Biology subjects

Xie, B.

Publications and source records attributed to Xie, B..

At least 19 recordsLinked to original sources

bioRxiv2026

A Multi-Omics Study of Cognitive Resilience to Alzheimer's Disease

Alzheimers disease (AD) is the most severe form of dementia. While significant efforts have been made to identify AD risk factors and develop therapeutics, much less attention has been given to neurobiological factors and molecular signatures associated with cognitive resilience. Substantial evidence suggests that modifiable factors, such as physical and mental activity, may contribute to cognitive reserve and resilience. To this end, we developed a resilient cohort of paired genetics, transcriptomics and proteomics data from the prefrontal cortex of 282 cognitively normal older adults. We conducted extensive preprocessing and rigorous quality control (QC), including QC on sequence metrics and sample matching across multiomics. This cohort can be leveraged for identification of molecular signatures of cognitive resilience to AD and is freely shared with the research community.

genomics↗

bioRxiv2026

Half-match recombination drives bridge RNA-guided excision and off-target insertion

IS110-family bridge recombinases are a recently identified class of compact, RNA-guided editors in which a bridge RNA (bRNA) directs the recombination of a donor DNA into a target site. In the current model, the bRNA engages fully complementary donor and target sequences within a single synaptic complex to drive double-stranded recombination, implying that the transposon is cut from its donor site rather than copied, yet neither the strandedness of the excised intermediate nor the requirement for full complementarity has been tested directly. Here we reconstituted IS621 recombination in a cell-free transcription-translation system, building representative arrangements of the excision and insertion reactions and characterizing the outcomes. We find that IS621 predominantly excises a single strand, releasing a single-stranded circle and leaving the donor site intact, consistent with copy-and-paste transposition. By introducing mismatches into the bRNA target sequences, we further find that excision proceeds independently of target-site complementarity, relying strictly on donor-arm recognition; we term this "half-match" recombination, because a substrate matching only half of the bRNA is sufficient. We also find half-match activity during insertion, both in vitro and in a published genome-editing experiment, where it accounts for approximately half of non-target insertion reads. Half-match recombination provides both a mechanistic explanation for off-target insertion and a framework for the rational design of high-fidelity bridge recombinases.

molecular biology↗

bioRxiv2026

Canonically minimal RNA-guided insertion sequences expand into large elements that disseminate antimicrobial resistance

IS110 has emerged as a powerful genome-editing tool because it is the smallest RNA-guided system capable of diverse programmable insertions. Naturally existing elements are conventionally modeled as compact[~] 1.5-kb systems comprising a single transposase and a bridge RNA (bRNA). Using high-throughput junction mapping together with large-scale comparative genomics, we redefined the in vivo structural boundaries, growth, and mobilization of IS110 elements. We uncovered a previously unrecognized size continuum extending to[~] 100 kb, driven by progressive local expansion, with expanded loci being widespread across bacterial genomes. Experiments confirmed the activity of natural IS110s both well below and above the size range of previously characterized elements. These large systems preferentially accumulate adaptive cargo, including antimicrobial resistance determinants and heavy-metal detoxification systems, and are strongly enriched for plasmid-derived DNA. Boundary configurations at expanded loci and the range of partial excision intermediates they produce both indicate flexible sequence recognition by IS110, most commonly through half-matches between the bRNA and complementary DNA sequence. This sequence tolerance allows loci to expand with diverse cargo. Together, these findings redefine IS110 from a compact insertion sequence into a dynamic platform that disseminates adaptive cargo.

microbiology↗

bioRxiv2026

Remodeled cephalic arch geometry promotes disturbed flow at pre-maturation flow rates in hemodialysis patients

