@article{RN139, author = {Anand, G. M. and Megale, H. C. and Murphy, S. H. and Weis, T. and Lin, Z. and He, Y. and Wang, X. and Liu, J. and Ramanathan, S.}, title = {Controlling organoid symmetry breaking uncovers an excitable system underlying human axial elongation}, journal = {Cell}, volume = {186}, number = {3}, pages = {497-512 e23}, note = {Anand, Giridhar M Megale, Heitor C Murphy, Sean H Weis, Theresa Lin, Zuwan He, Yichun Wang, Xiao Liu, Jia Ramanathan, Sharad eng R01 HD100036/HD/NICHD NIH HHS/ RF1 MH123948/MH/NIMH NIH HHS/ Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't 2023/01/20 Cell. 2023 Feb 2;186(3):497-512.e23. doi: 10.1016/j.cell.2022.12.043. Epub 2023 Jan 18.}, abstract = {The human embryo breaks symmetry to form the anterior-posterior axis of the body. As the embryo elongates along this axis, progenitors in the tail bud give rise to tissues that generate spinal cord, skeleton, and musculature. This raises the question of how the embryo achieves axial elongation and patterning. While ethics necessitate in vitro studies, the variability of organoid systems has hindered mechanistic insights. Here, we developed a bioengineering and machine learning framework that optimizes organoid symmetry breaking by tuning their spatial coupling. This framework enabled reproducible generation of axially elongating organoids, each possessing a tail bud and neural tube. We discovered that an excitable system composed of WNT/FGF signaling drives elongation by inducing a neuromesodermal progenitor-like signaling center. We discovered that instabilities in the excitable system are suppressed by secreted WNT inhibitors. Absence of these inhibitors led to ectopic tail buds and branches. Our results identify mechanisms governing stable human axial elongation.}, keywords = {Humans *Body Patterning *Mesoderm Wnt Signaling Pathway Embryo, Mammalian Organoids axial elongation bioengineering human stem cell models reproducible statistical inference}, ISSN = {1097-4172 (Electronic) 0092-8674 (Print) 0092-8674 (Linking)}, DOI = {10.1016/j.cell.2022.12.043}, url = {https://www.ncbi.nlm.nih.gov/pubmed/36657443}, year = {2023}, type = {Journal Article} } @article{RN135, author = {Carman, C. V. and Nikova, D. N. and Sakurai, Y. and Shi, J. and Novakovic, V. A. and Rasmussen, J. T. and Lam, W. A. and Gilbert, G. E.}, title = {Membrane curvature and PS localize coagulation proteins to filopodia and retraction fibers of endothelial cells}, journal = {Blood Adv}, volume = {7}, number = {1}, pages = {60-72}, note = {Carman, Christopher V Nikova, Dessislava N Sakurai, Yumiko Shi, Jialan Novakovic, Valerie A Rasmussen, Jan T Lam, Wilbur A Gilbert, Gary E eng R01 HL104006/HL/NHLBI NIH HHS/ Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S. 2022/07/19 Blood Adv. 2023 Jan 10;7(1):60-72. doi: 10.1182/bloodadvances.2021006870.}, abstract = {Prior reports indicate that the convex membrane curvature of phosphatidylserine (PS)-containing vesicles enhances formation of binding sites for factor Va and lactadherin. Yet, the relationship of convex curvature to localization of these proteins on cells remains unknown. We developed a membrane topology model, using phospholipid bilayers supported by nano-etched silica substrates, to further explore the relationship between curvature and localization of coagulation proteins. Ridge convexity corresponded to maximal curvature of physiologic membranes (radii of 10 or 30 nm) and the troughs had a variable concave curvature. The benchmark PS probe lactadherin exhibited strong differential binding to the ridges, on membranes with 4% to 15% PS. Factor Va, with a PS-binding motif homologous to lactadherin, also bound selectively to the ridges. Bound factor Va supported coincident binding of factor Xa, localizing prothrombinase complexes to the ridges. Endothelial cells responded to prothrombotic stressors and stimuli (staurosporine, tumor necrosis factor-alpha [TNF- alpha]) by retracting cell margins and forming filaments and filopodia. These had a high positive curvature similar to supported membrane ridges and selectively bound lactadherin. Likewise, the retraction filaments and filopodia bound factor Va and supported assembly of prothrombinase, whereas the cell body did not. The perfusion of plasma over TNF-alpha-stimulated endothelia in culture dishes and engineered 3-dimensional microvessels led to fibrin deposition at cell margins, inhibited by lactadherin, without clotting of bulk plasma. Our results indicate that stressed or stimulated endothelial cells support prothrombinase activity localized to convex topological features at cell margins. These findings may relate to perivascular fibrin deposition in sepsis and inflammation.}, keywords = {*Thromboplastin/metabolism *Phosphatidylserines/metabolism Endothelial Cells/metabolism Factor Va/chemistry/metabolism Pseudopodia/metabolism Fibrin}, ISSN = {2473-9537 (Electronic) 2473-9529 (Print) 2473-9529 (Linking)}, DOI = {10.1182/bloodadvances.2021006870}, url = {https://www.ncbi.nlm.nih.gov/pubmed/35849711}, year = {2023}, type = {Journal Article} } @article{RN133, author = {Elya, C. and Lavrentovich, D. and Lee, E. and Pasadyn, C. and Duval, J. and Basak, M. and Saykina, V. and de Bivort, B.