Biology subjects

Lee, J. K.

Publications and source records attributed to Lee, J. K..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Evaluation of a Functional Portable Hemodialysis Machine, XKIDNEY

Chronic kidney failure and end-stage renal disease (ESRD) are increasing globally, but home hemodialysis offers a critical means of improving patient quality of life and reducing national healthcare costs. This study investigates the performance of a portable hemodialysis (HD) device named XKIDNEY. The efficacy and safety of the device were determined with focus on solute clearance, fluid balancing accuracy, and blood cell integrity in an ex-vivo test environment. A comparison of the performance of XKIDNEY and a conventional HD unit showed that XKIDNEY had superior balancing accuracy without any technical malfunction. In addition, low molecular weight solutes, such as urea and creatinine, were effectively removed. These findings demonstrate that XKIDNEY enhances treatment portability without compromising performance and indicate XKIDNEY is a feasible home hemodialysis option.

bioengineering↗

bioRxiv2024

Heritability of movie-evoked brain activity and connectivity

The neural bases of sensory processing are conserved across people, but no two individuals experience the same stimulus in exactly the same way. Recent work has established that the idiosyncratic nature of subjective experience is underpinned by individual variability in brain responses to sensory information. However, the fundamental origins of this individual variability have yet to be systematically investigated. Here, we establish a genetic basis for individual differences in sensory processing by quantifying (1) the heritability of high-dimensional brain responses to movies and (2) the extent to which this heritability is grounded in lower-level aspects of brain function. Specifically, we leverage 7T fMRI data collected from a twin sample to first show that movie-evoked brain activity is heritable across the cortex, and that this heritability is greater for information encoded in lower temporal frequencies, especially in more associative cortical areas. Next, we use hyperalignment to decompose this heritability into genetic similarity in where vs. how sensory information is processed. We also show that the heritability of brain activity patterns can be partially explained by the heritability of the neural timescale, a one-dimensional measure of local circuit functioning. Finally, we generalize our findings by illustrating a similar pattern of results for the heritability of movie-evoked functional connectivity. These results demonstrate that brain responses to complex stimuli are heritable, and that this heritability is due, in part, to genetic control over stable aspects of brain function.

neuroscience↗

bioRxiv2023

Imaging Electrical Activity of Retinal Ganglion Cells with Fluores-cent Voltage and Calcium Indicator Proteins in Retinal Degenera-tive rd1 Blind Mice

In order to understand the retinal network, it is essential to identify functional connectivity among retinal neurons. For this purpose, imaging neuronal activity through fluorescent indicator proteins has been a promising approach offering simultaneous measurements of neuronal activities from different regions of the circuit. In this study, we used genetically encoded voltage and calcium indicators, Bongwoori-R3 and GCaMP6f, to visualize membrane voltage and calcium dynamics in the form of the spatial map within retinal ganglion cells from retina tissues of the photoreceptor degenerated rd1 mice. Retinal voltage imaging confirmed current-evoked responses from somatic spiking and intercellular conduction, while calcium imaging showed current evoked changes in calcium concentrations of presynaptic neurons. These results indicate that the combination of fluorescent protein sensors and high-speed imaging methods permits imaging electrical activity with cellular precision and millisecond resolution. Hence, we expect our method will provide a potent experimental platform for the study of retinal signaling pathways as well as the development of retinal stimulation strategies in visual prosthesis.

neuroscience↗

bioRxiv2023

Assessing the Predictive Ability of Computational Epitope Prediction Methods on Fel d 1 Allergen

While computational epitope prediction methods have found broad application, their use, specifically in allergy-related contexts, remains relatively less explored. This study benchmarks several publicly available epitope prediction tools, focusing on the allergenic IgE and T-cell epitopes of Fel d 1, an extensively studied allergen. Using a variety of tools accessible via the Immune Epitope Database (IEDB) and other resources, we evaluate their ability to identify the known linear IgE and T-cell epitopes of Fel d 1. Our results show a limited effectiveness for B-cell epitope prediction methods, with most performing only marginally better than random selection. We also explored the general predictive abilities on other allergens, and the results were largely random. When predicting T-cell epitopes, ProPred successfully identified all known Fel d 1 T-cell epitopes, whereas the IEDB approach missed two known epitopes and demonstrated a tendency to over-predict. However, when applied to a larger test set, both methods performed only slightly better than random selection. Our findings show the limitations of current computational epitope prediction methods in accurately identifying allergenic epitopes, emphasizing the need for methodological advancements in allergen research.

