Biology subjects

Hu, C.

Publications and source records attributed to Hu, C..

At least 109 records · Page 6Linked to original sources

bioRxiv2021

Angiotensin converting enzyme 2 (ACE2) is expressed in murine cutaneous under single-cell transcriptome resolution

Angiotensin converting enzyme 2 (Ace2) is widely distributed in human organs, which was identified as a functional receptor for severe acute respiratory syndrome (SARS) coronavirus in human beings. It was also confirmed that SARS-CoV-2 uses the same cell entry receptor, ACE2, as SARS-CoV. However, related research still not discover the expression data associated with murine skin under single cell RNA resolution. In this study, we performed single-cell RNA sequencing (scRNA-seq) on unsorted cells from mouse dorsal skin after 7 days post-wounding. 8312 sequenced cells from four skin samples met quality control metrics and were analyzed.

genomics↗

bioRxiv2021

The Epigenetic Pacemaker is a more sensitive tool than penalized regression for identifying moderators of epigenetic aging

Epigenetic clocks, DNA methylation based chronological age prediction models, are commonly employed to study age related biology. The error between the predicted and observed age is often interpreted as a form of biological age acceleration and many studies have measured the impact of environmental and other factors on epigenetic age. Epigenetic clocks are fit using approaches that minimize the error between the predicted and observed chronological age and as a result they reduce the impact of factors that may moderate the relationship between actual and epigenetic age. Here we compare the standard methods used to construct epigenetic clocks to an evolutionary framework of epigenetic aging, the epigenetic pacemaker (EPM) that directly models DNA methylation as a function of a time dependent epigenetic state. We show that the EPM is more sensitive than epigenetic clocks for the detection of factors that moderate the relationship between actual age and epigenetic state (ie epigenetic age). Specifically, we show that the EPM is more sensitive at detecting sex and cell type effects in a large aggregate data set and in an example case study is more sensitive sensitive at detecting age related methylation changes associated with polybrominated biphenyl exposure. Thus we find that the pacemaker provides a more robust framework for the study of factors that impact epigenetic age acceleration than traditional clocks based on linear regression models.

genetics↗

bioRxiv2021

Brain networks in human conscious visual perception

Consciousness is not explained by a single mechanism, rather it involves multiple specialized neural systems overlapping in space and time. We hypothesize that synergistic, large-scale subcortical and cortical attention and signal processing networks encode conscious experiences. To identify brain activity in conscious perception without overt report, we classified visual stimuli as perceived or not using eye measurements. Report-independent event-related potentials and functional magnetic resonance imaging (fMRI) signals both occurred at early times after stimuli. Direct recordings revealed a novel thalamic awareness potential linked to conscious visual perception based on report. fMRI showed thalamic and cortical detection, arousal, attentional salience, task-positive, and default mode networks were involved independent of overt report. These findings identify a specific sequence of neural mechanisms in human conscious visual perception. One-Sentence SummaryHuman conscious visual perception engages large-scale subcortical and cortical networks even without overt report.

neuroscience↗

bioRxiv2021

Cis-regulatory changes in locomotor genes are associated with the evolution of burrowing behavior

How evolution modifies complex, innate behaviors is largely unknown. Divergence in many morphological traits has been linked, at least in part, to cis-regulatory changes in gene expression, a pattern also observed in some behaviors of recently diverged populations. Given this, we compared the gene expression in the brains of two interfertile sister species of Peromyscus mice, including allele-specific expression (ASE) of their F1 hybrids, that show large and heritable differences in burrowing behavior. Because cis-regulation may contribute to constitutive as well as activity-dependent gene expression, we also captured a molecular signature of burrowing circuit divergence by quantifying gene expression in mice shortly after burrowing. We found that several thousand genes were differentially expressed between the two sister species regardless of behavioral context, with several thousand more showing behavior-dependent differences. Allele-specific expression in F1 hybrids showed a similar pattern, suggesting that much of the differential expression is driven by cis-regulatory divergence. Genes related to locomotor coordination showed the strongest signals of lineage-specific selection on burrowing-induced cis-regulatory changes. By comparing these candidate genes to independent quantitative trait locus (QTL) mapping data, we found that the closest QTL markers to these candidate genes are associated with variation in burrow shape, demonstrating an enrichment for candidate locomotor genes near segregating causal loci. Together, our results provide insight into how cis-regulated gene expression can depend on behavioral context as well as how this dynamic regulatory divergence between species can be integrated with forward genetics to enrich our understanding of the genetic basis of behavioral evolution.

