Biology subjects

Jang, J.

Publications and source records attributed to Jang, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Functional synaptic connectivity of engrafted spinal cord neurons with locomotor circuitry in the injured spinal cord

Spinal cord injury (SCI) results in significant neurological deficits, with no currently available curative therapies. Neural progenitor cell (NPC) transplantation has emerged as a promising approach for neural repair, as graft-derived neurons (GDNs) can integrate into the host spinal cord and support axon regeneration. However, the mechanisms underlying functional recovery remain poorly understood. In this study, we investigate the synaptic integration of NPC-derived neurons into locomotor circuits, the projection patterns of distinct neuronal subtypes, and their potential to modulate motor circuit activity. Using transsynaptic tracing in a mouse thoracic contusion SCI model, we found that NPC-derived neurons form synaptic connections with host locomotor circuits, albeit at low frequencies. Furthermore, we mapped the axon projections of V0C and V2a interneurons, revealing distinct termination patterns within host spinal cord laminae. To assess functional integration, we employed chemogenetic activation of GDNs, which induced muscle activity in a subset of transplanted animals. However, NPC transplantation alone did not significantly improve locomotor recovery, highlighting a key challenge in the field. Our findings suggest that while GDNs can integrate into host circuits and modulate motor activity, synaptic connectivity remains a limiting factor in functional recovery. Future studies should focus on enhancing graft-host connectivity and optimizing transplantation strategies to maximize therapeutic benefits for SCI.

neuroscience↗

bioRxiv2025

Deciphering precursor cell dynamics in esophageal preneoplasia via genetic barcoding and single-cell transcriptomics

Although histologically normal, esophageal preneoplastic cells harbor early genetic alterations and likely exhibit lineage plasticity. However, their origins and trajectories remain unclear. To address this, we combined genetic barcoding with single-cell RNA sequencing to trace the lineage of esophageal preneoplastic cells. We identified a distinct progenitor-like cell population with high plasticity. Through a newly developed scoring system, these high-plasticity cells are mapped, revealing their contributions to proliferative and basal cell populations. This approach uncovers molecular markers, including Nfib and Qk, that define these precursor cells, validated by spatial transcriptomics and a Trp53 Cdkn2a Notch1 mouse model. These findings provide critical insights into early tumorigenesis, highlighting the potential of precursor cells as biomarkers for early detection and therapeutic targets of esophageal squamous cell cancer. By elucidating the cellular dynamics underlying esophageal preneoplasia, this research lays the foundation for strategies to prevent malignant progression, offering broader implications for improving cancer diagnostics and treatment approaches. Significance StatementPreneoplastic cells often appear histologically normal yet carry early genetic and transcriptional changes that predispose them to malignant transformation. In this study, we combine genetic barcoding with single-cell transcriptomics to uncover the lineage dynamics of esophageal preneoplastic cells. We identify a distinct progenitor population, preneoplastic cells of esophageal squamous cell carcinoma (pESCC), characterized by high plasticity and a unique trajectory that gives rise to proliferating and basal cell populations. By developing a new computational scoring method to integrate lineage topology with differentiation state, we provide a framework for tracing cellular origins beyond conventional inference-based models. Our findings shed light on the earliest events in tumor initiation and offer a new paradigm for identifying biomarkers and intervention targets in the precancerous stages of esophageal cancer.

cancer biology↗

bioRxiv2025

Long-term innovative potential of genetic research and its suppression

Long-term innovation depends not only on discovering new elements but also on facilitating new recombination at the time of their co-availability. This notion of combinatorial innovation raises the question about whether scientific exploration and industry research persist over similar time horizons to meet innovative opportunities. Here, we analyze about 20 million papers and US, Chinese, and European patents to compare the courses of scientific and industrial activities in genetic research, a domain of far-reaching societal importance. We observe that research on new genes has declined since the early 2000s, but the exploration of novel gene combinations remains active for biotechnology innovation. Yet, fields of highly practical or commercial focus are less likely to test novel gene combinations. Furthermore, industry R&D on each gene tends to decline earlier than scientific interest in that gene. After this decline of the industrial momentum, continuous scientific research still sustains exploratory and innovative opportunities, involving novel gene combinations, clinical trials, and technologically-impactful work. Based on a hypothetical scenario of over-aligned science and industry, we estimate that up to 42.2-74.4% of the combinational opportunities would be unexplored if scientific research becomes hindered due to industrys retreat. This study suggests the potential complementary roles of scientific and industrial research with different temporal modes in innovation cycles, calling for balanced policies to foster innovation ecosystems.