}, title = {Neural mechanisms of parasite-induced summiting behavior in 'zombie' Drosophila}, journal = {Elife}, volume = {12}, note = {Elya, Carolyn Lavrentovich, Danylo Lee, Emily Pasadyn, Cassandra Duval, Jasper Basak, Maya Saykina, Valerie de Bivort, Benjamin eng GT11087/HHMI/Howard Hughes Medical Institute/ R01 NS121874/NS/NINDS NIH HHS/ Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. England 2023/05/15 Elife. 2023 May 15;12:e85410. doi: 10.7554/eLife.85410.}, abstract = {For at least two centuries, scientists have been enthralled by the "zombie" behaviors induced by mind-controlling parasites. Despite this interest, the mechanistic bases of these uncanny processes have remained mostly a mystery. Here, we leverage the Entomophthora muscae-Drosophila melanogaster "zombie fly" system to reveal the mechanistic underpinnings of summit disease, a manipulated behavior evoked by many fungal parasites. Using a high-throughput approach to measure summiting, we discovered that summiting behavior is characterized by a burst of locomotion and requires the host circadian and neurosecretory systems, specifically DN1p circadian neurons, pars intercerebralis to corpora allata projecting (PI-CA) neurons and corpora allata (CA), the latter being solely responsible for juvenile hormone (JH) synthesis and release. Using a machine learning classifier to identify summiting animals in real time, we observed that PI-CA neurons and CA appeared intact in summiting animals, despite invasion of adjacent regions of the "zombie fly" brain by E. muscae cells and extensive host tissue damage in the body cavity. The blood-brain barrier of flies late in their infection was significantly permeabilized, suggesting that factors in the hemolymph may have greater access to the central nervous system during summiting. Metabolomic analysis of hemolymph from summiting flies revealed differential abundance of several compounds compared to non-summiting flies. Transfusing the hemolymph of summiting flies into non-summiting recipients induced a burst of locomotion, demonstrating that factor(s) in the hemolymph likely cause summiting behavior. Altogether, our work reveals a neuro-mechanistic model for summiting wherein fungal cells perturb the fly's hemolymph, activating a neurohormonal pathway linking clock neurons to juvenile hormone production in the CA, ultimately inducing locomotor activity in their host.}, keywords = {Animals *Drosophila Drosophila melanogaster/physiology *Parasites Corpora Allata/metabolism Juvenile Hormones/metabolism D. melanogaster Entomophthora muscae behavior circadian rhythm genetics genomics juvenile hormone neuroscience parasitic mind-control summit disease}, ISSN = {2050-084X (Electronic) 2050-084X (Linking)}, DOI = {10.7554/eLife.85410}, url = {https://www.ncbi.nlm.nih.gov/pubmed/37184212}, year = {2023}, type = {Journal Article} } @article{RN138, author = {Galazo, M. J. and Sweetser, D. A. and Macklis, J. D.}, title = {Tle4 controls both developmental acquisition and early post-natal maturation of corticothalamic projection neuron identity}, journal = {Cell Rep}, volume = {42}, number = {8}, pages = {112957}, note = {Galazo, Maria J Sweetser, David A Macklis, Jeffrey D eng 2023/08/10 Cell Rep. 2023 Aug 9;42(8):112957. doi: 10.1016/j.celrep.2023.112957.}, abstract = {Identities of distinct neuron subtypes are specified during embryonic development, then maintained during post-natal maturation. In cerebral cortex, mechanisms controlling early acquisition of neuron-subtype identities have become increasingly understood. However, mechanisms controlling neuron-subtype identity stability during post-natal maturation are largely unexplored. We identify that Tle4 is required for both early acquisition and post-natal stability of corticothalamic neuron-subtype identity. Embryonically, Tle4 promotes acquisition of corticothalamic identity and blocks emergence of core characteristics of subcerebral/corticospinal projection neuron identity, including gene expression and connectivity. During the first post-natal week, when corticothalamic innervation is ongoing, Tle4 is required to stabilize corticothalamic neuron identity, limiting interference from differentiation programs of developmentally related neuron classes. We identify a deacetylation-based epigenetic mechanism by which TLE4 controls Fezf2 expression level by corticothalamic neurons. This contributes to distinction of cortical output subtypes and ensures identity stability for appropriate maturation of corticothalamic neurons.}, keywords = {CP: Developmental biology CP: Neuroscience Fezf2 Tle4 corticospinal neurons corticothalamic neurons epigenetic regulation neuron identity acquisition neuron identity stability subcerebral projection neurons}, ISSN = {2211-1247 (Electronic)}, DOI = {10.1016/j.celrep.2023.112957}, url = {https://www.ncbi.nlm.nih.gov/pubmed/37561632}, year = {2023}, type = {Journal Article} } @article{RN124, author = {Green, D. R. and Winkler, D. E. and Leichliter, J. and Harms, G. S. and Hatt, J. M. and Clauss, M. and Tutken, T.