Predicting Human Nucleosome Occupancy from Primary Sequence

Nucleosomes are the fundamental repeating unit of chromatin and comprise the structural building blocks of the living eukaryotic genome. Micrococcal nuclease (MNase) has long been used to delineate nucleosomal organization. Microarray-based nucleosome mapping experiments in yeast chromatin have revealed regularly-spaced translational phasing of nucleosomes. These data have been used to train computational models of sequence-directed nuclesosome positioning, which have identified ubiquitous strong intrinsic nucleosome positioning signals. Here, we successfully apply this approach to nucleosome positioning experiments from human chromatin. The predictions made by the human-trained and yeast-trained models are strongly correlated, suggesting a shared mechanism for sequence-based determination of nucleosome occupancy. In addition, we observed striking complementarity between classifiers trained on experimental data from weakly versus heavily digested MNase samples. In the former case, the resulting model accurately identifies nucleosome-forming sequences; in the latter, the classifier excels at identifying nucleosome-free regions. Using this model we are able to identify several characteristics of nucleosome-forming and nucleosome-disfavoring sequences. First, by combining results from each classifier applied de novo across the human ENCODE regions, the classifier reveals distinct sequence composition and periodicity features of nucleosome-forming and nucleosome-disfavoring sequences. Short runs of dinucleotide repeat appear as a hallmark of nucleosome-disfavoring sequences, while nucleosome-forming sequences contain short periodic runs of GC base pairs. Second, we show that nucleosome phasing is most frequently predicted flanking nucleosome-free regions. The results suggest that the major mechanism of nucleosome positioning in vivo is boundary-event-driven and affirm the classical statistical positioning theory of nucleosome organization

CFTR F508del and population structure in a cystic fibrosis population

Thesis (Master's)--University of Washington, 2020The Cystic Fibrosis Genome Project (CFGP) has assembled whole genome sequences on ~5K individuals with cystic fibrosis (CF) with the goal of identifying genetic modifiers of CF-related phenotypes. We hypothesized that the over-sampling of the clinal CFTR F508del haplotype in this dataset might make such studies particularly susceptible to deriving spurious associations between variants correlated with CFTR F508del genotype and CF-related outcomes. We assessed whether regions of the genome are associated with the CFTR F508del genotype by performing genome-wide association studies (GWAS’s) of CFTR F508del genotypes and measuring the type I error rate across the genome (genomic inflation) that results when not accounting for population structure. We determined that linear mixed models with orthogonally partitioned structure (LMM-OPS) adequately controlled for the underlying relatedness and population structure within our dataset, reducing signals in genomic locations correlated with CFTR. Our results support that performing a GWAS of a disease-causing variant is a useful method to assess the effectiveness of principal components and genetic relatedness estimates at controlling for confounding in datasets with over-sampling of a clinal variant

Molecular Epidemiological Investigations of HIV Transmission Patterns Among People Who Inject Drugs in Kenya

Thesis (Ph.D.)--University of Washington, 2023In Kenya people who inject drugs (PWID) have a 4-fold greater prevalence of HIV and at least 10-fold greater prevalence of hepatitis C compared to the general population. While preliminary epidemiological evidence suggests needle-sharing, and associated parenteral HIV transmission, is decreasing, more evidence is needed to evaluate these conclusions and to understand factors contributing to sexual HIV acquisition and transmission in this population. Phylogenetic and molecular epidemiology approaches can reveal transmission trends within and between populations to help determine the most impactful interventions; however, such studies must also be mindful of the vulnerability of populations, like PWID, to stigma or other group harms. To characterize the HIV epidemic among PWID in Kenya, we first used cluster analysis and ancestral state reconstruction to estimate the following relative frequencies of HIV transmission: transmission within the PWID population; between the PWID population and other key populations (female sex workers and men who have sex with men); between the PWID population and the general population; and between PWID from the coastal region and Nairobi. Second, we investigated whether PWID shared an HIV or hepatitis C transmission network with the sexual or injecting partners they identified through assisted partner services, based on genetic distances of the virus sequences. We found substantial mixing between HIV-1 sequences from PWID with those from other populations and no excess similarity between the HIV-1 sequences from pairs of individuals identified as injecting partners. These results support prior evidence of the effectiveness of needle-syringe programs and the shift towards sexual acquisition and transmission as an important factor in this epidemic for PWID. We propose a renewed emphasis on addressing risk factors for sexual transmission and on understanding the environment within which sexual HIV acquisition and transmission occurs for PWID. Further research on hepatitis C incidence and transmission risk factors could strengthen conclusions about changes in injecting behaviors. Finally, we explored ethical issues in molecular epidemiological research of pathogen transmission trends, noting a lack of productive change coming from the current discourse centered around privacy risks to research subjects. We recommend that by treating pathogen sequence data as primarily a community resource, we can both increase the responsiveness of researchers to community concerns and improve community acceptance of molecular epidemiology as a public health and research tool

