Biology subjects

Totty, M. S.

Publications and source records attributed to Totty, M. S..

11 recordsLinked to original sources

bioRxiv2026

Multiscale spatial transcriptomics resolves the cellular and molecular architecture of the human amygdala

The amygdala is a central hub for emotional learning that is dysregulated across numerous psychiatric disorders, yet its molecular architecture in humans remains poorly defined. We here present a spatial transcriptomic atlas of the human amygdala from nine neurotypical donors. Integrating Visium, Xenium, and VisiumHD technologies, we profiled over 1.1 million cells across 13 spatial domains spanning the basolateral complex, central, medial, and cortical nuclei, as well as the intercalated islands, each defined by distinct marker genes and gene co-expression networks. By integrating snRNA-seq reference atlases, we found that each subdivision of the basolateral subnucleus contains distinct excitatory neuron classes. We additionally found three transcriptionally distinct populations of intercalated neuron types, two of which form spatially distinct islands neighboring the basolateral complex, and were able to refine cell type diversity across the central nucleus and related amygdalostriatal transition areas. Finally, we localized psychiatric genetic risk across the amygdala, revealing both broad neuronal enrichment and subnuclear specificity. Together, this atlas provides a foundational resource and framework for accelerating cross-species comparisons and human disease-focused investigations.

neuroscience↗

bioRxiv2026

SpatialArtifacts: a computational framework for tissue artifact detection in spatial transcriptomics data

Spatial transcriptomics data are frequently compromised by technical artifacts, such as dry patches, tissue lifting, and uneven reagent coverage, which manifests as regions with low UMI counts, in particular at tissue borders. It can often be challenging to identify these regions using existing quality control methods. Here, we present SpatialArtifacts, a framework that combines median absolute deviation (MAD)-based outlier detection with mathematical morphology operations to identify and classify spatially contiguous tissue artifacts. Focal operations including 3x3 fill, 5x5 outline, and star-pattern connectivity link low-quality spots while preserving true biological domains. We use a hierarchical classification system to distinguish edge versus interior artifacts and large versus small regions, enabling downstream removal or targeted manual review. We demonstrate the performance of our method in human hippocampus, dorsolateral prefrontal cortex, and colorectal cancer tissues using 10x Genomics Visium and VisiumHD platforms. Our SpatialArtifacts package is freely available on Bioconductor at https://bioconductor.org/packages/SpatialArtifacts and on PyPI at https://pypi.org/project/spatial-artifacts/.

bioinformatics↗

bioRxiv2025

Spotsweeper-py: spatially-aware quality control metrics for spatial omics data in the Python ecosystem

Spatially-resolved transcriptomics (SRT) generates large and heterogeneous datasets where global (tissue-wide) quality control (QC) metrics often over-aggressively remove biologically meaningful regions or miss localized artifacts. Recently, spatially-aware QC metrics have been introduced in SpotSweeper, but this is limited to the R programming language, which makes it challenging to use these metrics within the Python/scverse ecosystem. Here, we present SpotSweeper-py, a Python equivalent package of SpotSweeper that computes neighborhood-aware z-scores for standard QC metrics such as total counts, log total counts, number of detected genes, and percentage of mitochondrial counts. We demonstrate the performance and usability of SpotSweeper-py on two public datasets from the 10x Genomics Visium and VisiumHD platforms. This implementation of local spatially-aware QC metrics enables direct integration with Python/scverse ecosystem, reduces false positives from global quality control while preserving tissue-specific architecture. Plotting utilities are also included for quick visualizations of flagged outliers. By making robust local QC accessible in Python, SpotSweeper-py strengthens the reliability of pipelines for analyzing SRT data. The open-source software is available on PyPI (https://pypi.org/project/spotsweeper).

bioinformatics↗

bioRxiv2025

Transcriptional response to chronic long-access fentanyl self-administration in rat habenula and amygdala

Fentanyl is a potent synthetic opioid associated with overdose. However, little is known about fentanyl-induced molecular adaptations in the habenula and amygdala, two brain regions implicated in opioid use and withdrawal. We performed bulk RNA-sequencing in the rat habenula and amygdala to identify transcriptomic changes associated with fentanyl intake. Rats self-administered intravenous saline or fentanyl over 22-24 days. Ninety minutes following the final session, brains were collected for transcriptomic profiling. In Hb, we identified 453 differentially expressed genes (DEGs) between saline and fentanyl rats, with upregulated genes associated with synaptic transmission and ionic conductance. In amygdala, we identified 3,041 fentanyl-associated DEGs with upregulated genes implicated in metabolic and vesicular functions. Downregulated genes in both regions were enriched for extracellular matrix functions. Integration of DEGs with single-cell RNA-sequencing data from rodents and humans revealed that fentanyl DEGs were enriched in specific habenula and amygdala cell type markers. Furthermore, fentanyl downregulated DEGs in amygdala were enriched in genes associated with risk for substance use disorders. Together, we define how fentanyl intake alters transcriptional programs in the rat habenula and amygdala, and we link these changes to specific human cell types and risk genes for neuropsychiatric disorders and addiction.

