Biology subjects

Lan, H.

Publications and source records attributed to Lan, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Genetic Architecture of Perivascular Space Morphology in the Pediatric Brain

IntroductionPerivascular spaces (PVS) support brain homeostasis through metabolite delivery and waste clearance, yet the genetic determinants of PVS morphology during childhood remain unknown. Here, we leveraged cross-sectional Adolescent Brain Cognitive Development Study data (N = 6,600; ages 9-10), including genomics and 3T structural MRI. MethodsLinear mixed-effects models examined associations between 45 single nucleotide polymorphisms (SNPs) previously linked to adult PVS structure or function and PVS count and volume fraction (VF) across six macroregions and 28 Desikan-Killiany subregions. ResultsFifteen SNPs demonstrated significant associations with PVS macroregion morphology, predominantly VF; 21 SNPs demonstrated associations with subregion morphology. Variants near SLC13A3 showed the strongest, most widespread associations with PVS VF. Additional replicated variants implicated Wnt signaling, cell adhesion, apoptosis, and glymphatic function. ConclusionThese findings suggest genetic associations with PVS morphology are detectable in childhood, while highlighting developmental and regional specificity. Longitudinal studies are now needed to determine whether childhood PVS genetic architecture predicts trajectories of glymphatic maturation and associated cognitive outcomes. Key PointsO_LIPerivascular space morphology, mapped across 28 white matter subregions, displays substantial regional and interindividual variability during childhood. C_LIO_LISix genetic associations with perivascular morphology were only detectable at subregion resolution, demonstrating that lobar averaging can obscure spatially restricted signals. C_LIO_LINearly 50% of adult-identified perivascular space risk variants replicated in 9-10 year-olds, with anatomically patterned associations reflecting patterns of neurovascular complexity and neurodevelopmental timing. C_LI

neuroscience↗

bioRxiv2026

Recessive POPDC1 Truncation Causes Lethal Short-QT Pattern Arrhythmogenic Cardiomyopathy with Multi-Ion Channel Remodeling and Ankyrin-G Scaffold Disruption

AimsBiallelic variants in Popeye domain containing 1 (POPDC1) classically cause limb-girdle muscular dystrophy, but their impact on cardiac system remains unclear. We investigated the functional consequence of a POPDC1 frameshift variant (c.448delT), first identified in a consanguineous family with arrhythmogenic cardiomyopathy (ACM) and sudden death. Methods and resultsComprehensive clinical and genetic evaluation was followed by mechanistic studies in an orthologous Popdc1 knock-in rat model. Functional characterization included biotelemetry and programed electrical stimulation, optical mapping, patch clamp, intracellular Ca2+ imaging, proteomics, and oxidative stress assays. Homozygous mutants (Popdc1fs/fs) exhibited a shortened QTc interval and high incidence of ventricular tachycardia compared to wild-type (Popdc1+/+). Urethane anesthesia provoked second-degree AV block in all 10 Popdc1fs/fs rats but in only 1 of 9 Popdc1+/+ littermates. Optical mapping demonstrated abbreviated action potentials, slowed conduction velocity, and inducible polymorphic VT. Patch clamp confirmed accelerated repolarization, with upregulated transient outward potassium currents (Ito) and L-type calcium currents (ICa, L), but downregulated peak sodium currents (INa). Multi-omics and ultrastructural analyses revealed a post-translational collapse of intercalated disc: POPDC1 loss destabilized Ankyrin-G and its membrane-anchored cargo, Nav1.5, coinciding with enhanced Kv4.3 and Cav1.2 protein levels. These disruptions create a convergence of delayed conduction and shortened refractoriness, forming substrate for malignant re-entry. ConclusionWe defined a recessive short-QT ACM leading to potentially fatal arrhythmias caused by biallelic POPDC1 truncation driving Ankyrin-G disruption, manifesting as a triad: (1) bradycardia/AV block, (2) accelerated repolarization as short-QT pattern/diffuse T-wave flattening or inversion, and (3) progressive cardiomyopathy and sudden death. Whats new?O_LIWe define a novel diagnostic triad for recessive short-QT arrhythmogenic cardiomyopathy (rSQT-ACM) in a loss-of-function POPDC1 truncation: (1) early-onset bradyarrhythmia (sinus bradycardia or AV block); (2) a paradoxical short-QT interval with maladaptive rate response/diffuse T-wave flattening or inversion; and (3) progressive cardiomyopathy accompanied accompanied by with SCD. C_LIO_LIMechanistically, biallelic POPDC1 truncation induces collapse of the POPDC1-AnkG hub, which triggers a unique "opposing remodeling" phenotype (severe INa reduction coupled with paradoxical upregulation of Kv4.3-mediated Ito), and established a unified "slow-conduction, short-wavelength" substrate that underpins malignant re-entry. C_LIO_LIImplications for safety and device therapy: Nav1.5 deficiency indicates that sodium channel blockers may be contraindicated, and early ICD implantation may be preferable to bradycardia pacing. C_LIO_LIMechanism-directed treatments: POPDC1s recessive inheritance and small gene size make it a strong candidate for AAV-mediated gene supplementation aimed at restoring the intercalated disc architecture and ion-channel anchoring. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/710328v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1012d79org.highwire.dtl.DTLVardef@5073dcorg.highwire.dtl.DTLVardef@1e69bc2org.highwire.dtl.DTLVardef@fc15ec_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

