Ash, Arlene S.; Eanet, Frances E; Fouayzi, Hassan; Hager, Kurt; Mick, Eric O.; Min, Hye Sung; Sabatino, Meagan J; Williams, Jeffrey (2023-11-09)
      The UMass Chan Medical School has worked with the Massachusetts Executive Office of Health and Human Services to develop risk adjustment tools for the Massachusetts Medicaid Program (MassHealth) since 2014. We have explored how social determinants of health (SDH) factors and medical complexity can be used jointly to predict healthcare cost. The first SDH model was implemented in 2016. It was replaced by SDH version 2.0 in 2018 and SDH versions 3.0 to 3.2 from 2020 through 2023. Here we describe the most recent work on SDH model 4.0, built using calendar year (CY) 2019 data for 1.03 million MassHealth members whose average total cost of care was $5,995. Model 4.0 includes some modifications based on MassHealth’s knowledge of policy and pricing changes that will be in effect in 2024 but had no influence on the 2019 data. Implementation of model 4.0 will start January 1, 2024.
    • Single-cell transcriptomic and genomic changes in the aging human brain [preprint]

      Jeffries, Ailsa M; Yu, Tianxiong; Ziegenfuss, Jennifer S; Tolles, Allie K; Kim, Yerin; Weng, Zhiping; Lodato, Michael A (2023-11-07)
      Aging brings dysregulation of various processes across organs and tissues, often stemming from stochastic damage to individual cells over time. Here, we used a combination of single-nucleus RNA-sequencing and single-cell whole-genome sequencing to identify transcriptomic and genomic changes in the prefrontal cortex of the human brain across life span, from infancy to centenarian. We identified infant-specific cell clusters enriched for the expression of neurodevelopmental genes, and a common down-regulation of cell-essential homeostatic genes that function in ribosomes, transport, and metabolism during aging across cell types. Conversely, expression of neuron-specific genes generally remains stable throughout life. We observed a decrease in specific DNA repair genes in aging, including genes implicated in generating brain somatic mutations as indicated by mutation signature analysis. Furthermore, we detected gene-length-specific somatic mutation rates that shape the transcriptomic landscape of the aged human brain. These findings elucidate critical aspects of human brain aging, shedding light on transcriptomic and genomics dynamics.
    • 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.
    • 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.
    • PARP knockdown promotes synapse reformation after axon injury [preprint]

      Belew, Micah Y; Huang, Wenjia; Florman, Jeremy T; Alkema, Mark J; Byrne, Alexandra B (2023-11-05)
      Injured nervous systems are often incapable of self-repairing, resulting in permanent loss of function and disability. To restore function, a severed axon must not only regenerate, but must also reform synapses with target cells. Together, these processes beget functional axon regeneration. Progress has been made towards a mechanistic understanding of axon regeneration. However, the molecular mechanisms that determine whether and how synapses are formed by a regenerated motor axon are not well understood. Using a combination of in vivo laser axotomy, genetics, and high-resolution imaging, we find that poly (ADP-ribose) polymerases (PARPs) inhibit synapse reformation in regenerating axons. As a result, regenerated parp(-) axons regain more function than regenerated wild-type axons, even though both have reached their target cells. We find that PARPs regulate both axon regeneration and synapse reformation in coordination with proteolytic calpain CLP-4. These results indicate approaches to functionally repair the injured nervous system must specifically target synapse reformation, in addition to other components of the injury response.
    • 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.
    • Cathepsin W, T-cell receptor-associated transmembrane adapter 1, lymphotactin and killer cell lectin like receptor K1 are sensitive and specific RNA biomarkers of canine epitheliotropic lymphoma

