Biology subjects

Basu, J.

Publications and source records attributed to Basu, J..

18 recordsLinked to original sources

bioRxiv2026

Implications for Faster Healing with Fewer Applications: Sustained Graft Persistence and Favorable Wound-Healing Biology of a Proprietary Processed Placental Tissue Allograft

Introduction Placental tissue allografts are widely utilized as wound coverings and barriers. In addition to tissue source, manufacturing and processing methodologies can influence extracellular matrix (ECM) architecture, mechanical stability, protease susceptibility, degradation kinetics, and graft persistence following implantation. An optimized placental tissue allograft should maintain sufficient matrix integrity during the active period of tissue repair while preserving the biological characteristics associated with a favorable wound healing environment. Our previously published work demonstrated that a proprietary processed human amniotic membrane allograft exhibited a more favorable wound healing biologic profile than conventionally processed placental tissue. The finding that no XWRAP treated wound had reached the reapplication threshold at Day 14, considered together with previously demonstrated favorable wound healing biology, provides a mechanistic rationale for the hypothesis that XWRAP may support faster healing with fewer applications over a course of wound management. Methods Graft integrity was evaluated every 2 days for 14 days following application to standardized full thickness excisional wounds in Sprague Dawley rats. XWRAP, a proprietary processed human amniotic membrane allograft, was compared with a donor matched conventionally processed human amniotic membrane comparator and a commercial placental tissue comparator. Graft integrity was scored from 0 to 5, where 0 represented complete graft loss or resorption and 5 represented an intact graft. A score [≤]1 represented the protocol defined threshold for reapplication during non terminal visits. Longitudinal graft integrity trajectories, original graft degradation, documented reapplications, and the proportion of wounds reaching the reapplication threshold were evaluated. At each visit, graft integrity in XWRAP treated wounds was compared with the pooled comparator groups (primary comparison) and with each comparator separately using animal level Mann Whitney tests, with Holm adjustment across visits; reapplication frequency was compared using exact Poisson rate ratios. Results XWRAP demonstrated markedly greater late phase persistence than both comparator products. At Day 14, mean graft integrity score was 3.88 for XWRAP compared with 0.93 for donor matched conventionally processed amnion and 1.69 for the commercial comparator. From Days 10 through 14, XWRAP graft integrity was significantly greater than both comparators (all p[≤]0.001), with Cliff's {delta} values of 0.95 to1.00. Compared with the pooled comparator groups, XWRAP graft integrity was significantly greater from Day 8 (3.31 vs. 2.93; p=0.022) through Day 14 (3.88 vs. 1.33; p<0.001); differences at Days 10 to14 remained significant after Holm adjustment, and no significant differences were observed during Days 2 to 6. At the terminal Day 14 assessment, none of the XWRAP treated wounds had reached the protocol defined reapplication threshold (0/16; 0%), compared with 11/14 (79%) wounds treated with donor matched conventional amnion and 5/16 (31%) wounds treated with the commercial comparator. Analysis limited to original grafts demonstrated the same persistence pattern, with Day 14 integrity scores of 3.92, 0.90, and 1.83, respectively. The proportion of wounds at the reapplication threshold at Day 14 was significantly lower with XWRAP than with the pooled comparators (0/16 vs. 16/30; p<0.001). Documented reapplications, all of which occurred during Days 2 to 6, did not differ between XWRAP and the pooled comparators (3.24 vs. 3.40 per 100 wound days; rate ratio 0.95, 95% CI 0.33 to2.53; p=1.00). Discussion Proprietary processing produced a substantially different graft persistence profile, with XWRAP remaining largely intact while comparator tissues progressed toward resorption. Importantly, this greater graft persistence complements our previously published findings demonstrating that XWRAP also produced a more favorable wound healing biologic profile across multiple measures of cellular proliferation, inflammation, tissue injury, and wound resolution. Taken together, these findings support two complementary attributes of XWRAP: sustained graft persistence and favorable wound healing biology. The finding that no XWRAP treated wound had reached the reapplication threshold at Day 14 provides a mechanistic rationale for the hypothesis that this combination may extend application intervals and reduce application requirements over a course of wound management.