genetics↗

bioRxiv2026

Spiral-on-a-Curve: wireless photoacoustic neuromodulation patch

Focused ultrasound neuromodulation offers a promising noninvasive strategy for precise deep-brain stimulation, yet conventional piezoelectric phased arrays rely on bulky hardware, high-voltage electronics, and complex phase control, limiting their scalability and wearable integration. Photoacoustic approaches enable wireless ultrasound generation but remain constrained by a trade-off between focusing precision, penetration depth, and robustness to optical misalignment. Here, we present a geometrically encoded passive photoacoustic patch (PPP) based on a spherical double logarithmic spiral (SDLS) array that achieves intrinsically stable and programmable acoustic focusing without electronic phase modulation. By distributing hemispherical CNT/PDMS photoacoustic emitters quasi-uniformly over an equal-path spherical surface and orienting each emitter toward a predefined focal point, the device establishes geometry-dominated wavefront convergence. Numerical simulations demonstrate that curved geometry is a prerequisite for phase-free focusing, while the nonperiodic spiral topology suppresses sidelobes and mitigates interference artifacts Compared with continuous spherical or periodic concentric arrays, the SDLS architecture exhibits substantially enhanced robustness to optical axis displacement, reducing focal tilt from > 14{degrees} to approximately 5{degrees} under 2 mm lateral misalignment. Experimental three-dimensional hydrophone mapping confirms millimeter-scale focusing at approximately 7 mm depth with a full width at half-maximum of 1.3 mm and peak pressures up to 8 MPa under safe laser exposure ([≤] 20 mJ/cm2). The focal region can be continuously tuned by adjusting illumination aperture size without altering device geometry or excitation schemes. The patch demonstrates excellent thermal and acoustic stability during prolonged operation and enables region-specific motor cortex stimulation in vivo, eliciting distinct electromyographic responses in forelimb and hindlimb muscles. By shifting ultrasound beam formation from electronic phase control to intrinsic three-dimensional geometry, this work establishes a lightweight, wire-free, and optically programmable platform for robust wearable neuromodulation and scalable bioacoustic interfaces.

bioengineering↗

bioRxiv2026

The genetic repertoire of the deep sea: from sequence to structure and function

The deep sea as the largest and maybe most hostile environment on Earth is still underexplored especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures, and used it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity, yet substantial structural conservation of proteins. Especially proteins involved in replication, recombination, and repair were identified to be under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as a unique evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.

bioinformatics↗

bioRxiv2025

Cross-competition shapes CD8+ T cell hierarchies and differentiation after RNA vaccination

