@article {69482, title = {Aging atlas reveals cell-type-specific effects of pro-longevity strategies.}, journal = {Nat Aging}, year = {2024}, month = {2024 May 30}, abstract = {

Organismal aging involves functional declines in both somatic and reproductive tissues. Multiple strategies have been discovered to extend lifespan across species. However, how age-related molecular changes differ among various tissues and how those lifespan-extending strategies slow tissue aging in distinct manners remain unclear. Here we generated the transcriptomic Cell Atlas of Worm Aging (CAWA, http://mengwanglab.org/atlas ) of wild-type and long-lived strains. We discovered cell-specific, age-related molecular and functional signatures across all somatic and germ cell types. We developed transcriptomic aging clocks for different tissues and quantitatively determined how three different pro-longevity strategies slow tissue aging distinctively. Furthermore, through genome-wide profiling of alternative polyadenylation (APA) events in different tissues, we discovered cell-type-specific APA changes during aging and revealed how these changes are differentially affected by the pro-longevity strategies. Together, this study offers fundamental molecular insights into both somatic and reproductive aging and provides a valuable resource for in-depth understanding of the diversity of pro-longevity mechanisms.

}, issn = {2662-8465}, doi = {10.1038/s43587-024-00631-1}, author = {Gao, Shihong Max and Qi, Yanyan and Zhang, Qinghao and Guan, Youchen and Lee, Yi-Tang and Ding, Lang and Wang, Lihua and Mohammed, Aaron S and Li, Hongjie and Fu, Yusi and Wang, Meng C} } @article {69251, title = {The cell-type-specific spatial organization of the anterior thalamic nuclei of the mouse brain.}, journal = {Cell Reports}, volume = {43}, year = {2024}, month = {2024 Feb 29}, pages = {113842}, abstract = {

Understanding the cell-type composition and spatial organization of brain regions is crucial for interpreting brain computation and function. In the thalamus, the anterior thalamic nuclei (ATN) are involved in a wide variety of functions, yet the cell-type composition of the ATN remains unmapped at a single-cell and spatial resolution. Combining single-cell RNA sequencing, spatial transcriptomics, and multiplexed fluorescent in situ hybridization, we identify three discrete excitatory cell-type clusters that correspond to the known nuclei of the ATN and uncover marker genes, molecular pathways, and putative functions of these cell types. We further illustrate graded spatial variation along the dorsomedial-ventrolateral axis for all individual nuclei of the ATN and additionally demonstrate that the anteroventral nucleus exhibits spatially covarying protein products and long-range inputs. Collectively, our study reveals discrete and continuous cell-type organizational principles of the ATN, which will help to guide and interpret experiments on ATN computation and function.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2024.113842}, author = {Kapustina, Margarita and Zhang, Angela A and Tsai, Jennifer Y J and Bristow, Brianna N and Kraus, Larissa and Sullivan, Kaitlin E and Erwin, Sarah R and Wang, Lihua and Stach, Tara R and Clements, Jody and Lemire, Andrew L and Cembrowski, Mark S} } @article {69548, title = {Cohesin prevents cross-domain gene coactivation.}, journal = {Nat Genet}, year = {2024}, month = {2024 Jul 24}, abstract = {

The contrast between the disruption of genome topology after cohesin loss and the lack of downstream gene expression changes instigates intense debates regarding the structure-function relationship between genome and gene regulation. Here, by analyzing transcriptome and chromatin accessibility at the single-cell level, we discover that, instead of dictating population-wide gene expression levels, cohesin supplies a general function to neutralize stochastic coexpression tendencies of cis-linked genes in single cells. Notably, cohesin loss induces widespread gene coactivation and chromatin co-opening tens of million bases apart in cis. Spatial genome and protein imaging reveals that cohesin prevents gene co-bursting along the chromosome and blocks spatial mixing of transcriptional hubs. Single-molecule imaging shows that cohesin confines the exploration of diverse enhancer and core promoter binding transcriptional regulators. Together, these results support that cohesin arranges nuclear topology to control gene coexpression in single cells.

