2019ACTRI Pilot Project Recipients

Clinical Research | Life Course Research | Academic-Community Pilot Project | Dissemination and Implementation Research Pilot Project

UC San Diego Altman Clinical and Translational Research Institute (ACTRI) announces the selection of 14 Pilot Project grant awardees for 2019. Pilot Project grants are one-year competitive cash awards for researchers to obtain preliminary data. Recipients were awarded in the categories of clinical and translational research and, for the first time, two were selected in the category of life course research. Funding priority is given to junior faculty members. Below are the 2019 projects.

Funding Period is 2019 through 2020 [pending IRB approval].


Clinical and Translational

PI: Gretchen Bandoli, Ph.D.
UC San Diego Department of Pediatrics

Title: Stress responsive biomarkers as predictors of preterm birth: an examination by maternal race

Preterm birth (prior to 37 weeks of gestation) is a leading cause of neonatal death in the United States, and a risk factor for medical and developmental morbidity that persists into adulthood.1 The large and persistent disparity between preterm birth rates among non-Hispanic White and African American women is well documented. Rates of preterm birth among African American women were 50% higher compared with non-Hispanic White women (14% vs. 9%) in 2016. Unlike non-Hispanic White women, preterm birth rates for African American women are insensitive to increase in socioeconomic status, maternal education, or paternal education.

Many have posited that the disparity in the rate of preterm birth is partially attributable to high levels of chronic stress in African American women. Cortisol, a hormone released as part of the stress-responsive hypothalamus pituitary adrenal (HPA) axis, has been inconsistently associated with preterm birth. Cortisol is critical in fetal development, organ maturation, and timing of parturition, but is strictly regulated by 11β-hydroxysteroid dehydrogenase type 2 (11βHSD2) in the placenta to prevent excess maternal glucocorticoid exposure to the fetus. To date, few studies have assessed stress responsive biomarkers by race in pregnancy, and to our knowledge, none have independently analyzed the role of 11βHSD2 by race. This is important, as chronic stress may lead to blunted cortisol response in African Americans, but still result in similar or higher fetal exposure levels if 11βHSD2 is under-expressed.

Previously, we reported that second-trimester serum cortisol was inversely related to gestational week at delivery; however, the sample size was insufficient to analyze this association by race. The objective of this pilot study is to expand this work in a sample sufficient to investigate this association by race, and include measures of 11βHSD2 as operationalized by the cortisone to cortisol ratio. The central hypothesis of this research is that higher maternal cortisol and lower 11βHSD2 functioning will predict preterm birth, but these patterns will differ by race.

This nested case-control study will utilize birth records and discharge summaries previously collected as part of the University of California San Francisco (UCSF) Preterm Birth Initiative (PTBi; PI: Jelliffe), and will link them to 300 banked maternal serum samples at the California Biobank Program. The samples, collected in the second trimester of pregnancy, will consist of 150 term births and 150 spontaneous preterm births, each selected 1:1 for non-Hispanic White and African American women. Samples will be assayed for cortisol and cortisone, and each biomarker, as well as the ratio, will be assessed to determine whether it predicts preterm birth, and whether these relationships differ by maternal race.

PI: Jill Buckley, M.D.
UC San Diego Department of Urology
(pending NIH approval)

Title: Magnetic Resonance Imaging Evaluation of Urethral Stricture Disease

Retrograde urethrography (RUG) and voiding cystourethrography (VCUG) have been the gold standard imaging modalities for urethral stricture disease for more than 50 years. As a combined approach VCUG and RUG can delineate stricture location and length but offer little further information and have multiple limitations. The quality of a RUG and VCUG are patient, operator, and interpreter dependent.  Obtaining imaging requires a moderate degree of invasiveness with injection of contrast transurethrally for a RUG and either catheterization or use of a suprapubic tube for VCUG. If a strong voiding effort is not made the location of the proximal extent of the stricture is obscured and the stricture location in reference to the external urethral sphincter, the ring of skeletal muscle around the urethra responsible for urinary continenc, is unclear.

VCUG and RUG also do not offer any information on the degree of spongiofibrosis which is a critical element in deciding which surgical repair technique is appropriate. Additionally, both imaging modalities are associated with operator and patient ionizing radiation exposure. This is an especially important consideration in the pediatric patient who is more susceptible to radiation injury.

Urethral magnetic resonance imaging (MRI) represents an opportunity to address the limitations of RUG and VCUG to both improve the quality of urethral imaging and potentially patient surgical outcomes. Definite advantages of MRI over RUG and VCUG include the elimination of diagnostic imaging associated ionizing radiation to patient and provider. The urethral sphincter is identifiable on MRI and the relationship with more proximal strictures, in which surgery could threaten continence, is apparent for patient counseling. Additionally, patient habitus, positioning and voiding effort are eliminated as variables.

