UCSF

Brain function depends on a tightly regulated interplay between vascular delivery, neuronal activity, glial support, and energy metabolism. Disturbances in this coupling are central to two of the most common causes of age-related cognitive decline — Alzheimer's disease (AD) and cerebral small vessel disease (cSVD) — yet the tools most commonly used to study them in vivo remain fragmented. Positron emission tomography (PET) with [¹⁸F]FDG reports glucose uptake but requires ionizing radiation and cyclotron infrastructure; magnetic resonance imaging (MRI) offers structural, vascular, and spectroscopic contrast but has historically lacked a practical, non-ionizing readout of glucose metabolism, and the multimodal datasets it produces have outpaced the analyses applied to them. This dissertation advances metabolic MRI as an integrated framework along three steps: combining established MRI contrasts to phenotype a monogenic cerebrovascular disease; developing a new MRI contrast to fill a gap in the metabolic toolkit; and integrating both into a multimodal multivariate study design that disentangles complex genetic and pathological contributions to brain dysfunction.Chapter 3 deploys an established multimodal MRI palette — T2-weighted, FLAIR, susceptibility-weighted (SWI), and gadolinium-enhanced T1-weighted imaging at 14.1 Tesla — to phenotype five Col4a1 missense mouse lines that model the clinical spectrum of Gould syndrome, the monogenic prototype of cSVD. A U-Net-assisted, Allen-Brain-Atlas-registered analysis pipeline quantifies allele-dependent volumetric, lesion-burden, and regional-distribution differences and introduces a combined SWI + Gd-T1WI rubric that distinguishes acute hemorrhagic from chronic iron-laden lesions, validated against Prussian blue, TER-119, and GFAP histology.Chapter 4 develops a non-ionizing deuterium metabolic imaging (DMI) approach using 2-deoxy-2-[²H₂]-D-glucose (2-DG-d2), a chemically synthesizable, hexokinase-trapped analog of [¹⁸F]FDG. A multi-band CVX-designed selective radiofrequency pulse paired with a Bloch-simulation-optimized three-dimensional balanced steady-state free precession (bSSFP) sequence at 14.1 Tesla suppresses the dominant HDO signal by more than 550-fold while preserving 2-DG-d2, enabling sub-4-µL voxel imaging of cerebral glucose uptake in under 20 minutes — a resolution and speed that approach clinical [¹⁸F]FDG PET without ionizing radiation.Chapter 5 integrates the multimodal-design philosophy of Chapter 3 with metabolic-MRI methods developed in Chapter 4 and elsewhere into a single multivariate feature-extraction study. ¹H MRSI, dynamic susceptibility contrast perfusion, hyperpolarized [1-¹³C]pyruvate MRSI, and [¹⁸F]FDG PET/CT are applied to a 2×2 APOE × hAPP knock-in cohort at late middle age. Robust Sparse Linear Discriminant Analysis with leave-one-out cross-validation shows that APOE4 reshapes hippocampal glycolysis–GABA coupling, hAPP collapses perfusion–metabolism coupling, and APOE4 × hAPP uniquely shifts cerebrovascular regulation from neuronal to astrocytic drivers — a shift that coincides with hippocampal amyloid-beta deposition. Few of these signatures emerge from any single imaging metric considered alone.Together, these studies demonstrate that metabolic MRI — comprising purpose-built deuterium, proton, and hyperpolarized carbon acquisition strategies combined with structural and vascular imaging and multivariate feature extraction — can non-invasively resolve genotype-specific signatures of neurodegenerative and cerebrovascular disease in vivo. The work provides methodology and biomarker candidates that motivate translational studies of brain function in aging and disease.

