Biology subjects

Chen, J. C.

Publications and source records attributed to Chen, J. C..

14 recordsLinked to original sources

bioRxiv2026

A Dynamically Regulated Designed IL-2 for Tumor-localized Signaling

Cytokines mediate cell-cell communication to coordinate immune responses and hold clinical promise as immunotherapies. While natural cytokines are exquisitely regulated by immune cells, engineered cytokines have not yet matched this sophisticated regulation, limiting clinical efficacy and safety. IL-2 is an important cytokine involved in antitumor response, but its production is disrupted in the immune-suppressive tumor microenvironment. Here we designed a regulated IL-2 module, OUTSMART designed IL-2 (dIL-2), that functions robustly in solid tumors and reduces systemic activity that could trigger toxicity: we computationally redesigned IL-2 to have a novel topology that increases stability, preserves native IL-2R{beta}{gamma} interfaces, ablates IL-2R binding, and delivers IL-2 signaling to CD8+ immune-effector cells. This designed cytokine is genetically regulated by a T cell activation-responsive promoter, allowing dynamic production from chimeric antigen receptor (CAR) T cells. Like wild type IL-2, OUTSMART dIL-2 drives T cell proliferation and enhances effector function. Unlike wild type IL-2, it preferentially stimulates CD8+ T cells and Natural Killer (NK) cells, avoids T regulatory cells, and stimulates CAR-T proliferation while preserving stemness, achieving durable tumor elimination in two solid tumor animal models. These design principles can be applied to create other dynamically-regulated cytokine systems that address mechanisms of complex disease.

synthetic biology↗

bioRxiv2026

A Rationally Designed Transgene Drives CAR T Functional Persistence and Durable Regression of Solid Tumors

The eradication of solid tumors by chimeric antigen receptor (CAR) T cells requires dynamic therapies capable of outlasting an immune suppressive tumor microenvironment (TME). However, biological barriers--including rapid exhaustion, poor expansion, and loss of stem-like memory--quickly neutralize these therapies. Because single-technology interventions often introduce unacceptable tradeoffs between efficacy and safety, durable remission demands a paradigm where multiple engineered solutions work in concert. To holistically address these mechanisms, we rationally designed a single-vector transgene that intrinsically drives CAR T functional persistence. The platform integrates four synergistic technologies: a high-avidity mesothelin (MSLN)-targeting CAR optimized to resist shed decoy antigens, a T-cell activation-responsive promoter (OUTLAST OP1) resisting exhaustion, a CD8-targeted designed IL-2 cytokine (OUTSMART dIL-2) driving intratumoral CAR-T expansion, and an EGFRopt safety switch. In lung and ovarian cancer models, this rational integration was required to drive antigen-dependent T cell expansion and eradicate established tumors at extremely low CAR T doses. Furthermore, engineered cells established a self-renewing pool of stem-like memory T cells capable of rejecting tumor rechallenge months later. Ultimately, this work demonstrates that intrinsic T cell dysfunction and extrinsic tumor-derived barriers can be simultaneously overcome by integrating synergistic technologies.

synthetic biology↗

bioRxiv2026

Developmental expression of the skeletal muscle determination gene, MyoD, is regulated by novel enhancer elements that interact with the core enhancer and distal regulatory region

MyoD plays a central role in determining the skeletal muscle lineage in vertebrate embryos. The core enhancer (CE) and distal regulatory region (DRR) are the only known MyoD enhancers, and together, they recapitulate all major aspects of MyoD expression in the embryo. However, knocking out each enhancer individually has only modest effects on MyoD expression. Here, we show that embryos lacking both enhancers maintain muscle-specific MyoD expression, indicating the existence of unknown MyoD regulatory elements. Precision run-on sequencing together with available ChIP-seq and DNase I hypersensitivity datasets identified three new candidate enhancer regions within 96 kb of MyoD 5 flanking sequences. Transgenic analysis revealed that DNA elements at -36 and -60 kb are active in all muscle-forming regions, each recapitulating aspects of endogenous MyoD expression. Enhancer activities in muscle regulatory factor-deficient mice suggest that they are components of the auto- and cross-regulatory circuitry that maintains MyoD expression. Analysis of Hi-C data showed that the entire -96 kb region constitutes a loop domain, within which multiple interactions between elements and with the MyoD gene were detected. A larger loop domain delimited by CTCF sites was also identified from -96 kb to +220 kb relative to the MyoD transcriptional start site. These data indicate that the newly identified enhancers are key components of a cis regulatory network that controls the activation and maintenance of MyoD expression in the embryo. One sentence summaryCis regulation of MyoD transcription during development

