Faculty Bibliography

Digital spatial profiling (DSP) facilitates RNA sequencing (RNA-seq) of small populations of cells, specifically ~20 pyramidal neurons in postmortem formalin-fixed paraffin-embedded (FFPE) human brain tissue. This approach enables precise expression profiling via RNA-seq data linked to spatially characterized samples utilizing tissue-bound probes. We present a comprehensive protocol for manual slide preparation using the GeoMx DSP system as preliminary steps to spatial characterization of lamina-specific pyramidal neurons in human postmortem Brodmann area 9 (BA9) frontal cortex brain tissue.

Dentate gyrus (DG) function depends on the neurotrophin brain-derived neurotrophic factor (BDNF) which shows robust synthesis in the principal cells, the granule cells (GCs). However, BDNF protein is present in the inner molecular layer (IML), where most afferents to GCs are from hilar mossy cells (MCs). Therefore, we asked whether MCs express BDNF mRNA and protein. Using adult mice, we found that MC BDNF mRNA and protein were expressed in the majority of MC somata and few other hilar neurons. Interestingly, IML BDNF was significantly greater in the ventral compared to dorsal DG. Additionally, dorsal IML BDNF was significantly higher in females on proestrous morning, when serum levels of estrogen peak, relative to metestrous morning, when estrogen is lower. Consistent with this observation, ventral MC somata, which project to the dorsal IML, showed more BDNF mRNA on proestrous morning than metestrous morning. Next, we asked if strong IML BDNF protein expression on proestrous morning was due to estrogen action at estrogen receptors (ERs) because estrogen binding to ERs can increase BDNF synthesis. We found that MCs have high expression of all ERs: ERα, ERβ and GPER1 in both sexes. When sexes were pooled, the percent of MCs labeled by ERβ and GPER1 exceeded the percent of MCs expressing ERα. When proestrous females were examined, GPER1-labeled MCs were greater than MCs labeled by ERα. The results demonstrate robust MC somatic expression of BDNF, relatively high ventral IML expression of BDNF, and estrous cycle dependence. The results also highlight robust MC ER expression, especially ERβ and GPER1, making the hilus a previously underestimated site of estrogen and BDNF action.

The rise of Alzheimer's disease (AD) immunotherapies underscores the need for accessible, time-efficient biomarkers for early diagnosis. MRI-based deep learning shows promise in this regard, yet few models have undergone comprehensive clinical validation. Using the SILCODE cohort (722 Chinese participants, 1,105 scans), we test the transportability of our classifier (pretrained on Western samples) to an independent Chinese cohort without retraining. The associations between risk scores and disease progression, cognitive performance, and plasma biomarkers are examined. In addition, an interpretable framework is developed to generate individualized brain risk maps and identify subtypes. The model classifies AD with an AUC of 0.913 and 95.2% sensitivity, identifying 90.5% of high-risk individuals 2-3 years before clinical diagnosis. Risk scores correlate significantly with cognitive and plasma indices, particularly p-tau 217. Brain risk maps reveal AD subtypes, including a subgroup with rapid cognitive decline. These findings establish a population-robust, clinically relevant MRI-based model for early AD detection and risk stratification.

The relationship between SARS-CoV-2-specific T cell responses and COVID-19 risk is incompletely understood, particularly after variant-adapted booster receipt. We assessed Spike-specific and Nucleocapsid-specific CD4⁺ and CD8⁺ T cell responses, measured by validated 27-color intracellular cytokine staining assay, as correlates of COVID-19 risk over 6 months in COVAIL recipients of a second SARS-CoV-2 booster on Day 1 (D1). Among one-dose mRNA recipients, D15 CD4 + T cell IFN-γ and/or IL-2 Spike BA.4/5 responses correlated inversely with COVID-19 risk for previously-infected (non-naïve) [hazard ratio (HR) = 0.62 (95% CI 0.39, 0.99) per 3-fold increase], but not SARS-CoV-2 naïve [HR = 1.03 (0.81, 1.32)], participants (22 non-naïve, 122 naïve cases). Spike-specific CD4⁺ T cells and neutralizing antibodies each independently predicted COVID-19 in non-naïve participants [Cox bivariate model HRs per standard deviation: D1 Spike CD4 + T cell 0.81 (0.68, 0.96), D15 titer 0.43 (0.27, 0.69), co-correlatep < 0.001]. Among non-naïve participants, high Spike-specific CD4⁺ T cell responses and neutralizing antibody titers marked low risk, as did polyfunctional Spike-specific CD4⁺ T cells expressing ≥ three cytokine(s)/markers. At the same high D15 CD4+ Spike-specific T cell levels, risk was lower for non-naïve vs. naïve participants, suggesting that these T cell responses are a proxy for unmeasured protective immune mechanism(s) operant post-SARS-CoV-2 infection.

The extent to which conserved neural circuit architectures depend on shared molecular specification programs remains unclear. Here, we address this question by examining the somatosensory system of the little skate, Leucoraja erinacea, an early-diverging vertebrate that retains ancestral features of both finned and limb-based body plans. We show that core features of somatosensory circuit organization, including laminar organization of the spinal cord and dorsally restricted targeting of sensory afferents, are deeply conserved. Unexpectedly, the molecular programs specifying dorsal root ganglion (DRG) sensory subtypes diverge extensively from those of mammals. Although DRG neuron subtype specification and spinal connectivity rely on target-derived cues, skates employ distinct neurotrophin receptor and transcription factor identity codes. These findings support a model in which conserved spinal circuit architectures provide a stable scaffold that leverages flexible sensory neuron specification programs, enabling the evolutionary diversification of vertebrate somatosensory systems.

