Faculty Bibliography

BACKGROUND:In 2012, the United States Preventative Services Task Force (USPSTF) formally recommended against all Prostate Specific Antigen (PSA) screening for prostate cancer. Our goal was to characterize PSA screening trends in the Veterans Health Administration (VA) before and after the USPSTF recommendation, and to determine if PSA screening was more likely to be ordered based on a Veteran's race or age. METHODS:Using the VA Corporate Data Warehouse, we created 10 annual groups of PSA-eligible men covering 2009-2018. We identified all PSA tests performed in the VA to determine yearly rates of PSA screening. All statistical tests were two-sided. RESULTS:The overall rate of PSA testing in the VA decreased from 63.3% in 2009 to 51.2% in 2018 (p<.001). PSA screening rates varied markedly by age group during our study period, with men aged 70-80 having the highest initial rate and greatest decline (70.6% in 2009 to 48.4% in 2018, p<.001). Men aged 55-69 saw a smaller decline (65.2% in 2009 to 58.9% in 2018, p<.001) while the youngest men, aged 40-54, had an increase in PSA screening (26.2% in 2009 to 37.8 in 2018, p<.001). CONCLUSIONS:In this analysis of PSA screening rates among veterans before and after the 2012 USPSTF recommendation against screening, we found that overall PSA screening decreased only modestly, continuing for more than half of the men in our study. Veterans of different races had similar screening rates, suggesting that VA care may minimize racial disparities. Veterans of varying age experienced significantly different trends in PSA screening.

Although many bacterial species do not possess proteasome systems, the actinobacteria, including the human pathogen Mycobacterium tuberculosis, use proteasome systems for targeted protein removal. Previous structural analyses of the mycobacterial proteasome ATPase Mpa revealed a general structural conservation with the archaeal PAN (proteasome-activating nucleotidase) and eukaryotic proteasomal Rpt1-6 ATPases, such as the N-terminal coiled coil domain, the OB (oligosaccharide/oligonucleotide-binding) domain, and the ATPase domain. However, Mpa has a unique β-grasp domain that in the ADP-bound crystal structure appears to interfere with the docking to the 20S proteasome core particle. Thus, it is unclear how Mpa binds to proteasome core particles. In this report, we show by cryo-EM that the Mpa hexamer in the presence of a degradation substrate and ATP forms a gapped ring, with two out of its six ATPase domains being highly flexible. We found that the linkers between the oligonucleotide binding and ATPase domains undergo conformational changes that are important for function, revealing a previously unappreciated role of the linker region in ATP-hydrolysis-driven protein unfolding. We propose that this gapped ring configuration is an intermediate state that helps rearrange its β-grasp domains and activating C-termini to facilitate engagement with proteasome core particles. This work provides new insights into the crucial process of how an ATPase interacts with a bacterial proteasome protease.

Rationale: MicroRNA-33 post-transcriptionally represses genes involved in lipid metabolism and energy homeostasis. Targeted inhibition of miR-33 increases plasma HDL cholesterol and promotes atherosclerosis regression, in part, by enhancing reverse cholesterol transport and dampening plaque inflammation. However, how miR-33 reshapes the immune microenvironment of plaques remains poorly understood. Objective: To define how miR-33 inhibition alters the dynamic balance and transcriptional landscape of immune cells in atherosclerotic plaques. Methods and Results: We used single cell RNA-sequencing of aortic CD45⁺ cells, combined with immunohistologic, morphometric and flow cytometric analyses to define the changes in plaque immune cell composition, gene expression and function following miR-33 inhibition. We report that anti-miR-33 treatment of Ldlr^-/- mice with advanced atherosclerosis reduced plaque burden and altered the plaque immune cell landscape by shifting the balance of pro- and anti-atherosclerotic macrophage and T cell subsets. By quantifying the kinetic processes that determine plaque macrophage burden, we found that anti-miR-33 reduced levels of circulating monocytes and splenic myeloid progenitors, decreased macrophage proliferation and retention, and promoted macrophage attrition by apoptosis and efferocytotic clearance. scRNA-sequencing of aortic arch plaques showed that anti-miR-33 reduced the frequency of MHCIIhi "inflammatory" and Trem2hi "metabolic" macrophages, but not tissue resident macrophages. Furthermore, anti-miR-33 led to derepression of distinct miR-33 target genes in the different macrophage subsets: in resident and Trem2hi macrophages, anti-miR-33 relieved repression of miR-33 target genes involved in lipid metabolism (e.g., Abca1, Ncoa1, Ncoa2, Crot), whereas in MHCIIhi macrophages, anti-miR-33 upregulated target genes involved in chromatin remodeling and transcriptional regulation. Anti-miR-33 also reduced the accumulation of aortic CD8+ T cells and CD4+ Th1 cells, and increased levels of FoxP3+ regulatory T cells in plaques, consistent with an immune-dampening effect on plaque inflammation. Conclusions: Our results provide insight into the immune mechanisms and cellular players that execute anti-miR-33's atheroprotective actions in the plaque.