developmental biology↗

bioRxiv2025

Twin-arginine transport complex plays an essential role in Caulobacter cell shape and viability

Two main pathways are responsible for protein secretion across the cytoplasmic membrane in prokaryotes. While the general secretory (Sec) pathway transports proteins across the membrane in an unfolded state, the twin-arginine translocation (Tat) pathway transports proteins primarily in their folded conformation. Although the Tat system appears dispensable in multiple model bacteria, some species require it for viability, and the reason for the distinction is nebulous. Here we show that all three subunits of the Tat complex -- TatA, TatB, and TatC -- are essential in the alpha-proteobacterium Caulobacter crescentus. Additionally, depletion of the Tat complex results in abnormal cell morphology. We found that localization to the cell periphery, as well as midcell localization upon osmotic upshift, of the essential peptidoglycan transpeptidase PBP2 is dependent on the Tat apparatus. In contrast, subcellular localization of the actin homolog MreB and the penicillin-binding protein PBP1a is not perturbed upon depletion of the Tat complex. PBP2 transpeptidase activity links glycan chains at sites of cell wall remodeling and is essential for cell elongation. Together these results suggest that PBP2 localization is a key responsibility of the Tat system in Caulobacter and possibly other alpha-proteobacteria. Significance StatementO_LIThe twin-arginine translocation (Tat) system is essential for viability in some bacteria but not others. The essential role that the Tat pathway plays in these bacteria is not well understood. C_LIO_LIThe Tat complex is essential in Caulobacter crescentus and required for the cell wall synthesis protein PBP2 to localize to the cell envelope. C_LIO_LIPBP2 is critical for viability and maintenance of cell shape in Caulobacter, and essentiality of the Tat complex may be partly attributed to its role in localizing PBP2. C_LI

microbiology↗

bioRxiv2025

Genetic targeting of myelinated primary afferent neurons using a new NefhCreERT2 knock-in mouse

Primary afferent neurons that convey somatosensory modalities comprise two large, heterogeneous populations: small-diameter neurons that give rise to slowly conducting unmyelinated axonal C fibers and medium-to-large diameter neurons with fast myelinated A fibers. Despite these two major groupings, tools to differentiate between unmyelinated and myelinated primary afferent fibers by genetic targeting have not been available; in particular, whereas numerous mouse driver lines exist to target different C fiber populations, genetic tools that target myelinated primary afferent populations are scarce. Here we describe a knock-in mouse line expressing tamoxifen-dependent CreERT2 under control of the Nefh gene, which encodes neurofilament heavy chain (NFH or NF200), a protein that is highly enriched in myelinated fibers. This mouse enables highly selective and efficient recombination of Cre-dependent reporters for functional and anatomical interrogation of myelinated fibers while excluding unmyelinated C fibers. In combination with other recombinase-expressing mouse lines, this genetic tool will be valuable for intersectional targeting of subpopulations of myelinated primary afferent fibers.

neuroscience↗

bioRxiv2025

A NaV1.8FlpO mouse enabling selective intersectional targeting of low threshold C fiber mechanoreceptors and nociceptors