bioengineering↗

bioRxiv2026

XWRAP Human Amniotic Membrane in Combination with an Amniotic-Fluid-Derived Biologic Promotes Collagen Fibril Regeneration in a Preclinical Rabbit Model of Medial Collateral Ligament Injury

Current treatment of orthopedic ligament injury relies principally on non-regenerative materials and surgical repair rather than strategies that promote intrinsic tissue regeneration. This study evaluated whether biologic augmentation with XWRAP, a human amniotic membrane allograft, combined with a cryopreserved amniotic-fluid-derived biologic containing micronized human amnion membrane, promotes regeneration of ligament architecture in a rabbit medial collateral ligament (MCL) gap-defect model. Standardized 4-mm mid-substance MCL gap defects were created in New Zealand White rabbits (n=3) and either treated with the amniotic membrane/amniotic-fluid biologic combination or left untreated, with intact contralateral or adjacent MCL serving as native controls; ligaments were evaluated by transmission electron microscopy at 2 and 6 weeks post-procedure, with collagen fibril diameter quantified from calibrated high-magnification micrographs. Treated defects developed significantly larger mean collagen fibril diameters than untreated defects at both time points (75 vs. 50 nm at 2 weeks and 88 vs. 62 nm at 6 weeks; p<0.0001 for each comparison), reaching approximately 90% of native, uninjured ligament fibril diameter (98 nm) by 6 weeks. Treated defects also developed a broader, bimodal fibril-diameter distribution resembling native ligament architecture, whereas untreated defects remained characterized by a narrow, unimodal population of small-diameter fibrils typical of scar-associated repair. These findings indicate that biologic augmentation with XWRAP combined with an amniotic-fluid-derived biologic promotes a regenerative, rather than purely reparative, healing response following ligament injury, progressively restoring collagen fibril architecture toward that of native tissue in this preclinical model.

bioengineering↗

bioRxiv2026

Proprietary Processing of Placental Tissue Allografts Influences Wound Healing Trajectories in a Rodent Excisional Skin Wound Model

Introduction: Placental tissue allografts are widely utilized in the management of chronic wounds, including diabetic foot ulcers. In addition to serving as wound coverings, these products may influence wound repair through extracellular matrix architecture and biologically active signaling molecules native to human amniotic tissue. Manufacturing and processing methodologies vary considerably across commercially available products and may substantially impact biologic activity, tissue remodeling, and wound-healing trajectories. In this study, a rodent wound-healing model was utilized to compare a proprietary processed placental tissue allograft with a conventionally processed placental tissue comparator. Methods: Two arms of a five-arm pilot rodent wound-healing study were evaluated to compare a proprietary processed human amniotic tissue allograft against a conventionally processed comparator; the remaining arms evaluated test articles under development and will be reported separately. Male rats (n=8 per arm), matched for weight, age, and diet, each received two full-thickness dorsal excisional wounds approximately 10 mm in diameter and 2 mm deep. Test articles were reapplied upon resorption over a 14-day period. At Day 14, sections were scored semi-quantitatively (0-4 Severity Injury Score) across histologic and immunohistochemical parameters spanning epidermal repair, inflammation, angiogenesis, proliferation, and remodeling. Cranial and caudal wounds were averaged within each animal, retaining the animal as the experimental unit. A Day 14 Histology Resolution Score was derived as a signed composite of pro- and anti-regenerative markers and evaluated alongside percent wound closure. Inferential statistics (Welch ANOVA with Games-Howell post hoc) were derived from the full five-arm cohort (n=40). Results: Animals treated with the proprietary processed allograft showed more advanced progression toward wound resolution than those receiving the conventionally processed comparator, across both surface and tissue-level endpoints. Mean animal-level wound closure at Day 14 was 95.2% with the proprietary processed allograft versus 89.9% with the conventional comparator. The integrated Day 14 Histology Resolution Score, a composite of epidermal repair, inflammation, angiogenesis, proliferation, and remodeling endpoints was 8.94 versus 5.13, corresponding to a shift from the poor-resolution range into the partial-resolution range on the pre-defined interpretive scale. Welch ANOVA across the full five-arm cohort (n=40) detected a significant overall effect of treatment on this composite (p = 0.010). The pairwise contrast between these two arms did not reach significance under Games-Howell correction across ten comparisons (p = 0.337); at n=8 per arm the study was not powered to resolve individual pairwise differences, and the observed standardized difference was large (Hedges' g = 0.93). Injury endpoints were consistently lower in the proprietary processed allograft: 69% lower acute inflammation, 60% lower dermal necrosis, approximately 57% lower epithelial erosion, 46% lower ulceration, and 42% less hemorrhage. Importantly, these reductions in residual tissue injury occurred while maintaining robust granulation tissue formation, angiogenesis, collagen remodeling, cellular proliferation, and macrophage recruitment. Discussion: These findings suggest that processing methodologies can materially influence the biologic performance of placental tissue allografts. The proprietary processed allograft was associated with lower residual tissue injury and greater regenerative and reparative activity relative to a conventionally processed comparator. These observations support the concept that placental tissue allografts should not necessarily be viewed as biologically equivalent and may have important implications for clinical outcomes and product selection in wound care.

