Publications

Spatial transcriptomics (ST) unlocks new potential for studying gene functions in cellular processes, as these functions often depend on the or-chestration of transcription across space. However, despite their growing number, analysis tools for ST remain largely aimed at data exploration, with few resources for theory-driven hypothesis testing. What’s missing is a way to test whether a factor of interest affects functionally relevant parameters of a gene’s spatial distribution. We present a tool to fill this gap, which we call a warped sigmoidal Poisson-process mixed-effects (WSP, pronounced “wisp”) model. WSP models are the first ST tool allowing researchers to test biologically critical questions without bespoke preprocessing pipelines for identifying key spatial parameters. By aligning coordinates to an axis of interest and letting a likelihood-based regression find between-group effects on expression rates and boundaries, WSP models replace error-prone manual preprocessing with minimally biased hypothesis testing. Integration with genome databases such as GO and KEGG is straightforward, as WSP model estimates of effects take the form of log fold change values. Using MERFISH data collected from wild-type mouse pups, we demonstrate utility by using a WSP model to test the hypothesis that there are interacting effects of age and laterality on gene expression during whisker barrel development.

Some of the most complex cognitive functions are possible because different sides of your brain control them. Chief among them is speech perception, the ability to interpret language. In people, the speech perception process is typically dominated by the left hemisphere.

Your brain breaks apart fleeting streams of acoustic information into parallel channels – linguistic, emotional and musical – and acts as a biological multicore processor. Although scientists have recognized this division of cognitive labor for over 160 years, the mechanisms underpinning it remain poorly understood.

Researchers know that distinct subgroups of neurons must be tuned to different frequencies and timing of sound. In recent decades, studies on animal models, especially in rodents, have confirmed that splitting sound processing across the brain is not uniquely human, opening the door to more closely dissecting how this occurs.

Yet a central puzzle persists: What makes near-identical regions in opposite hemispheres of the brain process different types of information?

Answering that question promises broader insight into how experience sculpts neural circuits during critical periods of early development, and why that process is disrupted in neurodevelopmental disorders.

Lateralized auditory processing is essential for specialized functions such as speech processing, typically dominated by the Left Auditory Cortex (ACx) in humans. Hemispheric specializations also occur in the adult mouse ACx, but their developmental origins are unclear. Our study finds that the Left and Right ACx in mice reach developmental milestones at different ages. Thalamocortical responses and maturation of synaptic dynamics develop earlier in the Right ACx than the Left. We show that this timing offset predicts hemisphere-dependent differences in sensory-driven plasticity. Juvenile tone exposure at specific times results in imbalanced adult tone frequency representations in the Right and Left ACx. Additionally, sex influences the timing of plasticity; female Right ACx plasticity occurs before male Right ACx, and female Left ACx aligns with male Right ACx plasticity. Our findings demonstrate that sex and hemispheric identity drive asynchronous development and contribute to functional differences in sensory cortices.

DNA repair mechanisms are essential for cellular development and function. This is particularly true in post-mitotic neurons, where deficiencies in DNA damage response proteins can result in severe neurodegenerative and neurodevelopmental disorders. One highly conserved factor involved in DNA repair is Mut-S Homolog 2 (Msh2), which is responsible for correcting base- base mismatches and insertion/deletion loops during cell proliferation. However, its role in mature neuronal function remains poorly understood. This study investigates the impact of Msh2 loss on sensory processing in a mouse model. Using electrophysiological and molecular assays, we identified significant deficits in cortical and thalamic sound processing in Msh2ᐨᐟᐨ mice. These deficits were linked to dysfunction of the thalamic reticular nucleus (TRN), a brain region that critically regulates corticothalamic and thalamocortical activity. Our findings revealed increased oxidative damage, aberrant neuronal activity, and elevated parvalbumin (PV) expression in PVᐩ interneurons in the TRN of Msh2ᐨᐟᐨ mice. Additionally, we observed the presence of connexin plaques, indicating that disrupted gap junction formation may contribute to impaired TRN function. These results underscore the critical role of Msh2 in supporting the functionality of PVᐩ interneurons in the TRN, thereby profoundly influencing sensory processing pathways. This study provides new insights into the importance of DNA repair mechanisms in neuronal development and function, potentially contributing to our understanding of their role in neurological disorders.