scientific communication and education↗

bioRxiv2024

Actin dysregulation induces immune evasion via oxidative stress-activated PD-L1 in gastric cancer

Diffuse gastric adenocarcinoma (DGAC) is an aggressive malignancy with limited therapeutic options, poor prognosis, and poorly understood biology. CRACD, an actin polymerization regulator, is often inactivated in gastric cancer, including DGAC. We found that genetic engineering of murine gastric organoids with Cracd ablation combined with Kras mutation and Trp53 loss induced aberrant cell plasticity, hyperproliferation, and hypermucinosis, the features that recapitulate DGAC transcriptional signatures. Notably, CRACD inactivation remodeled the immune landscape for immune evasion through PD-L1 enrichment in tumor cells. Mechanistically, CRACD loss disrupted actin dynamics, generating reactive oxygen species that activated HIF1, which transactivated PD-L1. Pharmacologic inhibition of HIF1 or PD-L1 restored immune surveillance and suppressed tumorigenesis. These findings reveal a novel role of actin homeostasis in limiting cell plasticity and immune evasion, position CRACD as a potential biomarker for stratifying patients with DGAC, and highlight HIF1 and PD-L1 as actionable therapeutic targets.

cancer biology↗

bioRxiv2024

RBP4 functions as an antagonistic ligand of orphan DR6

Death receptor (DR) is a unique transmembrane receptor mediating extrinsic factor-induced programmed cell death pathways. For most DRs, the regulatory mechanism has been revealed to involve agonistic death ligand (e.g., TRAIL, TNF-)-driven receptor clustering and activation, offering an in-depth understanding of the mechanistic basis for cell death regulation and therapeutic strategies. However, only death receptor 6 (DR6) remains orphan, and its molecular mechanism is poorly understood. Here, we identified retinol binding protein 4 (RBP4), a major vitamin-A carrier protein, as an antagonistic ligand of DR6. Single-molecule photobleaching and single-receptor tracking analyses revealed that RBP4 drives DR6 dimerization on the plasma membrane to prevent DR6 prodegenerative heterointeractions and consequent neurodegenerative processes. DR6 homodimerization predominantly depends on an extracellular intrinsically disordered region, allowing the agonistic propensity of increasing Ca2+ levels. Collectively, our study establishes the distinct molecular mechanism of DR6 and highlights the non-canonical role of RBP4 as a cell death regulator.

molecular biology↗

bioRxiv2024

Aquaporin-4 mis-localization slows glymphatic clearance of α-synuclein and promotes α-synuclein pathology and aggregate propagation

The appearance of misfolded and aggregated proteins is a pathological hallmark of numerous neurodegenerative diseases including Alzheimers disease and Parkinsons disease. Sleep disruption is proposed to contribute to these pathological processes and is a common early feature among neurodegenerative disorders. Synucleinopathies are a subclass of neurodegenerative conditions defined by the presence of -synuclein aggregates, which may not only enhance cell death, but also contribute to disease progression by seeding the formation of additional aggregates in neighboring cells. The mechanisms driving intercellular transmission of aggregates remains unclear. We propose that disruption of sleep-active glymphatic function, caused by loss of precise perivascular AQP4 localization, inhibits -synuclein clearance and facilitates -synuclein propagation and seeding. We examined human post-mortem frontal cortex and found that neocortical -synuclein pathology was associated with AQP4 mis-localization throughout the gray matter. Using a transgenic mouse model lacking the adapter protein -syntrophin, we observed that loss of perivascular AQP4 localization impairs the glymphatic clearance of -synuclein from intersititial to cerebrospinal fluid. Using a mouse model of -synuclein propogation, using pre-formed fibril injection, we observed that loss of perivascular AQP4 localization increased -synuclein aggregates. Our results indicate -synuclein clearance and propagation are mediated by glymphatic function and that AQP4 mis-localization observed in the presence of human synucleinopathy may contribute to the development and propagation of Lewy body pathology in conditions such as Lewy Body Dementia and Parkinsons disease. SummaryIn a human postmortem case series, we observe that neocortical Lewy body pathology is associated with mis-localization of the astroglial water channel aquaporin-4 (AQP4). In mice, -synuclein is cleared from the brain along perivascular pathways, while loss of perivascular AQP4 localization impairs glymphatic -synuclein clearance to the CSF. Furthermore, loss of perivascular AQP4 localization promotes the development and propagation of -synuclein aggregates.