Short SummaryImmunodominance is a universal feature of adaptive immunity that constrains T cell expansion, clonal diversity and breadth resulting in a narrowly focused T cell response. While observed across diverse priming settings and vaccine platforms, the influence of immunodominance on T cell phenotype remains unclear. Using an mRNA lipoplex vaccine encoding multiple antigens to study how immunodominance influences CD8+ T cell fate, we found that dominant CD8+ T cell responses alter the magnitude and phenotype of subdominant responses through peptide-MHC-I stability-mediated T cell cross-competition. Dominant CD8+ T cell responses preferentially acquired markers associated with terminal differentiation and cytotoxic function, while sub-dominant responses adopted memory-precursor and stem-like features. Removal of dominant responses allowed increased expansion of sub-dominant T cell responses and adoption of terminally differentiated effector phenotypes. These findings reveal that immunodominance dynamically shapes the magnitude, breadth and differentiation of CD8+ T cell responses and highlights opportunities to fine-tune T cell responses for therapeutic vaccination.

immunology↗

bioRxiv2025

Sex and gender differences in perivascular space in early adolescence

Perivascular spaces (PVS) surrounding cerebral blood vessels play an important role in the blood-brain barrier and glymphatic system. Although it was once thought that PVS were either absent or too small to be seen or quantified during healthy development with MRI, recent studies have found visible, quantifiable PVS exist throughout the white matter of the cerebrum in childhood and adolescence. As a result, researchers have begun to explore individual differences, including potential sex-based variations in developing PVS. Meta-analyses in adults have shown that PVS are larger on average in males than in females, and several studies have shown a similar relationship in children. In contrast, no studies to date have examined the association between gender and PVS at any age. This cross-sectional study examined 6,538 youths from a large, nationwide sample of 9- to 11-year-olds in the U.S. to examine the relationship between sex, felt-gender, and PVS count and volume. Using a model-building approach, we conducted a series of linear mixed-effects models to determine the maximum variance explained in PVS count and volume, including age, pubertal development status, race, parent education, BMI z-score, and regional white matter volume, while also adjusting for MRI scanner and site. BMI z-score, age, and parent education were significant predictors of both PVS volume and count. Adding sex to the model improved model fit in all regions, and the further addition of felt-gender significantly improved model fit for PVS count in 5/6 regions of interest. Moreover, we found increases in PVS volume and count were associated with reduced executive function, learning, and memory. As the first study to report an association between felt-gender and PVS, our findings demonstrate the importance of considering gender in addition to sex as a potential source of structural variance in PVS in adolescents.

neuroscience↗

bioRxiv2025

A deep learning and co-conservation framework enable discovery of non-canonical Cas proteins

CRISPR-Cas systems are central to prokaryotic adaptive immunity, widely harnessed for biotechnology. Yet, their vast and uncharacterized diversity, especially non-canonical variants, impedes full exploitation. Here we present BioPrinCRISPR, a class-agnostic computational framework leveraging gene co-conservation, protein domain co-occurrence, and embedding similarity to identify and characterize CRISPR-Cas systems across prokaryotic genomes. Applying BioPrinCRISPR to over one million bacterial genomes, we uncovered extensive canonical and uncharacterized systems, revealing a rich landscape of atypical Cas proteins and novel domain architectures. Notably, we identified recurrent fusion proteins with unique enzymatic combinations, suggesting roles in regulatory control or nucleic acid remodeling. Experimental validation of two divergent Cas13an-like effectors demonstrated RNA knockdown capacity in human cells, confirming our frameworks predictive power. These findings expand the functional repertoire of CRISPR-associated proteins and highlight unexplored modes of microbial immunity. BioPrinCRISPR thus stands as a powerful tool for comprehensively mapping CRISPR-Cas diversity, offering new insights into prokaryotic defense and facilitating discovery of novel candidates for next-generation genome engineering. An accompanying interactive web platform was also developed to facilitate data exploration.

synthetic biology↗

bioRxiv2025

Outdoor Air Pollution, Perivascular Space Morphology, and Cognition in Preadolescence