Brain asymmetry in the sensitivity to spectrotemporal modulation is an established functional feature that underlies the perception of speech and music. The left auditory cortex (ACx) is believed to specialize in processing fast temporal components of speech sounds, and the right ACx slower components. However, the circuit features and neural computations behind these lateralized spectrotemporal processes are poorly understood. To answer these mechanistic questions we use mice, an animal model that captures some relevant features of human communication systems. In this study, we screened for circuit features that could subserve temporal integration differences between the left and right ACx. We mapped excitatory input to principal neurons in all cortical layers and found significantly stronger recurrent connections in the superficial layers of the right ACx compared to the left. We hypothesized that the underlying recurrent neural dynamics would exhibit differential characteristic timescales corresponding to their hemispheric specialization. To investigate, we recorded spike trains from awake mice and estimated the network time constants using a statistical method to combine evidence from multiple weak signal-to-noise ratio neurons. We found longer temporal integration windows in the superficial layers of the right ACx compared to the left as predicted by stronger recurrent excitation. Our study shows substantial evidence linking stronger recurrent synaptic connections to longer network timescales. These findings support speech processing theories that purport asymmetry in temporal integration is a crucial feature of lateralization in auditory processing.

Background

Transcranial direct current stimulation (DCS) has lasting effects that may be explained by a boost in synaptic long-term potentiation (LTP). We hypothesized that this boost is the result of a modulation of somatic spiking in the postsynaptic neuron, as opposed to indirect network effects. To test this directly we record somatic spiking in a postsynaptic neuron during LTP induction with concurrent DCS.

Methods

We performed rodent in-vitro patch-clamp recordings at the soma of individual CA1 pyramidal neurons. LTP was induced with theta-burst stimulation (TBS) applied concurrently with DCS. To test the causal role of somatic polarization, we manipulated polarization via current injections. We also used a computational multi-compartment neuron model that captures the effect of electric fields on membrane polarization and activity-dependent synaptic plasticity.

Results

TBS-induced LTP was enhanced when paired with anodal DCS as well as depolarizing current injections. In both cases, somatic spiking during the TBS was increased, suggesting that evoked somatic activity is the primary factor affecting LTP modulation. However, the boost of LTP with DCS was less than expected given the increase in spiking activity alone. In some cells, we also observed DCS-induced spiking, suggesting DCS also modulates LTP via induced network activity. The computational model reproduces these results and suggests that they are driven by both direct changes in postsynaptic spiking and indirect changes due to network activity.

Conclusion

DCS enhances synaptic plasticity by increasing postsynaptic somatic spiking, but we also find that an increase in network activity may boost but also limit this enhancement.

The neural circuits responsible for social communication are among the least understood in the brain. Human studies have made great progress in advancing our understanding of the global computations required for processing speech, and animal models offer the opportunity to discover evolutionarily conserved mechanisms for decoding these signals. In this review article, we describe some of the most well-established speech decoding computations from human studies and describe animal research designed to reveal potential circuit mechanisms underlying these processes. Human and animal brains must perform the challenging tasks of rapidly recognizing, categorizing, and assigning communicative importance to sounds in a noisy environment. The instructions to these functions are found in the precise connections neurons make with one another. Therefore, identifying circuit-motifs in the auditory cortices and linking them to communicative functions is pivotal. We review recent advances in human recordings that have revealed the most basic unit of speech decoded by neurons is a phoneme, and consider circuit-mapping studies in rodents that have shown potential connectivity schemes to achieve this. Finally, we discuss other potentially important processing features in humans like lateralization, sensitivity to fine temporal features, and hierarchical processing. The goal is for animal studies to investigate neurophysiological and anatomical pathways responsible for establishing behavioral phenotypes that are shared between humans and animals. This can be accomplished by establishing cell types, connectivity patterns, genetic pathways and critical periods that are relevant in the development and function of social communication.

The left hemisphere's dominance in processing social communication has been known for over a century, but the mechanisms underlying this lateralized cortical function are poorly understood. Here, we compare the structure, function, and development of each auditory cortex (ACx) in the mouse to look for specializations that may underlie lateralization. Using Fos brain volume imaging, we found greater activation in the left ACx in response to vocalizations, while the right ACx responded more to frequency sweeps. In vivo recordings identified hemispheric differences in spectrotemporal selectivity, reinforcing their functional differences. We then compared the synaptic connectivity within each hemisphere and discovered lateralized circuit-motifs that are hearing experience-dependent. Our results suggest a specialist role for the left ACx, focused on facilitating the detection of specific vocalization features, while the right ACx is a generalist with the ability to integrate spectrotemporal features more broadly.

Connectivity determines the function of neural circuits and it is the gateway to behavioral output. The emergent properties of the Auditory Cortex (ACx) have been difficult to unravel partly due to our assumption that it is organized similarly to other sensory areas. But detailed investigations of its functional connectivity have begun to reveal significant differences from other cortical areas that perform different functions. Using Laser Scanning Photostimulation we previously discovered unique circuit features in the ACx. Specifically, we found that the functional asymmetry of the ACx (tonotopy and isofrequency axes) is reflected in the local circuitry of excitatory inputs to Layer 3 pyramidal neurons. In the present study we extend the functional wiring diagram of the ACx with an investigation of the connectivity patterns of inhibitory subclasses. We compared excitatory input to parvalbumin (PV) and somatostatin (SOM)-expressing interneurons and found distinct circuit-motifs between and within these subpopulations. Moreover, these connectivity motifs emerged as intrinsic differences between the left and right ACx. Our results support a functional circuit based approach to understand the role of inhibitory neurons in auditory processing.

