bluuebunny/crossref_metadata_2025_split huggingface dataset:
Piezo1 activates non-canonical EGFR endocytosis and signaling
Authors: Pardo-Pastor Carlos , Rosenblatt Jody 
Published: May 2022

SummaryEGFR-ERK signaling controls cell cycle progression during development, homeostasis, and disease. Both the soluble extracellular ligand, EGF, and mechanical inputs like matrix stiffness, cell adhesion, or stretch activate EGFR-ERK signaling. However, the molecules transducing mechanical forces into EGFR signaling remain unidentified. We previously found that stretch promotes mitosis by mechanically activating the ion channel Piezo1 to trigger ERK signaling. Here, we show that Piezo1 provides the missing link to mechanical EGFR-ERK activation. Both EGF ligand and mechanical or agonist activation of Piezo1 trigger clathrin-mediated endocytosis of EGFR and ERK activation, established markers of EGFR signaling. However, while EGF stimulation requires canonical EGFR tyrosine autophosphorylation, EGFR activation by Piezo1 instead requires Src-p38 kinase-dependent serine EGFR phosphorylation. Additionally, in contrast to the homeostatic signaling downstream EGF activation, direct agonist stimulation of Piezo1 promoted cell cycle re-entry and proliferation in mouse airway epitheliaex vivovia long-term nuclear accumulation of ERK, AP-1 (FOS and JUN), and YAP, typical of regenerative and malignant signaling. Our results suggest two modes of EGFR signaling: basal EGF-dependent signaling via tyrosine autophosphorylation and mechanically activated Piezo1-dependent signaling via serine phosphorylation, resulting in sustained proliferation, critical to repair, regeneration, and cancer growth. Given the limited success of tyrosine kinase inhibitors in cancer, this new axis may provide a more relevant target for cancer treatment.
Experience alters hippocampal and cortical network communication via a KIBRA-dependent mechanism
Authors: Quigley Lilyana D. , Pendry Robert , Mendoza Matthew L. , Pfeiffer Brad. E. , Volk Lenora J. 
Published: May 2022

AbstractSynaptic plasticity is hypothesized to underlie “replay” of salient experience during hippocampal sharp-wave/ripple (SWR)-based ensemble activity and to facilitate systems-level memory consolidation coordinated by SWRs and cortical sleep spindles. However, it remains unclear how molecular changes at synapses contribute to experience-induced modification of network function. The synaptic protein KIBRA regulates plasticity and memory, although its impact on circuit dynamics remains unknown. Here, we recorded in vivo neural activity from WT mice and littermates lacking KIBRA to examine circuit function before, during, and after novel experience. In WT mice, experience altered network dynamics in a manner consistent with incorporation of new information content in replay and enhanced hippocampal-cortical communication. However, while baseline SWR features were normal in KIBRA cKO mice, experience-dependent alterations in SWRs were absent. Furthermore, intra-hippocampal and hippocampal-cortical communication during SWRs was disrupted following KIBRA deletion. These results reveal molecular mechanisms that underlie network-level memory formation and consolidation.
Non-Invasive monitoring of normal tissue radiation damage using quantitative ultrasound spectroscopy
Authors: Rafat Marjan , Kaffas Ahmed El , Swarnakar Ankush , Shostak Anastasia , Graves Edward E. 
Published: May 2022

AbstractBackgroundWhile radiation therapy (RT) is an critical component of breast cancer therapy and is known to decrease overall local recurrence rates, recent studies have shown that normal tissue radiation damage may increase recurrence risk. Fibrosis is a well-known consequence of RT, but the specific sequence of molecular and mechanical changes induced by RT remains poorly understood.PurposeThere is currently a need to understand the contribution of the irradiated tissue microenvironment to recurrence to improve cancer therapy outcomes. This study seeks to evaluate the use of quantitative ultrasound spectroscopy (QUS) for real time determination of the normal tissue characteristic radiation response and to correlate these results to molecular features in irradiated tissues.MethodsMurine mammary fat pads (MFPs) were irradiated to 20 Gy, and QUS was used to analyze tissue physical properties pre-irradiation as well as at 1, 5, and 10 days post-irradiation. Tissues were processed for scanning electron microscopy imaging as well as histological and immunohistochemical staining to evaluate morphology and structure.ResultsTissue morphological and structural changes were observed non-invasively following radiation using mid-band fit (MBF), spectral slope (SS), and spectral intercept (SI) measurements obtained from QUS. Statistically significant shifts in MBF and SI indicate structural tissue changes in real time, which matched histological observations. Radiation damage was indicated by increased adipose tissue density and extracellular matrix (ECM) deposition.ConclusionsOur findings demonstrate the potential of using QUS to non-invasively evaluate normal tissue changes resulting from radiation damage. This supports further pre-clinical studies to determine how the tissue microenvironment and physical properties change in response to therapy, which may be important for improving treatment strategies.
Functional brain-wide network mapping during acute stress exposure in rats: Interaction between the lateral habenula and cortical, amygdalar, hypothalamic and monoaminergic regions
Authors: Durieux Laura , Herbeaux Karine , Borcuk Christopher , Hildenbrand Cécile , Andry Virginie , Goumon Yannick , Barbelivien Alexandra , Mathis Chantal , Bataglia Demian , Majchrzak Monique , Lecourtier Lucas 
Published: May 2022