}, title = {Formation and Replacement of Bone And Tooth Mineralized Tissues in Green Iguanas (Iguana Iguana) Revealed by In-Vivo Fluorescence Marking}, journal = {Integr Comp Biol}, note = {Green, Daniel R Winkler, Daniela E Leichliter, Jennifer Harms, Gregory S Hatt, Jean-Michel Clauss, Marcus Tutken, Thomas eng England 2023/07/21 Integr Comp Biol. 2023 Jul 20:icad089. doi: 10.1093/icb/icad089.}, abstract = {Hard tissue formation patterns and rates reveal details of animal physiology, life history, and environment, but are understudied in reptiles. Here, we use fluorescence labels delivered in vivo and laser confocal scanning microscopy to study tooth and bone formation in a managed group of green iguanas (Iguana iguana, Linne 1758) kept for 1.5 years under experimentally controlled conditions and undergoing several dietary switches. We constrain rates of tooth elongation, which we observe to be slow when enamel is initially deposited (c. 9 microm/day), but then increases exponentially in the dentin root, reaching c. 55 microm/day or more after crown completion. We further constrain the total timing of tooth formation to approximately 40-60 days, and observe highly variable timings of tooth resorption onset and replacement. Fluorescent labels clearly indicate cohorts of teeth recruited within Zahnreihen replacement waves, with faster sequential tooth recruitment and greater wave sizes posteriorly, where each wave initiates. Rates of hard tissue formation in long bones range from 0.4-3.4 microm/day, correlating with animal weight gain, and cortical bone recording the entire history of the experiment. We suggest additional labeling experiments to study hard tissue formation patterns in other reptiles, and propose strategies for chemical analyses of hard tissues in order to extract temporal information about past environments, behaviors and diets from reptilian fossils throughout the Phanerozoic.}, ISSN = {1557-7023 (Electronic) 1540-7063 (Linking)}, DOI = {10.1093/icb/icad089}, url = {https://www.ncbi.nlm.nih.gov/pubmed/37475667}, year = {2023}, type = {Journal Article} } @article{RN140, author = {Itoh, Y. and Sahni, V. and Shnider, S. J. and McKee, H. and Macklis, J. D.}, title = {Inter-axonal molecular crosstalk via Lumican proteoglycan sculpts murine cervical corticospinal innervation by distinct subpopulations}, journal = {Cell Rep}, volume = {42}, number = {3}, pages = {112182}, note = {Itoh, Yasuhiro Sahni, Vibhu Shnider, Sara J McKee, Holly Macklis, Jeffrey D eng R01 NS049553/NS/NINDS NIH HHS/ R01 NS045523/NS/NINDS NIH HHS/ K12 HD093427/HD/NICHD NIH HHS/ F31 NS063516/NS/NINDS NIH HHS/ R01 NS104055/NS/NINDS NIH HHS/ R01 NS075672/NS/NINDS NIH HHS/ DP1 NS106665/NS/NINDS NIH HHS/ Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't 2023/03/20 Cell Rep. 2023 Mar 28;42(3):112182. doi: 10.1016/j.celrep.2023.112182. Epub 2023 Mar 17.}, abstract = {How CNS circuits sculpt their axonal arbors into spatially and functionally organized domains is not well understood. Segmental specificity of corticospinal connectivity is an exemplar for such regional specificity of many axon projections. Corticospinal neurons (CSN) innervate spinal and brainstem targets with segmental precision, controlling voluntary movement. Multiple molecularly distinct CSN subpopulations innervate the cervical cord for evolutionarily enhanced precision of forelimb movement. Evolutionarily newer CSN(BC-lat) exclusively innervate bulbar-cervical targets, while CSN(medial) are heterogeneous; distinct subpopulations extend axons to either bulbar-cervical or thoraco-lumbar segments. We identify that Lumican controls balance of cervical innervation between CSN(BC-lat) and CSN(medial) axons during development, which is maintained into maturity. Lumican, an extracellular proteoglycan expressed by CSN(BC-lat), non-cell-autonomously suppresses cervical collateralization by multiple CSN(medial) subpopulations. This inter-axonal molecular crosstalk between CSN subpopulations controls murine corticospinal circuitry refinement and forelimb dexterity. Such crosstalk is generalizable beyond the corticospinal system for evolutionary incorporation of new neuron populations into preexisting circuitry.}, keywords = {Animals Mice *Spinal Cord/physiology Lumican *Axons/physiology Neurons/physiology Movement Pyramidal Tracts CP: Neuroscience Lumican proteoglycan axon collateralization axon development circuit refinement corticospinal neurons corticospinal segmental specificity evolutionary circuit diversification forelimb dexterity inter-axonal molecular crosstalk}, ISSN = {2211-1247 (Electronic)}, DOI = {10.1016/j.celrep.2023.112182}, url = {https://www.ncbi.nlm.nih.gov/pubmed/36934325}, year = {2023}, type = {Journal Article} } @article{RN127, author = {Kapate, N. and Dunne, M. and Kumbhojkar, N. and Prakash, S. and Wang, L. L. and Graveline, A. and Park, K. S. and Chandran Suja, V. and Goyal, J. and Clegg, J. R. and Mitragotri, S.