BackgroundAmbient air pollution exposure is associated with structural brain differences and poorer cognition in children; however, mechanisms of toxicity remain unclear. Perivascular spaces (PVS), key for brain waste clearance, may play a role in the neurotoxicity of air pollution. This study explored associations between air pollution exposure, PVS morphology, and cognition in preadolescents. MethodsWe analyzed cross-sectional Adolescent Brain Cognitive DevelopmentSM (ABCD) Study(R) data from 6,949 9-10-year-old participants. Annual average exposures to PM2.5, O3, NO2, and 15 PM2.5 components were estimated using spatiotemporal models mapped to residential addresses. PVS count and volume were derived from T1w and T2w MRI, and cognition was estimated using NIH Toolbox scores. Linear mixed-effects models examined independent associations between air pollution, PVS, and cognition; weighted quantile sum regression assessed co-exposure effects of PM2.5 mixtures. FindingsLinear models revealed that exposures to Zn, NH4 +, and Br were positively associated with PVS count in several regions. Higher PVS count in five key regions was associated with poorer cognitive performance across several NIH Toolbox domains. Higher Ca, Zn, and NH 4 + exposures were associated with poorer cognition (PFDR < 0.01). Higher frontal lobe PVS count mediated the association between Zn exposure and poorer total cognition (P < 0.01). Co-exposure models revealed that PM2.5 mixtures were associated with higher temporal and cingulate PVS count, and poorer working memory and crystallized intelligence (P < 0.01). InterpretationOutdoor air pollution was associated with higher PVS count and reduced cognition, suggesting that brain clearance may be a novel mechanism linking pollution to neurodevelopmental harm in preadolescents. FundingThis work was supported by the National Institutes of Health (NIH) National Institute of Environmental Health Sciences (NIEHS) (Grant Nos. R01ES032295 and R01ES031074 [to MMH]; T32ES013678 [to JM]; P30ES07048 [to JM and MAR]; 3P30ES000002-55S [to MAR]), National Institute of Mental Health (NIMH) (Grant RF1MH123223 [to JC]), National Institute of Neurological Disorders and Stroke (Grant R01NS128486 [to JC]), and EPA grants (Grant Nos. 83587201 and 83544101 [to JS]).

neuroscience↗

bioRxiv2025

N-acetylcarnosine attenuates age-associated declines in multi-organ systems to improve survival

Histidine containing dipeptides (HCDs) such as N-acetylcarnosine are endogenous metabolites that are ergogenic and mitigate metabolic dysfunction. We previously demonstrated that short-term N-acetylcarnosine treatment is highly efficacious in protecting muscle atrophy induced by disuse. Here we demonstrate that a 6-months treatment of N-acetylcarnosine attenuates a broad spectrum of age-associated maladies and improved survival by [~]50% in female mice. A comprehensive survey of organ systems revealed that N-acetylcarnosine prevents decline in adiposity, diastolic function, vasodilation, muscle strength, and bone density. Together, N-acetylcarnosine substantially delays the onset of system-wide end-stage pathology to prolong lifespan. As an endogenously present metabolite, treatment with N-acetylcarnosine may be a safe and promising intervention to promote healthy aging in humans.

physiology↗

bioRxiv2025

Relaxed DNA substrate specificity of transposases involved in programmed genome rearrangement

During post-zygotic development, the ciliate Oxytricha trifallax undergoes massive programmed genome rearrangement that involves over 225,000 DNA cleavage and joining events. An Oxytricha family of Tc1/mariner transposons, known as Telomere-Bearing Elements (TBEs), encodes a transposase that has been implicated in rearrangement, but its high copy number (>34,000 paralogs) has precluded genetic strategies to investigate its DNA recognition properties directly in Oxytricha. Here, we developed a heterologous strategy to assay TBE transposase expression and activity in E. coli, revealing highly promiscuous DNA cleavage properties. Systematic ChIP-seq experiments allowed us to define the DNA binding specificities of multiple distinct transposase subfamilies, which exhibited a binding and cleavage preference for short, degenerate sequence motifs that resemble features present within the TBE transposon ends. The relaxed sequence preference is striking for autonomous transposases, which typically recognize their end sequences with strict specificity to avoid compromising host fitness. Finally, we developed a custom antibody to investigate TBE transposases in their native environment and found that they precisely localize to the developing nucleus exclusively during the rearrangement process. Collectively, this work establishes a robust heterologous workflow for the biochemical investigation of enzymes that have been repurposed for large-scale genome rearrangements.