Genetic targeting of select populations of cells in the mouse nervous system is often hampered by a lack of selectivity, as candidate genes for such targeting are commonly expressed by multiple cell populations, also in the same region. Intersectional targeting using two or more genes has been enabled by the development of reporter tools dependent on more than one recombinase or gene regulator. Still, widespread adoption of intersectional tools is complicated by a scarcity of driver mice expressing recombinases otherthan Cre. Here we report the generation and characterization of a new driver mouse that expresses the FlpO recombinase from the endogenous locus of the Scn10a gene encoding NaV1.8, a voltage-gated sodium channel that is almost exclusively expressed in the afferent limb of the peripheral nervous system. Moreover, among sensory neurons the channel is preferentially expressed in nociceptors and in low-threshold C-fiber mechanoreceptors (C-LTMRs). The mouse showed high recombination efficiency (97 %) and selectivity (93 %) in dorsal root ganglia. Reporter-expressing fibers were observed in a variety of peripheral tissues, including skin, skeletal muscle, genitalia, bladder and intestines. To validate the suitability of the FlpO mouse line for intersectional targeting, we crossed it with a mouse line expressing CreERT2 from the Th (tyrosine hydroxylase) locus. This approach resulted in strikingly selective and efficient targeting of C-LTMRs, showing robust visualization of nerve endings of these fibers in skin and spinal cord at the light and electron microscopic level. Thus, the NaV1.8Flpo mouse line presented here constitutes a selective and versatile tool for intersectional genetic targeting of NaV1.8 expressing primary afferent neurons.

neuroscience↗

bioRxiv2025

A fast nociceptive subsystem mediating rapid reflexive behavior but not affective pain

Spinal nociceptive withdrawal reflexes are widely believed to rely on unmyelinated and thinly myelinated nociceptive fibers that also signal affective and motivational aspects of pain. Here we discover a population of myelinated mechanoreceptive nociceptor that forms free nerve endings as well as circumferential endings around hair follicles, and exclusively terminate in the deep spinal dorsal horn. Optogenetic activation of these fibers triggers rapid withdrawal reflexes that are precise and selective for the targeted limb, while silencing increases the threshold of mechanical nociceptive withdrawal reflexes. By contrast, optogenetic stimulation of the fibers is not associated with place aversion nor with changes in facial expression. Thus, we conclude that this nerve fiber population is uniquely positioned to rapidly respond to mechanical threats via selective withdrawal of the targeted body part, whereas other fast and slow nociceptive pathways are required for affective-motivational aspects of pain.

neuroscience↗

bioRxiv2024

Sinorhizobium meliloti BR-bodies promote fitness during host colonization

Biomolecular condensates, such as the nucleoli or P-bodies, are non-membrane-bound assemblies of proteins and nucleic acids that facilitate specific cellular processes. Like eukaryotic P-bodies, the recently discovered bacterial ribonucleoprotein bodies (BR-bodies) organize the mRNA decay machinery, yet the similarities in molecular and cellular functions across species have been poorly explored. Here, we examine the functions of BR-bodies in the nitrogen-fixing endosymbiont Sinorhizobium meliloti, which colonizes the roots of compatible legume plants. Assembly of BR-bodies into visible foci in S. meliloti cells requires the C-terminal intrinsically disordered region (IDR) of RNase E, and foci fusion is readily observed in vivo, suggesting they are liquid-like condensates that form via mRNA sequestration. Using Rif-seq to measure mRNA lifetimes, we found a global slowdown in mRNA decay in a mutant deficient in BR-bodies, indicating that compartmentalization of the degradation machinery promotes efficient mRNA turnover. While BR-bodies are constitutively present during exponential growth, the abundance of BR-bodies increases upon cell stress, whereby they promote stress resistance. Finally, using Medicago truncatula as host, we show that BR-bodies enhance competitiveness during colonization and appear to be required for effective symbiosis, as mutants without BR-bodies failed to stimulate plant growth. These results suggest that BR-bodies provide a fitness advantage for bacteria during infection, perhaps by enabling better resistance against the host immune response. SignificanceWhile eukaryotes often organize their biochemical pathways in membrane-bound organelles, bacteria generally lack such subcellular structures. Instead, membraneless compartments called biomolecular condensates have recently been found in bacteria to enhance biochemical activities. Bacterial ribonucleoprotein bodies (BR-bodies), as one of the most widespread biomolecular condensates identified to date, assemble the mRNA decay machinery via the intrinsically disordered regions (IDRs) of proteins. However, the implications of such assemblies are unclear. Using a plant-associated symbiont, we show that the IDR of its mRNA degradation protein is necessary for condensate formation. Absence of BR-bodies results in slower mRNA decay and ineffective symbiosis, suggesting that BR-bodies play critical roles in regulating biochemical pathways and promoting fitness during host colonization.

