UCSF

While it is now known that human chromosomes are pervasively transcribed, the relative contribution of the coding and lncRNA genomes to cell differentiation is unknown. Using genome-wide CRISPR interference (CRISPRi) screens in human pluripotent stem cells, we systematically assessed 18,905 protein-coding and 10,678 lncRNA targets for function in neural induction, identifying 419 coding and 201 lncRNA genes that regulate this step of development. Comparative multi-omic analyses discovered broad properties of coding and lncRNA genome function, such as an enrichment of lncRNA genes for roles in differentiation rather than proliferation. In contrast, coding genes were enriched for function in cell proliferation. CRISPRi single-cell RNA-Seq (Perturb-Seq) analysis resolved differentiation phenotypes at the level of specific cellular states, revealing additional distinctions in how coding and lncRNA genes regulate neural induction. These systematic studies demonstrated key functional differences between the coding and lncRNA genomes during this critical stage of neurodevelopment.

Malaria is a parasite infection transmitted by mosquitoes that infected 229 million cases and resulted in 409,000 deaths worldwide in 2019. In the Greater Mekong Sub-region (GMS), resistance to primary malaria treatments has emerged and is threatening to set back recent control successes. As countries ambition to eliminate malaria by 2030, infections clusters in forest-going populations that are increasingly targeted for prevention and treatment efforts by national control programs across the GMS. Yet, as pointed out by a recent review of the literature on forest-goers, a more detailed characterization of forest-going population is needed to accelerate malaria elimination in the GMS.

In chapter 1, we evaluated the association between deforestation and malaria incidence in northern and southern Lao PDR. Our approach leveraged surveillance records collected by the national program and high-resolution forest data to characterize the importance of forest-going population on malaria transmission in the GMS. Our results highlighted the challenges to transition from Plasmodium falciparum to Plasmodium vivax elimination and suggest programs may benefit from monitoring areas of on-going deforestation using remotely sensed data.

In chapter 2, three population-based surveys and one rolling survey among forest-goers from a randomized controlled trial in southern Lao PDR were combined to estimate the size of forest-going populations. Population size estimates (PSEs) were produced at three different time points and the capture-recapture methodology was used to estimate the total number of forest-goers in the study area over the study period. This study highlighted an important seasonality in malaria risk behaviors among forest-goers and illustrates population size estimation methods that can be replicated to support national control programs in the GMS.

In chapter 3, GPS logging devices were leveraged to measure and describe fine-scale mobility patterns of forest-goers recruited in a focal test and treat (FTAT) active case detection intervention conducted in southern Lao PDR. Combining clustering analyses and machine learning regressions, our results assessed the diversity within forest-going trips but did not translate into a clear segmentation of forest-goers’ role in malaria transmission in the GMS.

Taken together, this work characterizes the importance, size and mobility of forest-going populations in Lao PDR. These results are key for national control programs across the GMS to assess and meet their 2030 malaria elimination goals.

Forty years into the HIV epidemic, the most impacted group continues to be Black gay and bisexual men, for whom living with HIV comes with a substantial social burden, particularly in communities with high levels of HIV-stigma and homophobia. One way in which this is manifested is in the complex disclosure/nondisclosure process. HIV status disclosure has been, and continues to be privileged in public health research, as it is seen as critical to educating others, reducing sexual transmission, and garnering needed social support. Most of this research has been centered on the individual and has focused on understanding the decision-making process about how, when, and to whom they will disclose. Other research aims to identify barriers and facilitators of disclosure, with the ultimate goal of encouraging disclosure. At the individual level, however, exploring the disclosure process requires an understanding of previous experiences, social environments, and the dynamics of social relationships as HIV risk, diagnosis, and disclosure are each embedded in ongoing social relations. This dissertation takes a sociological approach to understanding the dynamics of HIV disclosure among Black gay and bisexual men living with HIV (BGBM-LWH) in Baton Rouge, Louisiana. BGBM, existing at the intersections of race, class, and sexuality, account for the majority of new infections in the state of Louisiana, and their experiences are embedded in a culture of silence and shame around sexuality and HIV. Thus, their HIV diagnosis and disclosure experiences offer a crucial site for this intersectional analysis which explores disclosure and its outcomes as socially and structurally constituted. Between June 2019 and June 2020, I conducted semi-structured, in-depth, qualitative interviews with 30 BGBM-LWH. I used a grounded theory analysis to explore not only men’s HIV disclosure-specific narratives, but to situate them in the context of their biographies, their social and cultural environment, and their ongoing social and familial relationships.