AbstractUpon stress exposure a broad network of structures comes into play in order to provide adequate responses and restore homeostasis. It has been known for decades that the main structures engaged during the stress response are the medial prefrontal cortex, the amygdala, the hippocampus, the hypothalamus, the monoaminergic systems (noradrenaline, dopamine, serotonin), and the periaqueductal gray. The lateral habenula (LHb) is an epithalamic structure directly connected to prefrontal cortical areas and to the amygdala, whereas it functionally interacts with the hippocampus. Also, it is a main modulator of monoaminergic systems. The LHb is activated upon exposure to basically all types of stressors, suggesting it is also involved in the stress response. However, it remains unknown if and how the LHb functionally interacts with the broad stress response network. In the current study we performed in rats a restraint stress procedure followed by immunohistochemical staining of the c-Fos protein throughout the brain. Using Graph Theory-based functional connectivity analyses, we confirm the principal hubs of the stress network (e.g. prefrontal cortex, amygdala, periventricular hypothalamus), and show that the LHb is engaged during stress exposure in close interaction with the medial prefrontal cortex, the lateral septum, and the medial habenula. In addition, we performed DREADD-induced LHb inactivation during the same restraint paradigm in order to explore its consequences on the stress response network. This last experiment gave contrasting results as the DREADD ligand alone, clozapine-N-oxide, was able to modify the network.GRAPHICAL ABSTRACTGRAPHICAL ABSTRACT TEXTIn this study, using immunohistochemical staining of the immediate early gene c-fos and graph theory-based functional correlational analyses, we aimed at unravelling the possible engagement of the lateral habenula (LHb) within the stress response network during acute stress exposure (10-min restraint) in rats. We found that the medial part of the LHb (LHbM) was preferentially engaged, and that this engagement was concomitant to this of structures such as the medial prefrontal cortex (mPFC), the insular cortex (Ins), hypothalamic (PVH) and thalamic (PVT) paraventricular nuclei, the extended amygdala, comprising the Bed nucleus of the stria terminalis (BNST) and the entire amygdala (AMG), as well as the dopaminergic ventral tegmental area (VTA) and the serotonergic dorsal raphe nucleus (RD). This suggests upon stressful situations the LHbM serves as a relay of cortical, thalamic, hypothalamic and temporal information, further transmitted to midbrain monoaminergic systems to probably initiate coping strategies.
Topology of gene regulatory compartments relative to the nuclear matrix
Authors: Park Gunhee , Ryu Kwangmin , Lee Junho , Kim Geunhee , Park Tae Lim , Shim Hwanyong , Lee YigJi , Kim Changyeop , Cho Won-Ki 
Published: May 2022

Summary ParagraphInside the nucleus, there are special compartments with characterized functions, some of which are involved in gene expression1. These compartments include transcriptional condensates and nuclear speckles, which contain factors required for transcription and splicing, respectively. While the characteristics of these intranuclear compartments were extensively investigated, spatial relationship between them is yet unclear. Meanwhile, RNA-protein structural network named the nuclear matrix has been observed inside the nucleus and suggested as a framework for the spatial segregation of the intranuclear space2–6. However, concept of the nuclear matrix was not widely accepted due to its lack of in vivo evidence7. Here, we report visualization of the nuclear matrix and intranuclear compartments using super-resolution fluorescence microscopy. We found the nuclear matrix is dynamic in live cells and easily disrupted upon transcription inhibition. Remarkably, we observed an orderly layered distribution of transcriptional condensates and nuclear speckles relative to the nuclear matrix. We also observed a separation of chromosome territories from transcriptional condensates and nuclear speckles by the nuclear matrix. Based on our findings, we propose a topological model for the regulation of transcription across the nuclear matrix.
Neural signals encoded by specific frequencies of closed-loop electrical stimulation structurally and functionally reconstruct spinal sensorimotor circuits after spinal cord injury
Authors: Zhou Kai , Yang Dan , Wei Wei , Zhang Hui , Yang Wei , Zhang Yunpeng , Nie Yingnan , Hao Mingming , Zhang Ting , Wang Shouyan , Liu Yaobo 
Published: May 2022