animal behavior and cognition↗

bioRxiv2021

Pancreatic Brsk2 amplifies parasympathetic signals to promote type 2 diabetes

The parasympathetic nervous system (PNS) modulates postprandial glucose metabolism via innervating pancreas; however, its significance in the pathogenesis of type 2 diabetes (T2DM) remains unclear. Here we show that brain-specific serine/threonine-protein kinase 2 (Brsk2), accumulated in obese mouse islets, responds to PNS activation and initiates pre-absorptive insulin release. In inducible mouse models, excessive Brsk2 amplifies parasympathetic signaling to {beta} cells and increases their secretion, ensuing insulin resistance and T2DM. Conversely, Brsk2 inhibition prevents and treats HFD-induced metabolic abnormities via avoiding {beta}-cell oversecretion. Mechanistically, parasympathetic acetylcholine activates cholinergic receptor M3 (Chrm3), then Chrm3 recruits and stabilizes Brsk2, which in turn phosphorylates phospholipase A2 activating protein (Plaa). A Chrm3-Brsk2-Plaa axis stimulates {beta}-cell hypersecretion during both pre-absorptive and absorptive stages in HFD-feeding mice, thus imposing insulin resistance and {beta}-cell dysfunction. Blocking parasympathetic signaling to {beta} cells by Brsk2 protein restoration, autonomic mediation drugs, or vagotomy restricted diabetes development. Moreover, three human BRSK2 variants are associated with hyperinsulinemia, insulin resistance, and T2DM in the Chinese population. These findings reveal that Brsk2 links parasympathetic nervous system to nutrition-overload induced T2DM.

pathology↗

bioRxiv2021

Robust Acquisition of High Resolution Spatial Transcriptomes from Preserved Tissues with Immunofluorescence Based Laser Capture Microdissection

The functioning of tissues is fundamentally dependent upon not only the phenotypes of the constituent cells but also their spatial organization in the tissue. However, acquisition of comprehensive transcriptomes of spatially- and phenotypically-defined cells in situ remains challenging. Here we present a general and robust method based on immunofluorescence-guided laser capture microdissection (immuno-LCM-RNAseq) to acquire finely resolved spatial transcriptomes including isoforms with as few as tens of cells from snap-frozen or RNAlater-treated clinical tissues, circumventing the problem of significant RNA degradation during this time-consuming process. The efficacy of this approach is exemplified by the characterization of differences at the transcript isoform level between the mouse small intestine lacteal cells at the tip versus the main capillary body. With the extensive repertoire of specific antibodies that are presently available, our method provides a powerful means by which spatially resolved cellular states can now be delineated in situ with preserved tissues. Moreover, such high quality spatial transcriptomes defined by immunomarkers can be used to compare with the phenotypes derived from single-cell RNAseq of dissociated cells as well as applied to bead-based spatial transcriptomic approaches that require such information a priori for cell identification.

genomics↗

bioRxiv2021

Beta human papillomavirus 8 E6 allows colocalization of non-homologous end joining and homologous recombination repair factors.