Preliminary studies have shown that urethral magnetic resonance urography and RUG combined with VCUG, the current gold standard for urethral stricture evaluation, have similar rates of diagnosis. MRI provides supplemental clinically valuable information in a significant portion of evaluated patients. This includes a more accurate delineation of stricture length and degree of spongiofibrosis.1-3
To date there is very limited further information regarding this promising imaging modality. In collaboration with radiology expert colleagues we will create a urethra specific MRI protocol to evaluate anterior urethral stricture disease in male patients. Accuracy of stricture length will be compared to the information provided by RUG with VCUG and intraoperative findings. The feasibility of delineating urethral stricture disease from the external urinary sphincter will be confirmed. The degree of spongiofibrosis will be evaluated and graded by radiology and urology to begin to create a staging system for urethral stricture severity.

Future work will include application of our findings to a larger cohort to see if the severity of spongiofibrosis on MRI is predictive of endourologic management and urethroplasty outcomes. We hope this work will help surgeons choose an appropriate surgical technique and improve patient outcomes.

PI: Cathleen Collins, M.D., Ph.D.
UC San Diego Department of Pediatrics

Title: Understanding the Role of T Follicular Helper Cells During Vaccination in Children of Different Ages

Children often have difficulty mounting effective immune response to encapsulated bacteria, leading to increased susceptibility to severe sinopulmonary infections caused by bacteria such as Streptococcus pneumoniae and Bordetella pertussis. The cost in terms of morbidity and mortality is staggering; for pertussis in particular, WHO estimated 142,512 cases and 89,000 deaths globally in 2015, but modeling suggests as many as 24 million cases and 160,700 deaths, with children disproportionately affected. There has been a resurgence of pertussis in the United States in the last decade, with California as the leading state in terms of number of cases. In addition, the poor immunogenicity of vaccines in children results in need for multiple booster injections throughout childhood which represents a barrier to vaccination for some children.

The mechanisms for the discrepancy in immune response between children and adults are unclear. T follicular helper (Tfh) cells are an important during the generation of humoral immunity, for providing the necessary "help" to B cells so they can undergo isotype switching and somatic hypermutation, resulting in long-term production of higher affinity antibodies with appropriate effector activities. Since Tfh cells reside typically within lymph nodes, they have been notoriously difficult to study. Dr. Dan's work at the La Jolla Institute of Allergy Immunology has given insight into Tfh responses by identification of cytokine-independent activation markers (AIM) that are specifically increased during antigen responses. Importantly these responses are detectable in peripheral blood in response to vaccination.

The goal of this project is to apply this technique to characterize Tfh responses after vaccination with the pneumococcal protein conjugate vaccine (Prevnar-13), the pneumococcal polysaccharide vaccine (Pneumovax23), and the acellular pertussis vaccine (DTaP and Tdap), in children and adults. We will children sent to the Allergy/Immunology Clinic for evaluation of atopic or immune disorders who are undergoing evaluation with blood tests for these conditions, and perform the AIM assay. We will compare these results with adults over 18 whose blood has already been collected by the La Jolla Institute. We will correlate the AIM responses with data about date of immunization, age of the child, gender and clinical data such as diagnosis of allergies or immune deficiency. We hypothesize that we may see lower Tfh activation in younger children, while teens may be equivalent to adults in percent of cells activated. This hypothesis is important to study since it has been hypothesized that boosting Tfh cell activation may be an effective adjuvant strategy. We will also compare the AIM assay results with antibody titers to see whether there is a correlation between these two tests, and whether this may be another way to study the efficacy of vaccination responses.

PI: Anjan Debnath, Ph.D.
UC San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences

Title: Fexinidazole and its Metabolites: New Drug Leads for Helicobacter pylori Infection

Helicobacter pylori infects more than half of the world's population and is responsible for most cases of inflammatory gastritis, peptic ulcer disease, and gastric cancer. The standard treatment of H. pylori infection involves two antibiotics (clarithromycin plus amoxicillin or metronidazole) and a proton pump inhibitor. However, poor patient compliance, emergence of antibiotic-resistant H. pylori strains, adverse effects, and high cost associated with multiple antibiotics frequently lead to therapy failure. Clearly, new anti-H. pylori treatments with both superior therapeutic efficacy and negligible adverse effects are urgently needed.

We, for the first time, identified potent activity of fexinidazole and its metabolites, fexinidazole sulfoxide and fexinidazole sulfone against H. pylori. We found that a 24-hour incubation of H. pylori with 10 µM fexinidazole completely inhibited their growth whereas same concentration of metronidazole did not inhibit bacterial growth. The effect of both metabolites on the activity of H. pylori was relatively fast, occurring within 12-h of incubation with 2 µM of sulfoxide and sulfone metabolites. We hypothesize that fexinidazole and its metabolites will have efficacy against H. pylori clinical isolates including drug resistant isolates. Using an H. pylori Sydney strain (SS1) mouse model, we will thoroughly evaluate the antimicrobial efficacy and pharmacokinetics of fexinidazole and its metabolites against H. pylori.

