Biology subjects

Sherman, S.

Publications and source records attributed to Sherman, S..

8 recordsLinked to original sources

bioRxiv2024

Spatial characterization of interface dermatitis in cutaneous lupus reveals novel chemokine ligand-receptor pairs that drive disease

BackgroundChemokines play critical roles in the recruitment and activation of immune cells in both homeostatic and pathologic conditions. Here, we examined chemokine ligand-receptor pairs to better understand the immunopathogenesis of cutaneous lupus erythematosus (CLE), a complex autoimmune connective tissue disorder. ObjectivesOur objectives were to (1) characterize the cellular and proteomic constitution of interface dermatitis in CLE using blister biopsies, (2) map chemokine:ligand receptor pairs that govern recruitment of immune cells to form interface dermatitis in CLE, and (3) perform unbiased analyses in tandem on different clinical subtypes to identify novel genes and proteins underlying discoid versus subacute CLE. MethodsWe used suction blister biopsies to measure cellular infiltrates with spectral flow cytometry in the interface dermatitis reaction, as well as 184 protein analytes in interstitial skin fluid using 96-plex immunoassay targeted proteomics. Flow and 96-plex immunoassay data concordantly demonstrated significant increases in T cells and antigen presenting cells (APCs). We also performed spatial transcriptomics and spatial proteomics of punch biopsies using digital spatial profiling (DSP) technology on CLE skin and healthy margin controls to examine discreet locations within the tissue. ResultsSpatial and 96-plex immunoassay data confirmed elevation of interferon (IFN) and IFN-inducible CXCR3 chemokine ligands. Comparing involved versus uninvolved keratinocytes in CLE samples revealed upregulation of essential inflammatory response genes in areas near interface dermatitis, including AIM2. 96-plex immunoassay data confirmed upregulation of Caspase 8, IL-18 which is the final product of AIM2 activation, and induced chemokines including CCL8 and CXCL6 in CLE lesional samples. Chemotaxis assays using PBMCs from healthy and CLE donors revealed that T cells are equally poised to respond to CXCR3 ligands, whereas CD14+CD16+ APC populations are more sensitive to CXCL6 via CXCR1 and CD14+ are more sensitive to CCL8 via CCR2. ConclusionsTaken together, our data map a pathway from keratinocyte injury to lymphocyte recruitment in CLE via AIM2-Casp8-IL-18-CXCL6/CXCR1 and CCL8/CCR2, and IFNG/IFNL1-CXCL9/CXCL11-CXCR3, and identify potential novel biomarkers of disease. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/574422v2_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1e86dbeorg.highwire.dtl.DTLVardef@7d0208org.highwire.dtl.DTLVardef@1108aa8org.highwire.dtl.DTLVardef@ff255f_HPS_FORMAT_FIGEXP M_FIG C_FIG Model of chemokine systems governing recruitment of immune cell subsets to form interface dermatitis in cutaneous lupus. A. Summary of fresh tissue blister biopsy studies demonstrating increases in HLADR+ cells in nonlesional lupus biopsies as assessed by flow cytometry, and increased CXCL6 and CCL8 as assessed by 96 plex immunoassay. Lesional lupus biopsies also demonstrated significant increases in T cells and CXCL9/10/11 production. B. Model of chemokine-directed formation of interface dermatitis in cutaneous lupus. 1. Whole transcriptome atlas (WTA) digital spatial profiling (DSP) revealed increased AIM2 in keratinocytes proximal to inflammation, which is reported to be induced by environmental triggers including UV light and toxins. We also noted increased Caspase 8 (Casp8) and IL18 at the protein level, which can be induced downstream of AIM2. Chemokines including CXCL6 and CCL8 can be induced downstream of IL18, explaining how CCL8 and CXCL6 might be induced. 2. Recruitment of myeloid cell first responders by CCL8 and CXCL6. CD14+CD16+ myeloid cells, which were recently described in nonlesional lupus skin, express CXCR1 and migrate towards CXCL6, whereas CD14+CD16-myeloid cells express more CCR2 and migrate towards CCL8. 3. The CXCR3 ligands CXCL9/10/11 are expressed by keratinocytes, but more strongly in CD45+ immune cell and T cell regions of interest (ROIs). 4. T cells express CXCR3 and migrate towards CXCL9 and to a greater extent CXCL11. 5. The recruited HLADR+ myeloid populations and T cells contribute to formation of interface dermatitis. Thus, we propose a model in which keratinocyte/myeloid crosstalk can reinforce chemokine systems to optimally recruit lymphocytes and other immune cells to form interface dermatitis. Created with Biorender.com. Plain language summaryLupus skin rashes arise during flares, after exposure to medications or sunlight, or in response to other triggers of inflammation. To understand how white blood cells enter the skin to cause these rashes, we used new technologies to look at proteins that attract them into the skin. We found proteins that are expressed by skin cells in lesions that can recruit specific types of white blood cells that are thought to be the initiators of skin rashes. Once in the skin, these and other white blood cells can make additional proteins that bring in more and more cells. We hope that our findings will be used to test new topical treatments for lupus and other autoimmune skin rashes.