}, title = {A backpack-based myeloid cell therapy for multiple sclerosis}, journal = {Proc Natl Acad Sci U S A}, volume = {120}, number = {17}, pages = {e2221535120}, note = {Kapate, Neha Dunne, Michael Kumbhojkar, Ninad Prakash, Supriya Wang, Lily Li-Wen Graveline, Amanda Park, Kyung Soo Chandran Suja, Vineeth Goyal, Juhee Clegg, John R Mitragotri, Samir eng Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. 2023/04/19 Proc Natl Acad Sci U S A. 2023 Apr 25;120(17):e2221535120. doi: 10.1073/pnas.2221535120. Epub 2023 Apr 19.}, abstract = {Multiple sclerosis (MS) is an incurable autoimmune disease and is currently treated by systemic immunosuppressants with off-target side effects. Although aberrant myeloid function is often observed in MS plaques in the central nervous system (CNS), the role of myeloid cells in therapeutic intervention is currently overlooked. Here, we developed a myeloid cell-based strategy to reduce the disease burden in experimental autoimmune encephalomyelitis (EAE), a mouse model of progressive MS. We developed monocyte-adhered microparticles ("backpacks") for activating myeloid cell phenotype to an anti-inflammatory state through localized interleukin-4 and dexamethasone signals. We demonstrate that backpack-laden monocytes infiltrated into the inflamed CNS and modulated both the local and systemic immune responses. Within the CNS, backpack-carrying monocytes regulated both the infiltrating and tissue-resident myeloid cell compartments in the spinal cord for functions related to antigen presentation and reactive species production. Treatment with backpack-monocytes also decreased the level of systemic pro-inflammatory cytokines. Additionally, backpack-laden monocytes induced modulatory effects on T(H)1 and T(H)17 populations in the spinal cord and blood, demonstrating cross talk between the myeloid and lymphoid arms of disease. Backpack-carrying monocytes conferred therapeutic benefit in EAE mice, as quantified by improved motor function. The use of backpack-laden monocytes offers an antigen-free, biomaterial-based approach to precisely tune cell phenotype in vivo, demonstrating the utility of myeloid cells as a therapeutic modality and target.}, keywords = {Mice Animals *Multiple Sclerosis/therapy Myeloid Cells *Encephalomyelitis, Autoimmune, Experimental Central Nervous System Monocytes Mice, Inbred C57BL Cns Immunoengineering macrophages myeloid phenotype}, ISSN = {1091-6490 (Electronic) 0027-8424 (Print) 0027-8424 (Linking)}, DOI = {10.1073/pnas.2221535120}, url = {https://www.ncbi.nlm.nih.gov/pubmed/37075071}, year = {2023}, type = {Journal Article} } @article{RN129, author = {McNamara, S. L. and Seo, B. R. and Freedman, B. R. and Roloson, E. B. and Alvarez, J. T. and O'Neill, C. T. and Vandenburgh, H. H. and Walsh, C. J. and Mooney, D. J.}, title = {Anti-inflammatory therapy enables robot-actuated regeneration of aged muscle}, journal = {Sci Robot}, volume = {8}, number = {76}, pages = {eadd9369}, note = {McNamara, S L Seo, B R Freedman, B R Roloson, E B Alvarez, J T O'Neill, C T Vandenburgh, H H Walsh, C J Mooney, D J eng K99 AG065495/AG/NIA NIH HHS/ T32 GM007753/GM/NIGMS NIH HHS/ T32 GM144273/GM/NIGMS NIH HHS/ F31 AR075367/AR/NIAMS NIH HHS/ R01 DE013349/DE/NIDCR NIH HHS/ Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. 2023/03/23 Sci Robot. 2023 Mar 22;8(76):eadd9369. doi: 10.1126/scirobotics.add9369. Epub 2023 Mar 22.}, abstract = {Robot-actuated mechanical loading (ML)-based therapies ("mechanotherapies") can promote regeneration after severe skeletal muscle injury, but the effectiveness of such approaches during aging is unknown and may be influenced by age-associated decline in the healing capacity of skeletal muscle. To address this knowledge gap, this work used a noninvasive, load-controlled robotic device to impose highly defined tissue stresses to evaluate the age dependence of ML on muscle repair after injury. The response of injured muscle to robot-actuated cyclic compressive loading was found to be age sensitive, revealing not only a lack of reparative benefit of ML on injured aged muscles but also exacerbation of tissue inflammation. ML alone also disrupted the normal regenerative processes of aged muscle stem cells. However, these negative effects could be reversed by introducing anti-inflammatory therapy alongside ML application, leading to enhanced skeletal muscle regeneration even in aged mice.}, keywords = {Animals Mice *Regeneration/physiology *Robotics Muscle, Skeletal/physiology Anti-Inflammatory Agents}, ISSN = {2470-9476 (Electronic) 2470-9476 (Linking)}, DOI = {10.1126/scirobotics.add9369}, url = {https://www.ncbi.nlm.nih.gov/pubmed/36947599}, year = {2023}, type = {Journal Article} } @article{RN134, author = {Nadler, M. J. S. and Chang, W. and Ozkaynak, E. and Huo, Y. and Nong, Y. and Boillot, M. and Johnson, M. and Moreno, A. and Matthew, P. Anderson}, title = {Hominoid SVA-lncRNA AK057321 targets human-specific SVA retrotransposons in SCN8A and CDK5RAP2 to initiate neuronal maturation}, journal = {Commun Biol}, volume = {6}, number = {1}, pages = {347}, note = {Nadler, Monica J S Chang, Weipang Ozkaynak, Ekim Huo, Yuda Nong, Yi Boillot, Morgane Johnson, Mark Moreno, Antonio Matthew P Anderson eng R01 MH112714/MH/NIMH NIH HHS/ R01 MH114858/MH/NIMH NIH HHS/ R21 MH100868/MH/NIMH NIH HHS/ R21 HD079249/HD/NICHD NIH HHS/ U54 HD090255/HD/NICHD NIH HHS/ P30 HD018655/HD/NICHD NIH HHS/ Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't England 2023/03/31 Commun Biol. 2023 Mar 30;6(1):347. doi: 10.1038/s42003-023-04683-8.