      Olayinka, Jadesola Temitope; Nagarkar, Akanksha; Ma, Diana Junyue; Wong, Neil B; Romasco, Andrew; Piedra-Mora, Cesar; Wrijil, Linda; David, Clement N; Gardner, Heather L; Robinson, Nicholas A; et al. (2023-11-03)
      Cutaneous T-cell lymphoma (CTCL) is an uncommon type of lymphoma involving malignant skin-resident or skin-homing T cells. Canine epitheliotropic lymphoma (EL) is the most common form of CTCL in dogs, and it also spontaneously arises from T lymphocytes in the mucosa and skin. Clinically, it can be difficult to distinguish early-stage CTCLs apart from other forms of benign interface dermatitis (ID) in both dogs and people. Our objective was to identify novel biomarkers that can distinguish EL from other forms of ID, and perform comparative transcriptomics of human CTCL and canine EL. Here, we present a retrospective gene expression study that employed archival tissue from biorepositories. We analyzed a discovery cohort of 6 canines and a validation cohort of 8 canines with EL which occurred spontaneously in client-owned companion dogs. We performed comparative targeted transcriptomics studies using NanoString to assess 160 genes from lesional skin biopsies from the discovery cohort and 800 genes from the validation cohort to identify any significant differences that may reflect oncogenesis and immunopathogenesis. We further sought to determine if gene expression in EL and CTCL are conserved across humans and canines by comparing our data to previously published human datasets. Similar chemokine profiles were observed in dog EL and human CTCL, and analyses were performed to validate potential biomarkers and drivers of disease. In dogs, we found enrichment of T cell gene signatures, with upregulation of IFNG, TNF, PRF1, IL15, CD244, CXCL10, and CCL5 in EL in dogs compared to healthy controls. Importantly, CTSW, TRAT1 and KLRK1 distinguished EL from all other forms of interface dermatitis we studied, providing much-needed biomarkers for the veterinary field. XCL1/XCL2 were also highly specific of EL in our validation cohort. Future studies exploring the oncogenesis of spontaneous lymphomas in companion animals will expand our understanding of these disorders. Biomarkers may be useful for predicting disease prognosis and treatment responses. We plan to use our data to inform future development of targeted therapies, as well as for repurposing drugs for both veterinary and human medicine.
    • Changes in Health Care Utilization During the First 2 Years of Massachusetts Medicaid Accountable Care Organizations

      Sabatino, Meagan J; Mick, Eric O.; Ash, Arlene S.; Himmelstein, Jay; Alcusky, Matthew J (2023-10-30)
      On March 1, 2018, the Massachusetts Medicaid and Children's Health Insurance Program (MassHealth) launched an ambitious accountable care organization (ACO) program that sought to integrate care across the physical, behavioral, functional, and social services continuum while holding ACOs accountable for cost and quality. The study objective was to describe changes in health care utilization among MassHealth members during the pre-ACO baseline (2015-2017) and post-implementation periods (2018 and 2019). Using MassHealth administrative data, the authors conducted a repeated cross-sectional study of MassHealth members enrolled in ACOs during 2015-2019. Rates of primary care visits, all-cause and primary-care sensitive emergency department (ED) visits, ED boarding, hospitalizations, acute unplanned admissions, and readmissions were reported during the baseline period (2015-2017) and year 1 (2018) and year 2 (2019). Primary care visit rates increased for adult members throughout the study period from a baseline mean of 7.2-9.2 per member per year (observed-to-expected [O:E]: 1.16) in 2019. Observed all-cause hospitalization rates fell below expected values with O:E ratios of 0.96 among adults and 0.79 among children in 2018, and 0.96 and 0.92 among adults and children, respectively, in 2019. All-cause ED visit rates increased slightly, and rates of pediatric asthma-related admissions, unplanned admissions for adults with ambulatory care sensitive conditions, and unplanned admissions and ED boarding for adults with substance use disorder and serious mental illness all declined for the study period. These findings are suggestive of utilization shifts to higher-value, lower-cost care under Massachusetts's innovative and comprehensive ACO model.
    • Addressing the dNTP bottleneck restricting prime editing activity [preprint]