Brain regions contain diverse populations of neurons that project to different long-range targets. The study of these subpopulations in circuit function and behavior requires a toolkit to characterize and manipulate their activity in vivo. We have developed a novel set of reagents based on Pseudorabies Virus (PRV) for efficient and long-term genetic tagging of neurons based on their projection targets. By deleting IE180, the master transcriptional regulator in the PRV genome, we have produced a mutant virus capable of infection and transgene expression in neurons but unable to replicate in or spread from those neurons. IE180-null mutants showed no cytotoxicity, and infected neurons exhibited normal physiological function more than 45 days after infection, indicating the utility of these engineered viruses for chronic experiments. To enable rapid and convenient construction of novel IE180-null recombinants, we engineered a bacterial artificial chromosome (BAC) shuttle-vector system for moving new constructs into the PRV IE180-null genome. Using this system we generated an IE180-null recombinant virus expressing the site-specific recombinase Cre. This Cre-expressing virus (PRV-hSyn-Cre) efficiently and robustly infects neurons in vivo and activates transgene expression from Cre-dependent vectors in local and retrograde projecting populations of neurons in the mouse. We also generated an assortment of recombinant viruses expressing fluorescent proteins (mCherry, EGFP, ECFP). These viruses exhibit long-term labeling of neurons in vitro but transient labeling in vivo. Together these novel IE180-null PRV reagents expand the toolkit for targeted gene expression in the brain, facilitating functional dissection of neuronal circuits in vivo.

Neurons integrate inputs arriving in different cellular compartments to produce action potentials that are transmitted to other neurons. Because of the voltage- and time-dependent conductances in the dendrites and soma, summation of synaptic inputs is complex. To examine summation of membrane potentials and firing rates, we performed whole-cell recordings from layer 5 cortical pyramidal neurons in acute slices of the rat's somatosensory cortex. We delivered subthreshold and suprathreshold stimuli at the soma and several sites on the apical dendrite, and injected inputs that mimic synaptic barrages at individual or distributed sites. We found that summation of subthreshold potentials differed from that of firing rates. Subthreshold summation was linear when barrages were small but became supralinear as barrages increased. When neurons were discharging repetitively the rules were more diverse. At the soma and proximal apical dendrite summation of the evoked firing rates was predominantly sublinear whereas in the distal dendrite summation ranged from supralinear to sublinear. In addition, the integration of inputs delivered at a single location differed from that of distributed inputs only for suprathreshold responses. These results indicate that convergent inputs onto the apical dendrite and soma do not simply summate linearly, as suggested previously, and that distinct presynaptic afferents that target specific sites on the dendritic tree may perform unique sets of computations.

Autism spectrum disorders (ASDs) are highly heritable developmental disorders caused by a heterogeneous collection of genetic lesions. Here we use a mouse model to study the effect on cortical connectivity of disrupting the ASD candidate gene PTEN (phosphatase and tensin homolog deleted on chromosome 10). Through Cre-mediated recombination, we conditionally knocked out PTEN expression in a subset of auditory cortical neurons. Analysis of long-range connectivity using channelrhodopsin-2 revealed that the strength of synaptic inputs from both the contralateral auditory cortex and from the thalamus onto PTEN-cko neurons was enhanced compared with nearby neurons with normal PTEN expression. Laser-scanning photostimulation showed that local inputs onto PTEN-cko neurons in the auditory cortex were similarly enhanced. The hyperconnectivity caused by PTEN-cko could be blocked by rapamycin, a specific inhibitor of the PTEN downstream molecule mammalian target of rapamycin complex 1. Together, our results suggest that local and long-range hyperconnectivity may constitute a physiological basis for the effects of mutations in PTEN and possibly other ASD candidate genes.

The primary auditory cortex (A1) is organized tonotopically, with neurons sensitive to high and low frequencies arranged in a rostro-caudal gradient. We used laser scanning photostimulation in acute slices to study the organization of local excitatory connections onto layers 2 and 3 (L2/3) of the mouse A1. Consistent with the organization of other cortical regions, synaptic inputs along the isofrequency axis (orthogonal to the tonotopic axis) arose predominantly within a column. By contrast, we found that local connections along the tonotopic axis differed from those along the isofrequency axis: some input pathways to L3 (but not L2) arose predominantly out-of-column. In vivo cell-attached recordings revealed differences between the sound-responsiveness of neurons in L2 and L3. Our results are consistent with the hypothesis that auditory cortical microcircuitry is specialized to the one-dimensional representation of frequency in the auditory cortex.