bioinformatics↗

bioRxiv2023

Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations

Available genetically-defined cancer models are limited in genotypic and phenotypic complexity and underrepresent the heterogeneity of human cancer. Herein, we describe a combinatorial genetic strategy applied to an organoid transformation assay to rapidly generate diverse, clinically relevant bladder and prostate cancer models. Importantly, the clonal architecture of the resultant tumors can be resolved using single-cell or spatially resolved next-generation sequencing to uncover polygenic drivers of cancer phenotypes.

cancer biology↗

bioRxiv2023

Active maintenance of CD8+ T cell naivety through regulation of global genome architecture

The differentiation of naive CD8+ cytotoxic T lymphocytes (CTLs) into effector and memory states results in large scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organisation reflect or underpin these transcriptional programs. We utilised Hi-C to map changes in the spatial organisation of long-range genome contacts within naive, effector and memory virus-specific CD8+ T cells. We observed that the architecture of the naive CD8+ T cell genome was distinct from effector and memory genome configurations with extensive changes within discrete functional chromatin domains. However, deletion of the BACH2 or SATB1 transcription factors was sufficient to remodel the naive chromatin architecture and engage transcriptional programs characteristic of differentiated cells. This suggests that the chromatin architecture within naive CD8+ T cells is preconfigured to undergo autonomous remodelling upon activation, with key transcription factors restraining differentiation by actively enforcing the unique naive chromatin state. One Sentence SummaryCD8+ T cell naivety is actively maintained by transcription factors that enforce a distinct, naive chromatin architecture. HighlightsO_LICD8+ T cell differentiation states are underscored by distinct chromatin looping architectures. C_LIO_LIChromatin loops juxtapose CTL state appropriate enhancers, transcription factors and genes. C_LIO_LIEffector and memory CTLs have similar genome architectures, explaining rapid memory recall. C_LIO_LICTL differentiation is restrained by BACH2 and SATB1, which enforce a naive loop architecture. C_LI

immunology↗

bioRxiv2023

Antigen-dependent IL-12 signaling in CAR T cells promotes regional to systemic disease targeting

Chimeric antigen receptor (CAR) T cell therapeutic responses are hampered by limited T cell trafficking, persistence, and durable anti-tumor activity in solid tumor microenvironments. However, these challenges can be largely overcome by relatively unconstrained synthetic engineering strategies, which are being harnessed to improve solid tumor CAR T cell therapies. Here, we describe fully optimized CAR T cells targeting tumor-associated glycoprotein-72 (TAG72) for the treatment of solid tumors, identifying the CD28 transmembrane domain upstream of the 4-1BB co-stimulatory domain as a driver of potent anti-tumor activity and IFN{gamma} secretion. These findings have culminated into a phase 1 trial evaluating safety, feasibility, and bioactivity of TAG72-CAR T cells for the treatment of patients with advanced ovarian cancer (NCT05225363). Preclinically, we found that CAR T cell-mediated IFN{gamma} production facilitated by IL-12 signaling was required for tumor cell killing, which was recapitulated by expressing an optimized membrane-bound IL-12 (mbIL12) molecule on CAR T cells. Critically, mbIL12 cell surface expression and downstream signaling was induced and sustained only following CAR T cell activation. CAR T cells with mbIL12 demonstrated improved antigen-dependent T cell proliferation and potent cytotoxicity in recursive tumor cell killing assays in vitro and showed robust in vivo anti-tumor efficacy in human xenograft models of ovarian cancer peritoneal metastasis. Further, locoregional administration of TAG72-CAR T cells with antigen-dependent IL-12 signaling promoted durable anti-tumor responses against both regional and systemic disease in mice and was associated with improved systemic T cell persistence. Our study features a clinically-applicable strategy to improve the overall efficacy of locoregionally-delivered CAR T cells engineered with antigen-dependent immune-modulating cytokines in targeting both regional and systemic disease.