Beta human papillomavirus ({beta}-HPV) are hypothesized to make DNA damage more mutagenic and potentially more carcinogenic. Double strand breaks in DNA (DSBs) are the most deleterious DNA lesion. They are typically repaired by homologous recombination (HR) or non-homologous end joining (NHEJ). HR occurs after DNA replication while NHEJ can occur at any point in the cell cycle. They are not thought to occur in the same cell at the same time. By destabilizing p300, {beta}-HPV type 8 protein E6 ({beta}-HPV8 E6) attenuates both repair pathways. However, {beta}-HPV8 E6 delays rather than abrogates DSB repair. Thus, {beta}-HPV8 E6 may cause DSBs to be repaired through a more mutagenic process. To evaluate this, immunofluorescence microscopy was used to detect colocalization, formation, and resolution of DSB repair complexes following damage. Flow cytometry and immunofluorescence microscopy were used to determine the cell cycle distribution of repair complexes. The resulting data show that {beta}-HPV8 E6 causes HR factors (RPA70 and RAD51) to colocalize with a persistent NHEJ factor (pDNA-PKcs). RPA70 complexes gave way to RAD51 complexes as in canonical HR, but RAD51 and pDNA-PKcs colocalization did not resolve within 32 hours of damage. The persistent RAD51 foci occur in G1 phase, consistent with recruitment after NHEJ fails. Chemical inhibition of p300, p300 knockout cells, and an {beta}-HPV8 E6 mutant demonstrate that these phenotypes are the result of {beta}-HPV8 E6-meidated p300 destabilization. Mutations associated with DSB repair were identified using next generation sequencing after a CAS9-induced DSB. {beta}-HPV8 E6 increases the frequency of mutations (>15 fold) and deletions (>20 fold) associated with DSB repair. These data suggest that {beta}-HPV8 E6 causes abnormal DSB repair where both NHEJ and HR occur at the same lesion and that his leads to deletions as the single stranded DNA produced during HR is removed by NHEJ. Author SummaryOur previous work shows that a master transcription regulator, p300, is required for two major DNA double strand break (DSB) repair pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). By degrading p300, beta genus Human Papillomavirus 8 protein E6 ({beta}-HPV8 E6) hinders DNA-PKcs activity, which is a key factor of NHEJ. {beta}-HPV8 E6 also stalls HR via p300 degradation resulting in the persistence of a core factor, RAD51. NHEJ and HR are known competitive to each other and only one pathway can be initiated to repair a DSB. Particularly, NHEJ tends to be used in G1 phase and HR occurs in S/G2 phase. Here, we show that {beta}-HPV8 E6 allows NHEJ and HR to occur at the same break site. This is expected to be mutagenic because HR generates overhangs while NHEJ removes them. Further, we show that {beta}-HPV8 E6 allows HR to occur in G1, which cannot be finished due to the lack of homologous templates. Finally, our sequencing results show that {beta}-HPV8 E6 significantly increases genomic variations including deletions and insertions following CAS9 induced DSB. This study supports the hypothesis that {beta}-HPV8 infections increases genomic instability.

cancer biology↗

bioRxiv2021

Glioblastoma mutations impair ligand discrimination by EGFR

The epidermal growth factor receptor (EGFR) is frequently mutated in human cancer, and is an important therapeutic target. EGFR inhibitors have been successful in lung cancer, where the intracellular tyrosine kinase domain is mutated, but not in glioblastoma multiforme (GBM) - where mutations (or deletions) occur exclusively in the EGFR extracellular region. Wild-type EGFR is known to elicit distinct signals in response to different growth factor ligands, exhibiting biased agonism. We recently showed that individual ligands stabilize distinct receptor dimer structures, which signal with different kinetics to specify outcome. EGF induces strong symmetric dimers that signal transiently to promote proliferation. Epiregulin (EREG) induces weak asymmetric dimers that generate sustained signaling and differentiation. Intriguingly, several GBM mutation hotspots coincide with residues that define the asymmetric and symmetric dimer structures. Here, we show that common extracellular GBM mutations prevent EGFR from distinguishing between EGF and EREG based on dimer structure and stability - allowing strong dimers to form with both ligands. Crystal structures show that the R84K mutation symmetrizes EREG-driven dimers, whereas the A265V mutation remodels key dimerization sites. Our results suggest that modulating EGFRs biased agonism plays an important role in GBM, and suggest new approaches for correcting aberrant EGFR signaling in cancer.

biochemistry↗

bioRxiv2021

METTL9 regulates N1-histidine methylation of zinc transporters to promote tumor growth

Methyltransferase like 9 (Mettl9) is a member of the methyltransferase like protein family which is characterized by the presence of binding domains for S-adenosyl methionine, (SAM), a co-substrate for methylation reactions. Despite METTL9 is predicted to be a methyltransferase, its enzymatic activity, substrate specificities and biological functions are still poorly characterized. In this study, we revealed a tumor-promoting role for METTL9. We found that deletion of Mettl9 in tumor cells suppresses tumor growth and elicits potent anti-tumor immunity. Mechanistically, METTL9 is a N1-histidine methyltransferase which methylates the histidine residues of a x-His-x-His (xHxH) motif on the substrates. This motif is found extensively in zinc transporter families SLC39s and SLC30s, particularly in SLC39A7. Deletion of Mettl9 impairs cytoplasmic zinc homeostasis, resulting in an altered gene expression program with increased endoplasmic reticulum (ER) stress and reduced cell cycle. Mutation of key METTL9 catalyzed methylhistidine residues of SLC39A7 impairs cytoplasmic zinc homeostasis and affects cell growth as well. Notably, METTL9 expression is increased in some cancer types and its higher expression is associated with worse clinical outcomes, particularly in liver and pancreatic cancer. In summary, our work identified METTL9 as a potential new oncogene and its mediated methylation is of regulatory importance. Identifying selective and potent small-molecule inhibitors of METTL9 could thus represent novel therapeutic strategy for anti-proliferative cancer drugs.

