Biology subjects

Chen, Y. Y.

Publications and source records attributed to Chen, Y. Y..

11 recordsLinked to original sources

bioRxiv2026

Arousal state modulates human hippocampal ripples

Hippocampal ripples are transient, high-frequency oscillations linked to memory replay and consolidation. Ripples are well-characterized in rodents to occur during periods of behavioral inactivity (i.e., sleep, rest), viewed as "offline" states where replay can emerge with limited sensory interference. However, human studies have increasingly observed ripples during active tasks, raising the questions of whether ripple genesis and function have been misunderstood or whether there are fundamental species differences. We propose that low arousal states--predominant during offline sleep and transient during wake--may constitute a common mechanism of ripple genesis that reconciles these observations. We recorded directly from human hippocampus during sleep and wake, measuring arousal via sleep staging, pupillometry, and heart rate. Ripple occurrence consistently tracked low arousal: rates were maximal in NREM sleep, small-pupil wake states, and slow heart rate periods across sleep and wake. This modulation was stronger in anterior than posterior hippocampus and was hippocampus specific: ripple-like activity outside the hippocampus showed an opposite modulation, increasing with high arousal. These results resolve apparent species differences and provide a unifying view of offline periods as arousal dips that can emerge across behavioral states, including transiently during active wake, suggesting hippocampal ripples, and memory consolidation, occur continuously intermixed with cognition.

neuroscience↗

bioRxiv2023

Individual-specific memory reinstatement patterns within human face-selective cortex

Humans have the remarkable ability to vividly retrieve sensory details of past events. According to the theory of sensory reinstatement, during remembering, brain regions involved in the sensory processing of prior events are reactivated to support this perception of the past. Recently, several studies have emphasized potential transformations in the spatial organization of reinstated activity patterns. In particular, studies of scene stimuli suggest a clear anterior shift in the location of retrieval activations compared with those during perception. However, it is not clear that such transformations occur universally, with evidence lacking for other important stimulus categories, particularly faces. Critical to addressing these questions, and to studies of reinstatement more broadly, is the growing importance of considering meaningful variations in the organization of sensory systems across individuals. Therefore, we conducted a multi-session neuroimaging study to first carefully map individual participants face-selective regions within ventral temporal cortex (VTC), followed by a second session to examine the correspondence of activity patterns during face memory encoding and retrieval. Our results showed distinct configurations of face-selective regions within the VTC across individuals. While a significant degree of overlap was observed between face perception and memory encoding, memory retrieval engagement exhibited a more selective and constricted reinstatement pattern within these regions. Importantly, these activity patterns were consistently tied to individual-specific neural substrates, but did not show any consistent direction of spatial transformation (e.g., anteriorization). To provide further insight to these findings, we also report on unique human intracranial recordings from VTC under the same experimental conditions. Our findings highlight the importance of considering individual variations in functional neuroanatomy in the context of assessing the nature of cortical reinstatement. Consideration of such factors will be important for establishing general principles shaping the neural transformations that occur from perception to memory.

neuroscience↗

bioRxiv2023

Transcriptional Regulation of the P-bodies Associated Psoriasis Candidate Gene CCHCR1

The coiled-coil alpha-helical rod protein 1 (CCHCR1) was first identified as a candidate gene in psoriasis and has lately been associated with COVID-19 susceptibility. Located within P-bodies and centrosomes, its exact cellular role and transcriptional control remain largely unknown. Here, we showed that CCHCR1 shares a bidirectional promoter with its neighboring gene, TCF19. This bidirectional promoter is activated by the G1/S-regulatory transcription factor E2F1, and both genes are co-induced during the G1/S transition of the cell cycle. A luciferase reporter assay suggests that the short intergenic sequence, only 287 bp in length, is sufficient for the G1/S induction of both genes, but the expression of CCHCR1 is further enhanced by the presence of exon 1 from both TCF19 and CCHCR1. This research uncovers the transcriptional regulation of the CCHCR1 gene, offering new perspectives on its function. These findings contribute to the broader understanding of diseases associated with CCHCR1 and may serve as a foundational step for future research in these vital medical fields.

cell biology↗

bioRxiv2023

Extracellular Domains of CAR Reprogram T-Cell Metabolism Without Antigen Stimulation

Metabolism is an indispensable part of T-cell proliferation, activation, and exhaustion, yet the metabolism of chimeric antigen receptor (CAR)-T cells remains incompletely understood. CARs are comprised of extracellular domains that determine cancer specificity, often using single-chain variable fragments (scFvs), and intracellular domains that trigger signaling upon antigen binding. Here we show that CARs differing only in the scFv reprogram T-cell metabolism differently. Even in the absence of antigens, some CARs increase proliferation and nutrient uptake in T cells. Using stable isotope tracers and mass spectrometry, we observe basal metabolic fluxes through glycolysis doubling and amino acid uptake overtaking anaplerosis in CAR-T cells harboring rituximab scFv, unlike other similar anti-CD20 scFvs. Disparate rituximab and 14g2a-based anti-GD2 CAR-T cells are similarly hypermetabolic and channel excess nutrients to nitrogen overflow metabolism. Since CAR-dependent metabolic reprogramming alters cellular energetics, nutrient utilization, and proliferation, metabolic profiling should be an integral part of CAR-T cell development.