The significant impacts of this project lie in two aspects: (i) discovery of an effective and safe drug for treatment of H. pylori, and (ii) repurpose a drug that has already undergone clinical development. This project combines the research expertise and resources of two complementary groups: Dr. Anjan Debnath in SSPPS has expertise in repurposing and development of new antimicrobials for parasitic diseases. Dr. Marygorret Obonyo in the Division of Infectious Diseases has expertise in molecular biology, host immune response, and animal models of H. pylori infection. These two groups have collaborated for 6 months to develop new therapeutics for treating H. pylori infection. Here we will exploit our combined expertise to pursue the following specific aims:

Aim 1: Assess in vitro activity of fexinidazole and fexinidazole metabolites against clinical isolates of H. pylori, drug-resistant H. pylori strains and dormant coccoid form of H. pylori.

SS1, metronidazole-resistant SS1 and clinical isolates (Shi470, Lithuania75, SouthAfrica7, India7, Gambia94/24, PeCan4, and SJM180) will be used in this study.

Aim 2: Evaluate in vivo efficacy of fexinidazole and fexinidazole metabolites for the treatment of H. pylori infection.

C57BL/6 mice will receive H. pylori by oral gavage and three weeks post-infection, mice will be treated with 20 mg/kg and 10 mg/kg of fexinidazole, fexinidazole sulfoxide, fexinidazole sulfone, or vehicle PO once daily for a consecutive 5 days.

Fexinidazole has completed phase II/III clinical trial for the treatment of human African trypanosomiasis, and this will offer decreased risk and shortened development timelines towards clinical use for H. pylori infection. Successful demonstration of efficacy in the proof-of-concept studies will enable further studies on pharmacokinetic using CTRI resources. We will seek extramural funding to conduct studies on pharmacokinetic, potential resistance development and mechanism of action against H. pylori.

PI: Angela Meier, M.D., Ph.D.
UC San Diego Department of Anesthesiology, Division of Critical Care

Title: Impact of Anesthetics on the Antimicrobial Treatment Response of Multi-Drug Resistant Organisms

According to the WHO and the CDC, antibiotic resistance is one of the biggest threats to global health. While risk profiles can vary, infection with antibiotic resistant microbes can affect everyone, including otherwise healthy individuals. With more antibiotic resistant microbes emerging every year, antibiotic treatment options are becoming more and more limited. Treatment success relies, in addition to a functional host defense, on the ability of antibiotics to inhibit growth or kill the offending organism. Patients infected with multi-drug resistant (MDR) organism are frequently treated in the intensive care unit once their infection is severe, many of which need sedation or undergo surgery requiring an anesthetic. With over 40 million anesthetics administered each year in the US alone, anesthetics are amongst commonly used drugs in the critically ill. While their impact on various aspects of the immune system as well as some direct impact on bacterial behaviour has been described, no data exists on their impact on antimicrobial efficacy. Emerging data from our laboratory and others suggest that the extracellular environment can significantly impact antimicrobial activity. Moreover, our preliminary data suggests that anesthetics can impact the minimal inhibitory concentrations of antimicrobials against MDR gram negative bacteria. With this proposal we aim to determine the effect of multiple commonly used anesthetics on the treatment efficacy of multiple antibiotics against several difficult to treat MDR organisms including organisms commonly found in hospitalized patients such as Pseudomonas, Klebsiella, Acinetobacter and Methicillin Resistant Staph Aureus in order to optimize treatment condition for our most vulnerable patients infected with difficult to treat infectious organisms.

We are proposing to use standard MIC testing, kinetic killing, transmission electron microscopy as well as murine pneumonia and bacteremia models in order to determine such impact of anesthetics on antimicrobial resistance. The proposed experiments will be conducted in the laboratory of Prof. Victor Nizet who is an expert in host pathogen interactions and drug discovery. They will be performed in collaboration with Dr. Monika Kumaraswamy from the department of infectious diseases who specializes in the treatment of MDR organisms. The results of our experiments will lay ground for future clinically focused studies with the ultimate goal of optimizing care for our most critically ill by specifically addressing if certain anesthetics should be encouraged or avoided during treatment of severe infections.

PI: Amy Non, M.D., MPH ( Also Daniel T. O’Connor Award Recipient)
UC San Diego, Division of Anthropology