In the United States, roughly 550,000 people receive routine hemodialysis for end-stage renal disease. This treatment requires an arteriovenous access, most commonly a brachiocephalic fistula. However, these accesses often fail due to stenosis in the cephalic arch (CA), a common complication whose underlying causes remain unclear (Bennet et al., 2015). To characterize the hemodynamic environment in the CA, we employed patient-specific millifluidic models that were perfused with blood-mimicking fluid containing fluorescently labelled beads to visualize flow behaviors. We perfused our models across physiologic (28-45 mL/min) and elevated (60-423 mL/min) flow rates and quantified wall shear stress (WSS) and streamline angle as a measure of flow disturbance. Our findings show that the bulk curvature and remodeled wall topography each create regions of persistently low WSS, consistent with prior clinical observations (Hammes et al., 2016). Moreover, remodeled wall topography promotes disturbed flow at elevated flow rates, a hemodynamic profile associated with various vascular pathologies (Chiu & Chien, 2011). Independently performed computational fluid dynamics (CFD) modeling complements these results, showing that remodeled wall topography promotes vortex formation at elevated flow rates, as assessed by Q-criterion. Collectively, our experimental and computational results provide strong evidence for geometry-driven disturbed flow in the CA at elevated flow rates. Notably, we observed disturbed flow at flow rates as low as 81 mL/min, far below the 600 mL/min required for hemodialysis. Disturbed flow thus offers a plausible mechanism that relates access flow rates to the vascular pathologies that precede access failure. Significance StatementHemodialysis requires an arteriovenous fistula (AVF) that must remodel and mature to withstand chronically elevated blood flow rates. However, how remodeled vessel geometry interplays with elevated flow to shape local hemodynamics remains poorly understood. Here, we used millifluidic models of the cephalic arch (CA) to show that vessel geometry and elevated flow rates promote regions of low wall shear stress and disturbed flow. Notably, geometry-driven disturbed flow is observed at flow rates above physiologic levels but well below 600 mL/min, the flow rate necessary for adequate dialysis. Because disturbed flow is injurious to the endothelium, our findings are the first to show that vascular damage begins before fistula maturation.

biophysics↗

bioRxiv2026

Clear cell renal cell carcinoma consensus transcriptomic programs reveal converging trajectories towards aggressive disease

Clear cell renal cell carcinoma (ccRCC) is characterized by a branching genomic trajectory in which early biallelic VHL inactivation splits into PBRM1- and BAP1-mutant lineages. However, driver mutations alone do not account for the molecular and phenotypic heterogeneity. To dissect this heterogeneity, we developed a non-negative matrix factorization (NMF)-based gene expression analytical framework for identifying recurrent transcriptional programs across factorization dimensionalities and across datasets. We applied it to three curated datasets (IMmotion151, n = 823; JAVELIN Renal 101, n = 726; TCGA, n = 614) to define 17 consensus transcriptomic programs (CTPs). Mapping CTPs onto single-cell RNAseq (scRNAseq) of human ccRCC tumors and patient-derived tumorgraft models linked these programs to their cellular sources, distinguishing RCC-intrinsic, tumor-cell-extrinsic, and mixed programs. RCC-intrinsic CTPs associated with canonical drivers, including VHL (R1), PBRM1 (R2), BAP1 (R4), PTEN/TSC1 (R3), TFE3/TFEB fusions (R5), NF2 (R6), and CDKN2A/TP53 (MP-Prolif). Additional CTPs captured tumor microenvironment (TME) composition (TME-Tcell, TME-Myelo, TME-Endo, TME-Stroma) and biological processes active across multiple cellular compartments, including proliferation, Y-chromosome-linked expression in male tumors, ciliary biology, and translation. Trajectory inference methods revealed PBRM1-like and BAP1-like branches that converged on a shared aggressive late transcriptomic stage (TS) associated with higher nuclear grade, additional driver alterations, myeloid/stromal infiltration, and poor clinical outcomes. Spatial transcriptomics (and multiregional sequencing) of paired conventional ccRCC and sarcomatoid regions linked TS advancement with morphological progression and clonal evolution. After adjusting for stage, grade, and BAP1/PBRM1 status, TS remained independently prognostic. Furthermore, our data suggest that immune checkpoint inhibitor combinations are particularly beneficial for MP-Prolif and not R1 utilizing specimens. In summary, we present an atlas of recurring transcriptomic programs in RCC and an ontological framework bridging genotype, tumor-cell-intrinsic gene expression, and microenvironment remodeling, with implications for risk stratification and treatment selection in ccRCC.