Mortality among patients with COVID-19 and respiratory failure is high and there are no known lower airway biomarkers that predict clinical outcome. We investigated whether bacterial respiratory infections and viral load were associated with poor clinical outcome and host immune tone. We obtained bacterial and fungal culture data from 589 critically ill subjects with COVID-19 requiring mechanical ventilation. On a subset of the subjects that underwent bronchoscopy, we also quantified SARS-CoV-2 viral load, analyzed the microbiome of the lower airways by metagenome and metatranscriptome analyses and profiled the host immune response. We found that isolation of a hospital-acquired respiratory pathogen was not associated with fatal outcome. However, poor clinical outcome was associated with enrichment of the lower airway microbiota with an oral commensal ( Mycoplasma salivarium ), while high SARS-CoV-2 viral burden, poor anti-SARS-CoV-2 antibody response, together with a unique host transcriptome profile of the lower airways were most predictive of mortality. Collectively, these data support the hypothesis that 1) the extent of viral infectivity drives mortality in severe COVID-19, and therefore 2) clinical management strategies targeting viral replication and host responses to SARS-CoV-2 should be prioritized.

Over-accumulation of oxalate in humans may lead to nephrolithiasis and nephrocalcinosis. Humans lack endogenous oxalate degradation pathways (ODP), but intestinal microbes can degrade oxalate using multiple ODPs and protect against its absorption. The exact oxalate-degrading taxa in the human microbiota and their ODP have not been described. We leverage multi-omics data (>3000 samples from >1000 subjects) to show that the human microbiota primarily uses the type II ODP, rather than type I. Further, among the diverse ODP-encoding microbes, an oxalate autotroph, Oxalobacter formigenes, dominates this function transcriptionally. Patients with Inflammatory Bowel Disease (IBD) frequently suffer from disrupted oxalate homeostasis and calcium oxalate nephrolithiasis. We show that the enteric oxalate level is elevated in IBD patients, with highest levels in Crohn's disease patients with both ileal and colonic involvement consistent with known nephrolithiasis risk. We show that the microbiota ODP expression is reduced in IBD patients, which may contribute to the disrupted oxalate homeostasis. The specific changes in ODP expression by several important taxa suggest that they play distinct roles in IBD-induced nephrolithiasis risk. Lastly, we colonize mice that are maintained in the gnotobiotic facility with O. formigenes, using either a laboratory isolate or an isolate we cultured from human stools, and observed a significant reduction in host fecal and urine oxalate levels, supporting our in silico prediction of the importance of the microbiome, particularly O. formigenes in host oxalate homeostasis.

B-cell non-Hodgkin lymphoma cell survival depends on poorly understood immune evasion mechanisms. In melanoma, the composition of the gut microbiota (GMB) is associated with immune system regulation and response to immunotherapy. We investigated the association of GMB composition and diversity with lymphoma biology and treatment outcome. Patients with diffuse large B-cell lymphoma (DLBCL), marginal zone (MZL), and follicular lymphoma (FL) were recruited at Mayo Clinic, Minnesota, and Perlmutter Cancer Center, NYU Langone Health. The pretreatment GMB was analyzed using 16S ribosomal RNA gene sequencing. We examined GMB compositions in 3 contexts: lymphoma patients (51) compared with healthy controls (58), aggressive (DLBCL) (8) compared with indolent (FL, MZL) (18), and the association of GMB with immunochemotherapy treatment outcomes (8 responders, 6 nonresponders). Respectively, we found that the pretreatment GMB in lymphoma patients had a distinct composition compared with healthy controls (P < .001); GMB compositions in DLBCL patients were significantly different than indolent patients (P = .01) with a trend toward reduced microbial diversity in DLBCL patients (P = .08); and pretreatment GMB diversity and composition were significant predictors of treatment responses (P = .01). The impact of these pilot results is limited by our small sample size, and should be considered a proof of principle. If validated, our results could lead toward improved treatment outcomes by improving medication stewardship and informing which GMB-targeted therapies should be tested to improve patient outcomes.

Mortality among patients with COVID-19 and respiratory failure is high and there are no known lower airway biomarkers that predict clinical outcome. We investigated whether bacterial respiratory infections and viral load were associated with poor clinical outcome and host immune tone. We obtained bacterial and fungal culture data from 589 critically ill subjects with COVID-19 requiring mechanical ventilation. On a subset of the subjects that underwent bronchoscopy, we also quantified SARS-CoV-2 viral load, analyzed the microbiome of the lower airways by metagenome and metatranscriptome analyses and profiled the host immune response. We found that isolation of a hospital-acquired respiratory pathogen was not associated with fatal outcome. However, poor clinical outcome was associated with enrichment of the lower airway microbiota with an oral commensal ( Mycoplasma salivarium ), while high SARS-CoV-2 viral burden, poor anti-SARS-CoV-2 antibody response, together with a unique host transcriptome profile of the lower airways were most predictive of mortality. Collectively, these data support the hypothesis that 1) the extent of viral infectivity drives mortality in severe COVID-19, and therefore 2) clinical management strategies targeting viral replication and host responses to SARS-CoV-2 should be prioritized.