Cochlear implants (CIs) stimulate auditory neurons with electric pulse trains whose amplitudes are modulated using envelopes extracted from different frequency bands, conveying essential speech cues. This study investigated how the rate of stimulation pulses affects envelope processing and speech perception in ten post-lingually deaf CI users. Amplitude modulation (AM) detection and consonant identification were examined using acoustic stimuli processed by multi-channel and single-channel strategies, with pulse rates ranging from 125 to 2000 pulses per second (pps) for multi-channel stimulation and from 125 to 4000pps for single-channel stimulation. The single-channel conditions encoded the overall broad-band speech envelope by a single electrode and were used to isolate within-electrode temporal modulation coding. For AM detection, the modulation frequency was 25 Hz ensuring sufficient modulation sampling across all carrier rates tested. Even at 125pps, the 25-Hz modulation was represented by five pulses per modulation cycle. Results revealed a significant decline in both AM detection and consonant identification at 125pps, suggesting that poorer speech recognition at low rates may be partly attributable to limitations in temporal modulation processing rather than solely to a restricted range of representable envelope frequencies. Consonant recognition performance remained stable across clinically relevant pulse rates (250-2000pps), though significant listener- and feature-specific effects were observed. Notably, while AM detection and consonant recognition were not significantly correlated within this small cohort, significant correlations were found between single-channel and multi-channel performance in both tasks. These findings support an important role for within-electrode temporal coding in CI speech perception and highlight the clinical relevance of individual variability in pulse rate effects.

Can the transcriptomic profile of a neuron predict its physiological properties? Using a Patch-seq dataset of the primary visual cortex, we addressed this question by focusing on spike rate adaptation (SRA), a well-known phenomenon that depends on small conductance calcium (Ca)-dependent potassium (SK) channels. We first show that in parvalbumin-expressing (PV) and somatostatin-expressing (SST) interneurons, expression levels of genes encoding the ion channels underlying action potential generation are correlated with the half-width (HW) of spikes. Surprisingly, the SK encoding genes are not correlated with the degree of SRA (dAdap). Instead, genes that encode proteins upstream from the SK current, as well as the low-voltage-activated calcium channel, are correlated with dAdap. This general principle is supported by datasets from the mouse primary motor cortex and multiple macaque brain regions. Finally, we generate testable predictions by constructing a minimal computational model.

Astrocyte contributions to CNS antigen presentation remain poorly defined. We show that interferon gamma (IFN-γ, the sole type II interferon), with proinflammatory cytokines, induces astrocytes to express components mediating attraction of and antigen presentation to CD4⁺ T cells. Re-analysis of astrocyte-enriched single-cell sequencing from bacterial mimetic-injected mice revealed a transcriptionally distinct, IFN-responsive astrocyte population enriched for antigen-presentation genes 24 h after peripheral immune challenge. In vivo, type II major histocompatibility complex (MHC-II⁺)GFAP⁺ astrocytes localize to the brain surface across multiple mouse models of neuroinflammation and in human neurological disease tissue. In vitro, purified astrocytes stimulated with IFN-γ and proinflammatory cytokines expressed MHC-II, costimulatory molecules, and lymphocyte-recruiting chemokines, and in co-culture supported rapid antigen-dependent expansion of previously activated CD4⁺ T cells. Human iPSC-derived CNS cultures showed equivalent induction of antigen-presentation machinery in human astrocytes following inflammatory cytokine stimulation. These findings define a cytokine-induced astrocyte state expressing antigen-presentation machinery at neuroimmune interfaces that can support local CD4⁺ T cell responses.

Functional abnormalities of the globus pallidus interna (GPi) are linked to psychosis severity and treatment response in schizophrenia. Transcranial ultrasound stimulation (TUS) is a noninvasive method for precisely targeting deep brain structures. The effects of GPi-targeted TUS on psychosis had not been examined. We conducted a random-order, sham-controlled, crossover pilot study assessing safety, tolerability, and preliminary efficacy of right GPi TUS for psychotic symptoms. Ten outpatients (mean age 37.5; 50% female) with schizophrenia or schizoaffective disorder and persistent psychosis received one TUS and one sham session, one week apart. TUS was MRI-guided, targeting right GPi with a 350 kHz transducer (100 Hz pulse repetition frequency, 5% duty cycle, in situ I _spta 400 mW/cm²). Outcomes-delusion experience sampling assessment (DESA) and auditory hallucinations rating scale (AHRS)-were measured before, during, and immediately, 1 h, 1, and 7 days after stimulation. DESA scores decreased significantly more after TUS than sham (p = 0.002, Cohen's d = 0.68); AHRS and cognition changes were not significant. Mild transient adverse effects occurred in both conditions; none were serious. GPi-targeted TUS was safe, well-tolerated, and associated with a preliminary reduction in delusional severity, warranting further study in larger, randomized trials. ClinicalTrials.gov: NCT05643196, registered 21 November 2022.