bioengineering↗

bioRxiv2026

Purinergic signaling promotes gliomagenesis through nuclear calcium transients

Intracellular Ca2+ transients drive key developmental and physiological processes, yet their role in oncogenesis remains incompletely understood. In glioblastoma (GBM), an aggressive brain malignancy, tumor cellular networks exhibit self-sustaining Ca2+ transients that promote tumor growth through unclear mechanisms. Using patient-derived GBM models, we show that these transients depend primarily on intracellular Ca2+ stores and extend to the nucleus to drive tumorigenesis. A neuromodulator screen identified extracellular purines ATP and ADP as potent inducers of both nuclear and cytosolic Ca2+ transients via activation of metabotropic purinergic P2RY1 receptors, whose knockdown attenuates tumorigenicity in vitro and in vivo. Mechanistically, Ca2+ transients promote tumorigenesis via the nuclear Ca2+/calmodulin-dependent kinase CAMK4, which regulates transcriptional and epigenetic programs, as well as ribosomal DNA transcription. From the therapeutic perspective, pharmacologic P2RY1 inhibition suppresses tumor growth in vitro and in vivo. Collectively, these findings reveal a pharmacologically targetable oncogenic mechanism in GBM and possibly other malignancies.

cancer biology↗

bioRxiv2026

Lateral entorhinal cortex supports behaviorally-induced hippocampal ensemble stability for reliable memory recall

Hippocampal pyramidal neurons function as place cells, showing location-specific activity during navigation, to form an internal spatial map of the environment. They are hypothesized to be the neural substrate of episodic memory. However, place cell receptive fields tend to drift or have poor tuning in low demand tasks, lacking operant goals such as random foraging, or in sensory context-deprived environments. Through chronic two-photon calcium imaging of hippocampal area CA1, we directly compare stability in a low versus a high demand task within the same animals over the course of learning and recall in the same environment. We find that compared to random foraging, an odor-context based navigational task stabilizes place cell representations and increases place cell quality and quantity. To investigate the circuit mechanism that may support this stability, we manipulated the activity of lateral entorhinal cortex (LEC) excitatory neurons, which provide both indirect and direct multisensory inputs about context, odor, and time to CA1. We chemogenetically suppressed activity of excitatory neurons in LEC during recall of the odor-context based navigation task and found that context discrimination is impaired at both the behavioral and neural level. With LEC silencing, mice had lower behavioral performance, less stable population activity, and greater similarity between opposing trial types. Our study finds that increasing task demand increases CA1 stability and that this stability is partially supported by LEC.

neuroscience↗

bioRxiv2026

Temporal Coding rather than Circuit Wiring allows Hippocampal CA3 Neurons to Dynamically Distinguish Different Cortical Inputs