Cancer Biology↗

bioRxiv2026

A correlational study of ABCA3 and SCN4B as exercise-related biomarkers of patients with Stanford type A aortic dissection

BackgroundAccumulating evidence indicates that moderate exercise may reduce the incidence of Stanford type A aortic dissection (TAAD), but the specific mechanisms remain unclear. This study aims to identify exercise-related biomarkers in TAAD patients and to investigate their underlying mechanisms. MethodsTranscriptome data related to TAAD and exercise-related genes were obtained from publicly available databases. Candidate biomarkers for TAAD were identified through an integrative approach incorporating differential expression analysis, machine learning, and expression level assessment, leading to the construction of a diagnostic model. Subsequently, functional enrichment, immune infiltration, regulatory network analysis, and computational drug prediction were conducted to systematically investigate the pathological mechanisms and translational potential of the indentified biomarkers. ResultsABCA3 and SCN4B were identified as exercise-related biomarkers in TAAD progression. A nomogram incorporating these two biomarkers exhibited strong diagnostic performance for identifying the disease. Functional enrichment analysis revealed potential involvement of these biomarkers in disease progression through pathways including circadian rhythm regulation and ribosome biosynthesis. Additionally, immune cells like M1 macrophages and naive B cells, as well as regulatory factors including hsa-miR-1343-3p and XIST, were found to be involved in this process. Finally, zonisamide and MRS1097 were identified through computation prediction as potential therapeutic drugs. ConclusionABCA3 and SCN4B were identified as exercise-related biomarkers associatied with TAAD and represent potential valuable targets for both diagnosis and treatment strategies.

bioinformatics↗

bioRxiv2025

Decoding the interactome for Cyclic-di-AMP-producing enzyme diadenylate cyclase (DacA)

Diadenylate cyclase (DacA) synthesizes the second messenger cyclic di-AMP (c-di-AMP), which regulates essential cellular processes across many Gram-positive and select Gram-negative bacteria/archaeal lineages. Although DacA is known to interact with regulators such as GlmM and CdaR, the breadth and functional relevance of its interactome remains poorly defined. Our study seeks to identify novel protein-protein interactions to further elucidate their unknown regulatory mechanisms and cellular roles. Using Streptococcus mutans as a model, we engineered a Flag-tagged strain (DacA-FLAG) and then performed co-immunoprecipitation under non-crosslinked and crosslinked conditions followed by mass spectrometry. We identified 22 candidates interacting proteins in non-crosslinked samples, 18 in crosslinked samples, and 6 shared between conditions. Selected partners were validated in vivo using split luciferase complementation. Notably, SMU_723 emerged as a key binding partner. AlphaFold-guided modeling predicated a direct DacA and SMU_723 interaction interface involving threonine 147, glutamine 148, and threonine 149 in DacA . Site-directed mutagenesis of these residues impaired binding, confirming their critical role. An SMU_723 deletion phenocopied a dacA deletion strain, sharing prolonged lag phase, aberrant cell morphology, reduced acid production and acid tolerance, impaired sorbitol metabolism, decreased colonization in a Drosophila model, and delayed growth upon calcium stimulation. These shared phenotypes suggest a functional and possibly regulatory link between DacA and SMU_723. Given SMU_723 sequence homology consistent with a calcium transporter, these data suggest that the DacA-723 interaction contributes to calcium homeostasis and/or calcium-responsive signaling. Collectively, our findings expand the DacA interaction network and implicate calcium transport in c-di-AMP-mediated regulation in S. mutans. ImportanceMapping the DacA interactome reveals how environmental and intracellular cues tune c-di-AMP signaling to control stress adaptation, ion balance, and virulence traits in S. mutans. By identifying new DacA-associated proteins and validating SMU_723 as a previously unrecognized interactor with genetic and phenotypic linkage to DacA, this study provides new insights into the mechanistic framework for c-di-AMP regulation in S. mutans. The connection between DacA and a putative calcium transporter highlights a plausible axis that couples second-messenger signaling to calcium homeostasis, with implications for biofilm physiology and pathogenesis. These insights open new avenues to therapeutically modulate c-di-AMP pathways.