Title: Examining epigenetic effects of stress in developing human neurons

Psychosocial stress has significant and lasting effects on health, potentially through epigenetic pathways early in development. Epigenetics has been defined as the study of stable changes in gene expression, independent of the underlying DNA sequence, that arise during cell development and proliferation (Jaenisch and Bird 2003). The role of epigenetic processes in mediating psychosocial stress exposures early in life is unclear. Evidence is particularly lacking in the key target tissue of the brain, even though neurons have more epigenetic variation, and have more potential to change in response to environmental stimuli than other cells (Iwamoto et al. 2011). Studies of prenatal stress suggest that pregnancy may be a particularly sensitive window to epigenetic change, as cells are proliferating and epigenetic marks are being established (Cao-Lei et al. 2017). However, little is known about methylation in healthy developing neurons during prenatal periods, and most human studies are observational, limiting causal inferences. We propose to address these gaps through a novel experiment to measure methylation using neural progenitor cells (NPCs) and neurons derived from human pluripotent stem cells exposed to the stress hormone cortisone across stages of prenatal development. In our preliminary work, we found that treating NPCs with 100uM of cortisone for 72hrs changed the cell’s expression profile, such that treated cells clustered separately from non-treated cells. We will build off these findings to conduct the first study to examine DNA methylation changes across multiple time points of neural development in response to stress exposure. Our overall goal is to determine how exposure to a stress hormone can alter DNA methylation across the genome in neural progenitors and neurons, and to determine how stable are these changes over time as neurons differentiate. We hypothesize that we will find DNA methylation changes related to stress-related genes and pathways, such as genes that are part of the hypothalamic pituitary adrenal (HPA) axis.

PI: David Pride, M.D., Ph.D.
UC San Diego, Department of Pathology

Title: Assessing the role of high fat derived viruses in gut inflammation and microbiome modulation

The human microbiome is a collection of microorganisms that live on the inner and outer surfaces of the body. Although colloquially referred to as those bacteria that inhabit the body, there are also robust communities of viruses that inhabit these surfaces. Our recent work has uncovered previously unknown aspects of the viral ecology of the human body including that: 1) most of these viral community members are bacteriophages, 2) virome members are highly persistent over time, 3) viruses have individual-and body site-specific features, 4) viruses are shared between contacts such that viruses have the capacity to shape not just or own microbiomes, but those of our close contacts as well. Our discovery that these communities are populated largely by bacteriophages suggests that they have a tremendous capacity to shape host bacterial communities. Despite this hypothesis being around for years now, very few studies have shed light on the potential roles of these viral communities in shaping host microbial communities. This highlights the critical need for translational studies to assess the capacity of viromes to shape the host cellular microbiome and associated phenotypes.

One of the sentinel studies in a microbiome research was performed by Gordon and colleagues, where they transplanted feces from obese into lean mice and observed that lean mice became obese on normal diets. That study highlighted the important role of the bacterial community in metabolic processes and lean/obese phenotypes. Unfortunately, the GI tract virome in those studies went completely ignored. We have identified a strong GI tract viral community phenotype associated with high-fat-diets (HFD), which likely went unrecognized in those prior studies. It is likely that when bacteria were transplanted, billions of viruses also were transplanted and were involved in the development of the obesity phenotype. We hypothesize that viruses in the GI tract play a direct role in shaping the cellular microbiome, and alone are sufficient to reproduce obese phenotypes.

The long-term goal of our work is to identify a role for viruses in driving ecological trends in the lower GI tract that result in host phenotype shifts. In doing so, we can shift the paradigm in microbiome research to account for the often ignored viral communities in driving health- and disease-associated phenotypes. Our specific aims are to: 1) harvest and develop a delivery system and for HFD-virome exposures, 2) identify microbiota changes associated with HFD-virome perturbations, and 3) to assess inflammatory and metabolic changes associated with HFD-virome exposures. Because we already have established a significant viral community phenotype associated with HFD, we believe that through the proposed exploratory experiments, we can establish that HFD-derived viral communities are sufficient to drive inflammatory and obesity-related phenotypes. By doing so, we would uncover aspects of the viral community previously unbeknownst to scientists and open up new avenues of research in pursuit of viromes that may drive health-associated phenotypes.

We believe that demonstrating the role of HFD-derived viral communities will establish a new field in characterizing viruses in human disease-associated phenotypes and lead to NIH funding opportunities.

PI: Stephanie Stanford, Ph.D.
UC San Diego, Department of Medicine
(pending NIH approval)

Title: Exploration of LMPTP as a new target for fibrosis therapy

The objective of this proposal is to obtain pilot evidence that the low molecular weight protein tyrosine phosphatase (LMPTP) is a new target for treatment of systemic sclerosis (SSc). SSc is an autoimmune disease characterized by progressive fibrosis of the skin and internal organs. Novel signaling mediators that promote the pro-fibrotic response by fibroblasts are viewed as potential targets for the development of SSc therapies. While protein kinases – enzymes that phosphorylate proteins- have been extensively studied in pro-fibrotic pathways, very little is known about the roles of the protein phosphatases – enzymes that remove phosphates from proteins-that regulate fibrosis and SSc. We performed a survey of expression levels of all protein tyrosine phosphatases (PTPs) in cultured dermal fibroblasts from SSc patients. We noticed that the phosphate LMPTP is highly expressed in these cells. Since nothing was known about the role of LMPTP in SSc, we sought to explore whether LMPTP regulates pro-fibrotic responses in human dermal fibroblasts. We have preliminary data suggesting that LMPTP inhibition impairs the pro-fibrotic responses in human dermal fibroblasts and that LMPTP knockout mice are protected from development of skin fibrosis. These findings suggest a novel role for LMPTP in promoting collagen deposition and suggest that LMPTP could be a new therapeutic target for SSC and other fibrotic diseases. Here, our goal is to obtain pilot experimental evidence that will enable us to secure long-term funding to assess the potential of LMPTO as an SSc target. We propose to examine LMPTP expression in fibrotic skin samples of SSc patients, to determine if LMPTP promotes pro-fibrotic responses in human lung fibroblasts, and to assess whether pharmacological LMPTP inhibition ameliorates skin fibrosis in vivo. We plan to leverage the findings obtained from this award to secure long-term funding to mere deeply investigate the molecular mechanism of action of LMPTP and to further assess the therapeutic potential of LMPTP for SSc and other fibrotic diseases.