      Ponnienselvan, Karthikeyan; Liu, Pengpeng; Nyalile, Thomas; Oikemus, Sarah; Joynt, Anya T; Kelly, Karen; Guo, Dongsheng; Chen, Zexiang; Lee, Jeong Min; Schiffer, Celia A; et al. (2023-10-29)
      Prime editing efficiency is modest in cells that are quiescent or slowly proliferating where intracellular dNTP levels are tightly regulated. MMLV-reverse transcriptase - the prime editor polymerase subunit - requires high intracellular dNTPs levels for efficient polymerization. We report that prime editing efficiency in primary cells and in vivo is increased by mutations that enhance the enzymatic properties of MMLV-reverse transcriptase and can be further complemented by targeting SAMHD1 for degradation.
    • Changes in Antidementia Medications upon Admission to the Nursing Home: Who Decides and Why? Results From a National Survey of Nursing Home Administrators

      Lapane, Kate L; Ott, Brian R; Hargraves, J Lee; Cosenza, Carol; Liang, Shiwei; Alcusky, Matthew J (2023-10-28)
      Objective: Little is known about who is involved and what factors influence changes in antidementia medications for older adults living in nursing homes. The study sought to describe factors associated with initiation and discontinuation of antidementia medications in nursing home residents with dementia. Design: National survey of nursing homes with ≥30 beds; homes with dementia units were oversampled. Settings and participants: Nursing home administrators [eg, Directors of Nursing (DoNs)]. Methods: In 2022, 1293 homes were surveyed (response rate: 26.6%, n = 340). Weighted analyses provided nationally representative results corrected for nonresponse (n = 14,455). Results: DoNs reported that people always/almost always involved in antidementia medication decisions included nursing home prescriber (84.4%), nursing staff (33.2%), family (23.4%), resident (13.8%), community primary care provider (12.1%), and dementia specialist (5.8%). DoNs reported that antidementia medications were much more likely to be initiated if residents (55.8%) and family members (53.2%) wanted antidementia medications, a dementia specialist was involved (51.9%), resident had aggressive behaviors (44.8%), resisted care (31.6%), or had severe physical/cognitive impairment (22.3%). DoNs reported that antidementia medications were much more likely to be discontinued with dementia specialist involvement (46.5%), progression to severe impairment (39.2%), hospice involvement (31.5%), <6 months' prognosis (28.5%), emergence of aggressive behaviors (25.2%), or resisting care (19.0%) and much less likely to be discontinued if residents (30.2%) and family (27.3%) were reluctant to discontinue. One in 6 homes reported that residents had no immediate family/caregivers usually or almost always/always. Conclusions and implications: DoNs report that family/caregivers and dementia specialists have significant influence on antidementia medication decisions in nursing homes, but many residents lack their involvement. Real-world evidence on the risks and benefits of antidementia medications in nursing homes is needed to inform clinical guidance about appropriate use of antidementia medications in nursing homes.
    • Prevalence and predictors of shared decision-making in goals-of-care clinician-family meetings for critically ill neurologic patients: a multi-center mixed-methods study

      Fleming, Victoria; Prasad, Abhinav; Ge, Connie; Crawford, Sybil; Meraj, Shazeb; Hough, Catherine L; Lo, Bernard; Carson, Shannon S; Steingrub, Jay; White, Douglas B; et al. (2023-10-21)
      Background: Shared decision-making is a joint process where patients, or their surrogates, and clinicians make health choices based on evidence and preferences. We aimed to determine the extent and predictors of shared decision-making for goals-of-care discussions for critically ill neurological patients, which is crucial for patient-goal-concordant care but currently unknown. Methods: We analyzed 72 audio-recorded routine clinician-family meetings during which goals-of-care were discussed from seven US hospitals. These occurred for 67 patients with 72 surrogates and 29 clinicians; one hospital provided 49/72 (68%) of the recordings. Using a previously validated 10-element shared decision-making instrument, we quantified the extent of shared decision-making in each meeting. We measured clinicians' and surrogates' characteristics and prognostic estimates for the patient's hospital survival and 6-month independent function using post-meeting questionnaires. We calculated clinician-family prognostic discordance, defined as ≥ 20% absolute difference between the clinician's and surrogate's estimates. We applied mixed-effects regression to identify independent associations with greater shared decision-making. Results: The median shared decision-making score was 7 (IQR 5-8). Only 6% of meetings contained all 10 shared decision-making elements. The most common elements were "discussing uncertainty"(89%) and "assessing family understanding"(86%); least frequent elements were "assessing the need for input from others"(36%) and "eliciting the context of the decision"(33%). Clinician-family prognostic discordance was present in 60% for hospital survival and 45% for 6-month independent function. Univariate analyses indicated associations between greater shared decision-making and younger clinician age, fewer years in practice, specialty (medical-surgical critical care > internal medicine > neurocritical care > other > trauma surgery), and higher clinician-family prognostic discordance for hospital survival. After adjustment, only higher clinician-family prognostic discordance for hospital survival remained independently associated with greater shared decision-making (p = 0.029). Conclusion: Fewer than 1 in 10 goals-of-care clinician-family meetings for critically ill neurological patients contained all shared decision-making elements. Our findings highlight gaps in shared decision-making. Interventions promoting shared decision-making for high-stakes decisions in these patients may increase patient-value congruent care; future studies should also examine whether they will affect decision quality and surrogates' health outcomes.
    • Investigating effects of environmentally acquired epigenetic factors on the mammalian embryo transcriptome