The human neocortex contains extraordinary cellular diversity generated through spatially and temporally coordinated developmental programs. Recent molecular atlases identified distinct progenitor populations and transcriptional programs underlying human cortical development, but molecular state alone does not resolve the lineage relationships linking progenitors to their differentiated progeny. In this dissertation, I combine prospective lineage tracing, single-cell genomics, and developmental model systems to investigate how progenitor identity and developmental timing shape lineage output in the developing human cortex. First, using high-throughput barcoded lineage tracing in primary human cortical tissue, I linked individual progenitors to their clonal output across the transition from neurogenesis to gliogenesis during midgestation. This study revealed a progressive shift in lineage output from predominantly glutamatergic toward increased GABAergic neurogenesis and identified a role for truncated radial glia in prolonged deep-layer glutamatergic neurogenesis. Next, to understand how ventral progenitors generate expanded interneuron and oligodendrocyte diversity in primates, I applied lineage tracing in developing macaque tissue to identify candidate regulators of fate specification and guide ongoing perturbation experiments. Finally, I investigated the molecular mechanisms underlying tRG emergence, demonstrating that activation of a single signaling pathway was sufficient to induce tRG-like cells in iPSC-derived cortical organoids, accompanied by progenitor expansion and increased deep-layer neurogenesis. Together, this work establishes lineage tracing as a central framework for understanding progenitor diversification and links developmental timing, progenitor identity, and gene regulatory mechanisms to the generation of cellular diversity in the human brain.

Background: There is a lack of research focusing exclusively on the sexual and reproductive healthcare of lesbian-identified Black women compared to studies with samples of heterosexual-identified and bisexual-identified Black women. Lesbian-identified Black women are likely to have different sexual and reproductive healthcare needs and concerns than heterosexual-identified Black women. An example of such needs includes the need for tailored safer sex options and education on alternative ways of achieving pregnancy, as well as other cultural considerations.Objectives: This dissertation sought to 1) examine and interpret how lesbian-identified Black women navigate accessing sexual and reproductive healthcare, 2) identify and interpret barriers and facilitators to accessing sexual and reproductive healthcare among lesbian-identified Black women, and 3) examine resiliency and protective factors employed by lesbian-identified Black women when navigating sexual and reproductive healthcare.Method: To accomplish these aims, a scoping literature review was conducted to synthesize the current literature on the sexual and reproductive healthcare experiences of lesbian-identified Black women. Using the theoretical frameworks of Intersectionality and Ecological Systems Theory, a qualitative interpretative phenomenological study was conducted to explore the lived experiences and meaning-making processes of lesbian-identified Black women. This study first examined and analyzed the origins of sexual and reproductive health experiences by positing the following research questions: 1) What were the experiences of lesbian-identified Black women during puberty, including menarche? 2) How do lesbian-identified Black women interpret their puberty experiences? And 3) In what ways do puberty experiences, including menarche, shape the way lesbian-identified Black women view and interact with sexual and reproductive healthcare in adulthood?The second analysis built upon how participants’ pubertal experiences affect and influence adult SRH practices and interactions. This part of the study aimed to answer the research questions: 1) What are the experiences of lesbian-identified Black women when experiencing pain or discomfort related to sexual and reproductive health conditions or disorders, such as fibroids, endometriosis, and general dysmenorrhea? 2) How do lesbian-identified Black women interpret their experiences with pain and discomfort related to sexual and reproductive conditions or disorders? 3) What are the facilitators and barriers for lesbian-identified Black women when seeking care for pain or discomfort related to sexual and reproductive conditions or disorders?Individual, semi-structured, in-depth interviews were conducted with 10 purposively sampled lesbian-identified Black women between January 2025 and September 2025. Two 60 to 120-minute interviews were conducted via Zoom, and video and audio recordings were made. The recordings were professionally transcribed verbatim and checked for accuracy. Data were managed via qualitative data analysis software ATLAS.ti, coded and analyzed using thematic and narrative analyses. The University of California, San Francisco Committee on Human Research approved the study (IRB #: 24-42513; Reference # 424569).Results: The scoping review identified 18 primary research studies published between 1988 and 2023 that examined lesbian-identified Black women’s sexual and reproductive healthcare experiences (Scott-Henderson, Franck, Asiodu, McLemore, et al., 2025). Key themes revealed the widespread influence of heteronormative assumptions by providers, barriers to lesbian-identified Black women disclosing sexual orientation, and deep-seated mistrust resulting from both racial and sexual orientation-based discrimination. Lesbian-identified Black women reported that these dynamics significantly obstructed their engagement with sexual and reproductive healthcare services, with many preferring Black, LGBTQ+-affirming providers and facilities. The findings also highlighted the underestimation of sexually transmitted infection risk and observed how insufficient provider knowledge contributes to gaps in care. Ultimately, the review illustrates how intersecting identities such as race, gender, and sexual orientation aggravate healthcare inequities, emphasizing the need for inclusive, culturally safe clinical environments and research frameworks.The findings of the first analysis presented thoughtful and reflective accounts of puberty experiences, including secondary sex characteristics and menarche. Participant narrative and reflective descriptions are captured under five themes: 1) “I wasn’t prepared:” Lack of Puberty Preparedness, 2) “I just figured it out on my own:” The Need for Self-study, 3) “Taboo:” Influence of Religion, 4) Influence of Sexuality/Gender Roles, and 5) Reproductive Challenges. The analysis presents overarching themes and narrative excerpts from the entire sample, illustrating the shared pubertal experiences of lesbian-identified Black women and aligning with the approach used by other interpretative phenomenological analysis (IPA) researchers.In the second analysis, through interviews, participants described long-standing challenges related to recognizing, managing, and seeking treatment for sexual and/or reproductive-related pain. Four significant barriers and three main facilitators emerged, each of which aligns with Bronfenbrenner’s Ecological Systems Theory, and fell within the tenets of Intersectionality. At the macrosystem level, and aligned with the social inequality tenet of intersectionality, participants identified providers’ lack of LGBTQ+ knowledge as a key barrier, often resulting in inappropriate assumptions and inadequate care. Exosystem-level barriers that centered on navigating financial obstacles, including insurance coverage, medical bills, and fear of unexpected costs, were captured by the social inequality tenet of Intersectionality. Mesosystem-level barriers reflected cultural expectations of “thugging it out,” normalizing pain, and discouraging timely care-seeking, exemplifying the social context component of Intersectionality. Microsystem-level barriers included experiencing healthcare judgment, including being dismissed or stereotyped, and facing weight-related or identity-based bias, which exemplifies the social inequality element of Intersectionality.Conclusion: The current literature revealed a lack of studies exclusive to the personal sexual and reproductive healthcare experiences of lesbian-identified Black women and how these experiences affect their engagement in care. Although several studies applied intersectionality frameworks and include sizeable samples, important gaps remain in how lesbian-identified Black women’s sexual and reproductive health experiences are conceptualized and examined. Much of the existing literature focuses broadly on “Black sexual minority women,” resulting in limited disaggregation by sexual identity and an incomplete understanding of the specific experiences of lesbian-identified Black women.The first analysis highlights the complexity of pubertal experiences of lesbian-identified Black women and reveals ways in which lingering sexual and reproductive healthcare knowledge deficits, compounded by religious restrictions, shame, ridicule, and the adultification of Black girls’ pubescent bodies, stem from systemic issues that disproportionately affect minoritized populations, particularly Black women who identify as gay or lesbian. The second analysis examined current sexual and reproductive healthcare interactions by examining and identifying barriers and facilitators to lesbian-identified Black women seeking care for pain or discomfort related to sexual or reproductive conditions or disorders. Barriers identified include structural and cultural factors, such as Black women normalizing (“thugging out”) pain, being dismissed by healthcare providers, and experiencing discriminatory judgment in healthcare settings and encounters. Facilitators include convenient technological tools, increased self-advocacy related to job title or professional prestige, and access to safe spaces and social support networks. By focusing on inclusive provider training, leveraging technology, and strengthening support networks, obstacles to sexual and reproductive care and treatment can be overcome.Impacts and implications of this dissertation study include sexual and reproductive health resources targeting lesbian-identified Black women, early support and intervention for Black girls during puberty, inclusive and intersectional education and training for healthcare providers, leveraging the benefits of technology for increasing access to and autonomy in healthcare interactions, and increasing and strengthening social support networks for this population.