PI:  Tiffany Tanaka, M.D.
UC San Diego, Department of Medicine

Title: Understanding how clonal hematopoiesis mediates cardiovascular risk through targeted exome, single cell transcriptome and epigenome analysis of clonal immune cells

Significance: The prevalence of clonal hematopoiesis (CH), defined by the presence of cancer-associated somatic mutations in nucleated blood cells, is remarkably high, approaching 10-20% of individuals over the age of 70 (Jaiswal NEJM 2014, Genovese NEJM 2014). CH is associated with a small increased risk of developing a hematologic malignancy, and surprisingly, a sizeable mortality risk largely attributed to cardiovascular events. With the UCSD Center for Epigenomics, we acquired the majority of funds needed for a pilot project to investigate the link between CH and cardiovascular disease, but need to cover the cost of sequencing samples to identify those with CH.

Innovation: The mechanisms by which CH mediates hematologic and cardiovascular disease are incompletely understood. A recent analysis of 4 independent populations of >8,000 subjects found that cancer-associated somatic mutations conferred a 1.9-4.0 fold increased risk of coronary artery disease (CAD), comparable to elevated LDL cholesterol or hypertension (Jaiswal NEJM 2017). 67-100% of patients younger than 50 years with mutations in DNMT3A, TET2 and ASXL1 had premature onset CAD, suggesting that these mutations are direct risk factors. The mutated genes are all epigenetic regulators, suggesting that epigenetic and transcriptomic changes contribute to cardiovascular risk. Recent work using transgenic mouse models suggested that CH mutations create a pro-inflammatory phenotype that promotes atherogenesis (Fuster Science 2017), however, the precise mechanisms by which these mutations cause CAD in humans is unknown. I hypothesize that single cell analysis will help us understand how clonal immune cells are unique from non-clonal cells in individuals with CAD, revealing pathways involved in CH-mediated cardiovascular risk with potential to guide risk modification.

Approach: I am applying for funds to cover targeted exome sequencing costs for 80 patients, required to identify the expected 10-20% of patients with a CH mutation. In collaboration with the UCSD Center for Epigenomics, Dr. Chris Glass, Dr. Sotirios Tsimikas and Dr. Rafael Bejar, we have the expertise and funding to complete single-cell (sc) analysis to identify differences in the transcriptome and chromatin accessibility using scRNA-seq and scATAC-seq, respectively, between clonally derived peripheral blood mononuclear cell (PBMC) subpopulations versus non-clonal PBMCs within each individual. We will enroll at least 6 patients with CAD, with and without CH, and 6 patients without CAD, with and without CH, from my and Dr. Bejar’s clinics (IRB #131550) and from the UCSD Cardiovascular Center (Dr. Tsimikas’ IRB 120902).

Interdisciplinary Collaborations: There are no effective therapies or standardized management for patients with CH. To this end, Dr. Bejar and I established the Clonal Hematopoiesis Clinic at UCSD, a multi-disciplinary team dedicated to the longitudinal study of patients with CH. Our clinical and scientific team is comprised of experts in Hematology, Cardiology and Epigenetics.

Future Directions: We will extend our collaboration to profile a more complete spectrum of CH mutations in a larger CAD cohort. We will also apply our techniques to other challenging clinical settings, including how populations of cells with CH mutations progress towards MDS, and how CH clones may expand following chemotherapy for solid and hematologic malignancies.

PI: Wynnis Tom, M.D.
UC San Diego, Departments of Dermatology and Pediatrics

Title: Pediatric Psoriasis and Non-Alcoholic Fatty Liver Disease (NAFLD): Spectrum and Significance for Co-Management

Beyond having thick, scaly skin lesions, children with psoriasis have 2-fold higher risk of metabolic syndrome and non-alcoholic fatty liver disease (NAFLD). Yet data is sparse on NAFLD severity and appropriate management for children with both conditions. This is a critical knowledge gap given the liver’s central role in drug metabolism, its risk for toxicity, and the potential for unaddressed inflammation to progress to scarring/fibrosis, cirrhosis, and liver failure with time. Our overarching goal is to identify systemic drug therapies appropriately safe for the skin and liver, and ideally, dually efficacious for pediatric psoriasis and NAFLD. We have preliminary data showing that some treatments (such as Tumor Necrosis Factor-alpha [TNF-α] inhibitors) may be more optimal in this setting, yet the hepatic effects of the majority of available systemic agents are unknown at this time. We seek to address these gaps via a multicenter study detailing the clinical and histologic features of NAFLD in children with psoriasis. Our consortium has unique access to liver biopsy specimens already collected from affected children. Specific Aim 1 is to determine the severity and spectrum of NAFLD in children with psoriasis compared to non-psoriatic controls. Specific Aim 2 is to perform immunohistochemistry studies for molecular targets relevant to existing and upcoming psoriasis therapies.