neuroscience↗

bioRxiv2025

Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain

In the human brain, the dorsal anterior cingulate cortex (dACC) plays key roles in various components of cognitive control, and is particularly relevant for reward processing and conflict monitoring. The dACC regulates expression of fear and pain, and its dysfunction is implicated in a number of neuropsychiatric disorders. Compared to more recently specialized neocortical areas, such as the dorsolateral prefrontal cortex (dlPFC), the dACC is evolutionarily older. The regions agranular structure, and other evolutionary specializations, such as the presence of von Economo neurons (VENs), contribute to its specialized roles in cognitive and emotional processing. Here, we generated paired spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from adjacent tissue sections of the dACC in ten adult neurotypical donors to define molecular profiles for dACC cell types and spatial domains. Using non-negative matrix factorization (NMF), we integrated these data by identifying gene expression patterns within the snRNA-seq data, which were projected onto the SRT data to infer the spatial localization. Combining these data with publicly available resources, we revealed insights about molecular profiles, spatial topography, enrichment of disease risk, and putative connectivity of spatially-localized dACC cell types, including VENs. Utilizing published dlPFC snRNA-seq and SRT data collected in the same neurotypical brain donors used here, we deployed cross-region comparison analyses between dACC and dlPFC to understand spatio-molecular specializations and laminar organization across human brain evolution. To make this comprehensive molecular resource accessible to the scientific community, we made both raw and processed data freely available, including through interactive web applications.

neuroscience↗

bioRxiv2025

Hippocampal-prelimbic coupling during context-dependent extinction retrieval in rats

After fear conditioning, repeated presentation of the conditioned stimulus (CS) alone produces a context-dependent extinction of learned fear. The hippocampus has a critical role in this process, but the mechanism by which contextual information encoded by the hippocampus leads to fear suppression is unknown. We hypothesize that contextual information encoded by the dorsal hippocampus supports the recall of extinction memory by the medial prefrontal cortex (mPFC). To test this hypothesis, we evaluated the oscillatory coherence and directional coupling of the hippocampus and mPFC during context-dependent extinction retrieval in a previously published experiment. In this experiment, male and female rats were subjected to auditory fear conditioning followed by fear extinction and extinction retrieval procedures. Previous analyses focused on oscillatory coupling during the CS; here, we performed new analyses to assess hippocampal-prefrontal coupling in the context in which extinction occurred. We found that, after extinction, re-exposing the animals to the extinction context produces a marked increase in dorsal hippocampal theta (6-8 Hz) oscillations. This increase was associated with enhanced coherence with the prelimbic (PL), but not the infralimbic (IL), division of the mPFC. Moreover, Granger causality analyses revealed that hippocampal theta oscillations preceded theta in the PL throughout the extinction retrieval session. This effect emerged during exposure to the extinction context and persisted during the presentation of the CSs and the expression of freezing behavior. Interestingly, this pattern of coherence was not observed in the IL. These results reveal that oscillatory coupling between the dorsal hippocampus and PL facilitates the context-dependent retrieval of the extinguished fear memory.

neuroscience↗

bioRxiv2024

Transcriptomic diversity of amygdalar subdivisions across humans and nonhuman primates

The amygdaloid complex mediates learning, memory, and emotions. Understanding the cellular and anatomical features that are specialized in the amygdala of primates versus other vertebrates requires a systematic, anatomically-resolved molecular analysis of constituent cell populations. We analyzed five nuclear subdivisions of the primate amygdala with single-nucleus RNA sequencing in macaques, baboons, and humans to examine gene expression profiles for excitatory and inhibitory neurons and confirmed our results with single-molecule FISH analysis. We identified distinct subtypes of FOXP2+ interneurons in the intercalated cell masses and protein-kinase C-{delta} interneurons in the central nucleus. We also establish that glutamatergic, pyramidal-like neurons are transcriptionally specialized within the basal, lateral, or accessory basal nuclei. Understanding the molecular heterogeneity of anatomically-resolved amygdalar neuron types provides a cellular framework for improving existing models of how amygdalar neural circuits contribute to cognition and mental health in humans by using nonhuman primates as a translational bridge.