microbiology↗

bioRxiv2025

Multiple Allosteric Sites Allow for Synergistic Enhancement of GPCR Signaling

Allosteric modulation of G protein-coupled receptors (GPCRs) is an emerging therapeutic paradigm that has proven effective, yet the cooperative action of multiple modulators remains unexplored. Here, we reveal how positive allosteric modulators (PAMs) synergistically enable extraordinary signal amplification through the D1 dopamine receptor (D1R). We developed UNC9815 and UNC10062 as enhanced D1R PAMs from the parent compound MLS6585, and then employed cryo-electron microscopy to reveal concurrent occupancy of three distinct allosteric sites by PAMs of different scaffolds, including LY3154207, BMS-A1, and our UNC compounds. Remarkably, we discovered two adjacent allosteric pockets at the transmembrane helix (TM) 1-7 interface: BMS-A1 occupies an intracellular site promoting activation through TM7 conformational shifts, while the UNC compounds complementarily stabilize the extracellular side of the interface. When combined with LY3154207, this cooperative architecture enhances dopamine potency by more than 1,000-fold. These findings elucidate the first structural blueprint for multi-site GPCR cooperativity, unlocking transformative therapeutic strategies inaccessible to orthosteric and single- site allosteric drugs.

molecular biology↗

bioRxiv2025

Protein Folding accompanied by disulfide bond formation drives glutenin polymerization into multidimensional gluten networks

Wheat flour dough, which is routinely used to make bread, pasta and noodles, can be stretched several thousand-fold without rupture. The molecular basis of this extraordinary property arises due to the ability to crosslink glutenin subunits, the major constituent of dough, into linear and branched elastic networks. The mechanism by which the glutenin subunits self-assemble and polymerize is unknown. Here, we show, using mass spectrometry, confocal imaging and molecular dynamics simulations that structuring of two hydrophobic residues, phenylalanine and tyrosine, in the core region of the monomeric glutenin 1Dx5 N-terminal domain (1Dx5-NTD) initiates inter molecular interactions and network formation. Upon folding of monomeric 1Dx5-NTD, two cysteine residues (Cys10 and Cys40) form an intramolecular disulfide bond and poises the third cysteine (Cys25) to engage in inter molecular crosslink with other glutenin subunits. Propagation of such a disulfide linkage pattern results in the formation of a cohesive linear gluten network. In alternate pathways, crosslinking of Cys10 with Cys25 with a third glutenin subunit results in the creation of a junction, which drives the formation of a three-dimensional network. The disulfide patterns in the networks accord well with the measured chemical reactivity of each cysteine residue and the solvent accessibility of the associated side chains during 1Dx5-NTD interactions. Our study shows that the diversity in the folding of a single glutenin subunit that exposes the third cysteine to the solvent is the key event that initiates polymerization and directs the formation of networks with differing architecture. Significance statementGlutenin proteins polymerize to form intricate molecular networks that support the expansion of dough by several thousand-fold. Although network formation occurs spontaneously, the polymerization mechanism is unknown. There are multiple cysteine residues in glutenin that can form intra and intermolecular disulfide bonds. Multiple experimental techniques and molecular dynamics simulations are used to show that folding of glutenin, initiated by two hydrophobic residues, exposes cysteines that are poised to form intermolecular disulfide bonds. The disulfide crosslinking pattern, determined by the initial folding process, dictates the creation of a linear or branched network. The study demonstrates that the propensity to form linear or branched networks is encoded by the diversity of the disulfide patterns created at the level of monomeric folding.