Memory relies on associating and indexing multimodal information. How does this occur within single neurons? The hippocampus integrates multisensory information from medial (MEC) and lateral (LEC) entorhinal cortices to form environmental representations1-6, yet their synaptic dynamics, circuit organization, and integrative functions remain elusive. Contrary to canonical models emphasizing anatomical and functional segregation, our dual-color optogenetic7 circuit mapping revealed that both MEC and LEC inputs converge on virtually every CA3 pyramidal neuron and exhibit similar input-output functions and modulation via GABAergic microcircuitry. Divergence occurs in their frequency-dependent short-term plasticity. With increasing frequencies, facilitating LEC-evoked responses undergo synaptic depression, whereas MEC-evoked responses continue facilitating. In vivo, MEC-originating dentate spikes fire CA3 more than LEC, likely due to their distinct temporal relationship with oscillatory activity. Our findings support that hippocampal area CA3 processes region-specific information from MEC and LEC via temporal coding, rather than hard-wired circuit organization, at both single-neuron and network levels.

neuroscience↗

bioRxiv2025

NK cell allorecognition shapes reprogramming of neutrophils infiltrating heart allografts

BackgroundRecent developments in neutrophil biology have demonstrated that neutrophils are phenotypically and functionally heterogeneous. Tissue microenvironments dictate changes in neutrophil cell states in infection and cancer, but little is known about how alloimmune responses or solid organ transplantation influence neutrophil heterogeneity and plasticity. MethodsHere, we used the murine heterotopic heart transplant model in conjunction with high dimensional flow cytometry and transcriptome analysis to interrogate how the alloimmune response and microenvironment of a transplanted organ influence neutrophil subset differentiation and plasticity. Complete MHC mismatched A/J (H2a) or syngeneic B6 (H2b) hearts were transplanted to C57BL/6 or B6 background genetically modified recipients. ResultsWe uncovered striking differences between neutrophils infiltrating complete MHC mismatched allografts and syngeneic isografts. Bone marrow neutrophil development was highly skewed towards an immature, interferon stimulated gene (ISG)+ subset (marked by IFIT1 expression) early after transplant in both allo- and iso-graft recipients. ISG+ neutrophils were also the dominant population in the peripheral blood of both recipient groups. In contrast, neutrophils maintained the ISG+ phenotype after infiltrating an allograft but appeared to turn off this program upon infiltrating an isograft. The heart graft microenvironment imposed additional reprogramming independent of donor-recipient mismatch, as neutrophils from both allo- and iso-grafts were skewed towards a mature, aged and proangiogenic dcTRAIL-R1+ phenotype. Interestingly, while the existing literature indicates that IFIT1-expressing ISG+ neutrophils and proangiogenic dcTRAIL-R1+ neutrophils are distinct subsets, we identified a novel IFIT1+ dcTRAIL-R1+ hybrid population that is highly enriched in allografts. Mechanistically, NK cell-mediated innate allorecognition drives this early intra-allograft specific neutrophil phenotypic programing. ConclusionsThese findings provide novel insights into the innate immune allorecognition-mediated regulation of the plasticity of recently described key neutrophil subsets and will enable specific targeting to neutralize detrimental neutrophil subsets and enhance solid organ transplant outcomes.

immunology↗

bioRxiv2025

Coin-tossing by Kinesin-1 Head and Tail Binding Collectively Drives Microtubule Patterns

Intracellular microtubule-based transport depends on an essential plus-ended molecular motor, kinesin-1. The N-terminal ATP-dependent head driving motility and a C-terminal cargo interacting tail, both bind microtubules. Previously, the interplay of both domains were hypothesized to play a role in collective microtubule sliding patterns, but the mechanisms remained unclear. Here, we show that full-length Drosophila kinesin-1 generates striking spatiotemporal patterns in gliding assays including bending, looping, and oscillations as well as stop-and-go motion of filaments. In presence of the motor domain alone these patterns are absent, but with the tail only construct, microtubules bind passively, with the tail acting as a static anchor. An equimolar mixture of these two domain constructs reproduces these spatio-temporal patterns both in terms of increased bending with length and velocity distributions. Our results support a simple coin-toss model, where either head or tail bind microtubules with equal probability, leading to antagonistic interactions that drives emergent motility patterns and velocity distributions. Thus the kinesin tail plays an active mechanical role beyond regulation or cargo binding, modulating microtubule behavior through inter-domain competition.