}, issn = {1546-1718}, doi = {10.1038/s41588-024-01852-1}, url = {https://doi.org/10.1038/s41588-024-01852-1}, author = {Dong, Peng and Zhang, Shu and Gandin, Valentina and Xie, Liangqi and Wang, Lihua and Lemire, Andrew L and Li, Wenhong and Otsuna, Hideo and Kawase, Takashi and Lander, Arthur D and Chang, Howard Y and Liu, Zhe J} } @article {69542, title = {Neural circuit basis of placebo pain relief.}, journal = {Nature}, year = {2024}, month = {2024 Jul 24}, abstract = {

Placebo effects are striking demonstrations of mind-body interactions . During pain perception, in the absence of any treatment, an expectation of pain relief can reduce the experience of pain, a phenomenon known as placebo analgesia . However, despite the strength of placebo effects and their impact on everyday human experience and failure of clinical trials for new therapeutics , the neural circuit basis of placebo effects has remained elusive. Here, we show that analgesia from the expectation of pain relief is mediated by rostral anterior cingulate cortex (rACC) neurons that project to the pontine nucleus (rACC{\textrightarrow}Pn), a pre-cerebellar nucleus with no established function in pain. We created a behavioral assay that generates placebo-like anticipatory pain relief in mice. In vivo calcium imaging of neural activity and electrophysiological recordings in brain slices showed that expectations of pain relief boost the activity of rACC{\textrightarrow}Pn neurons and potentiate neurotransmission in this pathway. Transcriptomic studies of Pn neurons revealed an abundance of opioid receptors, further suggesting a role in pain modulation. Inhibition of the rACC{\textrightarrow}Pn pathway disrupted placebo analgesia and decreased pain thresholds, whereas activation elicited analgesia in the absence of placebo conditioning. Finally, Purkinje cells exhibited activity patterns resembling those of rACC{\textrightarrow}Pn neurons during pain relief expectation, providing cellular-level evidence of a role for the cerebellum in cognitive pain modulation. These findings open the possibility of targeting this prefrontal cortico-ponto-cerebellar pathway with drugs or neurostimulation to treat pain.

}, issn = {1476-4687}, doi = {10.1038/s41586-024-07816-z}, author = {Chen, Chong and Niehaus, Jesse K and Dinc, Fatih and Huang, Karen L and Barnette, Alexander L and Tassou, Adrien and Shuster, S Andrew and Wang, Lihua and Lemire, Andrew and Menon, Vilas and Ritola, Kimberly and Hantman, Adam and Zeng, Hongkui and Schnitzer, Mark J and Scherrer, Gr{\'e}gory} } @article {68501, title = {Neuronal cell types, projections, and spatial organization of the central amygdala}, journal = {iScience}, volume = {25}, year = {2022}, month = {2022 Dec 22}, pages = {105497}, abstract = {

The central amygdala (CEA) has been richly studied for interpreting function and behavior according to specific cell types and circuits. Such work has typically defined molecular cell types by classical inhibitory marker genes; consequently, whether marker-gene-defined cell types exhaustively cover the CEA and co-vary with connectivity remains unresolved. Here, we combined single-cell RNA sequencing, multiplexed fluorescent\ in situ\ hybridization, immunohistochemistry, and long-range projection mapping to derive a {\textquotedblleft}bottom-up{\textquotedblright} understanding of CEA cell types. In doing so, we identify two major cell types, encompassing one-third of all CEA neurons, that have gone unresolved in previous studies. In spatially mapping these novel types, we identify a non-canonical CEA subdomain associated with\ Nr2f2\ expression and uncover an\ Isl1-expressing medial cell type that accounts for many long-range CEA projections. Our results reveal new CEA organizational principles across cell types and spatial scales and provide a framework for future work examining cell-type-specific behavior and function.