neuroscience↗

bioRxiv2024

Targeting MDSC-HTR2B to Improve Immune Checkpoint Inhibitors in Breast to Brain Metastasis

Myeloid Derived Suppressor Cells (MDSCs) support breast cancer growth via immune suppression and non-immunological mechanisms. Although 15% of patients with breast cancer will develop brain metastasis, there is scant understanding of MDSCs contribution within the breast-to-brain metastatic microenvironment. Utilizing co-culture models mimicking a tumor-neuron-immune microenvironment and patient tissue arrays, we identified serotonergic receptor, HTR2B, on MDSCs to upregulate pNF-{kappa}B and suppress T cell proliferation, resulting in enhanced tumor growth. In vivo murine models of metastatic and intracranial breast tumors treated with FDA-approved, anti-psychotic HTR2B antagonist, clozapine, combined with immunotherapy anti-PD-1 demonstrated a significant increase in survival and increased T cell infiltration. Collectively, these findings reveal a previously unknown role of MDSC-HTR2B in breast-to-brain metastasis, suggesting a novel and immediate therapeutic approach using neurological drugs to treat patients with metastatic breast cancer.

cancer biology↗

bioRxiv2024

Abo1 ATPase facilitates the dissociation of FACT from chromatin.

The histone chaperone FACT is a heterodimeric complex consisting of Spt16 and Pob3, crucial for preserving nucleosome integrity during transcription and DNA replication. Loss of FACT leads to cryptic transcription and heterochromatin defects. FACT was shown to interact with Abo1, an AAA+ family histone chaperone involved in nucleosome dynamics. Depletion of Abo1 causes FACT to stall at transcription start sites (TSS) and mimics FACT mutants, indicating a functional association between Abo1 and FACT. However, the precise role of Abo1 in FACT function remains poorly understood. Here, we reveal that Abo1 directly interacts with FACT and facilitates the dissociation of FACT from chromatin. Specifically, the N-terminal region of Abo1 utilizes its FACT interacting (FIN) helix to bind to the N-terminal domain (NTD) of Spt16. In addition, using single-molecule fluorescence imaging, we discovered that Abo1 facilitates the ATP-dependent dissociation of FACT from nucleosomes. Furthermore, we demonstrate that the interaction between Abo1 and FACT is essential for maintaining heterochromatin in fission yeast. In summary, our findings suggest that Abo1 regulates FACT turnover in an ATP-dependent manner, proposing a model of histone chaperone recycling driven by inter-chaperone interactions.

biochemistry↗

bioRxiv2024

Consistency of affective responses to naturalistic stimuli across individuals using intersubject correlation analysis based on neuroimaging data

In this study, we used functional magnetic resonance imaging (fMRI) data obtained for naturalistic emotional stimuli to examine the consistency of neural responses among participants in specific regions related to valence. We reanalyzed fMRI data from 17 participants as they watched episodes of "Sherlock" and used emotional ratings from 125 participants. To determine regions where neural response patterns were synchronized across participants based on the pattern of valence changes, intersubject correlation analysis was conducted. As a validation analysis, multidimensional scaling was conducted to investigate emotional representation for significant regions of interest. The results revealed that the ventromedial prefrontal cortex, bilateral superior frontal cortices, left posterior cingulate cortex, thalamus, right anterior cingulate cortex, and bilateral inferior frontal cortices showed increased neural synchrony as positive scenes were presented. Also, the bilateral superior temporal gyrus and bilateral medial temporal gyrus exhibited increased neural synchrony as negative scenes were presented. Moreover, the left inferior frontal cortex and right superior frontal gyrus were found to be engaged in emotion representation and display increased neural synchrony. These findings provide insights into the differential neural responses to emotionally evocative naturalistic stimuli as compared to conventional experimental stimuli. Also, this study highlights the future potential for using intersubject correlation analysis for examining consistency of neural responses to naturalistic stimuli.