immunology↗

bioRxiv2022

A single-cell resolution gene expression atlas of the larval zebrafish brain

The advent of multimodal brain atlases promises to accelerate discoveries in neuroscience by offering in silico queries of cell types, connectivity and gene expression in regions of interest. We employed multiplexed fluorescent in situ RNA hybridization chain reaction (HCR) to generate expression maps for an initial set of 200 marker genes across the larval zebrafish brain. The data were registered to the Max Planck Zebrafish Brain (mapzebrain) atlas, thus allowing co-visualization of gene expression patterns, single-neuron tracings, transgenic lines and anatomical segmentations. Additionally, brain activity maps of freely swimming larvae were generated at single-cell resolution using HCR labeling of the immediate-early gene cfos and integrated into the atlas. As a proof of concept, we identified a novel class of cerebellar eurydendroid cells that express calb2a, project to the hypothalamus and are activated in animals that have recently ingested food. Thus, a cellular-resolution gene expression atlas will not only help with rapid identification of marker genes for neuronal populations of interest, but also bridge the molecular and circuit levels by anchoring genetic information to functional activity maps and synaptic connectivity.

neuroscience↗

bioRxiv2021

Retinal input influences pace of neurogenesis but not cell-type configuration of the visual forebrain

The brain is assembled during development by both innate and experience-dependent mechanisms1-7, but the relative contribution of these factors is poorly understood. Axons of retinal ganglion cells (RGCs) connect the eye to the brain, forming a bottleneck for the transmission of visual information to central visual areas. RGCs secrete molecules from their axons that control proliferation, differentiation and migration of downstream components7-9. Spontaneously generated waves of retinal activity, but also intense visual stimulation, can entrain responses of RGCs10 and central neurons11-16. Here we asked how the cellular composition of central targets is altered in a vertebrate brain that is depleted of retinal input throughout development. For this, we first established a molecular catalog17 and gene expression atlas18 of neuronal subpopulations in the retinorecipient areas of larval zebrafish. We then searched for changes in lakritz (atoh7-) mutants, in which RGCs do not form19. Although individual forebrain-expressed genes are dysregulated in lakritz mutants, the complete set of 77 putative neuronal cell types in thalamus, pretectum and tectum are present. While neurogenesis and differentiation trajectories are overall unaltered, a greater proportion of cells remain in an uncommitted progenitor stage in the mutant. Optogenetic stimulation of a pretectal area20,21 evokes a visual behavior in blind mutants indistinguishable from wildtype. Our analysis shows that, in this vertebrate visual system, neurons are produced more slowly, but specified and wired up in a proper configuration in the absence of any retinal signals.

neuroscience↗

bioRxiv2021

Spexin modulates molecular thermogenic profile of adipose tissue and thermoregulatory behaviors

Thermoregulation is a physiological process by which a mammal regulates body temperature in response to its environment. Within the human body, thermoregulatory behaviors and metabolism are modulated by circulating metabolic factors. In our study, we tested the ability of the neuropeptide spexin, which shares sequence homology to galanin, to regulate these functions in female mice. Supraphysiological levels of spexin in C57BL/6 mice were insufficient to protect against diet-induced obesity after 50 days of treatment. Behavioral analysis of long-term spexin treatment appeared to modulate anxiety-like behaviors by promoting exploratory behaviors and thermoregulatory behaviors of nest building that ceased when animals were housed at thermoneutral temperatures. Upon examination of the molecular profile of brown and white adipose tissue, treatment disrupted the thermogenic profile of white adipose tissue, in which {beta}3-adrenergic receptor expression was downregulated. Our results reveal novel functions for spexin as a modulator of thermoregulatory behaviors and adipose tissue metabolism. HighlightsO_LISpexin treatment did not protect against diet-induced obesity in female mice. C_LIO_LISpexin-treatment promoted thermoregulatory behaviors of nest building. C_LIO_LIBehaviors normalized when animals were housed in thermoneutral temperatures. C_LI Funding SourcesNot applicable Disclosure SummaryNothing to disclose

molecular biology↗

bioRxiv2021

Visual recognition of social signals by a tecto-thalamic neural circuit

Social affiliation emerges from individual-level behavioral rules that are driven by conspecific signals1-5. Long-distance attraction and short-distance repulsion, for example, are rules that jointly set a preferred inter-animal distance in swarms6-8. However, little is known about their perceptual mechanisms and executive neuronal circuits3. Here we trace the neuronal response to self-like biological motion9,10 (BM), a visual trigger for affiliation in developing zebrafish2,11. Unbiased activity mapping and targeted volumetric two-photon calcium imaging revealed 19 activity hotspots distributed throughout the brain and clustered BM-tuned neurons in a multimodal, socially activated nucleus of the dorsal thalamus (DT). Individual DT neurons encode fish-like local acceleration but are insensitive to global or continuous motion. Electron microscopic reconstruction of DT neurons revealed synaptic input from the optic tectum (TeO/superior colliculus) and projections into nodes of the conserved social behavior network12,13. Chemogenetic ablation of the TeO selectively disrupted DT responses to BM and social attraction without affecting short-distance repulsion. Together, we discovered a tecto-thalamic pathway that drives a core network for social affiliation. Our findings provide an example of visual social processing, and dissociate neuronal control of attraction from repulsion during affiliation, thus revealing neural underpinnings of collective behavior.