cancer biology↗

bioRxiv2023

Compulsivity is linked to maladaptive choice variability but unaltered reinforcement learning under uncertainty

Compulsivity has been associated with variable behavior under uncertainty. However, previous work has not distinguished between two main sources of behavioral variability: the stochastic selection of choice options that do not maximize expected reward (choice variability), and random noise in the reinforcement learning process that updates option values from choice outcomes (learning variability). Here we studied the relation between dimensional compulsivity and behavioral variability, using a computational model which dissociates its two sources. We found that compulsivity is associated with more frequent switches between options, triggered by increased choice variability but no change in learning variability. This effect of compulsivity on the trait component of choice variability is observed even in conditions where this source of behavioral variability yields no cognitive benefits. These findings indicate that compulsive individuals make variable and maladaptive choices under uncertainty, but do not hold degraded representations of option values.

animal behavior and cognition↗

bioRxiv2022

Adaptive tuning of human learning and choice variability to unexpected uncertainty

Human value-based decisions are strikingly variable under uncertainty. This variability is known to arise from two distinct sources: variable choices aimed at exploring available options, and imprecise learning of option values due to limited cognitive resources. However, whether these two sources of decision variability are tuned to their specific costs and benefits remains unclear. To address this question, we compared the effects of expected and unexpected uncertainty on decision-making in the same reinforcement learning task. Across two large behavioral datasets, we found that humans choose more variably between options but simultaneously learn less imprecisely their values in response to unexpected uncertainty. Using simulations of learning agents, we demonstrate that these opposite adjustments reflect adaptive tuning of exploration and learning precision to the structure of uncertainty. Together, these findings indicate that humans regulate not only how much they explore uncertain options, but also how precisely they learn the values of these options. TeaserHumans regulate not only how much they explore uncertain options, but also how precisely they learn their values.

animal behavior and cognition↗

bioRxiv2022

Sniper2L, a high-fidelity Cas9 variant with high activity

Although several high-fidelity SpCas9 variants that have reduced activities at mismatched target sequences have been reported, it has been observed that this increased specificity is associated with reduced on-target activity, limiting the applications of the high-fidelity variants when efficient genome editing is required. Here, we developed an improved version of Sniper-Cas9, Sniper2L, which represents an exception to this trade-off trend as it showed higher specificity with retained high activity. We evaluated Sniper2L activities at a large number of target sequences, and developed DeepSniper, a deep-learning model that can predict the activity of Sniper2L. We also confirmed that Sniper2L can induce highly efficient and specific editing at a large number of target sequences when it is delivered as a ribonucleoprotein complex. Mechanically, the high specificity of Sniper2L originates from its superior ability to avoid unwinding a target DNA containing even a single mismatch. We envision that Sniper2L will be useful when efficient and specific genome editing is required.

bioengineering↗

bioRxiv2022

Artificial Gravity During a Spaceflight Analog Alters Brain Sensory Connectivity

Spaceflight has numerous untoward effects on human physiology. Various countermeasures are under investigation including artificial gravity (AG). Here, we investigated whether AG alters resting-state brain functional connectivity changes during head-down tilt bed rest (HDBR), a spaceflight analog. Participants underwent 60 days of HDBR. Two groups received daily AG administered either continuously (cAG) or intermittently (iAG). A control group received no AG. We assessed resting-state functional connectivity before, during, and after HDBR. We also measured balance and mobility changes from pre-to post-HDBR. We examined how functional connectivity changes throughout HDBR and whether AG is associated with differential effects. We found differential connectivity changes by group between posterior parietal cortex and multiple somatosensory regions. The control group exhibited increased functional connectivity between these regions throughout HDBR whereas the cAG group showed decreased functional connectivity. This finding suggests that AG alters somatosensory reweighting during HDBR. We also observed brain-behavioral correlations that differed significantly by group. Control group participants who showed increased connectivity between the putamen and somatosensory cortex exhibited greater mobility declines post-HDBR. For the cAG group, increased connectivity between these regions was associated with little to no mobility declines post-HDBR. This suggests that when somatosensory stimulation is provided via AG, functional connectivity increases between the putamen and somatosensory cortex are compensatory in nature, resulting in reduced mobility declines. Given these findings, AG may be an effective countermeasure for the reduced somatosensory stimulation that occurs in both microgravity and HDBR.