biophysics↗

bioRxiv2025

Glucosylation of Endogenous Haustorium-inducing factors Underpins Kin Avoidance in Parasitic Plants

Parasitic plants rarely attack themselves, suggesting the activity of a kin-avoidance mechanism. In the root parasitic plant Phtheirospermum japonicum, prehaustorium formation is triggered by host-secreted haustorium-inducing factors (HIFs), but it is unresponsive to its own root exudates. Here we report the identification of the spontaneous prehaustorium 1 (spoh1) mutant, which forms prehaustoria without external HIFs. spoh1 harbors a point mutation in the gene encoding UDP-glycosyltransferase GT72B1, an enzyme that glucosylates and thereby inactivates phenolic HIFs. Notably, PjGT72B1 possesses a different substrate specificity from its ortholog of the host Arabidopsis. Introduction of PjGT72B1 in Arabidopsis reduced HIF activity, indicating that HIF glucosylation regulates haustorium induction by hosts. Our findings suggest that parasitic plants have evolved kin-avoidance mechanisms through the glucosylation of endogenous HIFs.

plant biology↗

bioRxiv2025

Epithelia mediate inflammation with myeloid cells in Crohn's disease patients under treatment

Many Crohn's disease patients fail to respond to biologic therapies targeting canonical immune pathways, and the mechanisms underlying treatment non-response remain poorly understood. Integrating single-cell and spatial transcriptomics, we generated a comprehensive mucosal atlas of 380,000 cells spanning the terminal ileum and ascending colon of healthy donors and Crohn's disease patients receiving biologics. We revealed site-specific programs centered on TNF-expressing macrophages embedded within epithelial-stromal networks: follicle-associated enterocytes dictated immune activation in the ileum, while FAP-expressing stromal cells served this role in the colon. Co-expression network analysis further identified lineage-specific programs associating non-response, including a novel epithelial marker BPIFB1 independent of known genetic risk loci. Co-expression marker Z-scores significantly differed between responders and non-responders in published datasets. Together, these findings define a non-responder-specific epithelial-stromal-immune ecosystem that sustains chronic inflammation, providing a framework for stratifying treatment resistance and informing therapeutic strategies in Crohn's disease and other barrier organ disorders.

immunology↗

bioRxiv2025

In vivo validation of the palmitoylation cycle as a therapeutic target in NRAS-mutant cancer

Ras proteins are functionally dependent on one or more lipid modifications.1,2 The dynamic palmitoylation of N-Ras by DHHC palmitoyl acyltransferases and depalmitoylation by ABHD17 serine hydrolases is essential for the growth of NRAS-mutant acute myeloid leukemia (AML) cells.3-6 Here we show that ABD778, an in vivo-active ABHD17 inhibitor, selectively reduces the growth of NRAS-mutant AML and melanoma cell lines and is synergistic with the MEK inhibitor PD0325901 (PD901; mirdametinib). Mechanistically, ABD778 and PD901 induce deep and durable suppression of mitogen activated protein kinase (MAPK) pathway activation. Co-treatment extended the survival of mice transplanted with NrasG12D AMLs, which acquired by-pass mutations at relapse that conferred drug resistance and restored MAPK activation. ABD778 augmented the anti-leukemia activity of PI3 kinase, pan-Ras tri-complex, and FLT3 inhibitors, and restored gilteritinib sensitivity in a patient-derived xenograft model of FLT3 inhibitor resistance. These studies validate the palmitoylation cycle as a therapeutic target in NRAS-mutant cancers.

cancer biology↗

bioRxiv2025

Longitudinal analysis of retinal cell state transitions in RB1-deficient retinal organoids reveals the nascent cone precursors are the earliest cell-origin of human retinoblastoma