}, abstract = {SINE-VNTR-Alu (SVA) retrotransposons arose and expanded in the genome of hominoid primates concurrent with the slowing of brain maturation. We report genes with intronic SVA transposons are enriched for neurodevelopmental disease and transcribed into long non-coding SVA-lncRNAs. Human-specific SVAs in microcephaly CDK5RAP2 and epilepsy SCN8A gene introns repress their expression via transcription factor ZNF91 to delay neuronal maturation. Deleting the SVA in CDK5RAP2 initiates multi-dimensional and in SCN8A selective sodium current neuronal maturation by upregulating these genes. SVA-lncRNA AK057321 forms RNA:DNA heteroduplexes with the genomic SVAs and upregulates these genes to initiate neuronal maturation. SVA-lncRNA AK057321 also promotes species-specific cortex and cerebellum-enriched expression upregulating human genes with intronic SVAs (e.g., HTT, CHAF1B and KCNJ6) but not mouse orthologs. The diversity of neuronal genes with intronic SVAs suggest this hominoid-specific SVA transposon-based gene regulatory mechanism may act at multiple steps to specialize and achieve neoteny of the human brain.}, keywords = {Animals Humans *Retroelements/genetics *RNA, Long Noncoding/genetics Minisatellite Repeats Short Interspersed Nucleotide Elements Primates/genetics Chromatin Assembly Factor-1/genetics NAV1.6 Voltage-Gated Sodium Channel/genetics Nerve Tissue Proteins/genetics Cell Cycle Proteins/genetics}, ISSN = {2399-3642 (Electronic) 2399-3642 (Linking)}, DOI = {10.1038/s42003-023-04683-8}, url = {https://www.ncbi.nlm.nih.gov/pubmed/36997626}, year = {2023}, type = {Journal Article} } @article{RN131, author = {Pandey, S. and Moyer, A. J. and Thyme, S. B.}, title = {A single-cell transcriptome atlas of the maturing zebrafish telencephalon}, journal = {Genome Res}, volume = {33}, number = {4}, pages = {658-671}, note = {Pandey, Shristi Moyer, Anna J Thyme, Summer B eng DP1 HD094764/HD/NICHD NIH HHS/ R00 MH110603/MH/NIMH NIH HHS/ T32 HG008961/HG/NHGRI NIH HHS/ Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't 2023/04/19 Genome Res. 2023 Apr;33(4):658-671. doi: 10.1101/gr.277278.122. Epub 2023 Apr 18.}, abstract = {The zebrafish telencephalon is composed of highly specialized subregions that regulate complex behaviors such as learning, memory, and social interactions. The transcriptional signatures of the neuronal cell types in the telencephalon and the timeline of their emergence from larva to adult remain largely undescribed. Using an integrated analysis of single-cell transcriptomes of approximately 64,000 cells obtained from 6-day-postfertilization (dpf), 15-dpf, and adult telencephalon, we delineated nine main neuronal cell types in the pallium and eight in the subpallium and nominated novel marker genes. Comparing zebrafish and mouse neuronal cell types revealed both conserved and absent types and marker genes. Mapping of cell types onto a spatial larval reference atlas created a resource for anatomical and functional studies. Using this multiage approach, we discovered that although most neuronal subtypes are established early in the 6-dpf fish, some emerge or expand in number later in development. Analyzing the samples from each age separately revealed further complexity in the data, including several cell types that expand substantially in the adult forebrain and do not form clusters at the larval stages. Together, our work provides a comprehensive transcriptional analysis of the cell types in the zebrafish telencephalon and a resource for dissecting its development and function.}, keywords = {Animals Mice *Zebrafish/metabolism *Transcriptome Zebrafish Proteins/genetics Neurons/metabolism Telencephalon/metabolism}, ISSN = {1549-5469 (Electronic) 1088-9051 (Print) 1088-9051 (Linking)}, DOI = {10.1101/gr.277278.122}, url = {https://www.ncbi.nlm.nih.gov/pubmed/37072188}, year = {2023}, type = {Journal Article} } @article{RN136, author = {Prakash, S. and Kumbhojkar, N. and Lu, A. and Kapate, N. and Suja, V. C. and Park, K. S. and Wang, L. L. and Mitragotri, S.}, title = {Polymer Micropatches as Natural Killer Cell Engagers for Tumor Therapy}, journal = {ACS Nano}, note = {Prakash, Supriya Kumbhojkar, Ninad Lu, Andrew Kapate, Neha Suja, Vineeth Chandran Park, Kyung Soo Wang, Lily Li-Wen Mitragotri, Samir eng 2023/08/11 ACS Nano. 2023 Aug 11. doi: 10.1021/acsnano.3c03980.