neuroscience↗

bioRxiv2022

Targeting advanced prostate cancer with STEAP1 chimeric antigen receptor T cell therapy

Six transmembrane epithelial antigen of the prostate 1 (STEAP1) is a compelling tumor-associated cell surface antigen for therapeutic targeting in solid tumors. We identified broad expression of STEAP1 (87% positive) in lethal metastatic prostate cancer, even more so than prostate-specific membrane antigen (PSMA, 60% positive) which is a clinically established diagnostic and therapeutic target. Second-generation chimeric antigen receptor (CAR) T cells were engineered for reactivity against STEAP1 and demonstrated substantial antitumor activity in metastatic human prostate cancer models in immunodeficient mice. Adoptive transfer of STEAP1 CAR T cells was associated with prolonged peripheral persistence and either disease eradication or substantial tumor growth inhibition with progressive disease demonstrating antigen loss. As STEAP1 CAR T cells were also highly active in antigen density conditions as low as [~]1,500 molecules/cell, we generated a human STEAP1 (hSTEAP1) knock-in (KI) mouse to evaluate the potential for on-target off-tumor toxicities. hSTEAP1-KI mice demonstrated a pattern of systemic hSTEAP1 expression akin to that observed in humans with the greatest expression found in the prostate gland. Mouse-in-mouse studies of STEAP1 CAR T cell therapy in immunocompetent hSTEAP1-KI mice engrafted with disseminated mouse prostate cancer showed preliminary safety without evidence of gross toxicity, cytokine storm, or architectural disruption and increased T cell infiltration at sites of systemic hSTEAP1 expression. Tumor responses and extension of survival were appreciated but antigen loss was identified in recurrent and progressive disease. In summary, we report the extent of STEAP1 expression in treatment-refractory metastatic prostate cancer, the generation of a STEAP1 CAR T cell therapy with promising potency and safety in preclinical studies of advanced prostate cancer, and antigen escape as a mechanism of resistance to effective STEAP1 CAR T cell therapy.

cancer biology↗

bioRxiv2022

A Systematic Evaluation of the Computational Tools for Ligand-receptor-based Cell-Cell Interaction Inference

Cell-cell interactions (CCIs) are essential for multicellular organisms to coordinate biological processes and functions. Many molecules and signaling processes can mediate CCIs. One classical type of CCI mediator is the interaction between secreted ligands and cell surface receptors, i.e., ligand-receptor (LR) interaction. With the recent development of single-cell technologies, a large amount of single-cell RNA Sequencing (scRNA-Seq) data has become widely available. This data availability motivated the single-cell-resolution study of CCIs, particularly LR-based CCIs. Dozens of computational methods and tools have been developed to predict CCIs by identifying LR-based CCIs. Many of these tools have been theoretically reviewed. However, there is little study on current LR-based CCI prediction tools regarding their performance and running results on public scRNA-Seq datasets. In this work, to fill this gap, we tested and compared nine of the most recent computational tools for LR-based CCI prediction. We used fifteen mouse scRNA-Seq samples that correspond to nearly 100K single cells under different experimental conditions for testing and comparison. Besides briefing the methodology used in these nine tools, we summarized the similarities and differences of these tools in terms of both LR prediction and CCI inference between cell types. We provided insight into using these tools to make meaningful discoveries in understanding cell communications.

bioinformatics↗

bioRxiv2021

Bile Acid Regulates the Colonization and Dissemination of Candida albicans from the Gastrointestinal Tract by Controlling Host Defense System and Microbiota