cancer biology↗

bioRxiv2021

Ultrapotent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants

Accumulating mutations in the SARS-CoV-2 Spike (S) protein can increase the possibility of immune escape, challenging the present COVID-19 prophylaxis and clinical interventions. Here, 3 receptor binding domain (RBD) specific monoclonal antibodies (mAbs), 58G6, 510A5 and 13G9, with high neutralizing potency blocking authentic SARS-CoV-2 virus displayed remarkable efficacy against authentic B.1.351 virus. Each of these 3 mAbs in combination with one neutralizing Ab recognizing non-competing epitope exhibited synergistic effect against authentic SARS-CoV-2 virus. Surprisingly, structural analysis revealed that 58G6 and 13G9, encoded by the IGHV1-58 and the IGKV3-20 germline genes, both recognized the steric region S470-495 on the RBD, overlapping the E484K mutation presented in B.1.351. Also, 58G6 directly bound to another region S450-458 in the RBD. Significantly, 58G6 and 510A5 both demonstrated prophylactic efficacy against authentic SARS-CoV-2 and B.1.351 viruses in the transgenic mice expressing human ACE2 (hACE2), protecting weight loss and reducing virus loads. These 2 ultrapotent neutralizing Abs can be promising candidates to fulfill the urgent needs for the prolonged COVID-19 pandemic.

immunology↗

bioRxiv2021

Reduced graphene oxide membrane as supporting film for high-resolution cryo-EM

Although single-particle cryogenic electron microscopy (cryo-EM) has been applied extensively for elucidating many crucial biological mechanisms at the molecular level, this technique still faces critical challenges, the major one of which is to prepare the high-quality cryo-EM specimen. Aiming to achieve a more reproducible and efficient cryo-EM specimen preparation, novel supporting films including graphene-based two-dimensional materials have been explored in recent years. Here we report a robust and simple method to fabricate EM grids coated with single- or few-layer reduced graphene oxide (RGO) membrane in large batch for high-resolution cryo-EM structural determination. The RGO membrane has decreased interlayer space and enhanced electrical conductivity in comparison to regular graphene oxide (GO) membrane. Moreover, we found that the RGO supporting film exhibited nice particle-absorption ability, thus avoiding the air-water interface problem. More importantly, we found that the RGO supporting film is particularly useful in cryo-EM reconstruction of sub-100 kDa biomolecules at near-atomic resolution, as exemplified by the study of RBD-ACE2 complex and other small protein molecules. We envision that the RGO membranes can be used as a robust graphene-based supporting film in cryo-EM specimen preparation.

biophysics↗

bioRxiv2021

The rise and fall of the photoinhibition-related energy dissipation qI

Photosynthesis converts sunlight into chemical energy, sustaining the vast majority of the biosphere. Photosystem II (PSII), the oxygen-forming enzyme that initiates photosynthesis, is however particularly prone to light-induced damage in a process known as photoinhibition, which limits the productivity of both aquatic and land photosynthesis. Photoinhibition is associated with an energy dissipation process of unknown origin, termed qI. Here, we present a detailed biophysical and biochemical in vivo study of qI in model green alga Chlamydomonas reinhardtii. Time-resolved fluorescence measurements demonstrate the origin of qI, and indicate the PSII reaction centre as the site of the quencher. Oxygen-dependence of quenching site formation, but not photoinhibition itself, is shown, suggesting that two types of PSII damage - donor and acceptor-side impairment - can be separated. We then demonstrate that the quenching loss takes place in the absence of PSII repair, and is mediated by the degradation of photoinhibited PSII cores by the FtsH protease. Finally, we integrate data ranging from picoseconds to hours in the context of structure-function excitation energy-transferring membrane patches, revealing the extent of PSII heterogeneity from the onset of photoinhibition until the breakdown of damaged PSII. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/434601v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@d7c64dorg.highwire.dtl.DTLVardef@1c2943org.highwire.dtl.DTLVardef@d90b83org.highwire.dtl.DTLVardef@182cd12_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIUpon photoinhibition, oxygen sensitization results in an irreversible formation of quenching (qI) and inactivation of Photosystem II C_LIO_LIqI takes place in the PSII reaction centre C_LIO_LIPhotoinhibition-induced D1 cleavage is much slower than qI formation C_LIO_LIFtsH metalloprotease is required to degrade quenching PSII reaction centres C_LIO_LIA multiscale energy transfer model describes heterogeneity of PSII during photoinhibition C_LI