}, issn = {25890042}, doi = {10.1016/j.isci.2022.105497}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2589004222017692}, author = {O{\textquoteright}Leary, Timothy P. and Kendrick, Rennie M. and Bristow, Brianna N. and Sullivan, Kaitlin E. and Wang, Lihua and Clements, Jody and Lemire, Andrew L. and Cembrowski, Mark S.} } @article {67673, title = {Spatially patterned excitatory neuron subtypes and projections of the claustrum.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Aug 16}, abstract = {

The claustrum is a functionally and structurally complex brain region, whose very spatial extent remains debated. Histochemical-based approaches typically treat the claustrum as a relatively narrow anatomical region that primarily projects to the neocortex, whereas circuit-based approaches can suggest a broader claustrum region containing projections to the neocortex and other regions. Here, in the mouse, we took a bottom-up and cell-type-specific approach to complement and possibly unite these seemingly disparate conclusions. Using single-cell RNA-sequencing, we found that the claustrum comprises two excitatory neuron subtypes that are differentiable from the surrounding cortex. Multicolor retrograde tracing in conjunction with 12-channel multiplexed in situ hybridization revealed a core-shell spatial arrangement of these subtypes, as well as differential downstream targets. Thus, the claustrum comprises excitatory neuron subtypes with distinct molecular and projection properties, whose spatial patterns reflect the narrower and broader claustral extents debated in previous research. This subtype-specific heterogeneity likely shapes the functional complexity of the claustrum.

}, issn = {2050-084X}, doi = {10.7554/eLife.68967}, author = {Erwin, Sarah R and Bristow, Brianna N and Sullivan, Kaitlin E and Kendrick, Rennie M and Marriott, Brian and Wang, Lihua and Clements, Jody and Lemire, Andrew L and Jackson, Jesse and Cembrowski, Mark S} } @article {65798, title = {Behavioral state coding by molecularly defined paraventricular hypothalamic cell type ensembles.}, journal = {Science}, volume = {370}, year = {2020}, month = {2020 Oct 16}, abstract = {

Brains encode behaviors using neurons amenable to systematic classification by gene expression. The contribution of molecular identity to neural coding is not understood because of the challenges involved with measuring neural dynamics and molecular information from the same cells. We developed CaRMA (calcium and RNA multiplexed activity) imaging based on recording in vivo single-neuron calcium dynamics followed by gene expression analysis. We simultaneously monitored activity in hundreds of neurons in mouse paraventricular hypothalamus (PVH). Combinations of cell-type marker genes had predictive power for neuronal responses across 11 behavioral states. The PVH uses combinatorial assemblies of molecularly defined neuron populations for grouped-ensemble coding of survival behaviors. The neuropeptide receptor neuropeptide Y receptor type 1 (Npy1r) amalgamated multiple cell types with similar responses. Our results show that molecularly defined neurons are important processing units for brain function.

}, issn = {1095-9203}, doi = {10.1126/science.abb2494}, author = {Xu, Shengjin and Yang, Hui and Menon, Vilas and Lemire, Andrew L and Wang, Lihua and Henry, Fredrick E and Turaga, Srinivas C and Sternson, Scott M} } @article {65720, title = {Extensive and spatially variable within-cell-type heterogeneity across the basolateral amygdala.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Sep 01}, abstract = {

The basolateral amygdala complex (BLA), extensively connected with both local amygdalar nuclei as well as long-range circuits, is involved in a diverse array of functional roles. Understanding the mechanisms of such functional diversity will be greatly informed by understanding the cell-type-specific landscape of the BLA. Here, beginning with single-cell RNA sequencing, we identified both discrete and graded continuous gene-expression differences within the mouse BLA. Via in situ hybridization, we next mapped this discrete transcriptomic heterogeneity onto a sharp spatial border between the basal and lateral amygdala nuclei, and identified continuous spatial gene-expression gradients within each of these regions. These discrete and continuous spatial transformations of transcriptomic cell-type identity were recapitulated by local morphology as well as long-range connectivity. Thus, BLA excitatory neurons are a highly heterogenous collection of neurons that spatially covary in molecular, cellular, and circuit properties. This heterogeneity likely drives pronounced spatial variation in BLA computation and function.