microbiology↗

bioRxiv2023

Endocisternal interfaces for minimally invasive neural stimulation and recording of the brain and spinal cord

Minimally invasive neural interfaces can be used to diagnose, manage, and treat many disorders with substantially reduced risks of surgical complications. Endovascular neural interfaces implanted in the veins or arteries is one approach, but it requires prescriptions of anti-thrombotic medication and are likely not explantable after endothelialization. More critically, the approach is limited by the small size and location of blood vessels, such that many important cortical, subcortical, spinal targets cannot be reached. Here, we demonstrate a chronic endocisternal neural interface that approaches brain and spinal cord targets through inner and outer cerebral spinal fluid (CSF) spaces. These spaces surround the nervous system and lack the tortuosity of the circulatory system, giving us access to the entire brain convexity, deep brain structures within the ventricles, and the spinal cord from the spinal subarachnoid space. Combined with miniature magnetoelectric-powered bioelectronics, the entire wireless system is deployable through a percutaneous procedure. The flexible catheter electrodes can be freely navigated throughout the body from the spinal to cranial subarachnoid space, and from the cranial subarachnoid space to the ventricles. We show in a large animal model that we can also reposition the recording and stimulation electrodes or explant the neural interface after chronic implantation. This enables applications in therapies that require transient or permanent brain/machine interface such as stroke rehabilitation and epilepsy monitoring and opens a new class of minimally invasive endocisternal bioelectronics.

bioengineering↗

bioRxiv2022

Self-rectifying magnetoelectric metamaterials enable precisely timed remote neural stimulation and restoration of sensory motor functions

Magnetoelectric materials convert magnetic fields to electric fields and have applications in wireless data and power transmission, electronics, sensing, data storage, and biomedical technology. For example, magnetoelectrics could enable precisely timed remote stimulation of neural tissue, but the resonance frequencies where magnetoelectric effects are maximized are typically too high to stimulate neural activity. To overcome this challenge, we created the first self-rectifying magnetoelectric "metamaterial." This metamaterial relies on nonlinear charge transport across semiconductor layers that allow the material to generate a steady bias voltage in the presence of an alternating magnetic field. This "self-rectification" allows us to generate arbitrary electrical pulse sequences that have a time-averaged voltage in excess of 1 V. As a result, we can use magnetoelectric nonlinear metamaterials (MNMs) to remotely stimulate peripheral nerves with repeatable latencies of less than 5 ms, which is more than 120 times faster than previous neural stimulation approaches based on magnetic materials. These short latencies enable this metamaterial to be used in applications where fast neural signal transduction is necessary such as in sensory or motor neuroprosthetics. As a proof of principle, we show wireless stimulation to restore a sensory reflex in an anesthetized rat model as well as using the MNM to restore signal propagation in a severed nerve. The rational design of nonlinearities in the magnetic-to-electric transduction pathway as described here opens the door to many potential designs of MNMs tailored to applications spanning electronics, biotechnology, and sensing.

bioengineering↗

bioRxiv2021

Wireless endovascular nerve stimulation with a millimeter-sized magnetoelectric implant