Biological sex is a universal determinant of mammalian physiology, shaping reproductive traits and multiple non-reproductive systems such as the skeleton. Sex differences in the human musculoskeletal system manifest as divergent characteristics of bone and unequal burdens of diseases like osteoarthritis (OA). OA is a progressive joint disorder that disproportionately affects women in risk and progression. However, sex-related mechanisms remain understudied. Osteocytes, key regulators of bone remodeling and bone–cartilage crosstalk, also remain understudied in OA.This dissertation hypothesized that chromosomal and gonadal sex exert differential effects in osteocyte processes and osteoarthritis (OA). We used the Four Core Genotype (FCG) mice to decouple chromosomal sex (XX vs XY) from gonadal sex (ovaries vs testes) by generating and comparing XX-O, XY-O, XX-T, and XY-T groups. An FCG cohort experienced destabilization of medial meniscus (DMM) surgery at 16 weeks of age to induce OA, evaluating histology scores and longitudinal behavioral assays. All FCG genotypes developed post-traumatic OA, demonstrating that both chromosomally and gonadally female mice develop surgically induced OA. At 12 weeks post-surgery, XY chromosomes and the presence of testes exacerbated cartilage loss and bone modifications, whereas XX chromosomes and ovaries were protective. In behavioral assays, XY-T mice exhibited progressively heightened mechanical sensitivity and greater incapacitance, whereas XX-O mice displayed stability/resilience and better limb-loading performance. Testes were associated with increased total body mass, and XY-T mice showed reduced adiposity relative to other groups.A healthy FCG cohort at 14 weeks of age provided quantification of cortical and trabecular structure, mechanical properties, and osteocyte-intrinsic RNA expression. Trabecular bone parameters were predominantly driven by gonadal sex, with testes increasing trabecular measures. Cortical structure reflected both chromosomal and gonadal contributions, suggesting that XX chromosomes and testes contribute to the same phenotype. The elastic and plastic mechanical properties of bone showed differences in their regulation by sex, with elastic properties influenced by both gonadal and chromosomal sex and plastic properties showing no sex regulation. Bioinformatic analyses detected gonadal and chromosomal sex effects in gene expression. Wildtype animals examined high-fat and high-carbohydrate diets effects on osteocyte senescence markers, finding disrupted osteocyte homeostasis through TGFβ and senescence.Decoupling chromosomal from gonadal sex in the FCG mice revealed that XY chromosomes and testes exacerbate joint degeneration and pain-related impairments, whereas XX chromosomes and ovaries confer protection. Gonadal sex as drives trabecular bone structural properties, while cortical bone and bone mechanical properties show both chromosomal and gonadal sex effects. Osteocyte TGFβ signaling emerged as a central regulator linking diet to osteocyte bone quality. This dissertation shows how different sex effects and sex mechanisms can affect bone and musculoskeletal parameters in both healthy and unhealthy conditions.

Metastasis is a major cause of cancer mortality among patients with breast cancer. Currently, limited options exist for treatment of metastatic disease, none of which are specific to the various changes that tumor cells undergo as they journey from the primary tumor to a distant metastatic site. This dissertation explores mechanisms central to breast cancer metastasis to the lung through tumor cell-intrinsic and -extrinsic lenses. In chapter 1, we present an overview of breast cancer metastasis, the foundational studies that led to what is now known as the “metastatic cascade”, and a current perspective on tumor-intrinsic and -extrinsic mechanisms that can be targeted to treat metastasis which will be the focus of this dissertation. In chapter 2, we test two hypotheses about how pro- and anti-metastatic myeloid phenotypes arise in breast cancer: (1) that pro- and anti-metastatic myeloid microenvironments are discrete and unique, and (2) that pro- and anti-metastatic myeloid microenvironments are two ends of a spectrum of metastatic development. We profiled 12 differently metastatic patient-derived xenograft (PDX) models and discovered that distinct monocyte phenotypes dominate lowly and highly metastatic PDX models. However, we also find that anti-metastatic monocytes are present at early timepoints in highly metastatic tumor models and progressively shift towards a pro-metastatic phenotype. This work demonstrates that there is a window within the metastatic cascade where the lung myeloid microenvironment could be harnessed to suppress metastasis. In chapter 3, we explore a tumor cell-intrinsic approach to suppressing metastasis by investigating the effect of exposure to increased oxygen (“hyperoxia”) on breast cancer metastasis to the lung. We find that hyperoxia depletes electron transport chain subunits, and subsequently leads to a decrease in proliferation, anchorage independent colony-forming ability, and strikingly, spontaneous metastasis to the lung. Collectively, these two studies uncover promising susceptibilities of metastasis that merit further evaluation.