The microbiome plays an important role in human health by mediating the path from environmental exposures to health outcomes. The relative abundances of the high-dimensional microbiome data have an unit-sum restriction, rendering standard statistical methods in the Euclidean space invalid. To address this problem, we use the isometric log-ratio transformations of the relative abundances as the mediator variables. To select significant mediators, we consider a closed testing-based selection procedure with desirable confidence. Simulations are provided to verify the effectiveness of our method. As an illustrative example, we apply the proposed method to study the mediation effects of murine gut microbiome between subtherapeutic antibiotic treatment and body weight gain, and identify Coprobacillus and Adlercreutzia as two significant mediators.

BACKGROUND:Black men are disproportionately affected by prostate cancer, the most common non-cutaneous malignancy among men in the USA. The United States Preventive Services Task Force (USPSTF) encourages prostate-specific antigen (PSA) testing decisions to be based on shared decision-making (SDM) clinician professional judgment, and patient preferences. However, evidence suggests that SDM is underutilized in clinical practice, especially among the most vulnerable patients. The purpose of this study is to evaluate the efficacy of a community health worker (CHW)-led decision-coaching program to facilitate SDM for prostate cancer screening among Black men in the primary care setting, with the ultimate aim of improving/optimizing decision quality. METHODS:We proposed a CHW-led decision-coaching program to facilitate SDM for prostate cancer screening discussions in Black men at a primary care FQHC. This study enrolled Black men who were patients at the participating clinical site and up to 15 providers who cared for them. We estimated to recruit 228 participants, ages 40-69 to be randomized to either (1) a decision aid along with decision coaching on PSA screening from a CHW or (2) receiving a decision aid along with CHW-led interaction on modifying dietary and lifestyle to serve as an attention control. The independent randomization process was implemented within each provider and we controlled for age by dividing patients into two strata: 40-54 years and 55-69 years. This sample size sufficiently powered the detection differences in the primary study outcomes: knowledge, indicative of decision quality, and differences in PSA screening rates. Primary outcome measures for patients will be decision quality and decision regarding whether to undergo PSA screening. Primary outcome measures for providers will be acceptability and feasibility of the intervention. We will examine how decision coaching about prostate cancer screening impact patient-provider communication. These outcomes will be analyzed quantitatively through objective, validated scales and qualitatively through semi-structured, in-depth interviews, and thematic analysis of clinical encounters. Through a conceptual model combining elements of the Preventative Health Care Model (PHM) and Informed Decision-Making Model, we hypothesize that the prostate cancer screening decision coaching intervention will result in a preference-congruent decision and decisional satisfaction. We also hypothesize that this intervention will improve physician satisfaction with counseling patients about prostate cancer screening. DISCUSSION/CONCLUSIONS:Decision coaching is an evidence-based approach to improve decision quality in many clinical contexts, but its efficacy is incompletely explored for PSA screening among Black men in primary care. Our proposal to evaluate a CHW-led decision-coaching program for PSA screening has high potential for scalability and public health impact. Our results will determine the efficacy, cost-effectiveness, and sustainability of a CHW intervention in a community clinic setting in order to inform subsequent widespread dissemination, a critical research area highlighted by USPSTF. TRIAL REGISTRATION/BACKGROUND:The trial was registered prospectively with the National Institute of Health registry ( www.clinicaltrials.gov ), registration number NCT03726320 , on October 31, 2018.

In lung cancer, enrichment of the lower airway microbiota with oral commensals commonly occurs and ex vivo models support that some of these bacteria can trigger host transcriptomic signatures associated with carcinogenesis. Here, we show that this lower airway dysbiotic signature was more prevalent in group IIIB-IV TNM stage lung cancer and is associated with poor prognosis, as shown by decreased survival among subjects with early stage disease (I-IIIA) and worse tumor progression as measured by RECIST scores among subjects with IIIB-IV stage disease. In addition, this lower airway microbiota signature was associated with upregulation of IL-17, PI3K, MAPK and ERK pathways in airway transcriptome, and we identified Veillonella parvula as the most abundant taxon driving this association. In a KP lung cancer model, lower airway dysbiosis with V. parvula led to decreased survival, increased tumor burden, IL-17 inflammatory phenotype and activation of checkpoint inhibitor markers.