Biology subjects

Zhou, P.

Publications and source records attributed to Zhou, P..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Genetic Dependence and Genetic Diseases

The human life depends on the function of proteins that are encoded by about twenty-thousand genes. The gene-disease associations in majority genes are unknown and the mechanisms underlying pathogenicity of genes/variants and common diseases remain unclear. We studied how human life depends on the genes, i.e., the genetic-dependence, which was classified as genetic-dependent nature (GDN, vital consequence of abolishing a gene), genetic-dependent quantity (GDQ, quantitative genetic function required for normal life), and genetic-dependent stage (GDS, temporal expression pattern). Each gene differs in genetic-dependent features, which determines the gene-disease association extensively. The GDN is associated with the pathogenic potential/feature of genes and the strength of pathogenicity. The GDQ-damage relation determines the pathogenicity of variants and subsequently the pathogenic genotype, phenotype spectrum, and inheritance of variants. The GDS is mainly associated with the onset age/evolution/outcome and the nature of genetic disorders (disease/susceptibility). The varied and quantitative genetic-dependent feature of genome explains common mild phenotype/susceptibility. The genetic-dependence discloses the mechanisms underlying pathogenicity of gene/variants and common diseases. One sentence summaryGenetic dependent feature differs in genes and determines pathogenicity of genes/variants and the clinical features of genetic diseases.

genetics↗

bioRxiv2023

Bacterial pathogens deliver water/solute-permeable channels as a virulence strategy

Many animal and plant pathogenic bacteria utilize a type III secretion system to deliver effector proteins into the host cell1,2. Elucidation of how these effector proteins function in the host cell is critical for understanding infectious diseases in animals and plants3-5. The widely conserved AvrE/DspE-family effectors play a central role in the pathogenesis of diverse phytopathogenic bacteria6. These conserved effectors are involved in the induction of "water-soaking" and host cell death that are conducive to bacterial multiplication in infected tissues. However, the exact biochemical functions of AvrE/DspE-family effectors have been recalcitrant to mechanistic understanding for three decades. Here we show that AvrE/DspE-family effectors fold into a {beta}-barrel structure that resembles bacterial porins. Expression of AvrE and DspE in Xenopus oocytes results in (i) inward and outward currents, (ii) permeability to water and (iii) osmolarity-dependent oocyte swelling and bursting. Liposome reconstitution confirmed that the DspE channel alone is sufficient to allow the passage of small molecules such as fluorescein dye. Targeted screening of chemical blockers based on the predicted pore size (15-20 [A]) of the DspE channel identified polyamidoamine (PAMAM) dendrimers as inhibitors of the DspE/AvrE channels. Remarkably, PAMAMs broadly inhibit AvrE/DspE virulence activities in Xenopus oocytes and during Erwinia amylovora and Pseudomonas syringae infections. Thus, we have unraveled the enigmatic function of a centrally important family of bacterial effectors with significant conceptual and practical implications in the study of bacterial pathogenesis.

plant biology↗

bioRxiv2023

Deep spatial proteomic exploration of severe COVID-19-related pulmonary injury in post-mortem specimens

The lung, as a primary target of SARS-CoV-2, exhibits heterogeneous microenvironment accompanied by various histopathological changes following virus infection. However, comprehensive insight into the protein basis of COVID-19-related pulmonary injury with spatial resolution is currently deficient. Here, we generated a region-resolved quantitative proteomic atlas of seven major pathological structures within the lungs of COVID-19 victims by integrating histological examination, laser microdissection, and ultrasensitive proteomic technologies. Over 10,000 proteins were quantified across 71 dissected FFPE post-mortem specimens. By comparison with control samples, we identified a spectrum of COVID-19-induced protein and pathway dysregulations in alveolar epithelium, bronchial epithelium, and pulmonary blood vessels, providing evidence for the proliferation of transitional-state pneumocytes. Additionally, we profiled the region-specific proteomes of hallmark COVID-19 pulmonary injuries, including bronchiole mucus plug, pulmonary fibrosis, airspace inflammation, and hyperplastic alveolar type 2 cells. Bioinformatic analysis revealed the enrichment of cell-type and functional markers in these regions (e.g. enriched TGFBI in fibrotic region). Furthermore, we identified the up-regulation of proteins associated with viral entry, host restriction, and inflammatory response in COVID-19 lungs, such as FURIN and HGF. Collectively, this study provides spatial proteomic insights for understanding COVID-19-caused pulmonary injury, and may serve as a valuable reference for improving therapeutic intervention for severe pneumonia.

systems biology↗

bioRxiv2023

MicroRNA-122-mediated liver detargeting enhances the tissue specificity of cardiac genome editing