systems biology↗

bioRxiv2022

Modular Pooled Discovery of Synthetic Knockin Sequences to Program Durable Cell Therapies

Chronic stimulation can cause T cell dysfunction and limit efficacy of cellular immunotherapies. CRISPR screens have nominated gene targets for engineered T cells, but improved methods are required to compare large numbers of synthetic knockin sequences to reprogram cell functions. Here, we developed Modular Pooled Knockin Screening (ModPoKI), an adaptable platform for modular construction of DNA knockin libraries using barcoded multicistronic adaptors. We built two ModPoKI libraries of 100 transcription factors (TFs) and 129 natural and synthetic surface receptors. Over 20 ModPoKI screens across human TCR and CAR T cells in diverse conditions identified a transcription factor AP4 (TFAP4) construct to enhance long-term T cell fitness and anti-cancer function in vitro and in vivo. ModPoKIs modularity allowed us to generate a [~]10,000-member library of TF combinations. Non-viral knockin of a combined BATF-TFAP4 polycistronic construct further enhanced function in vivo. ModPoKI facilitates discovery of complex gene constructs to program cellular functions. HighlightsO_LIModular pooled knockins of hundreds of TF and surface receptor constructs combined with different antigen receptors C_LIO_LIChronic stimulation screens discover programs to improve T cell persistence C_LIO_LICombinatorial knockin screens with [~]10,000 transcription factor combinations C_LIO_LIBATF-TFAP4 dual knockin construct improves CAR T cell function in vitro and in vivo C_LI

immunology↗

bioRxiv2022

Distinct population and single-neuron selectivity for executive and episodic processing in human dorsal posterior cingulate

Posterior cingulate cortex (PCC) is an enigmatic region implicated in psychiatric and neurological disease, yet its role in cognition remains unclear. Human studies link PCC to episodic memory and default mode network (DMN), while findings from the non-human primate emphasize executive processes more associated with the cognitive control network (CCN) in humans. We hypothesized this difference reflects an important functional division between dorsal (executive) and ventral (episodic) PCC. To test this, we utilized human intracranial recordings of population and single unit activity targeting dorsal PCC during an alternated executive/episodic processing task. Dorsal PCC population responses were significantly enhanced for executive, compared to episodic, task conditions, consistent with the CCN. Single unit recordings, however, revealed four distinct functional types with unique executive (CCN) or episodic (DMN) response profiles. Our findings provide critical electrophysiological data from human PCC, bridging incongruent views within and across species, furthering our understanding of PCC function.

neuroscience↗

bioRxiv2021

Hybrid ssDNA repair templates enable high yield genome engineering in primary cells for disease modeling and cell therapy manufacturing

CRISPR-Cas9 offers unprecedented opportunities to modify genome sequences in primary human cells to study disease variants and reprogram cell functions for next-generation cellular therapies. CRISPR has several potential advantages over widely used retroviral vectors including: 1) site-specific transgene insertion via homology directed repair (HDR), and 2) reductions in the cost and complexity of genome modification. Despite rapid progress with ex vivo CRISPR genome engineering, many novel research and clinical applications would be enabled by methods to further improve knock-in efficiency and the absolute yield of live knock-in cells, especially with large HDR templates (HDRT). We recently reported that Cas9 target sequences (CTS) could be introduced into double-stranded DNA (dsDNA) HDRTs to improve knock-in, but yields and efficiencies were limited by toxicity at high HDRT concentrations. Here we developed a novel system that takes advantage of lower toxicity with single-stranded DNA (ssDNA). We designed hybrid ssDNA HDRTs that incorporate CTS sites and were able to boost knock-in percentages by >5-fold and live cell yields by >7-fold relative to dsDNA HDRTs with CTS. Knock-in efficiency and yield with ssCTS HDRTs were increased further with small molecule inhibitor combinations to improve HDR. We demonstrate application of these methods across a variety of target loci, knock-in constructs, and primary human cell types to reach ultra-high HDR efficiencies (>80-90%) which we use for pathogenic gene variant modeling and universal gene replacement strategies for IL2RA and CTLA4 mutations associated with mendelian immune disorders. Finally, we develop a GMP-compatible method for fully non-viral CAR-T cell manufacturing, demonstrating knock-in efficiencies of 46-62% and generating yields of >1.5 x 109 CAR+ T cells, well above current doses for adoptive cellular therapies. Taken together, we present a comprehensive non-viral approach to model disease associated mutations and re-write targeted genome sequences to program immune cell therapies at a scale compatible with future clinical application.