biophysics↗

bioRxiv2024

Topography of putative bidirectional interaction between hippocampal sharp wave ripples and neocortical slow oscillations

Systems consolidation relies on coordination between hippocampal sharp-wave ripples (SWRs) and neocortical UP/DOWN states during sleep. However, whether this coupling exists across neocortex and the mechanisms enabling it remain unknown. By combining electrophysiology in mouse hippocampus (HPC) and retrosplenial cortex (RSC) with widefield imaging of dorsal neocortex, we found spatially and temporally precise bidirectional hippocampo-neocortical interaction. HPC multi-unit activity and SWR probability was correlated with UP/DOWN states in mouse default mode network, with highest modulation by RSC in deep sleep. Further, some SWRs were preceded by the high rebound excitation accompanying DMN DOWN[->]UP transitions, while large-amplitude SWRs were often followed by DOWN states originating in RSC. We explain these electrophysiological results with a model in which HPC and RSC are weakly coupled excitable systems capable of bi-directional perturbation and suggest RSC may act as a gateway through which SWRs can perturb downstream cortical regions via cortico-cortical propagation of DOWN states.

neuroscience↗

bioRxiv2024

ClearScope: a fully integrated light sheet theta microscope for sub-cellular resolution imaging without lateral size constraints

Three-dimensional (3D) ex vivo imaging of cleared intact brains of animal models and large human and non-human primate postmortem brain specimens is important for understanding the physiological neural network connectivity patterns and the pathological alterations underlying neuropsychiatric and neurological disorders. Light-sheet microscopy has emerged as a highly effective imaging modality for rapid high-resolution imaging of large cleared samples. However, the orthogonal arrangements of illumination and detection optics in light sheet microscopy limits the size of specimen that can be imaged. Recently developed light sheet theta microscopy (LSTM) technology addressed this by utilizing a unique arrangement of two illumination light paths oblique to the detection light path, while allowing perpendicular arrangement of the detection light path relative to the specimen surface. Here, we report development of a next-generation, fully integrated, and user-friendly LSTM system for rapid sub-cellular resolution imaging uniformly throughout a large specimen without constraining the lateral (XY) size. In addition, we provide a seamlessly integrated workflow for image acquisition, data storage, pre- and post-processing, enhancement, and quantitative analysis. We demonstrate the system performance by high-resolution 3D imaging of intact mouse brains and human brain samples, and complete data analysis including digital neuron tracing, vessel reconstruction and design-based stereological analysis in 3D. This technically enhanced and user-friendly LSTM implementation will enable rapid quantitative mapping of molecular and cellular features of interests in diverse types of very large samples.

neuroscience↗

bioRxiv2024

Microtubule polymerization tuned by macromolecular crowdant size and density

Microtubule (MT) polymerization is regulated by biochemical as well as physical factors such as macromolecular crowding. Crowding agents or crowdants affect MT elongation rates differently depending on crowdant size due to opposing ef-fects on polymerization: microviscosity reduces polymer elongation, while volume exclusion increases reaction rates by local concentration. In order to address how crowdant size and concentration collectively affect MT populations, we combine in vitro MT polymerization experiments with kinetic Monte Carlo simulations. Our experiments in bulk with nucleators validate decreasing MT elongation rates with increasing concentrations of small molecular weight crowdants in bulk assays and a corresponding increase for large crowdants. Kinetic Monte Carlo simulations can explain the result with packing fractions dependence of small as compared to large crowdants increasing microviscosity more dramatically. In contrast MT bulk polymerization rates in absence of nucleators increased with crowdant con-centration, irrespective of their size, with a corresponding decrease in the critical concentration. Microscopy of filament growth dynamics demonstrates that small crowdants result in shorter filaments in a concentration dependent manner, consis-tent with their role in reducing elongation rates, but this decrease is compensated by increased number of filaments. Large crowdants increase the filament numbers while elongation is slightly decreased. Our results provide evidence for MT nucle-ation being rate-limited and elongation diffusion limited, resulting in differences in the effect of crowdant sizes on nucleation and elongation. These results are of gen-eral relevance to understand physical effects of crowding on collective cytoskeletal polymerization dynamics.