BackgroundThe cardiac troponin T (Tnnt2) promoter is broadly utilized for cardiac specific gene expression, particularly via adeno-associated virus (AAV)-based gene transfer. However, these vectors drive lower-level ectopic gene expression in other tissues, most notably in the liver. Whether the AAV-Tnnt2 vectors remain tissue-specific in applications sensitive to low or transient gene expression, such as gene editing, remains unclear. MethodsThe tissue specificity of AAV9-Tnnt2 vectors was evaluated in mice using Cre-LoxP-based fluorescence reporters and CRISPR/Cas9-mediated somatic mutagenesis. CRISPR/Cas9-triggered AAV integration into host genome was further assessed by quantitative PCR. ResultsIn mice treated with AAV-Tnnt2-GFP, GFP signal was specifically observed in the heart by confocal imaging. However, when AAV-Tnnt2-Cre was administered to mice carrying LoxP-STOP-LoxP fluorescence reporters, the reporter signals were observed in up to 50% hepatic cells. Similarly, the AAV-Tnnt2-SaCas9 vector extensively edited the hepatic genome as measured by targeted amplicon-sequencing. Cas9-triggered AAV integration into the host genome was also validated in the liver. Inclusion of target sequences for microRNA-122, a highly expressed, liver-specific microRNA, in the AAV transgenes 3 untranslated region (3 UTR) markedly reduced ectopic transgene expression, genome editing and AAV integration in the liver. ConclusionsThe heavily used AAV-Tnnt2 system exhibits liver leakiness that severely impairs the cardiac specificity of AAV-based genetic manipulation. This problem can be mitigated via miR122-mediated liver detargeting.

physiology↗

bioRxiv2023

SCFFBXW11 complex targets interleukin-17 receptor A for ubiquitin-proteasome-mediated degradation.

Interleukin-17 (IL-17) is a pro-inflammatory cytokine, participating in innate and adaptive immune responses, that plays an important role in host defense, autoimmune diseases, tissue regeneration, metabolic regulation, and tumor progression. Post-translational modifications (PTMs) are crucial for protein function, stability, cellular localization, cellular transduction, and cell death. However, PTMs of IL-17 receptor A (IL-17RA) have not been investigated. Here, we showed that human IL-17RA was targeted by F-box and WD repeats domain containing 11 (FBXW11) for ubiquitination, followed by proteasome-mediated degradation. We used bioinformatics tools and biochemical techniques to determine that FBXW11 ubiquitinated IL-17RA through a lysine 27-linked polyubiquitin chain, targeting IL-17RA for proteasomal degradation. Domain 665-804 of IL-17RA was critical for interaction with FBXW11 and subsequent ubiquitination. Our study demonstrates that FBXW11 regulates IL-17 signaling pathways at IL-17RA level.

biochemistry↗

bioRxiv2023

On the Mathematics of RNA Velocity II: Algorithmic Aspects

In a previous paper [CSIAM Trans. Appl. Math. 2 (2021), 1-55], the authors proposed a theoretical framework for the analysis of RNA velocity, which is a promising concept in scRNA-seq data analysis to reveal the cell state-transition dynamical processes underlying snapshot data. The current paper is devoted to the algorithmic study of some key components in RNA velocity workflow. Four important points are addressed in this paper: (1) We construct a rational time-scale fixation method which can determine the global gene-shared latent time for cells. (2) We present an uncertainty quantification strategy for the inferred parameters obtained through the EM algorithm. (3) We establish the optimal criterion for the choice of velocity kernel bandwidth with respect to the sample size in the downstream analysis and discuss its implications. (4) We propose a temporal distance estimation approach between two cell clusters along the cellular development path. Some illustrative numerical tests are also carried out to verify our analysis. These results are intended to provide tools and insights in further development of RNA velocity type methods in the future.

bioinformatics↗

bioRxiv2023

Mutator transposon insertions within maize genes often provide a novel outward reading promoter

The highly active family of Mutator (Mu) DNA transposons has been widely used for forward and reverse genetics in maize. There are examples of Mu-suppressible alleles which result in conditional phenotypic effects based on the activity of Mu. Phenotypes from these Mu- suppressible mutations are observed in Mu-active genetic backgrounds, but absent when Mu activity is lost. For some Mu-suppressible alleles, phenotypic suppression likely results from an outward-reading promoter within Mu that is only active when the autonomous Mu element is silenced or lost. We isolated 35 Mu alleles from the UniformMu population that represent insertions in 24 different genes. Most of these mutant alleles are due to insertions within gene coding sequences, but several 5 UTR and intron insertions were included. RNA-seq and de novo transcript assembly were utilized to document the transcripts produced from 33 of these Mu insertion alleles. For 20 of the 33 alleles, there was evidence of transcripts initiating within the Mu sequence reading through the gene. This outward-reading promoter activity was detected in multiple types of Mu elements and doesnt depend on the orientation of Mu. Expression analyses of Mu-initiated transcripts revealed the Mu promoter often provides gene expression levels and patterns that are similar to the wild-type gene. These results suggest the Mu promoter may represent a minimal promoter that can respond to gene cis-regulatory elements. Findings from this study have implications for maize researchers using the UniformMu population, and more broadly highlights a strategy for transposons to co-exist with their host. Article SummaryMutator (Mu) transposable elements are a widely used tool for insertional mutagenesis in maize and often insert in the 5 regions of genes. The characterization of transcripts for Mu insertion alleles reveals complex transcripts. These often result in one transcript that covers the first portion of the gene terminating in Mu and a second transcript initiating within Mu covering the latter portion of the gene. This may reflect a strategy for Mu to minimize the consequences of insertions within genes.