}, issn = {2050-084X}, doi = {10.7554/eLife.59003}, author = {O{\textquoteright}Leary, Timothy P and Sullivan, Kaitlin E and Wang, Lihua and Clements, Jody and Lemire, Andrew L and Cembrowski, Mark S} } @article {64874, title = {Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 Apr 12}, abstract = {

Understanding the principles governing neuronal diversity is a fundamental goal for neuroscience. Here we provide an anatomical and transcriptomic database of nearly 200 genetically identified cell populations. By separately analyzing the robustness and pattern of expression differences across these cell populations, we identify two gene classes contributing distinctly to neuronal diversity. Short homeobox transcription factors distinguish neuronal populations combinatorially, and exhibit extremely low transcriptional noise, enabling highly robust expression differences. Long neuronal effector genes, such as channels and cell adhesion molecules, contribute disproportionately to neuronal diversity, based on their patterns rather than robustness of expression differences. By linking transcriptional identity to genetic strains and anatomical atlases we provide an extensive resource for further investigation of mouse neuronal cell types.

}, issn = {2050-084X}, doi = {10.7554/eLife.38619}, author = {Sugino, Ken and Clark, Erin and Schulmann, Anton and Shima, Yasuyuki and Wang, Lihua and Hunt, David L and Hooks, Bryan M and Traenkner, Dimitri and Chandrashekar, Jayaram and Picard, Serge and Lemire, Andrew L and Spruston, Nelson and Hantman, Adam W and Nelson, Sacha B} } @article {65159, title = {A repeated molecular architecture across thalamic pathways.}, journal = {Nature Neuroscience}, volume = {22}, year = {2019}, month = {2019 Sep 16}, pages = {1925-35}, abstract = {

The thalamus is the central communication hub of the forebrain and provides the cerebral cortex with inputs from sensory organs, subcortical systems and the cortex itself. Multiple thalamic regions send convergent information to each cortical region, but the organizational logic of thalamic projections has remained elusive. Through comprehensive transcriptional analyses of retrogradely labeled thalamic neurons in adult mice, we identify three major profiles of thalamic pathways. These profiles exist along a continuum that is repeated across all major projection systems, such as those for vision, motor control and cognition. The largest component of gene expression variation in the mouse thalamus is topographically organized, with features conserved in humans. Transcriptional differences between these thalamic neuronal identities are tied to cellular features that are critical for function, such as axonal morphology and membrane properties. Molecular profiling therefore reveals covariation in the properties of thalamic pathways serving all major input modalities and output targets, thus establishing a molecular framework for understanding the thalamus.

}, issn = {1546-1726}, doi = {10.1038/s41593-019-0483-3}, author = {Phillips, James W and Schulmann, Anton and Hara, Erina and Winnubst, Johan and Liu, Chenghao and Valakh, Vera and Wang, Lihua and Shields, Brenda C and Korff, Wyatt and Chandrashekar, Jayaram and Lemire, Andrew L and Mensh, Brett and Dudman, Joshua T and Nelson, Sacha B and Hantman, Adam W} } @article {49496, title = {Distinct descending motor cortex pathways and their roles in movement.}, journal = {Nature}, volume = {563}, year = {2018}, month = {2018 Nov}, pages = {79-84}, abstract = {