}, abstract = {Natural killer (NK) cell therapies have emerged as a potential therapeutic approach to various cancers. Their efficacy, however, is limited by their low persistence and anergy. Current approaches to sustain NK cell persistence in vivo include genetic modification, activation via pretreatment, or coadministration of supporting cytokines or antibodies. Such supporting therapies exhibit limited efficacy in vivo, in part due to the reversal of their effect within the immunosuppressive tumor microenvironment and off-target toxicity. Here, we report a material-based approach to address this challenge. Specifically, we describe the use of polymeric micropatches as a platform for sustained, targeted activation of NK cells, an approach referred to as microparticles as cell engagers (MACE). Poly(lactide-co-glycolic) acid (PLGA) micropatches, 4-8 mum in diameter and surface-modified with NK cell receptor targeting antibodies, exhibited strong adhesion to NK cells and induced their activation without the need of coadministered cytokines. The activation induced by MACE was greater than that induced by nanoparticles, attesting to the crucial role of MACE geometry in the activation of NK cells. MACE-bound NK cells remained viable and exhibited trans-endothelial migration and antitumor activity in vitro. MACE-bound NK cells activated T cells, macrophages, and dendritic cells in vitro. Adoptive transfer of NK-MACE also demonstrated superior antitumor efficacy in a mouse melanoma lung metastasis model compared to unmodified NK cells. Overall, MACE offers a simple, scalable, and effective way of activating NK cells and represents an attractive platform to improve the efficacy of NK cell therapy.}, keywords = {NK cell NK cell activation NK engager adoptive cell transfer cross-linking lung metastasis microparticle}, ISSN = {1936-086X (Electronic) 1936-0851 (Linking)}, DOI = {10.1021/acsnano.3c03980}, url = {https://www.ncbi.nlm.nih.gov/pubmed/37565806}, year = {2023}, type = {Journal Article} } @article{RN130, author = {Reynolds, D. S. and de Lazaro, I. and Blache, M. L. and Liu, Y. and Jeffreys, N. C. and Doolittle, R. M. and Grandidier, E. and Olszewski, J. and Dacus, M. T. and Mooney, D. J. and Lewis, J. A.}, title = {Microporogen-Structured Collagen Matrices for Embedded Bioprinting of Tumor Models for Immuno-Oncology}, journal = {Adv Mater}, pages = {e2210748}, note = {Reynolds, Daniel S de Lazaro, Irene Blache, Manon L Liu, Yutong Jeffreys, Nicholas C Doolittle, Ramsey M Grandidier, Estee Olszewski, Jason Dacus, Mason T Mooney, David J Lewis, Jennifer A eng U01CA21436901/CA/NCI NIH HHS/ Germany 2023/05/10 Adv Mater. 2023 May 10:e2210748. doi: 10.1002/adma.202210748.}, abstract = {Embedded bioprinting enables the rapid design and fabrication of complex tissues that recapitulate in vivo microenvironments. However, few biological matrices enable good print fidelity, while simultaneously facilitate cell viability, proliferation, and migration. Here, a new microporogen-structured (microPOROS) matrix for embedded bioprinting is introduced, in which matrix rheology, printing behavior, and porosity are tailored by adding sacrificial microparticles composed of a gelatin-chitosan complex to a prepolymer collagen solution. To demonstrate its utility, a 3D tumor model is created via embedded printing of a murine melanoma cell ink within the microPOROS collagen matrix at 4 degrees C. The collagen matrix is subsequently crosslinked around the microparticles upon warming to 21 degrees C, followed by their melting and removal at 37 degrees C. This process results in a microPOROS matrix with a fibrillar collagen type-I network akin to that observed in vivo. Printed tumor cells remain viable and proliferate, while antigen-specific cytotoxic T cells incorporated in the matrix migrate to the tumor site, where they induce cell death. The integration of the microPOROS matrix with embedded bioprinting opens new avenues for creating complex tissue microenvironments in vitro that may find widespread use in drug discovery, disease modeling, and tissue engineering for therapeutic use.}, keywords = {cancer collagen embedded bioprinting immunotherapy microporogens}, ISSN = {1521-4095 (Electronic) 0935-9648 (Linking)}, DOI = {10.1002/adma.202210748}, url = {https://www.ncbi.nlm.nih.gov/pubmed/37163476}, year = {2023}, type = {Journal Article} } @article{RN128, author = {Salcedo, M. K. and Jun, B. H. and Socha, J. J. and Pierce, N. E. and Vlachos, P. P. and Combes, S. A.}, title = {Complex hemolymph circulation patterns in grasshopper wings}, journal = {Commun Biol}, volume = {6}, number = {1}, pages = {313}, note = {Salcedo, Mary K Jun, Brian H Socha, John J Pierce, Naomi E Vlachos, Pavlos P Combes, Stacey A eng Research Support, U.S. Gov't, Non-P.H.S. England 2023/03/25 Commun Biol. 2023 Mar 23;6(1):313. doi: 10.1038/s42003-023-04651-2.}, abstract = {An insect's living systems-circulation, respiration, and a branching nervous system-extend from the body into the wing. Wing hemolymph circulation is critical for hydrating tissues and supplying nutrients to living systems such as sensory organs across the wing. Despite the critical role of hemolymph circulation in maintaining healthy wing function, wings are often considered "lifeless" cuticle, and flows remain largely unquantified. High-speed fluorescent microscopy and particle tracking of hemolymph in the wings and body of the grasshopper Schistocerca americana revealed dynamic flow in every vein of the fore- and hindwings. The global system forms a circuit, but local flow behavior is complex, exhibiting three distinct types: pulsatile, aperiodic, and "leaky" flow. Thoracic wing hearts pull hemolymph from the wing at slower frequencies than the dorsal vessel; however, the velocity of returning hemolymph (in the hindwing) is faster than in that of the dorsal vessel. To characterize the wing's internal flow mechanics, we mapped dimensionless flow parameters across the wings, revealing viscous flow regimes. Wings sustain ecologically important insect behaviors such as pollination and migration. Analysis of the wing circulatory system provides a template for future studies investigating the critical hemodynamics necessary to sustaining wing health and insect flight.