plant biology↗

bioRxiv2021

Hyperspectral sensing of photosynthesis, stomatal conductance, and transpiration for citrus tree under drought condition

Obtaining variation in water use and photosynthetic capacity is a promising route toward yield increases, but it is still too laborious for large-scale rapid monitoring and prediction. We tested the application of hyperspectral reflectance as a high-throughput phenotyping approach for early identification of water stress and rapid assessment of leaf photosynthetic traits in citrus trees. To this end, photosynthetic CO2 assimilation rate (Pn), stomatal conductance (Cond) and transpiration rate (Trmmol) were measured with gas-exchange approaches alongside measurements of leaf hyperspectral reflectance from citrus grown across a gradient of soil drought levels. Water stress caused Pn, Cond and Trmmol rapid and continuous decreases in whole drought period. Upper layer was more sensitive to drought than middle and lower layers. Original reflectance spectra of three drought treatments were surprisingly of low diversity and could not track drought responses, whereas specific hyperspectral spectral vegetation indices (SVIs) and absorption features or wavelength position variables presented great potential. Performance of four machine learning algorithms were assessed and random forest (RF) algorithm yielded the highest predictive power for predicting photosynthetic parameters. Our results indicated that leaf hyperspectral reflectance was a reliable and stable method for monitoring water stress and yield increasing in large-scale orchards. HighlightAn efficient and stable methods using hyperspectral features for early and pre-visual identification of drought and machine learning techniques for predicting photosynthetic capacity.

physiology↗

bioRxiv2021

The Diameter Factor of Aligned Electrospinning Membranes Facilitates Cutaneous Wound Healing by Promoting Epithelialization

Topographical properties (such as pattern and diameter) of biomaterials play important roles in influencing cell activities and manipulating the related immune response during the skin wound healing. We prepared aligned electrospinning membranes with different fiber diameters including 319{+/-}100 nm (A300), 588{+/-}132 nm (A600) and 1048{+/-}130 nm (A1000). The A300 membranes significantly improved cell proliferation and spreading, and facilitated skin wound healing (epithelization and vascularization) with the regeneration of hair follicles. The transcriptome revealed the underlying molecular mechanism that A300 could promote macrophages transformation to reparative phenotypes with highly expressed IL10 and TGF{beta}, subsequently promoting epidermal cell migration via secreting matrix metalloproteinases 12 (MMP12). All the results indicate the A300 to be a potential candidate for guided skin regeneration applications. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/432929v3_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@17d754borg.highwire.dtl.DTLVardef@19fcb2forg.highwire.dtl.DTLVardef@1d4bc1eorg.highwire.dtl.DTLVardef@18a8091_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2021

A D-2-hydroxyglutarate biosensor based on specific transcriptional regulator DhdR

D-2-Hydroxyglutarate (D-2-HG) is a metabolite in many physiological metabolic processes. When D-2-HG is aberrantly accumulated due to mutations in isocitrate dehydrogenases or D-2-HG dehydrogenase, it functions in a pro-oncogenic manner and is thus considered a therapeutic target and biomarker in many cancers. In this study, DhdR from Achromobacter denitrificans NBRC 15125 was identified as an allosteric transcription factor that negatively regulates D-2-HG dehydrogenase expression and responds to presence of D-2-HG. It is the first known transcription regulator specifically responding to D-2-HG across all domains of life. Based on the allosteric effect of DhdR, a D-2-HG biosensor was developed by combining DhdR with amplified luminescent proximity homogeneous assay technology. The biosensor was able to detect D-2-HG in serum, urine, and cell culture with high specificity and sensitivity. Additionally, this biosensor was also successfully used to identify the role of D-2-HG metabolism in lipopolysaccharide biosynthesis of Pseudomonas aeruginosa, demonstrating its broad usages.