All cancers develop from malignant transformation of normal cells, while it is challenging to identify these "cells-of-origin" since it is impossible to witness the dynamic changes in human cancers. Retinoblastoma (Rb), an intraocular malignant cancer, is a typical model for study the molecular and cellular mechanisms of cancers. Although the maturing cone precursors (CPs) are proposed as the cellular origin of human Rb, it is unknow whether other retinal cells are also sensitive to RB1 inactivation. Here we developed RB1-deficient human retinal organoids (ROs) models from RB1-/- or RB1+/- human induced pluripotent stem cells (hiPSCs). RB1-/- hiPSCs developed into Rb tumors which recapitulated the features of human native Rb and had the ability to form consecutive orthotopic xenografts in mice. Importantly, RB1 loss induced the overproliferation of ATOH7+ neurogenic retinal progenitor cells (nRPCs), which disrupted the retinal development by generating proliferative, nascent retinal cells including retinal ganglion cells and CPs. scRNA-seq analysis verified the ATOH7+/RXR{gamma}+ nascent CPs survived and finally drove Rb development. In contrast, monoallelic RB1 inactivation with low pRB expression did not induce nascent CPs proliferation, but only induced nRPCs overproliferation which caused retinocytoma-like phenotype. Finally, a potential therapeutic agent for Rb was identified from multi-omics data. Our findings firstly indicate that nRPCs are the most sensitive cells to RB1 loss inducing nascent retinal cells abnormal proliferation, and ATOH7+ nascent CPs are the earliest cellular origin of human Rb, facilitating drug development for Rb.

cell biology↗

bioRxiv2025

KYLO-0603, a novel liver-targeting, thyroid hormone recep-tor-β agonist for the treatment of MASH

Metabolic dysfunction-associated steatohepatitis (MASH) is a progressive liver disease associated with liver-related complications and death. Kylo-0603 is a novel agonist for the thyroid hormone receptor {beta} (THR-{beta}) that has been developed by merging the structures of three acetylgalactosamine (GalNAc)-modified ASPGR ligands with a triiodothyronine (T3) analog. This unique design allows for both THR-{beta} activation and targeted delivery to hepatocytes, significantly reducing the risk of adversed effects related to increased systemic thyroid hormone-like effects. Additionally, it effectively lowers serum cholesterol by as much as 69.2% and low-density lipoprotein cholesterol (LDL-C) levels by up to 88.2% in the MASH mouse model. Meanwhile, Kylo-0603 was shown to reduce steatosis by up to 1.3 points (P < 0.001), inflammation by 1.8 points (P < 0.0001), and ballooning by 0.8 points (P < 0.01). The non-alcoholic steatohepatitis (NASH) activity score (NAS) decreased by up to 3.7 points (P < 0.0001), and the fibrosis score dropped by 0.6 points (P < 0.05). These findings suggest that Kylo-0603 is effective in enhancing liver tissue NASH status and inhibiting fibrosis progression. In summary, Kylo-0603, as a highly both tissue and target selective and low-toxicity THR-{beta} agonist, shows significant promise for treating MASH and is likely to emerge as a new therapeutic option for patients with this condition.

biochemistry↗

bioRxiv2024

Spatiotemporal Regulatory Logics of Mouse Gastrulation

Spatiotemporal coordination of cellular and molecular events is crucial for cell fate commitment during mouse gastrulation. However, the high-precision mechanisms governing the timing and spatial dynamics remain poorly understood. Here, we present a time-series single-cell multi-omic dataset from the mouse gastrulating embryos and construct a hierarchical gene regulatory landscape. Integrating this with real three-dimensional transcriptomic coordinate, we created ST-MAGIC and ST-MAGIC (+) atlas, dissecting the spatiotemporal logics of regulatory networks and signaling responsiveness underpinning the lineage commitment at gastrulation. Specifically, we delineated the multi-omic basis for left-right symmetry breaking events in the gastrula and also revealed the spatiotemporal molecular relay for axial mesendoderm lineage, where early and intermediate transcription factors first open the chromatin regions and setup the responsiveness to signaling, followed by terminal factors to consolidate the transcriptomic architecture. In summary, our study presents a spatiotemporal regulatory logic framework of mouse gastrulation, that advances our understanding of mammalian embryogenesis.