molecular biology↗

bioRxiv2024

A Comprehensive Proteogenomic and Spatial Analysis of Innate and Acquired Resistance of Metastatic Melanoma to Immune Checkpoint Blockade Therapies

While a subset of patients with metastatic melanoma achieves durable responses to immune checkpoint blockade (ICB) therapies, the majority ultimately exhibit either innate or acquired resistance to these treatments. However, the molecular mechanisms underlying resistance to ICB therapies remain elusive and are warranted to elucidate. Here, we comprehensively investigated the tumor and tumor immune microenvironment (TIME) of paired pre- and post-treatment tumor specimens from metastatic melanoma patients who were primary or secondary resistance to anti-CTLA-4 and/or anti-PD-1/PD-L1 therapies. Differentially expressed gene (DEG) analysis and single-sample gene set enrichment analysis (ssGSEA) with transcriptomic data identified cell cycle and c-MYC signaling as pathway-based resistance signatures. And weighted gene co-expression network analysis (WGCNA) revealed the activation of a cross-resistance meta-program involving key signaling pathways related to tumor progression in ICB resistant melanoma. Moreover, spatially-resolved, image-based immune monitoring analysis by using NanoStrings digital spatial profiling (DSP) and Cyclic Immunofluorescence (CyCIF) showed infiltration of suppressive immune cells in the tumor microenvironment of melanoma with resistance to ICB therapies. Our study reveals the molecular mechanisms underlying resistance to ICB therapies in patients with metastatic melanoma by conducting such integrated analyses of multi-dimensional data, and provides rationale for salvage therapies that will potentially overcome resistance to ICB therapies. Statement of translational relevanceThis study paves the way for the creation of innovative therapeutic strategies, aimed at subverting resistance to immune checkpoint blockade (ICB) therapies in metastatic melanoma patients. By unraveling the specific molecular mechanisms underlying resistance, scientists can design effective alternative treatments that target pathways such as pathways associated with cell cycle dysregulation and c-MYC signaling. Furthermore, through the application of advanced immune monitoring techniques such as NanoString Digital Spatial Profiling (DSP) and Cyclic Immunofluorescence (CyCIF), this study has significantly enriched our understanding of the tumor microenvironment. This enhanced characterization facilitates the discovery of potential biomarkers that may forecast a patients response to ICB treatment. Ultimately, these advancements could potentially refine patient outcomes and foster the development of more personalized cancer treatments in the future.

genetics↗

bioRxiv2024

FLASH Irradiation Regulates IFN-β induction by mtDNA via Cytochrome c Leakage

Ultrahigh dose rate radiotherapy (FLASH-RT) is under intensive investigation for its biological benefits. The mechanisms underlying its ability to spare normal tissues while suppress tumor growth still remain controversial. Here we reveal that compared to the low dose rate electron irradiation (0.36 Gy/s), FLASH electron irradiation at 61 or 610 Gy/s enhances the cytochrome c leakage from mitochondria in human breast cells MCF-10A, which elicits substantial caspase activation, suppresses both the cytosolic mitochondrial DNA (mtDNA) accumulation and IFN-{beta} secretion. Besides, the deletion of mtDNA severely decreases the radiation-induced cGAS-STING activation. Conversely, the cytochrome c leakage in carcinoma cells MDA-MB-231 post electron irradiation is limited, especially for the case of FLASH irradiation, resulting in less cytosolic cytochrome c but stronger cGAS-STING activation than those in MCF-10A cells. The enhanced difference of cytochrome c leakage between cancer cells and normal cells post FLASH irradiation indicates a potential mechanism of FLASH effect by regulating the apoptotic and inflammatory pathway.