Life Course Research

PI: Louise Laurent, M.D., Ph.D.
University of California, San Diego, Department of Reproductive Medicine

Title: Correlating maternal and neonatal microbiome profiles with pregnancy and postnatal outcomes: Urinary Microbiome vs. Vaginal and Rectal Microbiome during Pregnancy

There are trillions of microbes living on and within the human body, which all together define the human microbiota. There is a distinct physiology of pregnancy, and similarly, there is a distinct microbiota of pregnancy, which is likely associated with these physiologic changes. Importantly, there is growing evidence that the maternal microbiota may have a significant impact on pregnancy and postnatal outcomes. 

Defining the female urinary microbiome (FUM) is currently a growing field of research, and is accomplished by isolating the DNA and/or RNA of microbes from catheterized urine samples. However, there is very little that is known about the FUM in pregnancy. This is surprising, given that maternal voided urine is the one biospecimens that is routinely collected at prenatal clinic visits and hospital visits to screen for pathologic processes during pregnancy, including asymptomatic bacteriuria. Asymptomatic bacteriuria has been shown to be associated with adverse pregnancy outcomes, such as pyelonephritis and spontaneous preterm birth. Currently, urinalysis and/or standard urine culture are used to screen for and diagnose asymptomatic bacteriuria. We predict that the discovery of the FUM will have an important impact on the definition of asymptomatic bacteriuria, and on the management of pregnant patients in the future.

Our primary objective is to describe the FUM in pregnancy using catheterized urine samples, and to correlate this with voided clean-catch midstream urine samples, vaginal samples, and rectal samples. We hypothesize that there is a distinct microbiota unique to the bladder, which can be isolated from the microbiota that typically ascend from the gastrointestinal and genital tract to the urinary tract during pregnancy. By clearly defining the relationship between the microbiota of the bladder, vagina, and rectum, we hope to enhance the clinical utility of voided urine samples in clinical practice, which can be used to predict and prevent adverse pregnancy outcomes. As a secondary objective, we aim to compare the microbiome identified from the catheterized and voided urine samples, with the microbes isolated using urine cultures and enhanced quantitative urine culture (EQUC) techniques. As a tertiary objective, we aim to investigate how the FUM changes between pregnancy and the postpartum period.

Our study is a prospective cohort study, with current IRB approval for the enrollment of 100 patients. We are collecting catheterized urine, voided clean-catch midstream urine, vaginal, and rectal samples from term pregnant patients at the time of their cesarean delivery, and again at their postpartum visit.

This project has been awarded initial funding for 20 patients through the UCSD Health Sciences Academic Senate Grant. Since that time, there has been one recently published study characterizing the microbiome of the bladder in pregnancy. The results of this study support expanding the sample size to 50 patients, in order to identify the maximum number of unique species of bacteria isolated. By expanding our sample size, we anticipate that the data from this pilot project will be used to design future extramurally funded studies to definitively determine the FUM in pregnancy and its clinical significance.

PI: Dorota Skowronska-Krawczyk, Ph.D.
University of California, San Diego, Department of Ophthalmology

Title:  Advancing the understanding of neuroprotective function of senolytic drugs in glaucoma

Mammalian aging is a complex process where distinct molecular processes contribute to age-related tissue dysfunction. Several lines of evidence suggest that activation of senescence is an important contributor. Markers of cellular senescence such as expression of the p16Ink4a and secretion of senescent associated secretory phenotype (SASP) molecules dramatically increase during aging in both humans and mice. Several studies suggest that p16Ink4a+ cells act to shorten healthy lifespan by promoting age dependent changes that functionally impair certain tissues and organs. Intriguingly, many recent studies have shown that removal of senescent cells using senolytic drugs induces lifespan extension and improves health of animals. This approach has never been applied in age-related eye diseases.

Glaucoma is an eye disease that damages the optic nerve and results in vision loss. Of all the glaucoma-associated risk factors, patient’s age is by far the strongest and consistently reported. This leading cause of blindness is becoming increasingly more prevalent in the aging population. Concurrent with the age-related increase in the prevalence of glaucoma is the age-related decreased population of retinal ganglion cells (RGCs) in the retina. The RGCs are neuronal cells essential for retina function as they electrically connect the retina with the brain; it is also the cell type that is primarily damaged in glaucoma.