biophysics↗

bioRxiv2024

Modeling and Correction of Protein Conformational Disease in iPSC-derived Neurons through Personalized Base Editing

AbstractAltered protein conformation can cause incurable neurodegenerative disorders. Mutations in SERPINI1, the gene encoding neuroserpin, can alter protein conformation resulting in cytotoxic aggregation leading to neuronal death. Familial encephalopathy with neuroserpin inclusion bodies (FENIB) is a rare autosomal dominant progressive myoclonic epilepsy that progresses to dementia and premature death. We developed HEK293T and induced pluripotent stem cell (iPSC) models of FENIB, harboring a patient-specific pathogenic SERPINI1 variant or stably overexpressing mutant neuroserpin fused to GFP (MUT NS-GFP). Here, we utilized a personalized adenine base editor (ABE)-mediated approach to correct the pathogenic variant efficiently and precisely to restore neuronal dendritic morphology. ABE-treated MUT NS-GFP cells demonstrated reduced inclusion size and number. Using an inducible MUT NS-GFP neuron system, we identified early prevention of toxic protein expression allowed aggregate clearance, while late prevention halted further aggregation. To address several challenges for clinical applications of gene correction, we developed a neuron-specific engineered virus-like particle to optimize neuronal ABE delivery, resulting in higher correction efficiency. Our findings provide a targeted strategy which may treat FENIB and potentially other neurodegenerative diseases due to altered protein conformation such as Alzheimers and Huntingtons diseases.

molecular biology↗

bioRxiv2023

Entorhinal cortex glutamatergic and GABAergic projections bidirectionally control discrimination and generalization of hippocampal representations

Discrimination and generalization are crucial brain-wide functions for memory and object recognition that utilize pattern separation and completion computations. Circuit mechanisms supporting these operations remain enigmatic. We show lateral entorhinal cortex glutamatergic (LECGLU) and GABAergic (LECGABA) projections are essential for object recognition memory. Silencing LECGLU during in vivo two-photon imaging increased the population of active CA3 pyramidal cells but decreased activity rates, suggesting a sparse coding function through local inhibition. Silencing LECGLU also decreased place cell remapping between different environments validating this circuit drives pattern separation and context discrimination. Optogenetic circuit mapping confirmed that LECGLU drives dominant feedforward inhibition to prevent CA3 somatic and dendritic spikes. However, conjunctively active LECGABA suppresses this local inhibition to disinhibit CA3 pyramidal neuron soma and selectively boost integrative output of LEC and CA3 recurrent network. LECGABA thus promotes pattern completion and context generalization. Indeed, without this disinhibitory input, CA3 place maps show decreased similarity between contexts. Our findings provide circuit mechanisms whereby long-range glutamatergic and GABAergic cortico-hippocampal inputs bidirectionally modulate pattern separation and completion, providing neuronal representations with a dynamic range for context discrimination and generalization.

neuroscience↗

bioRxiv2022

Lateral entorhinal cortex inputs modulate hippocampal dendritic excitability by recruiting a local disinhibitory microcircuit