Interleukin-1 accounts for intrarenal th17 cell activation during ureteral obstruction

Interleukin 17A-secreting T-helper 17 (Th17) cells are pathogenic in inflammatory kidney diseases, but their intrarenal regulation is poorly understood. In order to better define Th17 cell dynamics during interstitial inflammation, we utilized the mouse unilateral ureteral obstruction model to analyze inflammatory cell subtypes by multicolor flow cytometry and cell sorting and by effects on in vitro-generated Th17 cells. Interleukin 17A expression localized to CCR6(+)CCR4(+/-)CD4(+) T-cells and progressively increased in obstructed kidneys. The number of CCR6(+)CD4(+) T-cells increased over 10-fold by 72h, were enriched for interleukin 17A production, and were highly proliferative based on in vivo bromodeoxyuridine incorporation. Secreted products of leukocytes isolated from obstructed kidneys enhanced the interleukin 17A production of in vitro-generated Th17 cells. This Th17-enhancing activity was identified as interleukin-1 produced by renal dendritic cells and monocytes. The in vivo validity of these findings was confirmed in mice lacking the interleulin-1 receptor and in mice treated with a recombinant interleukin-1 receptor antagonist, each of which exhibited reduced intrarenal Th17 activity compared with control mice. Thus, the inflamed kidney accumulates CCR6(+) Th17 cells that undergo activation and proliferation. Production of interleukin 1 family cytokines by resident dendritic cells and infiltrating monocytes enhances intrarenal Th17 activation in acute kidney injury. Kidney International (2012) 81, 379-390; doi:10.1038/ki.2011.348; published online 5 October 201

Interleukin-1 accounts for intrarenal th17 cell activation during ureteral obstruction

Interleukin 17A-secreting T-helper 17 (Th17) cells are pathogenic in inflammatory kidney diseases, but their intrarenal regulation is poorly understood. In order to better define Th17 cell dynamics during interstitial inflammation, we utilized the mouse unilateral ureteral obstruction model to analyze inflammatory cell subtypes by multicolor flow cytometry and cell sorting and by effects on in vitro-generated Th17 cells. Interleukin 17A expression localized to CCR6(+)CCR4(+/-)CD4(+) T-cells and progressively increased in obstructed kidneys. The number of CCR6(+)CD4(+) T-cells increased over 10-fold by 72h, were enriched for interleukin 17A production, and were highly proliferative based on in vivo bromodeoxyuridine incorporation. Secreted products of leukocytes isolated from obstructed kidneys enhanced the interleukin 17A production of in vitro-generated Th17 cells. This Th17-enhancing activity was identified as interleukin-1 produced by renal dendritic cells and monocytes. The in vivo validity of these findings was confirmed in mice lacking the interleulin-1 receptor and in mice treated with a recombinant interleukin-1 receptor antagonist, each of which exhibited reduced intrarenal Th17 activity compared with control mice. Thus, the inflamed kidney accumulates CCR6(+) Th17 cells that undergo activation and proliferation. Production of interleukin 1 family cytokines by resident dendritic cells and infiltrating monocytes enhances intrarenal Th17 activation in acute kidney injury. Kidney International (2012) 81, 379-390; doi:10.1038/ki.2011.348; published online 5 October 201

Prevalence and correlates of violence among sexual and injecting partners of people who inject drugs living with HIV in Kenya: a cross-sectional study

Abstract Background In Kenya, violence is common among people who inject drugs (PWID) living with HIV and their sexual and injecting partners and may lead to decreased uptake of HIV services, increased HIV risk behaviors, and increased HIV transmission. Violence is defined as any physical harm, threatened harm, or forced sexual acts inflicted on a person in the past year. Understanding the nature of violence and its correlates among PWID and their partners will inform population-specific public health interventions and policy recommendations. Methods This is a cross-sectional study nested in a prospective cohort study conducted in eight public health centers, methadone clinics, and needle syringe programs in Nairobi, Kilifi, and Mombasa counties in Kenya. 3,302 sexual and/or injecting partners of PWID living with HIV were recruited through assisted partner services and participated in the study. Prevalence and correlates of violence were identified using the Wald test and negative binomial regression. Results Out of 3302 study participants, 1439 (44%) had experienced violence within the past year. Physical violence was the most common form of violence experienced (35%), followed by being threatened (23%) or subjected to sexual violence (7%). In an adjusted analysis, female participants reported higher experiences of sexual violence (prevalence ratio [PR] = 2.46; 95% confidence interval [CI] 1.62, 3.74; p < 0.001) compared to male participants. In adjusted analysis, coastal residents had a higher experience of overall violence (PR = 1.48; 95% CI 1.27, 1.72; p < 0.001) than those living in Nairobi. This regional effect was relatively stronger among the female respondents (p interaction = 0.025). Participants’ sex modified the association between region and experiencing violence after adjusting potential confounding factors. Conclusions The study reveals the prevalence of violence among PWID and identifies high-risk sub-groups, including women, specifically for sexual violence, and coastal residents. Tailored interventions addressing their unique needs are essential. A holistic approach that combines violence prevention and response, comprehensive harm reduction, healthcare access, and community support is crucial to address the complex issue of drug use and HIV burden among PWID in Kenya for improved health outcomes