AbstractEpidural electrical stimulation restores locomotion in animals and humans with spinal cord injury (SCI). However, the coding rules underlying electrical stimulation remain poorly understood, which has greatly limited the application of such electrical neuromodulation techniques in SCI clinical treatment. To elucidate the coding rules of electrical stimulation on spinal sensorimotor circuit reconstruction after complete SCI, we initially developed a spinal−muscle closed-loop stimulation protocol to mimic feedforward and feedback electrical signals in spinal sensorimotor circuits. Afterwards, using methods of sensorimotor function evaluation, neural circuit tracing and neural signal recording, we discovered a unique stimulus frequency of 10−20 Hz under closed-loop conditions was required for structural and functional reconstruction of spinal sensorimotor circuits. The single-cell transcriptome analysis of activated motoneurons characterized molecular networks involved in spinal sensorimotor circuit reconstruction. This study provides insights into neural signal decoding during spinal sensorimotor circuit reconstruction, and indicates a technological approach for the clinical treatment of SCI.
Signaling protein abundance modulates the strength of the Spindle Assembly Checkpoint
Authors: Chen Chu , Humphrey Lauren , Jema Soubhagyalaxmi , Karmarkar Shriya , Ferrari Frank , Joglekar Ajit P. 
Published: May 2022

SummaryDuring mitosis, unattached kinetochores in a dividing cell signal to the Spindle Assembly Checkpoint to delay anaphase onset and prevent chromosome missegregation1–4. The signaling activity of these kinetochores and the likelihood of chromosome missegregation both depend on the amount of SAC signaling proteins that each kinetochore recruits5–8. Therefore, factors that control SAC protein recruitment to signaling kinetochores must be thoroughly understood. Phosphoregulation of kinetochore and SAC signaling proteins emerging from the concerted action of many kinases and phosphatases is a major determinant of SAC protein recruitment to signaling kinetochores9. Whether the abundance of SAC proteins also influences their recruitment and signaling activity at human kinetochores has not been studied8, 10. Here, we reveal that the low cellular abundance of the SAC signaling protein Bub1 limits kinetochore recruitment of Bub1 and BubR1 and reduces the SAC signaling activity of the kinetochore. Conversely, Bub1 overexpression results in higher protein recruitment and SAC activity producing longer delays in anaphase onset. We also find that the number of SAC proteins recruited by a signaling kinetochore is inversely correlated with the total number of signaling kinetochores in the cell. This correlation likely arises from the competition among the signaling kinetochores to recruit from a limited pool of signaling proteins. The inverse correlation between the number of signaling kinetochores in the cell and the signaling activity of individual kinetochores may allow the dividing cell to prevent the large number of signaling kinetochores in prophase from generating an unnecessarily large signal, while enabling the last unaligned kinetochore to signal at the maximum possible strength.
A Cdh3-Lam332 signaling axis in a leader cell subpopulation controls protrusion dynamics and tumor organoid collective migration
Authors: Hwang Priscilla Y , Mathur Jairaj , Cao Yanyang , Almeida Jose , Cornish Daphne , Clarke Maria , Pathak Amit , Longmore Gregory D 
Published: May 2022