neuroscience↗

bioRxiv2024

SpotSweeper: spatially-aware quality control for spatial transcriptomics

Quality control (QC) is a crucial step to ensure the reliability and accuracy of the data obtained from RNA sequencing experiments, including spatially-resolved transcriptomics (SRT). Existing QC approaches for SRT that have been adopted from single-nucleus RNA sequencing (snRNA-seq) methods are confounded by spatial biology and are inappropriate for SRT data. In addition, no methods currently exist for identifying histological tissue artifacts unique to SRT. Here, we introduce SpotSweeper, spatially-aware QC methods for identifying local outliers and regional artifacts in SRT. SpotSweeper evaluates the quality of individual spots relative to their local neighborhood, thus minimizing bias due to biological heterogeneity, and uses multiscale methods to detect regional artifacts. Using SpotSweeper on publicly available data, we identified a consistent set of Visium barcodes/spots as systematically low quality and demonstrate that SpotSweeper accurately identifies two distinct types of regional artifacts, resulting in improved downstream clustering and marker gene detection for spatial domains.

bioinformatics↗

bioRxiv2022

Thalamic nucleus reuniens coordinates prefrontal-hippocampal synchrony to suppress extinguished fear

Traumatic events result in vivid and enduring fear memories. Suppressing the retrieval of these memories is central to behavioral therapies for pathological fear. The medial prefrontal cortex (mPFC) and hippocampus (HPC) have been implicated in retrieval suppression, but how mPFC-HPC activity is coordinated during extinction retrieval is unclear. Here we show that after extinction training, coherent theta oscillations (6-9 Hz) in the HPC and mPFC are correlated with the suppression of conditioned freezing in male and female rats. Inactivation of the nucleus reuniens (RE), a thalamic hub interconnecting the mPFC and HPC, reduces extinction-related Fos expression in both the mPFC and HPC, dampens mPFC-HPC theta coherence, and impairs extinction retrieval. Conversely, theta-paced optogenetic stimulation of RE augments fear suppression and reduces relapse of extinguished fear. Collectively, these results demonstrate a novel role for RE in coordinating mPFC-HPC interactions to suppress fear memories after extinction.

neuroscience↗

bioRxiv2021

Convergent coding of recent and remote fear memory in the basolateral amygdala

BackgroundIn both rodents and humans, the basolateral amygdala (BLA) is essential for encoding and retrieving conditioned fear memories. Although the BLA is a putative storage site for these memories, recent evidence suggests that they become independent of the BLA with the passage of time. MethodsWe systematically examined the role for the BLA in the retrieval of recent (1 day) and remote (2 weeks) fear memory using optogenetic, electrophysiological, and calcium imaging methods in male and female Long-Evans rats. Critically, we used a behavioral design that permits within-subjects comparison of recent and remote memory at the same time point; freezing behavior served as the index of learned fear. ResultsWe found that BLA c-Fos expression was similar after the retrieval of recent or remote fear memories. Extracellular single-unit recordings in awake, behaving animals revealed that single BLA neurons exhibit robust increases in spike firing to both recent and remote conditional stimuli (CSs). Fiber photometry recordings revealed that these patterns of activity emerge from principal neurons. Consistent with these results, optogenetic inhibition of BLA principal neurons impaired conditioned freezing to both recent and remote CSs. There were no sex differences in any of the measures or manipulations. ConclusionsThese data reveal that BLA neurons encode both recent and remote fear memories, suggesting substantial overlap in the allocation of temporally distinct events. This may underlie the broad generalization of fear memories across both space and time. Ultimately, these results provide evidence that the BLA is a long-term storage site for emotional memories.

neuroscience↗

bioRxiv2021

Behavioral and brain mechanisms mediating conditioned flight behavior in rats

Environmental contexts and associative learning can inform animals of potential threats, though it is currently unknown how contexts bias defensive transitions. Here we investigated context-dependent flight responses in the Pavlovian serial-compound stimulus (SCS) paradigm. We show here that SCS-evoked flight behavior in male and female rats is dependent on contextual fear. Flight was reduced in the conditioning context after context extinction and could be evoked in a different shock-associated context. Although flight was exclusive to white noise stimuli, it was nonetheless associative insofar as rats that received an equal number of unpaired USs did not show flight-like behavior. Finally, we found that inactivation of either the central nucleus of the amygdala (CeA) or bed nucleus of the stria terminalis (BNST) attenuated both contextual fear and flight responses. This work demonstrates that contextual fear summates with cued and innate fear to drive a high fear state and freeze-to-flight transitions.

neuroscience↗