      Krykbaeva, Marina (2023-10-20)
      The major aim of this work is to shed light on epigenetic effects on embryonic development. To this end, we implemented two experimental paradigms. First, we investigated the effect of maternal diet on the embryonic transcriptome. We used in vitro fertilization to isolate gamete-carried factors and single-embryo RNA-Seq to produce a high-resolution data set in 4-cell, morula, and blastocyst embryos, as well as oocytes. We found that although differential expression was observed in most stages of development, these changes were fairly small in size. Likewise, offspring created using an embryo transfer procedure did not exhibit phenotypic differences as a result of maternal diet. However, alterations in gene expression of mitochondrial respiration and lipid and cholesterol metabolism genes were detected in offspring tissue with a clear sex bias. Second, we compared transcriptomes of embryos produced using three methods of fertilization – natural mating (NM), in vitro fertilization (IVF), and intracytoplasmic sperm injection (ICSI) as well as parthenogenesis. The largest differences were detected in IVF embryos, largely in the categories of translation and ribosome biogenesis. ICSI embryos exhibited a small deviation in differentiation-associated gene expression. Parthenogenesis, an embryo-like system with no paternal contributions, resulted in vast expression changes encompassing ~20% of expressed genes and was further used as a model system to confirm a role for sperm-carried RNAs in regulating embryo gene expression. Lastly, this single-embryo data set was used to characterize stochasticity in gene expression and confirm the presence of both “quiet” and “noisy” genes. Overall, we provide two large-scale data sets comprised of hundreds of embryos, which serves as a systematic approach to investigating the effect of epigenetic factors on the embryonic transcriptome.
    • Identifying vulnerabilities in sugar nucleotide metabolism of cancer cells

      Doshi, Mihir B (2023-10-20)
      Cancer cells exhibit elevated metabolic demands, imposing a need for metabolic reprogramming. The aim of the thesis is to identify a targetable metabolic vulnerability using an approach that leverages the altered pathways in cancer cells to induce the accumulation of inherently toxic metabolites to eliminate cancer cells selectively. Through a systematic analysis of transcriptomics and cancer dependency data, we identified UXS1, a Golgi enzyme responsible for converting UDP-glucuronic acid (UDPGA) to UDP-xylose that is conditionally essential in cells expressing high levels of its upstream enzyme UGDH. Here, we demonstrate that UGDH high cancer cells are dependent on UXS1 to prevent excess buildup of UDPGA, generated by UGDH. Excess UDPGA causes disruption of the structure and function of the Golgi, leading to aberrant protein glycosylation and improper protein trafficking of critical glycoproteins within cancer cells. We find that UGDH expression is elevated in various cancers, including lung adenocarcinoma and breast carcinoma. Furthermore, elevating UGDH expression is beneficial to cancer cells, because UDPGA functions as a substrate in the detoxification of chemotherapeutic agents. Therefore, chemo-resistant cells upregulate UGDH expression, enhancing their susceptibility to UXS1 ablation. Consequently, this study reveals the therapeutic potential of targeting UXS1 in cancer treatment, offering a novel approach to exploit the metabolism of sugar nucleotides in cancer cells.