The superior colliculus (SC) is a highly conserved sensorimotor midbrain structure implicated in the control of orienting movements. Yet, despite decades of research, it remains unclear how neural activity in this structure unfolds during internally-driven behaviors like spatial navigation, when orienting movements need to be coordinated with other ongoing behavioral and cognitive processes. This dissertation aims to address this gap. By recording from neurons in the intermediate and deep motor layers of the SC (dSC) of mice navigating a Y-maze, it is demonstrated that: 1) About 30% of neurons fire selectively for left or right turns at the maze bifurcation (left- or right-preferring ‘turn cells’). 2) Turn cell activity is rhythmically modulated during locomotion, firing in-phase with the ongoing stepping cycle of the animal, such that left and right turn cells fire at opposite phases of the stepping cycle. 3) Simultaneous recordings from turn cells and populations of hippocampal place cells reveal that turn cell activity is modulated in directional coordination with hippocampal representations of possible future paths (i.e., hippocampal ‘sweeps’). Critically, hippocampal sweeps prior to the bifurcation can predict turn cell activity at the bifurcation. 4) Consistent with an influence of hippocampal sweeps on turn cell activity, sweeps are associated with biases in the animal’s trajectory toward the represented path. 5) The remaining 70% of neurons in the dSC either exhibit no turn-selective firing at the maze bifurcation or exhibit turn-selective firing that depends on the animal’s starting position on the maze and its upcoming trajectory. Notably, these neurons can exhibit firing that encodes trajectories between two specific maze arms or trajectories converging on a single maze arm.Thus, during navigation, neural activity in the motor layers of the SC reflects not only multiple aspects of ongoing behavior—such as turns, steps, and trajectories—but also ongoing cognitive processes, such as internal representations of possible future paths. These results are consistent with the interpretation that the SC functions as a ‘movement template’, organized as an entire sequence of goal-directed movements, which can be used by higher brain centers for intentional actions (Ewert, 1970; Ingle, 1970; Schaefer, 1970). Drawing on 19th-century psychology, particularly the notion of ‘ideo-motor’ action (Carpenter, 1852; James, 1890), it is further hypothesized the SC plays a central role in transforming cognitive inputs into orienting movements, thereby linking thoughts to actions.

The ability to alter our behavior based on sensory inputs, such as odors or textures, is a necessity for adaptation. The medial prefrontal cortex (mPFC), important for cognitive function(Miller et al., 2001), produces gamma synchrony that is necessary for this behavioral flexibility tested in mice(Cho et al., 2015; Cho et al., 2020; Cho et al., 2023). It is unclear what contributes to this necessary gamma synchrony. The insula is also known to be necessary for proper cognitive function (Gehrlach et al., 2020; Menon et al., 2010; Kayyal et al., 2021), and also has bidirectional connectivity with the mPFC (Gehrlach et al., 2020). Here we apply optogenetic inhibition on the medial insular cortex (mIC) to mPFC projecting (mIC-mPFC) cell bodies and terminals during a Rule-Shifting task in mice to show that this projection is necessary for texture to odor cue rule shifts. We further determine the existence of gamma synchrony between mIC and mPFC parvalbumin interneurons (PVIs) during this task and find a difference in synchrony based on the cue type using a novel recording technique called transmembrane electrical measurements performed optically (TEMPO) (Marshall et al., 2016). This gamma synchrony was shown to be necessary for rule shifts to odor due to a deficit from out-of-phase optogenetic gamma stimulation. Overall, the results show the mIC is necessary for optimal rule shifting to an odor cue.

KCNT1-related epilepsy is a severe neurodevelopmental disorder caused by pathogenic variants in KCNT1, which encodes a sodium-activated potassium channel. In addition to frequent, often treatment-resistant seizures, affected individuals may experience respiratory complications, cardiac abnormalities, hypotonia, skeletal fragility, and gastrointestinal dysfunction. Standard anti-seizure medications are typically ineffective, leaving patients and their caregivers to manage a broad and complex set of symptoms. Although there has been a concerted effort to find better treatment and care for KCNT1 individuals, the underlying mechanism in which mutations in KCNT1 result in multi-organ disorder remains unclear. This dissertation focuses on the role of KCNT1 beyond the synapse, specifically on cilia. In chapter 2, we provide evidence that KCNT1 localizes to both motile and primary cilia across cell types and species and explored overexpression of KCNT1. In chapter 3, we characterized the clinical spectrum, noting multisystem involvement such as respiratory support, cardiac defects, urinary dysfunction, and spinal abnormalities. Next, using Xenopus as a model, we observed KCNT1 expression in developing ciliated tissues and showed that loss of KCNT1 disrupted development of multiciliated cells, reminiscent of recent work on the ion channel Piezo1. Consistently, pharmacological inhibition of Piezo signaling enhanced the ciliogenesis phenotype observed following KCNT1 inhibition, while activation of Piezo1 activity partially rescued ciliogenesis in the context of KCNT1 inhibition. Together, this work establishes that KCNT1 has embryonic functions in Xenopus beyond regulating neuronal activity, specifically in multiciliated cell development, and identifies an interaction with pharmacologically-tractable Piezo channels that may be productive for therapeutic efforts.