neuroscience↗

bioRxiv2020

Connectivity analysis of single cell RNA-sequencing derived transcriptional signature of lymphangioleiomyomatosis

Lymphangioleiomyomatosis (LAM) is a rare pulmonary disease affecting women of childbearing age that is characterized by the aberrant proliferation of smooth-muscle (SM)-like cells and emphysema-like lung remodeling. In LAM, mutations in TSC1 or TSC2 genes results in the activation of the mechanistic target of rapamycin complex 1 (mTORC1) and thus sirolimus, an mTORC1 inhibitor, has been approved by FDA to treat LAM patients. Sirolimus stabilizes lung function and improves symptoms. However, the disease recurs with discontinuation of the drug, potentially because of the sirolimus-induced refractoriness of the LAM cells. Therefore, there is a critical need to identify remission inducing cytocidal treatments for LAM. Recently released Library of Integrated Network-based Cellular Signatures (LINCS) L1000 transcriptional signatures of chemical perturbations has opened new avenues to study cellular responses to existing drugs and new bioactive compounds. Connecting transcriptional signature of a disease to these chemical perturbation signatures to identify bioactive chemicals that can "revert" the disease signatures can lead to novel drug discovery. We developed methods for constructing disease transcriptional signatures and performing connectivity analysis using single cell RNA-seq data. The methods were applied in the analysis of scRNA-seq data of naive and sirolimus-treated LAM cells. The single cell connectivity analyses implicated mTORC1 inhibitors as capable of reverting the LAM transcriptional signatures while the corresponding standard bulk analysis did not. This indicates the importance of using single cell analysis in constructing disease signatures. The analysis also implicated other classes of drugs, CDK, MEK/MAPK and EGFR/JAK inhibitors, as potential therapeutic agents for LAM.

systems biology↗

bioRxiv2019

Identification of the lymphangioleiomyomatosis cell and its uterine origin

Lymphangioleiomyomatosis (LAM) is a metastasizing neoplasm of reproductive age women that causes cystic lung remodeling and progressive respiratory failure. The source of LAM cells that invade the lung and the reasons that LAM targets women have remained elusive. We employed single cell and single nuclei RNA sequencing on LAM lesions within explanted LAM lungs, known to contain smooth muscle like cells bearing mTOR activating mutations in TSC1 or TSC2, and identified a unique population of cells that were readily distinguished from those of endogenous lung cells. LAMCORE cells shared closest transcriptomic similarity to normal uterus and neural crest. Immunofluorescence microscopy demonstrated the expression of LAMCORE cell signature genes within LAM lesions in both lung and uterus. Serum aptamer proteomics and ELISA identified biomarkers predicted to be secreted by LAMCORE cells. Single cell transcriptomics strongly supports a uterine neural crest origin of LAMCORE cells; providing insights into disease pathogenesis and informing future treatment strategies for LAM.\n\nSIGNIFICANCEPresent study identified a novel population of LAMCORE cells, which is likely originated from uterine neural crest; identified novel LAM cell-specific secretome proteins that hold promise as potential biomarkers and therapeutic targets. Advancing the understanding of LAM pathogenesis and metastasis model may yield broader insights into the biology of cancer.

cancer biology↗

bioRxiv2019

Characterizing macroinvertebrate community composition and abundance in freshwater tidal wetlands of the Sacramento-San Joaquin Delta

Restored tidal wetlands may provide important food web support for at-risk fish species in the Sacramento-San Joaquin Delta (Delta) of California, including Delta Smelt (Hypomesus transpacificus) and Chinook Salmon (Oncorhynchus tshawytscha). Since many tidal wetland restoration projects are planned or have recently been constructed in the Delta, understanding the diversity and variability of wetland invertebrates that are fish prey items is of increasing importance. During this study, two different invertebrate sampling techniques were tested (leaf packs and sweep nets) in four habitat types within three different wetland sites to evaluate which sampling technique provided the most reliable metric of invertebrate abundance and community composition. Sweep nets provided a better measure of fish food availability than leaf packs and were better able to differentiate between habitat types. Generalized linear models showed submerged and floating vegetation had higher abundance and species richness than channel habitats or emergent vegetation. Permutational multivariate analysis of variance showed significantly different communities of invertebrates in different habitat types and in different wetlands, and point-biserial correlation coefficients found a greater number of mobile taxa associated with sweep nets. There were more taxa associated with vegetated habitats than channel habitats, and one region had more taxa associated with it than the other two regions. These results suggest that restoration sites that contain multiple habitat types may enhance fish invertebrate prey diversity and resilience. However, the effect of habitat diversity must be monitored as restoration sites develop to assess actual benefits to at-risk fish species.

ecology↗