}, keywords = {Animals *Grasshoppers Biomechanical Phenomena Hemolymph Flight, Animal/physiology Insecta/physiology Wings, Animal/physiology}, ISSN = {2399-3642 (Electronic) 2399-3642 (Linking)}, DOI = {10.1038/s42003-023-04651-2}, url = {https://www.ncbi.nlm.nih.gov/pubmed/36959465}, year = {2023}, type = {Journal Article} } @article{RN125, author = {Spitzberg, J. D. and Ferguson, S. and Yang, K. S. and Peterson, H. M. and Carlson, J. C. T. and Weissleder, R.}, title = {Multiplexed analysis of EV reveals specific biomarker composition with diagnostic impact}, journal = {Nat Commun}, volume = {14}, number = {1}, pages = {1239}, note = {Spitzberg, Joshua D Ferguson, Scott Yang, Katherine S Peterson, Hannah M Carlson, Jonathan C T Weissleder, Ralph eng P01 CA069246/CA/NCI NIH HHS/ T32 CA079443/CA/NCI NIH HHS/ R01 CA237332/CA/NCI NIH HHS/ Research Support, N.I.H., Extramural England 2023/03/05 Nat Commun. 2023 Mar 4;14(1):1239. doi: 10.1038/s41467-023-36932-z.}, abstract = {Exosomes and extracellular vesicles (EV) are increasingly being explored as circulating biomarkers, but their heterogenous composition will likely mandate the development of multiplexed EV technologies. Iteratively multiplexed analyses of near single EVs have been challenging to implement beyond a few colors during spectral sensing. Here we developed a multiplexed analysis of EV technique (MASEV) to interrogate thousands of individual EVs during 5 cycles of multi-channel fluorescence staining for 15 EV biomarkers. Contrary to the common belief, we show that: several markers proposed to be ubiquitous are less prevalent than believed; multiple biomarkers concur in single vesicles but only in small fractions; affinity purification can lead to loss of rare EV subtypes; and deep profiling allows detailed analysis of EV, potentially improving the diagnostic content. These findings establish the potential of MASEV for uncovering fundamental EV biology and heterogeneity and increasing diagnostic specificity.}, keywords = {*Extracellular Vesicles *Exosomes Biomarkers Chromatography, Affinity Staining and Labeling}, ISSN = {2041-1723 (Electronic) 2041-1723 (Linking)}, DOI = {10.1038/s41467-023-36932-z}, url = {https://www.ncbi.nlm.nih.gov/pubmed/36870999}, year = {2023}, type = {Journal Article} } @article{RN137, author = {Tavakoli, S. and Garcia, V. and Gahwiler, E. and Adatto, I. and Rangan, A. and Messemer, K. A. and Kakhki, S. A. and Yang, S. and Chan, V. S. and Manning, M. E. and Fotowat, H. and Zhou, Y. and Wagers, A. J. and Zon, L. I.}, title = {Transplantation-based screen identifies inducers of muscle progenitor cell engraftment across vertebrate species}, journal = {Cell Rep}, volume = {42}, number = {4}, pages = {112365}, note = {Tavakoli, Sahar Garcia, Vivian Gahwiler, Eric Adatto, Isaac Rangan, Apoorva Messemer, Kathleen A Kakhki, Sara Ashrafi Yang, Song Chan, Victoria S Manning, Margot E Fotowat, Haleh Zhou, Yi Wagers, Amy J Zon, Leonard I eng R24 OD017870/OD/NIH HHS/ 2023/04/06 Cell Rep. 2023 Apr 4;42(4):112365. doi: 10.1016/j.celrep.2023.112365.}, abstract = {Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle, but this approach is limited by the deleterious effects of cell expansion in vitro and consequent poor engraftment efficiency. In an effort to overcome this limitation, we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here, we report the development and application of a cross-species small-molecule screening platform employing zebrafish and mice, which enables rapid, direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system, we screened a library of bioactive lipids to discriminate those that could increase myogenic engraftment in vivo in zebrafish and mice. This effort identified two lipids, lysophosphatidic acid and niflumic acid, both linked to the activation of intracellular calcium-ion flux, which showed conserved, dose-dependent, and synergistic effects in promoting muscle engraftment across these vertebrate species.}, keywords = {CP: Developmental biology cell therapy engraftment lysophosphatidic acid muscular dystrophy niflumic acid satellite cell}, ISSN = {2211-1247 (Electronic)}, DOI = {10.1016/j.celrep.2023.112365}, url = {https://www.ncbi.nlm.nih.gov/pubmed/37018075}, year = {2023}, type = {Journal Article} } @article{RN132, author = {Tian, H. and Davis, H. C. and Wong-Campos, J. D. and Park, P. and Fan, L. Z. and Gmeiner, B. and Begum, S. and Werley, C. A. and Borja, G. B. and Upadhyay, H. and Shah, H. and Jacques, J. and Qi, Y. and Parot, V. and Deisseroth, K. and Cohen, A. E.