neuroscience↗

bioRxiv2024

An active electronic bidirectional interface for high resolution interrogation of the spinal cord

ObjectiveEpidural electrical stimulation (EES) has shown promise as both a clinical therapy and research tool for studying nervous system function. However, available clinical EES paddles are limited to using a small number of contacts due to the burden of wires necessary to connect each contact to the therapeutic delivery device, limiting the treatment area or density of epidural electrode arrays. We aimed to eliminate this burden using advanced on-paddle electronics. ApproachWe developed a smart EES paddle with a 60-electrode programmable array, addressable using an active electronic multiplexer embedded within the electrode paddle body. The electronics are sealed in novel, ultra-low profile hermetic packaging. We conducted extensive reliability testing on the novel array, including a battery of ISO 10993-1 biocompatibility tests and determination of the hermetic package leak rate. We then evaluated the EES device in vivo, placed on the epidural surface of the ovine lumbosacral spinal cord for 15 months. Main resultsThe active paddle array performed nominally when implanted in sheep for over 15 months and no device-related malfunctions were observed. The onboard multiplexer enabled bespoke electrode arrangements across, and within, experimental sessions. We identified stereotyped responses to stimulation in lower extremity musculature, and examined local field potential responses to EES using high-density recording bipoles. Finally, spatial electrode encoding enabled machine learning models to accurately perform EES parameter inference for unseen stimulation electrodes, reducing the need for extensive training data in future deep models. SignificanceWe report the development and chronic large animal in vivo evaluation of a high-density EES paddle array containing active electronics. Our results provide a foundation for more advanced computation and processing to be integrated directly into devices implanted at the neural interface, opening new avenues for the study of nervous system function and new therapies to treat neural injury and dysfunction.

bioengineering↗

bioRxiv2024

PITPβ promotes COPI vesicle fission through lipid transfer and membrane contact formation

Intracellular transport among organellar compartments occurs in two general ways, by membrane-bound carriers or membrane contacts. Specific circumstances that involve the coordination of these two modes of transport remain to be defined. Studying Coat Protein I (COPI) transport, we find that phosphatidylcholine with short acyl chains (sPC) is delivered through membrane contact from the endoplasmic reticulum (ER) to sites of COPI vesicle formation at the Golgi to support the fission stage. Phosphatidylinositol transfer protein beta (PITP{beta}) plays a key role in this process, with the elucidation of this role advancing a new understanding of how PITP{beta} acts, providing a mechanistic understanding of a specific circumstance when vesicular transport requires membrane contact, and contributing to a basic understanding of how transport carriers in a model intracellular pathway are formed. SummarySpecific circumstances that membrane contact is needed for vesicular transport remain to be defined. We find that a critical lipid is delivered through membrane contact to support the fission stage of a model intracellular transport pathway.

cell biology↗

bioRxiv2024

Efficient DNA base editing via an optimized DYW-like deaminase

CRISPR-based cytosine base editors enable precise genome editing without inducing double-stranded DNA breaks, yet traditionally depend on a limited selection of deaminases from the APOBEC/AID or TadA families. Here, we introduce SsCBE, a novel CRISPR-based cytosine base editor utilizing SsdAtox, a DYW-like deaminase derived from the toxin of Pseudomonas syringae. Strategic engineering of SsdAtox has led to remarkable improvements in the base editing efficiency (by up to 8.4-fold) and specificity for SsCBE, while concurrently reducing cytotoxicity. Exhibiting exceptional versatility, SsCBE was delivered and efficiently applied using diverse delivery methods, including the engineered virus-like particles (eVLPs). Its application has enabled targeted cytosine base editing in mouse zygotes and pioneering edits in mitochondrial DNA. The advent of SsCBE marks a significant advancement in the CRISPR toolkit, providing a versatile tool for advanced research and therapeutic strategies.