The results of my analyses are presented in three chapters. First, I illustrate the ways in which HIV status disclosure can result in disruptions to one’s biography and can lead to long-term, negative, and unforseen consequences. These included loss of employment or housing, as well as disrupted social networks, familial relationships, and support systems. Further, I illustrate how their intersectional social locations alongside structural racism, homophobia, and HIV stigma shaped the nature of those disruptions and long-term consequences. Second, I reveal the emotion and emotion work that accompanied men’s disclosure experiences. Men described having to manage and control their own emotions and “dig deep” to get the nerve to disclose. In turn, they described having to manage others’ emotional reactions and feeling a sense of guilt for being the cause of sadness for their friends and family. Lastly, I develop a grounded theory of the social interactions and structures that produce and reproduce HIV stigma on an ongoing basis. These included: the transmission of misinformation at the community level; witnessing or experiencing acts of marginalization at the individual level; HIV criminal nondisclosure laws and sex education policies at the institutional level; as well as silence and gossip at the level of social interactions. This project expands on sociological and public health literatures to produce an analysis of HIV disclosure that places social and structural environment at the center, as opposed to the individual, and offers new sites for research and intervention.

Cancer is among the leading causes of mortality worldwide and the number of cancer-related deaths is expected to rise to 16.4 million by 2040. Given the wealth of publicly available cancer data that has been generated over the past few decades, it is now possible to investigate cancer at an unprecedented scale using computational approaches. This body of work covers three projects that leverage human tumor samples to evaluate cancer models, predict cancer therapeutics, and investigate the prognostic value of infiltrating B cell repertoires. In the first project, we compared cell lines from the Cancer Cell Line Encyclopedia to primary tumor samples from the Cancer Genome Atlas (TCGA) to evaluate how well each cell lines represents its primary tumors. We predicted subtype classifications for individual cell lines and proposed a new pan-cancer cell line panel with the most representative cell lines across 22 tumor types to facilitate pan-cancer studies. In the second project, we applied a computational drug repositioning approach to identify compounds to sensitize drug resistant breast cancers using patient samples from the I-SPY2 TRIAL and the Connectivity Map drug perturbation dataset. We identified a drug hit, fulvestrant, which we validated experimentally and found that it increased drug response in a paclitaxel-resistant breast cancer cell line. In the third project, we extracted B cell repertoires from TCGA RNA-seq samples and performed diversity and network analysis. We then evaluated the prognostic value of these repertoire features and identified significant associations with survival in a subset of tumor types. Together, this research demonstrates how computational methods can leverage publicly available datasets to extract new insights into cancer biology

Background: The aims of this study are to assess the prevalence of tobacco and cannabis use among adult patients visiting the UCSF Dental Center between January of 2019 and June of 2020, and to compare the periodontal diagnoses between tobacco/cannabis use groups, while accounting for demographic confounding factors, such as age, gender, race, ethnicity, and insurance.

Methods: Data were derived from UCSF Dental Center student, resident, and faculty clinics. The extracted data fit the inclusion criteria, which included individuals age ≥18 that had dental examinations completed between January 2019 to June 2020. Data analysis was performed to ascertain the relationship between use of tobacco (past and present) and/or cannabis products and periodontitis as defined by AAP/CDC definitions. Covariates included age, gender, and insurance status. Univariable and multivariable logistic regression analyses were carried out to evaluate the relationship between exposure (tobacco/cannabis use) and outcome (periodontitis).