The lateral entorhinal cortex (LEC) provides information about multi-sensory environmental cues to the hippocampus through direct inputs to the distal dendrites of CA1 pyramidal neurons. A growing body of work suggests that LEC neurons perform important functions for episodic memory processing, coding for contextually-salient elements of an environment or the experience within it. However, we know little about the functional circuit interactions between LEC and the hippocampus. In this study, we combine functional circuit mapping and computational modeling to examine how long-range glutamatergic LEC projections modulate compartment-specific excitation-inhibition dynamics in hippocampal area CA1. We demonstrate that glutamatergic LEC inputs can drive local dendritic spikes in CA1 pyramidal neurons, aided by the recruitment of a disinhibitory vasoactive intestinal peptide (VIP)-expressing inhibitory neuron microcircuit. Our circuit mapping further reveals that, in parallel, LEC also recruits cholecystokinin (CCK)-expressing inhibitory neurons, which our model predicts act as a strong suppressor of dendritic spikes. These results provide new insight into a cortically-driven GABAergic microcircuit mechanism that gates non-linear dendritic computations, which may support compartment-specific coding of multi-sensory contextual features within the hippocampus. HIGHLIGHTSO_LISlice electrophysiology experiments investigate how lateral entorhinal cortex influences hippocampal area CA1 C_LIO_LILEC drives local spikes in distal dendrites but not in somata of CA1 pyramidal neurons C_LIO_LILEC inputs recruit VIP IN and CCK IN populations in CA1, but not SST INs C_LIO_LIComputational modeling and circuit manipulation experiments identify a VIP IN-mediated disinhibitory microcircuit for gating local dendritic spike generation C_LI IN BRIEFBilash et al. found that a distal cortical input is capable of driving local dendritic spikes in hippocampal pyramidal neurons. This dendritic spike generation is promoted by cortical recruitment of a local VIP interneuron-mediated disinhibitory microcircuit. Their results highlight new circuit mechanisms by which dynamic interaction of excitation, inhibition, and disinhibition support supralinear single-cell computations.

neuroscience↗

bioRxiv2021

Behaviorally emergent hippocampal place maps remain stable during memory recall

The hippocampus is critical for the formation and recall of episodic memories1, 2 which store past experience of events ( what) occurring at particular locations ( where) in time ( when). Hippocampal place cells, pyramidal neurons which show location-specific modulation of firing rates during navigation3, 4, together form a spatial representation of the environment. It has long been hypothesized that place cells serve as the neural substrate for long-term episodic memory of space5, 6. However, recent studies call to question this tenet of the field by demonstrating unexpected levels of representational drift in hippocampal place cells with respect to the duration of episodic memories in mice7, 8. In the present study, we examined behaviorally driven long-term organization of the place map, to resolve the relationship between memory and place cells. Leveraging the stability of two-photon calcium imaging, we tracked activity of the same set of CA1 pyramidal neurons during learning and memory recall in an operant, head-fixed, odorcued spatial navigation task. We found that place cells are rapidly recruited into task-dependent spatial maps, resulting in emergence of orthogonal as well as overlapping representations of space. Further, task-selective place cells used a diverse set of remapping strategies to represent changing task demands that accompany learning. We found behavioral performance dependent divergence of spatial maps between trial types occurs during learning. Finally, imaging during remote recall spanning up to 30 days revealed increased stabilization of learnt place cell maps following memory consolidation. Our findings suggest that a subset of place cells is recruited by rule based spatial learning, actively reconfigured to represent task-relevant spatial relationships, and stabilized following successful learning and consolidation.

neuroscience↗

bioRxiv2021

RNF168-mediated localization of BARD1 recruits the BRCA1-PALB2 complex to DNA damage

DNA damage prompts a diverse range of alterations to the chromatin landscape. The RNF168 E3 ubiquitin ligase catalyzes the mono-ubiquitination of histone H2A at lysine (K)13/15 (mUb-H2A), forming a binding module for DNA repair proteins. BRCA1 promotes homologous recombination (HR), in part, through its interaction with PALB2, and the formation of a larger BRCA1-PALB2-BRCA2-RAD51 (BRCA1-P) complex. The mechanism by which BRCA1-P is recruited to chromatin surrounding DNA breaks is unclear. In this study, we reveal that an RNF168-governed signaling pathway is responsible for localizing the BRCA1-P complex to DNA damage. Using mice harboring a Brca1CC (coiled coil) mutation that blocks the Brca1-Palb2 interaction, we uncovered an epistatic relationship between Rnf168- and Brca1CC alleles, which disrupted development, and reduced the efficiency of Palb2-Rad51 localization. Mechanistically, we show that RNF168-generated mUb-H2A recruits BARD1 through a BRCT domain ubiquitin-dependent recruitment motif (BUDR). Subsequently, BARD1-BRCA1 accumulate PALB2-RAD51 at DNA breaks via the CC domain-mediated BRCA1-PALB2 interaction. Together, these findings establish a series of molecular interactions that connect the DNA damage signaling and HR repair machinery.