AbstractCarcinoma dissemination can occur when heterogeneous tumor and tumor stromal cells clusters migrate together via collective migration. Cells at the front lead and direct collective migration, yet how these leader cells form and interact with the microenvironment to direct migration are not fully appreciated. From live videos of primary mouse and human breast tumor organoids in a 3D microfluidic system that mimics the native breast tumor microenvironment, we developed 3D computational models which hypothesize that leader cells generate high protrusive forces and overcome extracellular matrix (ECM) resistance. Using single cell sequencing, we reveal leader cells are heterogeneous, and identify and isolate a unique Cadherin-3 (Cdh3) positive leader cell subpopulation that is necessary and sufficient to lead migration. Cdh3 controls leader cell protrusion dynamics through the local production of Laminin-332 which is required for integrin/focal adhesion function. Our findings highlight how a subset of leader cells interact with the microenvironment to direct collective migration.TeaserHigher protrusions of Cdh3+ leader cells polarize tumor organoids that then invade collagen via Lam332 adhesion feedback.
Calcium-activated big conductance (BK) potassium channels traffic through nuclear envelopes into kinocilia in skate electrosensory cells
Authors: Chen Abby L. , Wu Ting-Hsuan , Shi Lingfang , Clusin William T. , Kao Peter N. 
Published: May 2022

AbstractElectroreception through ampullae of Lorenzini in the little skate, Leucoraja erinacea, involves functional coupling between voltage-activated calcium channels (CaV1.3, cacna1d) and calcium-activated big conductance potassium (BK) channels (BK, kcnma1). Whole mount confocal microscopy was used to characterize expression of BK and CaV1.3 in intact ampullae. BK and CaV1.3 are present in electrosensory cell plasma membranes and colocalize with lamin B1 in nuclear envelopes and kinocilia. Predicted nuclear localization signals (NLS) were identified in BK and CaV1.3 by bioinformatic sequence analyses. The BK NLS is bipartite, occurs at an alternative splice site for the mammalian STREX exon and is modified by post-translational phosphorylation. Nuclear localization of skate BK channels was characterized in heterologously-transfected HEK293 cells. Double point mutations in the bipartite NLS (KR to AA, or SVLS to AVLA) independently attenuated BK channel nuclear localization, illustrating that BK trafficking into nuclei and electrosensory cell kinocilia is regulated through a newly identified bipartite NLS.
Expanding luciferase reporter systems for cell-free protein expression
Authors: Sato Wakana , Rasmussen Melanie , Deich Christopher , Engelhart Aaron E. , Adamala Katarzyna P. 
Published: May 2022

AbstractLuciferases are often used as a sensitive, versatile reporter in cell-free transcription-translation (TXTL) systems, for research and practical applications such as engineering genetic parts, validating genetic circuits, and biosensor outputs. Currently, only two luciferases (Firefly and Renilla) are commonly used without substrate cross-talk. Here we demonstrate expansion of the cell-free luciferase reporter system, with two orthogonal luciferase reporters: N. nambi luciferase (Luz) and LuxAB. These luciferases do not have cross-reactivity with the Firefly and Renilla substrates. We also demonstrate a substrate regeneration pathway for one of the new luciferases, enabling long-term time courses of protein expression monitoring in the cell-free system. Furthermore, we reduced the number of genes required in TXTL expression, by engineering a cell extract containing part of the luciferase enzymes. Our findings lead to an expanded platform with multiple orthogonal luminescence translation readouts for in vitro protein expression.
Three ALS genes regulate expression of the MHC class II antigen presentation pathway
Authors: Chi Binkai , Öztürk Muhammet M. , Paraggio Christina L. , Leonard Claudia E. , Sanita Maria E. , Dastpak Mahtab , O’Connell Jeremy D. , Coady Jordan A. , Zhang Jiuchun , Gygi Steven P. , Lopez-Gonzalez Rodrigo , Reed Robin 
Published: May 2022