microbiology↗

bioRxiv2021

Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis

Dosage compensation (DC) is a mechanism by which X chromosome transcription is equalized in the somatic cells of both males and females. In male fruit flies, expression levels of the X-chromosome are increased two-fold to compensate for their single X chromosome. In testis, dosage compensation is thought to cease during meiosis, however, the timing and degree of the resulting transcriptional suppression is difficult to separate from global meiotic downregulation of each chromosome. To address this, we analyzed testis single-cell RNA-sequencing (scRNA-seq) data from two Drosophila melanogaster strains. We found evidence that the X chromosome is equally transcriptionally active as autosomes in somatic and pre-meiotic cells, and less transcriptionally active than autosomes in meiotic and post-meiotic cells. In cells experiencing dosage compensation, close proximity to MSL (male-specific lethal) chromatin entry sites (CES) correlates with increased X chromosome transcription. We found low or undetectable level of germline expression of most msl genes, mle, roX1 and roX2 via sequencing or RNA-FISH, and no evidence of germline nuclear roX1/2 localization. Our results suggest that, although DC occurs in somatic and premeiotic germ cells in Drosophila testis, there might be non-canonical factors involved in the dosage compensation. The single-cell expression patterns and enrichment statistics of detected genes can be explored interactively in our database: https://zhao.labapps.rockefeller.edu/gene-expr/.

genetics↗

bioRxiv2021

DsbA-L protects against diabetic renal injury through the adipo-renal axis

Disulfide-bond A oxidoreductase-like protein (DsbA-L) is an adiponectin-interacting protein that is highly expressed in adipose tissue. The adipo-renal axis involves adipocyte release of signaling molecules that are recruited to kidney and regulate kidney function. We have found that the DsbA-L modulated the progression of diabetic nephropathy, but the precise mechanism of this modulation is unknown. Here, the transgenic mice overexpressing DsbA-L protein in fat (fDsbA-L) were used to verify that the renoprotective role of DsbA-L whether by adipo-renal axis. Mice were divided into four groups: a normal (Control) group, STZ induced diabetic mice, fDsbA-L mice and diabetic fDsbA-L mice (n=6). Diabetes was induced in mice by STZ 100mg/kg and continued HFD feeding for 12 weeks. Compared with the control group, the weight, blood glucose,and urine protein levels and the pathological changes in the kidney tissue of diabetic mice were increased significantly, accompanied by increased NLRP3,caspase-1, IL-1{beta}, IL-18, FN, and Collagen1 mRNA and protein expression, which were reduced in diabetic fDsbA-L mice. Interestingly, the level of adiponectin in serum and kidney expression in diabetic mice was reduced significantly compared to that in the control group. However this change was reversed in diabetic fDsbA-L mice. These data suggest that the overexpression of DsbA-L in the adipocytes of mice can protect against diabetic renal injury through anti-inflammatory mediators,and may be mediated by the adipo-renal axis.

genetics↗

bioRxiv2020

Identification of Cross-Reactive CD8+ T Cell Receptors with High Functional Avidity to a SARS-CoV-2 Immunodominant Epitope and Its Natural Mutant Variants

Despite the growing knowledge of T cell responses and their epitopes in COVID-19 patients, there is a lack of detailed characterizations for T cell-antigen interactions and T cell functions. Using a peptide library predicted with HLA class I-restriction, specific CD8+ T cell responses were identified in over 75% of COVID-19 convalescent patients. Among the 15 SARS-CoV-2 epitopes identified from the S and N proteins, N361-369 (KTFPPTEPK) was the most dominant epitope. Importantly, we discovered 2 N361-369-specific T cell receptors (TCRs) with high functional avidity, and they exhibited complementary cross-reactivity to reported N361-369 mutant variants. In dendritic cells (DCs) and the lung organoid model, we found that the N361-369 epitope could be processed and endogenously presented to elicit the activation and cytotoxicity of CD8+ T cells ex vivo. Our study evidenced potential mechanisms of cellular immunity to SARS-CoV-2, illuminating natural ways of viral clearance with high relevancy in the vaccine development.

immunology↗