biophysics↗

bioRxiv2024

PAMPHLET: A Robust Toolkit for Precise PAM Prediction and Unveiling PAM Consistency in Highly Co-occurrence CRISPR-Cas Systems

The CRISPR-Cas technology has sparked a new technological revolution, significantly enhancing our ability to understand and engineer organisms. The nuclease that underpins this technology is evolving from the "One Cas9 for all" model to a diverse CRISPR toolbox. Identifying PAM sequences is a critical bottleneck in developing novel Cas proteins. Given the limitations of experimental methods, bioinformatics approaches are essential for predicting PAM sequences of Cas proteins in advance. To date, there are only a few PAM sequence prediction programs, and their accuracy is relatively low due to the limited number of spacers in CRISPR-Cas systems. To overcome this challenge, we have developed a pipeline named PAMPHLET, which innovatively utilizes homology searches of Cas proteins to identify additional spacers. PAMPHLET was tested on 20 CRISPR-Cas systems with known PAMs, increasing the number of spacers by up to 18-fold compared to the original datasets and successfully predicting 18 PAM sequences for protospacers. For rigorous and high-quality wet-lab validation of the predictions made by PAMPHLET, we employed the published DocMF platform. This platform leverages next-generation sequencing chips to profile protein-DNA interactions and can simultaneously screen both 5 and 3 PAMs with high throughput. The PAMPHLET predictions showed high consistency with the DocMF results for four novel Cas proteins. We expect that PAMPHLET will overcome the current limitations in PAM sequence prediction, expedite the discovery of PAM sequences, and help to shorten the development cycle for CRISPR tools. Remarkably, PAMPHLET has revealed an intriguing genomic phenomenon: the C2c9 and C2c10 systems, which lack the canonical adaptation module, possess identical PAM sequences to those found in co-occurring type I systems, suggesting potential shared spacer acquisition mechanisms. This finding highlights the complex evolutionary relationships of CRISPR-Cas systems and propels us toward a deeper understanding of their mechanistic diversity and adaptability.

bioinformatics↗

bioRxiv2023

Massively Concurrent Sub-Cellular Traction Force Videography enabled by Single-Pixel Optical Tracers (SPOTs)

We report a large field-of-view and high-speed videography platform for measuring the sub-cellular traction forces of more than 10,000 biological cells over 13mm2 at 83 frames per second. Our Single-Pixel Optical Tracers (SPOT) tool uses 2-dimensional diffraction gratings embedded into a soft substrate to convert cells mechanical traction stress into optical colors detectable by a video camera. The platform measures the sub-cellular traction forces of diverse cell types, including tightly connected tissue sheets and near isolated cells. We used this platform to explore the mechanical wave propagation in a tightly connected sheet of Neonatal Rat Ventricular Myocytes (NRVMs) and discovered that the activation time of some tissue regions are heterogeneous from the overall spiral wave behavior of the cardiac wave. One-Sentence SummaryAn optical platform for fast, concurrent measurements of cell mechanics at 83 frames per second, over a large area of 13mm2.

bioengineering↗

bioRxiv2021

SE(3)-Equivariant Energy-based Models for End-to-End Protein Folding

Accurate prediction of protein structures is critical for understanding the biological function of proteins. Nevertheless, most structure optimization methods are built upon pre-defined statistical energy functions, which may be sub-optimal in formulating the conformation space. In this paper, we propose an end-to-end approach for protein structure optimization, powered by SE(3)-equivariant energy-based models. The conformation space is characterized by a SE(3)-equivariant graph neural network, with substantial modifications to embed the protein-specific domain knowledge. Furthermore, we introduce continuously-annealed Langevin dynamics as a novel sampling algorithm, and demonstrate that such process converges to native protein structures with theoretical guarantees. Extensive experiments indicate that SE(3)-Fold achieves comparable structure optimization accuracy, compared against state-of-the-art baselines, with over 1-2 orders of magnitude speed-up.

bioinformatics↗

bioRxiv2021

T-cell Repertoire Characteristics of Asymptomatic and Re-detectable Positive COVID-19 Patients