Candida albicans (CA), a commensal and opportunistic eukaryotic organism, frequently inhabits the gastrointestinal (GI) tract and causes life-threatening infections. Antibiotic-induced gut dysbiosis is a major risk factor for increased CA colonization and dissemination from the GI tract. We identified a significant increase of taurocholic acid (TCA), a major bile acid in antibiotic-treated mice susceptible to CA infection. In vivo findings indicate that administration of TCA through drinking water is sufficient to induce colonization and dissemination of CA in wild type and immunosuppressed mice. Treatment with TCA significantly reduced mRNA expression of immune genes ang4 and Cxcr3 in the colon. In addition, TCA significantly decreased the relative abundance of three culturable species of commensal bacteria, Turicibacter sanguinis, Lactobacillus johnsonii, and Clostridium celatum, in both cecal contents and mucosal scrapings from colon. Taken together, our results indicate that TCA promotes fungal colonization and dissemination of CA from the GI tract by controlling host defense system and intestinal microbiota that play a critical role in regulating CA in the intestine. ImportanceBroad-spectrum antibiotics, FDA-approved bile acid drugs, and probiotics used to control metabolic and infectious diseases profoundly alter the level of TCA in the gut. Furthermore, TCA level is highly altered in a subset of cancer, colitis and surgery patients who are highly susceptible to CA infection. Inadvertently, these therapies and disease conditions could be either promoting CA colonization and dissemination. Our findings indicate that TCA alone can induce fungal colonization and dissemination from the intestine. Results from this study will have a significant impact in understanding how bile acids interact with the microbiota and host in regulating invasive fungal infections that originate from the intestine and to develop potential new antifungal therapeutics.

microbiology↗

bioRxiv2021

The road not taken: disconnection of a human-unique cortical pathway in schizophrenia and its effects on naturalistic social cognition

BackgroundEfficient processing of complex and dynamic social scenes relies on intact connectivity of many underlying cortical areas and networks, but how connectivity deficits affect this functioning in social cognition remains unknown. Here we measure these relationships using functionally based localization of social cognition areas, resting-state functional connectivity, and movie-watching data. MethodsIn 42 schizophrenia participants (SzP) and 41 healthy controls (HC), we measured the functional connectivity of areas localized by face-emotion processing, theory-of-mind, and attention tasks. We quantified the weighted shortest path length between visual and medial prefrontal theory-of-mind areas in both populations to assess the impact of functional connectivity deficits on network structure. We then correlated connectivity along the shortest path in each group with movie-evoked activity in a key node of the theory-of-mind network (TPJp). ResultsSzP had pronounced connectivity deficits in temporoparietal junction/posterior superior temporal sulcus (TPJ-pSTS) areas involved in face-emotion processing (t(81)=4.4, p=0.00002). In HC the shortest path connecting visual and medial prefrontal theory-of-mind areas passed through TPJ-pSTS, whereas in SzP the shortest path passed through prefrontal cortex (PFC). While movie-evoked TPJp activity correlated with connectivity along the TPJ-pSTS pathway in both groups (r=0.43, p=0.002), it additionally correlated with connectivity along the PFC pathway only in SzP (rSzP=0.56, p=0.003). ConclusionsConnectivity along the human-unique TPJ-pSTS pathway affects both the network architecture and functioning of areas involved in processing complex dynamic social scenes. These results demonstrate how focal deficits can have widespread impacts across cortex.

neuroscience↗

bioRxiv2021

Nuclear stabilisation of p53 requires a functional nucleolar surveillance pathway

The nucleolar surveillance pathway (NSP) monitors nucleolar fidelity and responds to nucleolar stresses (i.e., inactivation of ribosome biogenesis) by mediating the inhibitory binding of ribosomal proteins (RPs) to mouse double minute 2 homolog (MDM2), a nuclear-localised E3 ubiquitin ligase, which results in p53 accumulation. Inappropriate activation of the NSP has been implicated in the pathogenesis of collection of human diseases termed "ribosomopathies", while drugs that selectively activate the NSP are now in trials for cancer. Despite the clinical significance, the precise molecular mechanism(s) regulating the NSP remain poorly understood. Using genome-wide loss of function screens, we demonstrate the ribosome biogenesis (RiBi) axis as the most potent class of genes whose disruption stabilises p53. Furthermore, we identified a novel suite of genes critical for the NSP, including a novel mammalian protein implicated in 5S ribonucleoprotein particle (5S-RNP) biogenesis, HEATR3. By selectively disabling the NSP, we unexpectedly demonstrate that a functional NSP is required for the ability of all nuclear acting stresses tested, including DNA damage, to robustly induce p53 accumulation. Together, our data demonstrates that the NSP has evolved as the dominant central integrator of stresses that regulate nuclear p53 abundance, thus ensuring RiBi is hardwired to cellular proliferative capacity.