synthetic biology↗

bioRxiv2020

Stability of ripple events during task engagement in human hippocampus

Periods of cognitive disengagement, such as rest or sleep, are thought to support the progressive consolidation of episodic memories. During these states, the hippocampus displays transient high-frequency oscillatory bursts, known as ripples, which are thought to promote interactions with the neocortex, consolidating memory traces. More recent findings have suggested ripples in the human hippocampus may also occur during task engagement, particularly for tasks requiring episodic memory processes. However, it is unclear if hippocampal ripples occur during other cognitive states or whether ripple properties are modulated by specific types of task demands. In addition, identifying genuine hippocampal ripple events in the human brain can be methodological challenging. To address these questions, we used intracranial recordings from the human hippocampus to quantify ripple events across perceptual, memory and resting task states. Using spectro-temporal identification of hippocampal ripples, we observed highly similar ripple event properties across tasks, with a modest yet significant increase in ripple properties (rate, duration & amplitude) during resting task states. These ripple event attributes did not differ between hemisphere, nor across or within the time of day examined. Supporting data further highlighted that while hippocampal ripples occurred during all task states, these rates were typically lower than that observed during sleep. Together, these findings highlight that hippocampal ripples occur consistently, but sparsely, during a broad range of cognitive task states. Such findings may be incorporated into existing models of systems consolidation, whereby hippocampal ripples help to initially establish latent memory traces.

neuroscience↗

bioRxiv2020

Rational Tuning of CAR Tonic Signaling Yields Superior T-Cell Therapy for Cancer

Chimeric antigen receptors (CARs) are modular proteins capable of redirecting immune cells toward a wide variety of disease-associated antigens. Here, we explore the effects of CAR protein sequence and structure on CAR-T cell function. Based on the empirical observation that CD20 CARs with similar sequences exhibit divergent tonic-signaling and anti-tumor activities, we devised engineering strategies that aimed to improve CAR-T cell function by tuning the intensity of tonic signaling. We found that CARs designed to exhibit low but non-zero levels of tonic signaling show robust effector function upon antigen stimulation while avoiding premature functional exhaustion by CAR-T cells. Through alterations of the CARs ligand-binding domain and overall protein conformation, we generated CD20 CAR variants that outperform the CD19 CAR in mouse models of human lymphoma. We further demonstrate that rational modification of protein confirmation can be generalized to improve GD2 CAR-T cell efficacy against neuroblastoma. These findings point to tonic signaling and basal T-cell activation as informative parameters to guide the rational design of next-generation CARs for cancer therapy.

bioengineering↗

bioRxiv2020

Mu oscillations and motor imagery performance: A reflection of success, not ability

Motor imagery, or our ability to imagine movement without actually engaging in the action, has been an increasingly popular tool in rehabilitation settings. Understanding its neural underpinning is crucial for further development of new interventions. Using scalp electroencephalography (EEG), many studies have shown that mu oscillations (8-13 Hz), a variant of the alpha band recorded over the motor cortex electrodes, are involved in both the imagination and performance of movements; however, the exact relationship between mu oscillations and motor imagery is unclear. To further our understanding of the functional significance of mu oscillations and their role in both motor learning and motor performance, our study sought to investigate how suppression in mu oscillations varies during a motor imagery task according to both within subject imagery success and between subject imagery ability. We examined EEG activity while a large sample of participants performed an objective test of motor imagery ability (Test of Ability in Movement Imagery, TAMI). Results demonstrated that mu oscillatory activity significantly decreased during successful imagery trials as compared to unsuccessful ones. However, the extent of reduction in mu oscillations did not correlate with individual imagery ability. These results provide further support for the involvement of mu oscillations in motor behaviours and indicate that suppression in mu oscillations may serve as an important index for determining successful motor imagery performance within an individual. The processes that underlie this success are likely similar to those that underlie successful motor execution, given motor imagerys proposed functional equivalence to motor imagery.

neuroscience↗

bioRxiv2020

Systematically optimized BCMA/CS1 bispecific CAR-T cells robustly control heterogeneous multiple myeloma

Chimeric antigen receptor (CAR)-T cell therapy has shown remarkable clinical efficacy against B-cell malignancies but also demonstrated marked vulnerability to antigen escape and tumor relapse. Here, we report the rational design and systematic optimization of bispecific CAR-T cells with robust activity against multiple myeloma (MM), including heterogeneous MM that is resistant to conventional CAR-T cell therapy targeting B-cell maturation antigen (BCMA). We demonstrate that BCMA/CS1 bispecific CAR-T cells exhibit significantly higher CAR expression levels and greater antigen-stimulated proliferation compared to T cells that co-express individual BCMA and CS1 CARs. Compared to single-input BCMA- or CS1-targeting CAR-T cells, BCMA/CS1 bispecific CAR-T cells significantly prolong the survival of animals bearing heterogeneous MM tumors. Combination therapy with anti-PD-1 antibody further accelerates the rate of initial tumor clearance in vivo, but CAR-T cell treatment alone was able to achieve durable tumor-free survival even upon tumor re-challenge. Taken together, the BCMA/CS1 bispecific CAR presents a promising treatment approach to prevent antigen escape in CAR-T cell therapy against MM, and the vertically integrated optimization process can be used to develop robust cell-based therapy against novel disease targets.

bioengineering↗