molecular biology↗

bioRxiv2024

Hijacked Immune Cells Traverse Microenvironmental Barriers by Positioning and Pushing their Intracellular Parasite Cargo

Cell migration is fundamental to development, homeostasis, and immunity, and requires cells to traverse space-limited microenvironments by deforming intracellular organelles such as the nucleus. Although nuclear mechanics are established as a rate-limiting factor during confined migration, how cells transport bulky foreign cargo remains unclear. Here, using Toxoplasma gondii, a disease-causing parasite that hijacks motile immune cells for dissemination while replicating into large intracellular assemblies, we discover that parasitic cargoes exceed the size and stiffness of host nuclei, and therefore constitute a primary bottleneck for migration. We uncover a mechanoadaptive response to parasite size, characterized by size-dependent intracellular repositioning, myosin-II contractility, and bleb-based protrusions. This reprogramming of forces and subcellular architecture enables the transport of oversized, mechanically rigid cargo through space-limited microenvironments. These findings establish a mechanobiological principle of how cells size-dependently adapt forces and their subcellular architecture to accommodate intracellular objects that challenge the physical limits of cell migration.

cell biology↗

bioRxiv2024

A temperature-sensitive and interferon-silent Sendai virus vector for CRISPR-Cas9 delivery and gene editing in primary human cells

The transformative potential of gene editing technologies hinges on the development of safe and effective delivery methods. In this study, we developed a temperature-sensitive and interferon-silent Sendai virus (ts SeV) as a novel delivery vector for CRISPR-Cas9 and for efficient gene editing in sensitive human cell types without inducing IFN responses. ts SeV demonstrates unprecedented transduction efficiency in human CD34+ hematopoietic stem and progenitor cells (HSPCs) including transduction of the CD34+/CD38-/CD45RA-/CD90+(Thy1+)/CD49fhigh stem cell enriched subpopulation. The frequency of CCR5 editing exceeded 90% and bi-allelic CCR5 editing exceeded 70% resulting in significant inhibition of HIV-1 infection in primary human CD14+ monocytes. These results demonstrate the potential of the ts SeV platform as a safe, efficient, and flexible addition to the current gene-editing tool delivery methods, which may help to further expand the possibilities in personalized medicine and the treatment of genetic disorders.

microbiology↗

bioRxiv2024

Mimicking the breast metastatic microenvironment: characterization of a novel syngeneic model of HER2+ breast cancer

Preclinical murine models in which primary tumors spontaneously metastasize to distant organs are valuable tools to study metastatic progression and novel cancer treatment combinations. Here, we characterize a novel syngeneic murine breast tumor cell line, NT2.5-lung metastasis (- LM), that provides a model of spontaneously metastatic neu-expressing breast cancer with quicker onset of widespread metastases after orthotopic mammary implantation in immune-competent NeuN mice. Within one week of orthotopic implantation of NT2.5-LM in NeuN mice, distant metastases can be observed in the lungs. Within four weeks, metastases are also observed in the bones, spleen, colon, and liver. Metastases are rapidly growing, proliferative, and responsive to HER2-directed therapy. We demonstrate altered expression of markers of epithelial-to-mesenchymal transition (EMT) and enrichment in EMT-regulating pathways, suggestive of their enhanced metastatic potential. The new NT2.5-LM model provides more rapid and spontaneous development of widespread metastases. Besides investigating mechanisms of metastatic progression, this new model may be used for the rationalized development of novel therapeutic interventions and assessment of therapeutic responses targeting distant visceral metastases SUMMARY STATEMENTWe characterize a new syngeneic, immune-competent murine model of breast cancer (NT2.5-LM) that yields rapid and widespread metastases, preserves spontaneous metastasis, and provides a model for studying novel therapeutic interventions.