Results: Within the patient population of UCSF Dental Center, that met the inclusion criteria, 6.2% of patients were current tobacco users, 12.0% were former tobaccos users, 6.5% were cannabis users, and 2.3% were both tobacco and cannabis users. Modelling with multiple logistic regression revealed that current and former cigarette users had 1.7x and 1.4x, respectively, the odds as never smokers of having periodontitis (adjusted OR = 1.7; 95% CI 1.4-2.2 and adjusted OR = 1.4; 95% CI 1.2-1.7, respectively). Cannabis users had 1.3x the odds of having periodontitis (adjusted OR = 1.3; 95% CI 1.0-1.5). The odds of having periodontal disease while using both cannabis and tobacco product were statistically significant (adjusted OR = 1.7; 95% CI 1.2-2.4). In addition to looking at the association between tobacco and/or cannabis product use and periodontal disease that included moderate disease, a logistic regression analysis was completed to assess whether there was an association between tobacco products, cannabis products, and tobacco and cannabis products and specifically severe periodontal disease. Compared to tobacco and cannabis non-use, current and former cigarette use was associated with 2.2x and 1.5x, respectively, the odds of a severe form of periodontal disease (adjusted OR = 2.2; 95% CI 1.9-2.7 and adjusted OR = 1.5; 95% CI 1.3-1.7, respectively). Cannabis use did not have a statistically significant association with severe periodontal disease (adjusted OR = 1.1; 95% CI 0.9-1.4). Using both cannabis and tobacco products was associated with approximately twice the odds of severe periodontal disease (adjusted OR = 2.4; 95% CI 1.7-3.2). Finally, an ordered logistic regression analysis was conducted. This analysis revealed that odds of being in a more severe category of periodontal disease increases with use of tobacco or cannabis products. After adjusting for covariates, current and former cigarette users had 2x greater odds of being in a more severe category of periodontal disease than never smokers (adjusted OR = 2.1; 95% CI 1.8-2.4 and adjusted OR = 1.5; 95% CI 1.3-1.7, respectively). Cannabis users had 1.2x greater odds than never smokers of being a more severe category of periodontal disease (adjusted OR = 1.2; 95% CI 1.1-1.4) Using both cannabis and tobacco products was also statistically significantly associated with higher odds of being at a greater severity level of periodontal disease (adjusted OR = 2.1; 95% CI 1.6-2.7).

Conclusion: In this sample of dental patients in a Northern California academic practice tobacco use, with and without cannabis use, was associated with periodontitis and severe periodontitis. In addition, the results of this study showed that cannabis use alone was associated with periodontitis, but not severe periodontal disease. With the recent legalization of medical and recreational cannabis use, there will likely be an increase in prevalence of cannabis use throughout the United States. It is important for health care clinicians to understand its potentials risks. Determining whether an association exists between cannabis and periodontal disease should be a priority for periodontal epidemiological studies. Dental and medical practitioners should take steps to raise awareness of the possibility of regular tobacco and cannabis use as potential risk factors for periodontal disease.