Activity in the motor cortex predicts movements, seconds before they are initiated. This preparatory activity has been observed across cortical layers, including in descending pyramidal tract neurons in layer 5. A key question is how preparatory activity is maintained without causing movement, and is ultimately converted to a motor command to trigger appropriate movements. Here, using single-cell transcriptional profiling and axonal reconstructions, we identify two types of pyramidal tract neuron. Both types project to several targets in the basal ganglia and brainstem. One type projects to thalamic regions that connect back to motor cortex; populations of these neurons produced early preparatory activity that persisted until the movement was initiated. The second type projects to motor centres in the medulla and mainly\ produced late preparatory activity and motor commands. These results indicate that two types of motor cortex output neurons have specialized roles in motor control.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0642-9}, author = {Economo, Michael N and Viswanathan, Sarada and Tasic, Bosiljka and Bas, Erhan and Winnubst, Johan and Menon, Vilas and Graybuck, Lucas T and Nguyen, Thuc Nghi and Smith, Kimberly A and Yao, Zizhen and Wang, Lihua and Gerfen, Charles R and Chandrashekar, Jayaram and Zeng, Hongkui and Looger, Loren L and Svoboda, Karel} } @article {49492, title = {The subiculum is a patchwork of discrete subregions.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Oct 30}, abstract = {

In the hippocampus, the classical pyramidal cell type of the subiculum acts as a primary output, conveying hippocampal signals to a diverse suite of downstream regions. Accumulating evidence suggests that the subiculum pyramidal cell population may actually be comprised of discrete subclasses. Here, we investigated the extent and organizational principles governing pyramidal cell heterogeneity throughout the mouse subiculum. Using single-cell RNA-seq, we find that the subiculum pyramidal cell population can be deconstructed into eight separable subclasses. These subclasses were mapped onto abutting spatial domains, ultimately producing a complex laminar and columnar organization with heterogeneity across classical dorsal-ventral, proximal-distal, and superficial-deep axes. We further show that these transcriptomically defined subclasses correspond to differential protein products and can be associated with specific projection targets. This work deconstructs the complex landscape of subiculum pyramidal cells into spatially segregated subclasses that may be observed, controlled, and interpreted in future experiments.

}, issn = {2050-084X}, doi = {10.7554/eLife.37701}, author = {Cembrowski, Mark S and Wang, Lihua and Lemire, Andrew L and Copeland, Monique and DiLisio, Salvatore F and Clements, Jody and Spruston, Nelson} } @article {47442, title = {Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016}, abstract = {

Clarifying gene expression in narrowly defined neuronal populations can provide insight into cellular identity, computation, and functionality. Here, we used next-generation RNA sequencing (RNA-seq) to produce a quantitative, whole genome characterization of gene expression for the major excitatory neuronal classes of the hippocampus; namely, granule cells and mossy cells of the dentate gyrus, and pyramidal cells of areas CA3, CA2, and CA1. Moreover, for the canonical cell classes of the trisynaptic loop, we profiled transcriptomes at both dorsal and ventral poles, producing a cell-class- and region-specific transcriptional description for these populations. This dataset clarifies the transcriptional properties and identities of lesser-known cell classes, and moreover reveals unexpected variation in the trisynaptic loop across the dorsal-ventral axis. We have created a public resource, Hipposeq (http://hipposeq.janelia.org), which provides analysis and visualization of these data and will act as a roadmap relating molecules to cells, circuits, and computation in the hippocampus.

}, issn = {2050-084X}, doi = {10.7554/eLife.14997}, author = {Cembrowski, Mark S and Wang, Lihua and Sugino, Ken and Shields, Brenda C and Spruston, Nelson} } @article {47278, title = {Spatial gene-expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons.}, journal = {Neuron}, year = {2016}, month = {2016 Jan 13}, abstract = {

Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types. This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but it may be further hampered by prominent within-class variability. Here, we considered a well-defined canonical neuronal population-hippocampal CA1 pyramidal cells (CA1 PCs)-and systematically examined the extent and spatial rules of transcriptional heterogeneity. Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences within CA1 along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous gene-expression gradients, producing a transcriptional profile consistent with a multifarious continuum of cells. This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.12.013}, author = {Cembrowski, Mark S and Bachman, Julia L and Wang, Lihua and Sugino, Ken and Shields, Brenda C and Spruston, Nelson} }