Implanted bioelectronic devices have the potential to treat disorders that are resistant to traditional pharmacological therapies; however, reaching many therapeutic nerve targets requires invasive surgeries and implantation of centimeter-sized devices. Here we show that it is possible to stimulate peripheral nerves from within blood vessels using a millimeter-sized wireless implant. By directing the stimulating leads through the blood vessels we can target specific nerves that are difficult to reach with traditional surgeries. Furthermore, we demonstrate this endovascular nerve stimulation (EVNS) with a millimeter sized wireless stimulator that can be delivered minimally invasively through a percutaneous catheter which would significantly lower the barrier to entry for neuromodulatory treatment approaches because of the reduced risk. This miniaturization is achieved by using magnetoelectric materials to efficiently deliver data and power through tissue to a digitally-programmable 0.8 mm2 CMOS system-on-a-chip. As a proof-of-principle we show wireless stimulation of peripheral nerve targets both directly and from within the blood vessels in rodent and porcine models. The wireless EVNS concept described here provides a path toward minimally invasive bioelectronics where mm-sized implants combined with endovascular stimulation enable access to a number of nerve targets without open surgery or implantation of battery-powered pulse generators.

bioengineering↗

bioRxiv2021

L-WNK1 is required for BK channel activation in intercalated cells

BK channels expressed in intercalated cells (ICs) in the aldosterone-sensitive distal nephron (ASDN) mediate flow-induced K+ secretion. In the ASDN of mice and rabbits, IC BK channel expression and activity increase with a high K+ diet. In cell culture, the long isoform of the kinase WNK1 (L-WNK1) increases BK channel expression and activity. Apical L-WNK1 expression is selectively enhanced in ICs in the ASDN of rabbits on a high K+ diet, suggesting that L-WNK1 contributes to BK channel regulation by dietary K+. We examined the role of IC L-WNK1 expression in enhancing BK channel activity in response to a high K+ diet. Mice with an IC-selective deletion of L-WNK1 (IC-L-WNK1-KO) and littermate control mice were placed on a high K+ (5% K+ as KCl) diet for at least 10 days. IC-L-WNK1-KO mice exhibited higher blood K+ concentrations ([K+]) than controls. BK channel-dependent whole-cell currents in ICs from cortical collecting ducts of high K+ fed IC-L-WNK1-KO mice were reduced compared to controls. Six-hour urinary K+ excretion in response a saline load was similar in IC-L-WNK1-KO mice and controls. The observations that IC-L-WNK1-KO mice have higher blood [K+] and reduced IC BK channel currents are consistent with impaired urinary K+ secretion, and suggest that IC L-WNK1 has a role in the renal adaptation to a high K+ diet.

physiology↗

bioRxiv2019

Novel quinolone resistance determinant, qepA8, in Shigella flexneri isolated in the United States, 2016

A qepA8+ Shigella flexneri was cultured from the stool of a traveler returning from India and East Asia. This chromosomally encoded qepA variant, has a six-base insertion, and may have been mobilized as part of a complex IS1-mediated composite transposon including catA1, aadA1, and blaOXA-1. In laboratory E. coli, qepA8 alone only conferred decreased ciprofloxacin susceptibility; however, it may work in combination with additional mechanisms to confer clinical resistance.

microbiology↗

bioRxiv2018

Magnetoelectric materials for miniature, wireless neural stimulation at therapeutic frequencies

A fundamental challenge for bioelectronics is to deliver power to miniature devices inside the body. Wires are common failure points and limit device placement. On the other hand, wireless power by electromagnetic or ultrasound waves must overcome absorption by the body and impedance mismatches between air, bone, and tissue. In contrast, magnetic fields suffer little absorption by the body or differences in impedance at interfaces between air, bone, and tissue. These advantages have led to magnetically-powered stimulators based on induction or magnetothermal effects. However, fundamental limitations in these power transfer technologies have prevented miniature magnetically-powered stimulators from applications in many therapies and disease models because they do not operate in clinical "high-frequency" ranges above 50 Hz. Here we show that magnetoelectric materials - applied in bioelectronic devices - enable miniature magnetically-powered neural stimulators that can operate up to clinically-relevant high-frequencies. As an example, we show that ME neural stimulators can effectively treat the symptoms of a hemi-Parkinsons disease model in freely behaving rodents. We further demonstrate that ME-powered devices can be miniaturized to mm-sized devices, fully implanted, and wirelessly powered in freely behaving rodents. These results suggest that ME materials are an excellent candidate for wireless power delivery that will enable miniature bioelectronics for both clinical and research applications.

bioengineering↗