}, title = {Video-based pooled screening yields improved far-red genetically encoded voltage indicators}, journal = {Nat Methods}, volume = {20}, number = {7}, pages = {1082-1094}, note = {Tian, He Davis, Hunter C Wong-Campos, J David Park, Pojeong Fan, Linlin Z Gmeiner, Benjamin Begum, Shahinoor Werley, Christopher A Borja, Gabriel B Upadhyay, Hansini Shah, Himali Jacques, Jane Qi, Yitong Parot, Vicente Deisseroth, Karl Cohen, Adam E eng RF1 MH117042/MH/NIMH NIH HHS/ RF1 NS126043/NS/NINDS NIH HHS/ HHMI/Howard Hughes Medical Institute/ Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. 2023/01/10 Nat Methods. 2023 Jul;20(7):1082-1094. doi: 10.1038/s41592-022-01743-5. Epub 2023 Jan 9.}, abstract = {Video-based screening of pooled libraries is a powerful approach for directed evolution of biosensors because it enables selection along multiple dimensions simultaneously from large libraries. Here we develop a screening platform, Photopick, which achieves precise phenotype-activated photoselection over a large field of view (2.3 x 2.3 mm, containing >10(3) cells, per shot). We used the Photopick platform to evolve archaerhodopsin-derived genetically encoded voltage indicators (GEVIs) with improved signal-to-noise ratio (QuasAr6a) and kinetics (QuasAr6b). These GEVIs gave improved signals in cultured neurons and in live mouse brains. By combining targeted in vivo optogenetic stimulation with high-precision voltage imaging, we characterized inhibitory synaptic coupling between individual cortical NDNF (neuron-derived neurotrophic factor) interneurons, and excitatory electrical synapses between individual hippocampal parvalbumin neurons. The QuasAr6 GEVIs are powerful tools for all-optical electrophysiology and the Photopick approach could be adapted to evolve a broad range of biosensors.}, keywords = {Mice Animals *Hippocampus/physiology *Electrophysiological Phenomena Cells, Cultured Neurons/physiology Interneurons}, ISSN = {1548-7105 (Electronic) 1548-7091 (Print) 1548-7091 (Linking)}, DOI = {10.1038/s41592-022-01743-5}, url = {https://www.ncbi.nlm.nih.gov/pubmed/36624211}, year = {2023}, type = {Journal Article} } @article{RN126, author = {Zwang, T. J. and Woost, B. and Bailey, J. and Hoglund, Z. and Richardson, D. S. and Bennett, R. E. and Hyman, B. T.}, title = {Spatial characterization of tangle-bearing neurons and ghost tangles in the human inferior temporal gyrus with three-dimensional imaging}, journal = {Brain Commun}, volume = {5}, number = {3}, pages = {fcad130}, note = {Zwang, Theodore J Woost, Benjamin Bailey, Joshua Hoglund, Zachary Richardson, Douglas S Bennett, Rachel E Hyman, Bradley T eng England 2023/06/16 Brain Commun. 2023 Apr 19;5(3):fcad130. doi: 10.1093/braincomms/fcad130. eCollection 2023.}, abstract = {Studies of post-mortem human tissue provide insight into pathological processes, but are inherently limited by practical considerations that limit the scale at which tissue can be examined, and the obvious issue that the tissue reflects only one time point in a continuous disease process. We approached this problem by adapting new tissue clearance techniques to an entire cortical area of human brain, which allows surveillance of hundreds of thousands of neurons throughout the depth of the entire cortical thickness. This approach allows detection of 'rare' events that may be difficult to detect in standard 5 micrometre-thick paraffin sections. For example, it is well established that neurofibrillary tangles begin within a neuron, and ultimately, in at least some instances, persist in the brain even after the neuron has died. These are referred to as 'ghost tangles', a term that appropriately implies their 'difficult to see' ephemeral qualities. We set out to find ghost tangles as one example of the power of the tissue clearance/image analysis techniques to detect rare events, and to learn what happens at the end-point of a tangle's life history. We were able to identify 8103 tau tangles, 132 465 neurons and 299 640 nuclei in tissue samples from three subjects with severe Alzheimer's disease (Braak V-VI) and 4 tau tangles, 200 447 neurons and 462 715 nuclei in tissue samples from three subjects with no significant tau pathology (Braak 0-I). Among these data, we located 57 ghost tangles, which makes them only 0.7% of the total tau tangles observed. We found that ghost tangles are more likely to be found in cortical layers 3 and 5 (49/57), with a select few scattered across other layers 1, 2, 4 and 6. This ability to find rare events, such as ghost tangles, in large enough quantities to statistically test their distribution exemplifies how tissue clearing can be used as a powerful tool for studying selective vulnerability or resilience to pathology across brain regions.}, keywords = {ghost tangles inferior temporal gyrus spatial mapping tau tissue clearing}, ISSN = {2632-1297 (Electronic) 2632-1297 (Linking)}, DOI = {10.1093/braincomms/fcad130}, url = {https://www.ncbi.nlm.nih.gov/pubmed/37324243}, year = {2023}, type = {Journal Article} }