cell biology↗

bioRxiv2021

Canagliflozin increases adenoma burden in female APCMin/+ mice

The diabetes drug canagliflozin acts primarily by inhibiting glucose reuptake by the sodium glucose transporter 2 (SGLT2) in the kidney proximal tubule, thereby lowering serum glucose levels. Canagliflozin also acts on SGLT1, a related transporter responsible for glucose uptake in the small intestine and more distal kidney tubules. Several cancers overexpress SGLT1 and SGLT2, where these transporters fuel tumor metabolism. A recent study by NIAs Interventions Testing Program (ITP) showed that canagliflozin treatment extends lifespan in male mice. Since cancer is the major cause of death in most mouse strains, including the UM-HET3 strain used by the ITP, this observation suggests that canagliflozin might exert anti-cancer effects in this context. Here, we treated a commonly-used mouse neoplasia model -- the intestinal adenoma-prone APCMin/+ strain -- with canagliflozin, to test the effects of drug treatment on tumor burden. Surprisingly, canagliflozin increased the total area of intestine involved by adenomas, an effect that was most marked in the distal intestine and in female mice. Immunohistochemical analysis suggested that canagliflozin may not influence adenoma growth via direct SGLT1/2 inhibition in neoplastic cells themselves. Instead, our results are most consistent with a model whereby canagliflozin aggravates adenoma development by altering the anatomic distribution of intestinal glucose absorption, as evidenced by increases in postprandial GLP-1 levels consistent with delayed glucose absorption. Our results suggest that canagliflozin exacerbates adenomatosis in the APCMin/+ model via complex, cell-non-autonomous mechanisms, and hint that sex differences in incretin responses may underlie differential effects of this drug on lifespan.

cancer biology↗

bioRxiv2020

The dendritic spatial code: branch-specific place tuning and its experience-dependent decoupling

Dendrites of pyramidal neurons integrate different sensory inputs, and non-linear dendritic computations drive feature selective tuning and plasticity. Yet little is known about how dendrites themselves represent the environment, the degree to which they are coupled to their soma, and how that coupling is sculpted with experience. In order to answer these questions, we developed a novel preparation in which we image soma and connected dendrites in a single plane across days using in vivo two-photon microscopy. Using this preparation, we monitored spatially tuned activity in area CA3 of the hippocampus in head-fixed mice running on a linear track. We identified "place dendrites", which can stably and precisely represent both familiar and novel spatial environments. Dendrites could display place tuning independent of their connected soma and even their sister dendritic branches, the first evidence for branch-specific tuning in the hippocampus. In a familiar environment, spatially tuned somata were more decoupled from their dendrites as compared to non-tuned somata. This relationship was absent in a novel environment, suggesting an experience dependent selective gating of dendritic spatial inputs. We then built a data-driven multicompartment computational model that could capture the experimentally observed correlations. Our model predicts that place cells exhibiting branch-specific tuning have more flexible place fields, while neurons with homogenous or co-tuned dendritic branches have higher place field stability. These findings demonstrate that spatial representation is organized in a branch-specific manner within dendrites of hippocampal pyramidal cells. Further, spatial inputs from dendrites to soma are selectively and dynamically gated in an experience-dependent manner, endowing both flexibility and stability to the cognitive map of space. One sentence summaryHippocampal pyramidal cells show branch-specific tuning for different place fields, and their coupling to their soma changes with experience of an environment.

neuroscience↗