SARS-CoV-2 antibody prevalence, correlates, and access to harm reduction services among people who inject drugs living with and without HIV and their partners in Kenya

Abstract Background In sub-Saharan Africa many people who inject drugs (PWID) are living with undiagnosed or untreated HIV and experience high levels of poverty and conditions that can contribute to worse outcomes from SARS-CoV-2 infection. Identifying the burden of SARS-CoV-2 infection in marginalized populations like PWID may contribute to controlling the pandemic. Methods This is a nested cross-sectional study within an ongoing cohort study that recruits PWID living with HIV and their injecting and/or sexual partners at needle and syringe program sites and methadone clinics in Kenya. Blood samples were collected from consenting participants at enrollment to determine SARS-CoV-2 antibodies using a Platellia BioRad SARS-CoV-2 total antibody enzyme-linked immunosorbent assay. Baseline data were collected on HIV status, antiretroviral therapy and methadone adherence. We used logistic regression to identify factors associated with antibody positivity and descriptive statistics to report SARS-CoV-2 antibody prevalence. Results One thousand participants were enrolled between April and July 2021, of whom 323 (32.3%) were women and 677 (67.7%) were men. Median age of participants was 36 years (interquartile range: 30, 42). SARS-CoV-2 antibody positivity was found in 309 (30.9%) participants. Disruption in obtaining methadone service was reported by 106 (24.3%) of the participants. Men were significantly less likely than women to have SARS-CoV-2 antibodies (adjusted odds ratio [aOR] = 0.68, 95% confidence interval [CI] 0.51, 0.95; p < 0.01) Participants who reported a sexual or injecting partner diagnosed with SARS-CoV-2 were twofold more likely to have SARS-CoV-2 antibodies detected (aOR = 2.21, 95% CI 1.06, 4.58; p < 0.032). Living with HIV was not associated with presence of SARS-CoV-2 antibodies. Conclusion The seroprevalence of SARS-CoV-2 of 30.9% in this cohort suggests high transmission rates within this population. SARS-CoV-2 seroprevalence was similar for people living with and without HIV. A large portion of this population was noted to have had disruption in access to harm reduction services

Assessing the Independent and Joint Effects of Unmedicated Prenatal Depressive Symptoms and Alcohol Consumption in Pregnancy and Infant Neurodevelopmental Outcomes

BACKGROUND: Prenatal alcohol exposure (PAE) is an established risk factor for neurodevelopmental deficits in the offspring. Prenatal depression has been associated with neurodevelopmental deficits in the offspring, although investigations into un-medicated prenatal depression have been inconsistent. We hypothesized that un-medicated prenatal depressive symptoms would independently and jointly with PAE predict neurodevelopmental outcomes in infant offspring. METHODS: We studied 344 participants from a randomized clinical trial of multivitamin supplements in pregnant women in Ukraine. Women were recruited based upon peri-conceptional alcohol use and followed up to 12 months postpartum. Prenatal depressive symptoms were assessed at approximately 32 weeks of gestation using the Beck Depression Scale. Neurodevelopment was assessed with the Bayley Scales for Infant Development II Mental Development Index (MDI) and Psychomotor Development Index (PDI) at 6 and 12 months postpartum. Generalized linear regression models were constructed to assess the independent and joint effects of prenatal depressive symptoms and PAE in models adjusted for sociodemographic and pregnancy characteristics. RESULTS: PAE was independently associated with deficits in neurodevelopmental outcomes at 6 and 12 months, however, level of prenatal depressive symptoms was not. We found marginal evidence of synergism of depressive symptoms and PAE, with larger deficits in those with both exposures observed for the PDI-6 months (p=0.05) and MDI-12 months (p=0.09). Additionally, there was a suggestion of sexual dimorphism; females had stronger deficits from joint exposures than males (depressive symptom (MDI-6 months) female: −8.28, 95% CI −13.06, −3.49; male: 0.68, 95% CI −4.58, 5.94; p for interaction 0.04). While not statistically significant for the MDI or PDI at 12 months, the trend persisted. CONCLUSION: Infants exposed to PAE and prenatal depression may be at an increased risk of neurodevelopmental deficits. Healthcare providers should be aware of this possible synergism in their efforts to mitigate the neurodevelopmental effects of these co-occurring exposures