Within medicine devoted to LGBTQ+ health, data are everywhere. Large databases teem with numbers waiting for evaluation, buggy online surveys offer rickety drop-down menus filled with identity terms, and clinic bulletin boards host calls for research participants to “stand up and be counted.” This dissertation will trace the life of what I will call “queer data” - that is, data documenting queer subjects as well as data that might potentially be understood as “queered” - as it is produced, analyzed, and mobilized. A rich moment for anthropological study emerges when quantification techniques requiring bounded categories are confronted by the foundational fluidity of queerness. This project draws from from anthropological fieldwork within research projects and clinical spaces in the California Bay Area, semi-structured interviews with individuals across the United States, as well as objects and virtual spaces that serve as ethnographic objects. Tracing such queer data through medical settings and discourses provides a unique opportunity to explore questions around the evidence-base of queerness and the ways in which queerness soaks into data processes in transformative ways.In this dissertation, I describe how this queer data production emerges as a co-constitutive process through which community norms and experiences shape the options for categorization, while at the same time such categories affect how individuals and communities make meaning around their identities, bodies, and desires. I examine how debates around the use of statistics within medical education reanimates counting as a contested space that exposes the political stakes of quantifying queerness and the affective impact of numbers. Data are also a potent force within clinical spaces. Through examinations of clinical intake forms, I describe how efforts to create healthcare spaces that are affirming to queer patients position data as a form of care. How such healthcare data are transformed by bureaucratic reporting requirements is discussed as an example of how queerness both resists and is subsumed by aggregation. The organ inventory is also taken up as an ethnographic object and explored for the ontological claims it makes around what a body is and how it should be cared for. By tracing such queer data, this dissertation explores how quantifying queerness is an act of transformation, but one that is necessarily incomplete. The ever-evolving nature of queerness leaves it in excess of static categories in a way that can productively draw attention to the generative work of quantification.

Acini are essential for the secretory function of multiple exocrine organs. During acini formation, a cluster of epithelial end bud progenitors must undergo secretory program initiation, maturation and cell polarization to form a unit of single layered secretory cells enclosing a central lumen. Yet, how this complex process is regulated remains unknown. Using the developing salivary gland as a model, we reveal the EGF receptor ERBB3 as a master driver of acinus formation. We discovered ERBB3 to be enriched in end buds, and through conditional deletion of epithelial Erbb3, to be essential in multiple steps of secretory cell program initiation, cell maturation, expansion and polarization. Moreover, we demonstrate that addition of a single factor, ERBB3 ligand neuregulin-1, to isolated epithelia ex vivo is sufficient to recapitulate the complex outcomes of in vivo acinus formation in multiple exocrine organs. Finally, we reveal a new ERBB3-mTOR1/2 signaling link that governs the full formation of the secretory acinus.

Neutrophils are professional migrators within our body, moving from the bloodstream through dense forests of extracellular matrix to reach sites of infection and initiate an immune response. While we have long appreciated the role of biochemical signals in neutrophil recruitment, increasing attention is being given to the role of physical signals during this process. For example, membrane tension and membrane shape changes arise as neutrophils navigate complex 3D environments in vivo, which can impact the path cells take through tissue. However, how this information is relayed back to the cytoskeleton has remained largely unexplored. In this thesis we probe the link between biochemical and physical inputs to better understand how neutrophils integrate environmental signals to ensure robust directed migration.

In Chapter 2 we establish how intrinsic protein self-organization and external membrane curvature work together to pattern the actin nucleation promoting factor WAVE. Using super-resolution microscopy, we find that WAVE forms rings at the saddle-shaped necks of membrane invaginations in the absence of actin polymer. Dual inputs from WAVE’s propensity to oligomerize and curvature sensitivity explain this enrichment pattern and inform our understanding of WAVE propagation in the presence of actin. Specifically, we find that WAVE localizes to the saddle-shaped lagging regions of the leading edge to support a uniformly advancing cell front. Elucidation of the mechanisms underpinning WAVE organization has provided initial insights into the integration of internal biochemical signals with external cell shape in organizing the actin cytoskeleton.

In Chapter 3 we continue on this theme and highlight how WASP, another actin nucleation promoting factor, uses a modification of these behaviors to link cell shape and cell polarity during neutrophil migration. Unlike WAVE, WASP persistently enriches to substrate-induced invaginations in the presence of actin. Additionally, WASP assembles into focal structures rather than linear structures. We find that these properties allow WASP to link sites of local membrane deformation to the cytoskeleton by promoting actin polymerization and aligned migration in textured environments. Strikingly, this property requires concomitant inputs from cell shape and cell polarity. WASP only engages with curved membranes at the cell front, which supports forward advance. We show that WASP is essential for integration of substrate features with directed migration, which could have implications for migration through collagen meshworks in vivo.