Mammalian brains vary in size, structure, and function, but the extent to which evolutionarily novel cell types contribute to this variation remains unresolved. Recent studies suggest there is a primate-specific population of striatal inhibitory interneurons, the TAC3 interneurons. However, broader taxonomic and developmental characterization is required to address novelty in cell type evolution. Here, we examine gene expression in inhibitory neurons across 11 mammalian species, spanning 160 million years divergence from primates. We find that the initial class of newborn TAC3 interneurons specified during development represents an ancestral, MGE-derived striatal population also present in pig and ferret cortex. This discovery prompted a reexamination of the Glire clade, including mice which are thought to lack the TAC3 type. Targeted enrichment of MGE precursors in mice reveals conservation of the TAC3 initial class, camouflaged by reduced expression of Tac2 (the mouse ortholog of TAC3) and a gain of Th expression. Extending our analysis to the adult striatum further supports the homology of primate TAC3 and mouse Th striatal interneurons, while uncovering a rare Tac2 subpopulation in mouse ventromedial striatum. This study suggests that initial classes of telencephalic inhibitory neurons are largely conserved and that during evolution, neuronal types in the mammalian brain change through redistribution and fate refinement, rather than by derivation of novel precursors early in development.

The size of ‘drug-like’ chemical space has been classically estimated to be on the order of 1060 theoretical molecules. Synthetic chemists and commercial vendors continuously expand the subset of tangible chemical space, molecules that can be made available within weeks for assay testing, at a nearly exponential rate. The curation of virtual libraries of tangible compounds makes their exploration feasible through methods such as molecular docking whereby billions of compounds can be modeled into a receptor binding site, scored empirically, and prioritize those most likely to bind. There is an objective truth that for any computational effort to identify a potent and efficacious molecule, that ligand must first exist with the virtual library being screened, with the chemical make-up of these spaces pivotal for success. This thesis applies molecular docking methods utilizing expanded virtual chemical space to ligand discovery at the opioid receptors to improve overall virtual screening hit-rates and initial potencies from diverse and novel scaffolds.Chapter 2 describes both method development and its practical application for the generation and exploration of ‘bespoke’ virtual chemical libraries. Here, we enumerate 14 million synthetically tangible analogs of a [2.2.2]bicyclic isoquinuclidine scaffold to be explored in virtual space for assessment of this unprecedented scaffold. We show how small and quick libraries around targeted chemistry, notably absent form current make-on-demand libraries, can identify the potent binders from among their ranks. Single digit-nanomolar and picomolar antagonists with polypharmacology for the Mu and Kappa opioid receptors were identified in a campaign of less than 50 synthesized compounds. Mouse studies displayed therapeutic potential for opioid withdrawal precipitation with reduced aversive side effect profiles compared to naloxone.Chapter 3 is a showcase of the current pre-published state of our applications of multi-billion scale library docking against the Mu Opioid Receptor (MOR) for ligands diverse in both structure and signaling. We show that as our make-on-demand libraries have grown over time, we continue to see improvements in our hits in terms of hit rate, initial potencies, and varied signaling modalities, even for a receptor with hundreds of years of pharmacology research behind it. We are also able to display the added value of ML/AI-based methods, such as Boltz2 rescoring, in combination with physics-based molecular docking to improve hit rates of the top ranking ligands via the rescuing potent ligands traditionally too low down the DOCK score ranked list. In this effort, we identified an array of nM binders spanning the range of signaling efficacies, including a full agonist with therapeutic potential directly from the docking hit-list.