cancer biology↗

bioRxiv2023

A software tool for at-home measurement of sensorimotor adaptation

Sensorimotor adaptation is traditionally studied in well-controlled laboratory settings with specialized equipment. However, recent public health concerns such as the COVID-19 pandemic, as well as a desire to recruit a more diverse study population, have led the motor control community to consider at-home study designs. At-home motor control experiments are still rare because of the requirement to write software that can be easily used by anyone on any platform. To this end, we developed software that runs locally on a personal computer. The software provides audiovisual instructions and measures the ability of the subject to control the cursor in the context of visuomotor perturbations. We tested the software on a group of at-home participants and asked whether the adaptation principles inferred from in-lab measurements were reproducible in the at-home setting. For example, we manipulated the perturbations to test whether there were changes in adaptation rates (savings and interference), whether adaptation was associated with multiple timescales of memory (spontaneous recovery), and whether we could selectively suppress subconscious learning (delayed feedback, perturbation variability) or explicit strategies (limited reaction time). We found remarkable similarity between in-lab and at-home behaviors across these experimental conditions. Thus, we developed a software tool that can be used by research teams with little or no programming experience to study mechanisms of adaptation in an at-home setting. SignificanceSensorimotor learning is traditionally studied in the laboratory, but recent public health emergencies have caused the community to consider at-home data collection. To accelerate this effort, we implemented a software tool that remotely tracks motor learning. Compared with previous remote data collection strategies, our software (1) generates experiments of arbitrary length that (2) run locally on a participants laptop which (3) can be modified without any programming expertise in the research laboratory. Here we show a close correspondence between behaviors captured by our tool and those observed in laboratory environments including savings, interference, spontaneous recovery, and variations in implicit and explicit learning due to changes in perturbation variance, reaction time constraints, and feedback delay. Our software and its corresponding manuals are available here: https://osf.io/e8b63/.

neuroscience↗

bioRxiv2023

Design and validation of a high-throughput in vitro model of the outer Blood-Retinal Barrier (oBRB) using the Curiochips Microphysiological System

Numerous diseases, including AMD (age-related macular degeneration), arise from the blood-retinal barrier and blood vessel abnormalities in the eye; unfortunately, there is a lack of reliable in-vitro models for their systematic study. This study describes a high-throughput microphysiological system (MPS) designed to model the outer Blood-Retinal Barrier (oBRB). The MPS platform is engineered to integrate seamlessly with high-content screening technologies, utilizing a design with a single oBRB model incorporating RPE (retina pigment epithelial cells) and endothelial cell co-culture to fit within a single 96-well. Arranged in the standard 96-well plate format, the platform allows high-throughput assessment of barrier integrity through 3D confocal imaging (ZO-1 staining), Trans Epithelial Electrical Resistance (TEER), and permeability measurements. The oBRB model enables the investigation of crosstalk among different cell types in co-culture. This includes assessing changes in the barrier integrity of the Retinal Pigment Epithelium (RPE) monolayer and investigating neovascularization events resulting from endothelial cell remodeling. The platform is positioned for utility in drug discovery and development efforts targeting diseases involving oBRB damage and choroidal neovascularization, such as age-related macular degeneration (AMD).

bioengineering↗

bioRxiv2023

Antibody-based immunotherapy targeting FAM19A5 reverses synaptic loss and improves cognitive function in Alzheimer's disease.

IntroductionAlzheimers disease (AD) is characterized by the dysregulation of synaptic balance, with progressive loss of synapses outpacing formation, ultimately leading to cognitive decline. However, the lack of effective strategies for restoring lost synapses poses a major barrier to improving clinical outcomes. MethodsWe developed NS101, a monoclonal antibody targeting FAM19A5, a brain-secreted protein. Its preclinical efficacy in restoring synapses and cognition was evaluated using APP/PS1 and P301S mice. The clinical safety and target engagement of NS101 were examined in human participants. ResultsFAM19A5 binds to LRRC4B, a postsynaptic adhesion molecule, leading to synapse reduction. Blocking this interaction with NS101 normalized the rate of synapse elimination in AD mice. This synaptic rebalancing restored the number and function of synapses, resulting in improved cognition. Systemically administered NS101 facilitated the transport of brain FAM19A5 into the bloodstream. DiscussionTargeting FAM19A5 may hold clinical promise for treating AD by restoring synaptic balance.

neuroscience↗