cell biology↗

bioRxiv2021

Specific cognitive signatures of information seeking in controllable environments

In uncertain environments, seeking information about alternative choice options is essential for adaptive learning and decision-making. However, information seeking is usually confounded with changes-of-mind about the reliability of the preferred option. Here, we exploited the fact that information seeking requires control over which option to sample to isolate its behavioral and neurophysiological signatures. We found that changes-of-mind occurring with control require more evidence against the current option, are associated with reduced confidence, but are nevertheless more likely to be confirmed on the next decision. Multimodal neurophysiological recordings showed that these changes-of-mind are preceded by stronger activation of the dorsal attention network in magnetoencephalography (MEG), and followed by increased pupil-linked arousal during the presentation of decision outcomes. Together, these findings indicate that information seeking increases the saliency of evidence perceived as the direct consequence of ones own actions. HighlightsO_LIExploration-exploitation dilemmas confound information seeking with changes-of-mind. C_LIO_LIUnlike changes-of-mind, information seeking requires control over information sampling. C_LIO_LIInformation seeking is associated with reduced confidence and active hypothesis testing. C_LIO_LIStronger neurophysiological correlates of attention and arousal during information seeking. C_LI

neuroscience↗

bioRxiv2020

Ophthalmic Changes in a Spaceflight Analog Are Associated with Brain Functional Reorganization

Following long-duration spaceflight, some astronauts exhibit ophthalmic structural changes referred to as Spaceflight Associated Neuro-ocular Syndrome (SANS). Optic disc edema is a common sign of SANS. The origin and effects of SANS are not understood as signs of SANS have not manifested in previous spaceflight analog studies. In the current spaceflight analog study, eleven subjects underwent 30 days of strict head down-tilt bed rest in elevated ambient carbon dioxide (HDBR+CO2). Using functional magnetic resonance imaging (fMRI), we acquired resting-state fMRI data at 6 time points: before (2), during (2), and after (2) the HDBR+CO2 intervention. Five participants developed optic disc edema during the intervention (SANS subgroup) and 6 did not (NoSANS group). This occurrence allowed us to explore whether development of signs of SANS during the spaceflight analog impacted resting-state functional connectivity during HDBR+CO2. In light of previous work identifying genetic and biochemical predictors of SANS, we further assessed whether the SANS and NoSANS subgroups exhibited differential patterns of resting-state functional connectivity prior to the HDBR+CO2 intervention. We found that the SANS and NoSANS subgroups exhibited distinct patterns of resting-state functional connectivity changes during HDBR+CO2 within visual and vestibular-related brain networks. The SANS and NoSANS subgroups also exhibited different resting-state functional connectivity prior to HDBR+CO2 within a visual cortical network and within a large-scale network of brain areas involved in multisensory integration. We further present associations between functional connectivity within the identified networks and previously identified genetic and biochemical predictors of SANS. Subgroup differences in resting-state functional connectivity changes may reflect differential patterns of visual and vestibular reweighting as optic disc edema develops during the spaceflight analog. This finding suggests that SANS impacts not only neuro-ocular structures, but also functional brain organization. Future prospective investigations incorporating sensory assessments are required to determine the functional significance of the observed connectivity differences. HIGHLIGHTSWe investigated resting-state functional connectivity (FC) during a spaceflight analog with elevated CO2 (HDBR+CO2). During the HDBR+CO2 intervention, a subset of participants developed optic disc edema, a sign of spaceflight-associated neuro-ocular syndrome (SANS). Participants with signs of SANS exhibited a distinct pattern of resting-state functional connectivity changes within visual and vestibular-related networks during HDBR+CO2. Participants who developed optic disc edema exhibited different FC prior to the spaceflight analog within a visual cortical network and within a large-scale network of brain areas involved in multisensory integration.

neuroscience↗