In a mouse model glaucoma/ischemic stress, we recently studied the effects of p16Ink4a on glaucoma pathogenesis. We observed that upon increased intraocular pressure (IOP) the expression of p16Ink4a is elevated, leading to enhanced senescence in the RGCs, which is what most likely directly causes RGC death. In addition, the analysis of p16KO mice suggests that the lack of p16Ink4a gene protects RGCs from cell death caused by elevated IOP. More importantly, we have also detected elevated expression of p16INK4a and senescence in human glaucomatous eyes. Therefore, our work has indicated for the first time that elevated expression of p16Ink4a is linked to RGC aging and death.Intriguingly, recent bioinformatic meta-analysis of a published set of genes associated with POAG pointed at senescence and inflammation as key factors in RGC degeneration in glaucoma.

We hypothesize that removing early senescent RGCs induced upon IOP elevation in the eye will protect remaining RGCs from senescence and death. As a preliminary approach, we used a well-accepted transgenic p16-3MR mouse model where the systemic administration of a small molecule selectively kills p16INK4a-expressing cells. Using this model, we could show that the removal of transgenically modified p16-expressing cells has a strong positive effect on RGC survival. Under this Pilot Award, we will test the neuroprotective effect of senescent cell clearance on RGC survival and function utilizing combinations of previously well described senolytic drugs. Moreover, we will investigate the integrity of visual path and single-cell transcriptomic signature of protected RGCs to understand the molecular basis of the effectiveness of the treatment. This exploratory project is designed to provide preliminary data for future investigations aimed at finding senolytic drugs that can be used to treat glaucoma patients as well as to understand the process of neuroprotection.


Academic-Community Pilot Project

Argentina Servin, M.D., MPH
University of California, San Diego, Division of Infectious Diseases & Global Public Health, Department of Medicine

Tsuyuki Kiyomi, Ph. D. MPH
University of California, San Diego, Division of Infectious Diseases & Global Public Health, Department of Medicine

Community Partner:
Kevin Mattson, CEO
San Ysidro Health

Title: Developing a youth-centered mobile app for Sex Ed and linkage into care in California

In 2016, the United States (U.S.) had higher rates of sexually transmitted infections (STIs) and adolescent pregnancy than most other industrialized countries.With more than two million cases of STIs reported among adolescents and young adults, the rates of syphilis, gonorrhea, and chlamydia reached a record high in the country. Furthermore, health disparities persist among racial and ethnic minority adolescents and in counties located along the U.S.-Mexico border region with African American (AA) and Latino adolescents reporting the highest rates of STIs, and despite declining birth rates, compared to other racial/ethnic groups, are three to four times as likely to give birth. Previous research has found that lack of comprehensive sexual education (Sex Ed) and access to quality health care are associated with increased sexual risk behaviors, STIs, and unintended pregnancy among adolescents. Currently, the U.S. has no universal standard for Sex Ed, with fewer than half of high schools in the country teaching essential sex education, and 7 states requiring the negative portrayal of sexual and gender minority (SGM) adolescents. However, advances in communication technologies provide emergent modalities to engage adolescents in comprehensive Sex Ed and linkage to care. The proposed study aims to develop the content, design, and prototype of a mobile health app that provides comprehensive Sex Ed for both heterosexual and SGM adolescents, and linkage into care based on the users location by partnering with San Ysidro Health (SYH) and their school-based clinic sites located in the U.S.–Mexico border region.

Specific aims include:

Aim 1. To develop a significant and innovative Sex Ed curriculum that is inclusive of heterosexual and SGM adolescents in the U.S.-Mexico border region. Focus groups (n=3) will be conducted with clients from the SYH school-based clinic sites (ages 15-18) to develop an inclusive, significant, and innovative Sex Ed curriculum that will serve as the content for the mobile app. 

Aim 2. To assess and conduct geo-mappping of existing services available for heterosexual and SGM adolescents in the US-Mexico border region. Formative interviews (n~20) will be conducted with SYH providers and local community organizations that work with adolescents in this region to identify barriers to accessing care, key services available and geo-mapping of these services.

Aim 3. To inform the design, app development approach, identification of mobile platforms, and development of the mobile app prototype. Based on the findings from Aim 1 and 2, we will work Mr. Palii (Co-I) to develop the user experience (UX) and user interface (UI) design, identification of mobile platforms and develop a mobile app prototype.

Aim 4. To conduct a alpha and beta-testing of the mobile app prototype among adolescents for refinement and future efficacy trial. Alpha (e.g., eliminate device specific bugs) and beta testing (e.g., target popuation testing) of the app prototype will be conducted via FGs (n=3) with clients from the school-based clinic sites. This will allow the adolescents’ to provide relevant feedback regarding the content and design of the app and quality assurance.