AbstractHere we report that the major histocompatibility complex II (MHC II) antigen presentation pathway is regulated by the ALS-causative genes, FUS, TAF15, or MATR3. Of >6000 proteins detected by quantitative mass spectrometry, the subunits of the MHC II heterodimer, HLA-DR, were the top 2 downregulated proteins in HeLa knock outs (KO) of these ALS genes, but not the related gene, EWSR1. Moreover, CD74, which is the 3rd essential component of HLA-DR, was downregulated in the 3 KOs. We show that the downregulations are due to loss of CIITA, a transcription factor dedicated to expression of MHC II genes. Thus, our results reveal the 1st shared cellular pathway regulated by multiple ALS genes, and this pathway is ALS genes -> CIITA -> MHC II genes. We obtained the same results in HMC3 cells, a microglia cell line, showing that loss of the MHC II pathway extends to an ALS-relevant cell type in the central nervous system (CNS). Furthermore, the MHC II pathway is downregulated in hematopoietic progenitor cells (HPCs) bearing the ALS FUSR495X mutation. This observation may be highly significant to ALS pathogenesis as HPCs give rise to a multitude of CNS-specific and systemic immune cells, both of which have known or suspected roles in ALS. Together, our data raise the possibility that loss of the MHC II pathway in a large range of immune cells results in global failure of the immune system to protect motor neurons from damage that leads to the disease. Consequently, CIITA and the other genes in the MHC II pathway may be important new therapeutic targets for the disease.
Systematic optimization of Cas12a base editors in wheat and maize using the ITER platform
Authors: Gaillochet Christophe , Pena Fernandez Alexandra , Goossens Vera , D’Halluin Katelijn , Drozdzecki Andrzej , Shafie Myriam , Van Duyse Julie , Van Isterdael Gert , Gonzalez Camila , Vermeersch Mattias , De Saeger Jonas , Develtere Ward , Audenaert Dominique , De Vleesschauwer David , Meulewaeter Frank , Jacobs Thomas B. 
Published: May 2022

AbstractThe ever-increasing number of CRISPR components creates a significant burden when developing new genome engineering tools. Plant biotechnology in particular has few high-throughput options to perform iterative design-build-test-learn cycles when creating new gene-editing reagents. We have established ITER (Iterative Testing of Editing Reagents) based on arrayed protoplast transfections and high-content imaging, allowing one optimization cycle – from design to results– within three weeks. We validated ITER in wheat and maize protoplasts using Cas9 cytosine and adenine base editors. Given that previous LbCas12a-ABEs have low or no activity in plants, we used ITER to develop an optimized LbCas12a-ABE. We show that the sequential improvement of five components –NLS, crRNA, LbCas12a, adenine deaminase and linker– led to a remarkable increase in ABE activity from almost undetectable levels to 40% on an extrachromosomal GFP reporter. We confirmed the activity of LbCas12a-ABE at endogenous targets and in stable wheat transformants and leveraged these improvements to develop a highly mutagenic LbCas12a nuclease and LbCas12a-CBE. Our data show that ITER is a sensitive, versatile, and high-throughput platform that can be harnessed to accelerate the development of genome editing technologies in plants.
Mutual repression between JNK/AP-1 and JAK/STAT stratifies cell behaviors during tissue regeneration
Authors: Jaiswal Janhvi , Engesser Raphael , Peyroton Andrea Armengol , Weichselberger Vanessa , Crucianelli Carlo , Grass Isabelle , Timmer Jens , Classen Anne-Kathrin 
Published: May 2022

AbstractEpithelial repair relies on the activation of stress signaling pathways to coordinate cellular repair behaviors. Their deregulation is implicated in chronic wound and cancer pathologies. Despite such translational importance, an understanding of how spatial patterns of signaling pathways and repair behaviors arise in damaged tissues remains elusive. Using TNF-α/Eiger-mediated inflammatory damage to Drosophila imaginal discs, we uncover that JNK/AP-1 signaling cells act as paracrine organizers and initiate a mutual repression network that spatially segregates JNK/AP-1 and JAK/STAT signaling cells into distinct populations. While JNK/AP-1 signaling cells produce JAK/STAT-activating Upd ligands, these signal-sending cells suppress activation of JAK/STAT via Ptp61F. Conversely, responding cells with activated JAK/STAT suppress JNK activation via Zfh2. The resulting bistable segregation of signaling domains is associated with distinct cellular tasks and regenerative potential. While JNK/AP-1 signaling cells at the wound center act as paracrine organizers, their cell cycle is senescently arrested. Thus, compensatory proliferation occurs exclusively in JAK/STAT signaling cells at the wound periphery. This spatial stratification is essential for proper tissue repair, as co-activation of JNK/AP-1 and JAK/STAT in the same cells creates conflicting inputs on cell cycle progression, leading to excess apoptosis of senescently arrested organizer cells. Finally, we demonstrate that bistable spatial segregation of JNK/AP-1 and JAK/STAT drives senescent and proliferative behaviors in transient as well as chronic tissue damage models, and importantly, in RasV12, scrib tumors under the influence of JNK/AP-1 activity. Revealing this previously uncharacterized regulatory network between JNK/AP-1, JAK/STAT and associated cell behaviors have important implications for our conceptual understanding of tissue repair, chronic wound pathologies and tumor microenvironments, where both pathways are strongly implicated.