Finally, Chapter 4 presents unpublished work exploring the molecular mechanisms of cell polarity through GTPase regulation by Rho GEFs and GAPs using HEK293T cells as a model system. Using CRISPR we endogenously label highly expressed GEFs and GAPs. We describe a system for polarizing HEK293T cells and report candidate GEFs and GAPs that enrich to induced cell protrusions. Finally, we supply a protocol for phenotyping the migration of HEK293T GEF or GAP knockout cell lines and provide a positive control in the form of Rac1 knockout. Ultimately, GEFs and GAPs exhibiting loss of function phenotypes would be followed up in the consitituively polarized, highly motile neutrophil cell line HL-60.

Because its geographic reach was not as vast as Britain, France, or Spain's, Imperial Germany is often rendered to the marginalia of colonial historiography. Yet Germany’s colonial endeavors, specifically its genocidal war against the Ovaherero and Nama (1904-1908) in German South West Africa is critically important as an expression of Lebensraum, a geopolitical understanding of ethnic identity and racialized space appropriated from biologist Oscar Peschel’s response to Charles Darwin’s theories of evolution and natural selection. In complementing Ovaherero and Nama efforts for reparations, this dissertation embraces an altercentric historiography — a genealogical materialism guided by ubuntu philosophy — and approach to biological science that narrativizes Germany’s first genocide as a material expression of the colonial biomedical logics that animated the the colonial project and endure in the present.

I am using three case studies that tether contemporary scientific and archival practice to colonial-era biomedical harms. First, the collection and ongoing incarceration of Ovaherero and Nama skulls and other skeletal remains in German and American and other archival collections is a feature of a broader regime of race-making and property rights. The the continued capture of these remains has been described by Ovaherero and Nama community members as a continuation of genocide through the linking of expropriative colonial actions to the “post”-colonial present. Secondly, an analysis of Eugen Fischer’s transnational “bastard studies” allows for an examination of the genocide continuity thesis. It connects the imperial German study of mixedness in southern Africa to eugenic study in Weimar and then Nazi Germany via the desire to manage perceived impurities to whiteness resulting from race-mixing. This illustration of continuity reveals how desires for racial management in each location yielded both consistent and differential racial structures and fates for the mixed-race communities in question. Finally, the deep interest in the sequencing and tracing of San genomes is inextricably linked to anthropological constructions of “hunter-gatherers” as ancient and primitive, and the Eurocentric compulsion to enclose and define and hierarchize human life with the creation of a “human” that always precludes African indigeneity. The always already racialized genomics projects and nation-state assertions of genomic sovereignty are occurring simultaneously to San communities being dispossessed of their land and turned into an underclass in the nation-states into which they are being forcibly assimilated.

Purpose – Purpose was to model cognitive fatigue and evening physical fatigue together to determine subgroups of patients with distinct cognitive fatigue AND evening physical fatigue profiles. Once these profiles were identified, differences among the subgroups in demographic and clinical characteristics, co-occurring symptoms, and quality of life outcomes were evaluated.Methods – Oncology patients (n=1332) completed self-report measures of cognitive fatigue and evening physical fatigue, six times over two cycles of chemotherapy. Latent profile analysis, that combined the two symptom scores, was done to identify subgroups of patients with distinct cognitive fatigue AND evening physical fatigue profiles. Results – Three distinct profiles (i.e., Low (20.5%), Moderate (39.6%), High (39.6%) were identified. Compared to the Low class, patients in the High class were younger, female, more likely to live alone and had a higher comorbidity burden and a lower functional status. In addition, these patients had a higher symptom burden and a poorer quality of life. Conclusion – Based on clinically meaningful cutoff scores, 80% of the patients in this study had moderate to high levels of both cognitive fatigue and evening physical fatigue. In addition, these patients experienced high levels of other common symptoms (e.g., anxiety, depression, sleep disturbance, pain). These co-occurring symptoms and other modifiable characteristics associated with membership in the Moderate and High classes may be potential targets for individualized symptom management interventions.