developmental biology↗

bioRxiv2024

Desmoplakin is a desmosomal mechanosensor

Desmosomes are essential cell-cell adhesion organelles that enable tension-prone tissue, like the skin and heart, to withstand mechanical stress. Desmosomal anomalies are associated with numerous epidermal disorders and cardiomyopathies. Despite their critical role in maintaining tissue resilience, an understanding of how desmosomes sense and respond to mechanical stimuli is lacking. Here, we use a combination of super-resolution imaging, FRET-based tension sensors, atomistic computer simulations, and biochemical assays to demonstrate that actomyosin forces induce a conformational change in desmoplakin, a critical cytoplasmic desmosomal protein. We show that in human breast cancer MCF7 cells, actomyosin contractility reorients keratin intermediate filaments and directs force to desmoplakin along the keratin filament backbone. These forces induce a conformational change in the N-terminal plakin domain of desmoplakin, converting this domain from a folded (closed) to an extended (open) conformation. Our findings establish that desmoplakin is mechanosensitive and responds to changes in cellular load by undergoing a force-induced conformational change.

cell biology↗

bioRxiv2024

Human-mouse proteomics reveals the shared pathways in Alzheimer's disease and delayed protein turnover in the amyloidome

Murine models of Alzheimers disease (AD) are crucial for elucidating disease mechanisms but have limitations in fully representing AD molecular complexities. We comprehensively profiled age-dependent brain proteome and phosphoproteome (n > 10,000 for both) across multiple mouse models of amyloidosis. We identified shared pathways by integrating with human metadata, and prioritized novel components by multi-omics analysis. Collectively, two commonly used models (5xFAD and APP-KI) replicate 30% of the human protein alterations; additional genetic incorporation of tau and splicing pathologies increases this similarity to 42%. We dissected the proteome-transcriptome inconsistency in AD and 5xFAD mouse brains, revealing that inconsistent proteins are enriched within amyloid plaque microenvironment (amyloidome). Determining the 5xFAD proteome turnover demonstrates that amyloid formation delays the degradation of amyloidome components, including A{beta}-binding proteins and autophagy/lysosomal proteins. Our proteomic strategy defines shared AD pathways, identify potential new targets, and underscores that protein turnover contributes to proteome-transcriptome discrepancies during AD progression.

biochemistry↗

bioRxiv2024

Engineered protein destabilization reverses intrinsic immune evasion for candidate vaccine pan-strain KSHV and SARS-CoV-2 antigens

Both Kaposi sarcoma herpesvirus LANA and SARS coronavirus 2 RdRp/nsp12 are highly conserved replication proteins that evade immune processing. By deleting the LANA central repeat 1 domain (LANA{Delta}CR1) or by dividing RdRp into two separated fragments (RdRpFrag) to maximize nascent protein mis-folding, cis peptide presentation was increased. Native LANA or RdRp SIINFEKL fusion proteins expressed in MC38 cancer cells were not recognized by activated OT-1 CD8+ cells against SIINFEKL but cytotoxic recognition was restored by expression of the corresponding modified proteins. Immunocompetent syngeneic mice injected with LANA- or RdRp-SIINFEKL MC38 cells developed rapidly-growing tumors with short median survival times. Mice injected with LANA{Delta}CR1- or RdRpFrag-SIINFEKL had partial tumor regression, slower tumor growth, longer median survival, as well as increased effector-specific tumor-infiltrating lymphocytes. These mice developed robust T cell responses lasting at least 90 days post-injection that recognized native viral protein epitopes. Engineered vaccine candidate antigens can unmask virus-specific CTL responses that are typically suppressed during native viral infection.

immunology↗