Dissemination and Implementation Research Pilot Project

PI: Jay Silverman, Ph.D.
University of California, San Diego, Department of Medicine

Community Partner:
Ilana Brongiel, MPH
San Ysidro Health

(pending NIH approval)
Title: Adapting an evidence-based model for reducing reproductive coercion and intimate partner violence, and increasing contraceptive use among Latina adolescents in southern San Diego: ARCHES Jovenes

With clinics located less than one mile north of the US-Mexico border, San Ysidro Health (SYH), is one of the largest community health centers in San Diego County serving an annual patient population of over 94,000 individuals, and has established itself as a locally and nationally recognized leader in border health issues, including youth-centered services.1 Intimate partner violence (IPV) and reproductive coercion (RC) (i.e. male partner, family member, or others’ behaviors that directly interfere with female attempts to use contraception, via coercion to become pregnant against her wishes or direct/indirect interference with her use of birth control) are consistently associated with unintended pregnancy among adolescent girls and young women.3-10 Latina adolescents in the United States, which are a primary demographic served by SYH, continue to be at highest risk for pregnancy (46.3 births per 1000) with those of Mexican origin at highest risk relative to other Latinas.11 ARCHES (Addressing Reproductive Coercion in Health Settings) is a brief clinical model delivered by existing providers in the context of family planning counseling via four primary strategies: a) Educational and empowerment counseling to minimize risk to women of interference by others in contraceptive use or pregnancy decisions; b) Identification and support of RC and IPV survivors; c) Supportive linkage of IPV survivors to local IPV services; and d) Provision of discreet educational materials on contraceptive methods to use without interference, RC, IPV and IPV services.12,24

ARCHES is the only clinical model shown to reduce risk of IPV and RC as demonstrated via two NIH-funded cluster RCTs in the U.S. among >4000 women.13-15 Based on this evidence for ARCHES, and the critical needs of adolescent girls and young women (AGYW) aged 15-24 in the border region, we will collaborate with SYH and their staff, AGYW patients, SYH Youth Advisory Board members and Peer Health Advocates, to adapt ARCHES, and create a highly acceptable, feasible, patient-centered and safe model for youth seeking contraceptive services. This study is grounded in IS frameworks proposed by Procter et al. and Aarons, Hurlburt and Horwitz,16,17 and is designed as a principally qualitative study with a quantitative and qualitative follow-up. All study activities will be conducted in the context of clinical and educational services provided by SYH, inclusive of their three school-based health centers, two Pediatric Clinics, SYH Teen Clinic, and eight primary health care clinics that collectively serve over 7,000 female adolescents each year in the border region.

PI: Irene Su, M.D.
University of California, San Diego, Department of Obstetrics, Gynecology and Reproductive Services

Title: Developing a multicomponent implementation strategy for fertility care for female adolescent and young adult cancer survivors

Unmet reproductive health care needs are highly prevalent among the nearly 550,000 newly diagnosed or post-treatment female adolescent and young adult (AYA) cancer survivors in the United States. AYA survivors undergo radiation, chemotherapy, surgery and/or endocrine therapy, treatments that can adversely impact their future reproductive health. Infertility from cancer treatment is devastating and significantly impairs quality of life in survivorship. Equally important is family planning to prevent unintended pregnancy in this high-risk population. These sequeale are preventable through fertility care, i.e. fertility and family planning counseling and associated procedures. The evidence-based practice of fertility care at cancer diagnosis and post-treatment in survivorship has been recommended by oncology, pediatric and gynecology clinical guidelines for more than a decade. Yet, there remains a significant care gap in delivering high quality reproductive health care for female AYA cancer survivors, arguably due to the lack of effective implementation strategies to facilitate fertility care across disparate clinical settings.

The objective of this proposal is to design and refine the implementation strategies for fertility care at cancer diagnosis and post-treatment in survivorship for female AYA cancer survivors at two disparate care settings in our community: UC San Diego Moores Cancer Center and Rady Children’s Hospital of San Diego. In Aim 1, we will conduct framework-based evaluations on existing and proposed implementation strategies, including mobile health (mHealth) tools, for delivering fertility care in female AYA cancer patients. Guided by the Consolidated Framework for Implementation Research (CFIR) constructs, we will undertake qualitative and quantitative studies through focus groups, semi-structured interviews, and questionnaires with stakeholders to study the context of fertility care in two disparate clinical settings and evaluate feasibility, appropriateness, and acceptability of existing and proposed implementation strategies. In Aim 2, we will develop and conduct usability testing of a multicomponent strategy, inclusive of mHealth tools, for delivering fertility care at two disparate cancer care settings. We will use end-user design approaches to engage stakeholders in the design of mHealth and additional implementation and strategy components. The significance of this study is improving reproductive health care in adolescents and young adults with cancer, an underserved population. In taking an implementation science approach, this study is innovative to the oncofertility discipline and will generate knowledge on how fertility care is delivered in disparate clinical settings, how to develop a multicomponent implementation strategy for this care gap, and how novel mHealth strategies may facilitate the delivery of cancer specialty care. Developing these mHealth strategies and shareable technology functionalities within the common EPIC electronic health record (EHR) platform is key to broader dissemination and implementation.