BackgroundThe prevention of COVID-19 pandemic is highly complicated by the prevalence of asymptomatic and recurrent infection. Many previous immunological studies have focused on symptomatic and convalescent patients, while the immune responses in asymptomatic patients and re-detectable positive cases remain unclear. MethodsHere we comprehensively analyzed the peripheral T-cell receptor (TCR) repertoire of 54 COVID-19 patients in different phases, including asymptomatic, symptomatic, convalescent and re-detectable positive cases. ResultsWe found progressed immune responses from asymptomatic to symptomatic phase. Furthermore, the TCR profiles of re-detectable positive cases were highly similar to those of asymptomatic patients, which could predict the risk of recurrent infection. ConclusionTherefore, TCR repertoire surveillance has the potential to strengthen the clinical management and the immunotherapy development for COVID-19. FundingThe Science and Technology Innovation Project of Foshan Municipality (2020001000431) and the National Key Research and Development Project (2020YFA0708001).

immunology↗

bioRxiv2021

NiftyTorch: A Deep Learning framework for NeuroImaging

We present NiftyTorch a Deep Learning Framework for NeuroImaging. The motivation behind the development of such a library is that there are scant amount of centralized tool for deploying 3D deep learning for NeuroImaging. In addition, most of the existing tools require expert technical knowledge in Deep Learning or programming, creating a barrier for entry. The goal is to provide a one stop package using which the users can perform classification tasks, Segmentation tasks and Image Transformation tasks. The intended audience are the members of NeuroImaging who would like to explore deep learning but have no background in coding. In this article we explore the capabilities of the framework, the performance of the framework and the future work for the framework.

neuroscience↗

bioRxiv2021

Spatial and temporal plasticity of neoantigen-specific T-cell responses bases on characteristics associated to antigen and TCR

Neoantigens derived from somatic mutations have been demonstrated to correlate with therapeutic responses mediated by treatment with immune checkpoint inhibitors. Neoantigens are therefore highly attractive targets for the development of personalized medicine approaches although their quality and associated immune responses is not yet well understood. In a case study of metastatic malignant melanoma, we performed an in-depth characterization of neoantigens and respective T-cell responses in the context of immunotherapy with Ipilimumab. Three neoantigens identified either by immunopeptidomics or in silico prediction were investigated using binding affinity analyses and structural simulations. We isolated seven T-cell receptors (TCRs) from the patient immune repertoire recognizing these antigens. TCRs were compared in-vitro and in-vivo with multi-parametric analyses. Identified immunogenic peptides showed similar binding affinities to the human leukocyte antigen (HLA) complex and comparable differences to their wildtype counterparts in molecular dynamic simulations. Nevertheless, isolated TCRs differed substantially in functionality and frequency. In fact, TCRs with comparably lower functional avidity and higher potential for cross-reactivity provided at least equal anti-tumor immune responses in vivo. Of note, these TCRs showed a reduced activation pattern upon primary in vitro stimulation. Exploration of the TCR-{beta} repertoire in blood and in different tumor-related tissues over three years, offered insights on the high frequency and particular long-term persistence of low-avidity TCRs. These data indicate that qualitative differences of neoantigen-specific TCRs and their impact on function and longevity need to be considered for neoantigen targeting by adoptive T-cell therapy using TCR-transgenic T cells. Statement of translational relevanceImmunotherapy has demonstrated high efficacy in diverse malignancies. Neoantigens derived from mutations provide promising targets for safe and highly tumor-specific therapeutic approaches. Yet, single determinants of an effective and enduring T-cell mediated tumor rejection are still not well understood. We analyzed in detail seven neoantigen-specific T-cell receptors (TCRs) derived from a melanoma patient targeting three different altered peptide ligands identified by mass spectrometry and prediction analyses. Functional characterization of these TCRs revealed potent anti-tumor reactivity of all TCRs. Of special interest, TCRs with comparably lower affinity demonstrated effective in vivo activity as well as dominant spatial and temporal distribution in blood and tissue. Functional differences of TCR may require further T-cell and/or TCR engineering and should be considered for future clinical trial designs.

immunology↗