plant biology↗

bioRxiv2023

Longitudinal analysis of memory T follicular helper cells and antibody response following CoronaVac vaccination

The inactivated vaccine CoronaVac is one of the most widely used COVID-19 vaccines globally. However, the longitudinal evolution of the immune response induced by CoronaVac remains elusive compared to other vaccine platforms. Here, we recruited 88 healthy individuals that received 3 doses of CoronaVac vaccine. We longitudinally evaluated their polyclonal and antigen-specific CD4+ T cells and neutralizing antibody response after receiving each dose of vaccine for over 300 days. Both the 2nd and 3rd dose of vaccination induced robust spike-specific neutralizing antibodies, with a 3rd vaccine further increased the overall magnitude of antibody response, and neutralization against Omicron sub-lineages B.1.1.529, BA.2, BA.4/BA.5 and BA.2.75.2. Spike-specific CD4+ T cell and circulating T follicular helper (cTFH) cells were markedly increased by the 2nd and 3rd dose of CoronaVac vaccine, accompanied with altered composition of functional cTFH cell subsets with distinct effector and memory potential. Additionally, cTFH cells are positively correlated with neutralizing antibody titers. Our results suggest that CoronaVac vaccine-induced spike-specific T cells are capable of supporting humoral immunity for long-term immune protection.

immunology↗

bioRxiv2023

Spatial Tracking Across Time (ST AT ): Tracking Neurons Across In-Vivo Imaging Sessions through Optimizing Local Neighborhood Motion Consistency

Chronic calcium imaging has become a powerful and indispensable tool for analyzing the long-term stability and plasticity of neuronal activity. One crucial step of the data processing pipeline is to register individual neurons across imaging sessions, which usually extend over a few days or even months, and show various levels of spatial deformation of the imaged field of view (FOV). Previous solutions align FOVs of all sessions first and then register the same neurons according to their shapes and locations [1, 2]. However, the FOV registration is computational intensive, especially in the case of nonrigid case. Here we propose a cell tracking method that does not require FOV image registration. Specifically, the algorithm STAT (short for Stay T ogether, Align Together, and for Spatial Tracking Across Time) represents neurons from two sessions as two sets of neuronal centroids, uses point set registration (PSR) to find a spatially smooth transformation to align them while assigning correspondences. The optimization method iteratively updates between the general motion and individual neuron identity tracking, an idea seen in the computer vision literatures [3, 4]. Our method can be thought of as a specialization and simplification of these more general methods to calcium imaging neuron tracking. We validate STAT on datasets with simulated nonrigid motion that is hard to motion correct without extensive manual intervention. Next, we test STAT on experimental data from singing birds collected on three different days, and observe stable song-locked activity across days. An example use case of this package is reference [5].

neuroscience↗

bioRxiv2023

Overexpression of the violaxanthin de-epoxidase confers faster NPQ and photosynthesis induction in rice

Plants in the field experience fluctuations in light conditions. Plants with swift responses to dynamic light conditions usually gain competitive advantage in the field. The dynamic photosynthesis can be reflected in dynamic changes in almost all processes in photosynthesis, with dominant factors being dynamic changes in non-photochemical quenching, Rubisco activation and stomatal dynamics. Each of these dynamic responses is controlled by defined mechanisms. In this study, we showed that overexpression of VDE, an enzyme involved in the xanthophyll cycle and non-photochemical quenching, in rice resulted in faster NPQ induction, less photoinhibition, and faster photosynthesis induction, which together caused increased biomass production by about 11[~]16%. This study, demonstrating a previously unnoticed role of VDE in altering the dynamics of photosynthesis induction besides decreasing photoinhibition, offers a potential strategy to improve canopy photosynthesis through capitalizing the ability of plants to use dynamic light. HighlightThe overexpression of VDE in rice resulted in faster NPQ induction, less photoinhibition, and faster photosynthesis induction, which together caused increased biomass in field.

plant biology↗

bioRxiv2023

Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift

Developing broad coronavirus vaccines requires identifying and understanding the molecular basis of broadly neutralizing antibody (bnAb) spike sites. In our previous work, we identified sarbecovirus spike RBD group 1 and 2 bnAbs. We have now shown that many of these bnAbs can still neutralize highly mutated SARS-CoV-2 variants, including the XBB.1.5. Structural studies revealed that group 1 bnAbs use recurrent germline encoded CDRH3 features to interact with a conserved RBD region that overlaps with class 4 bnAb site. Group 2 bnAbs recognize a less well-characterized "site V" on the RBD and destabilize spike trimer. The site V has remained largely unchanged in SARS-CoV- 2 variants and is highly conserved across diverse sarbecoviruses, making it a promising target for broad coronavirus vaccine development. Our findings suggest that targeted vaccine strategies may be needed to induce effective B cell responses to escape resistant subdominant spike RBD bnAb sites.

immunology↗

bioRxiv2023

Key common genes and pathways in ulcerative colitis and ankylosing spondylitis based on bioinformatics analysis

Associations between ulcerative colitis (UC) and ankylosing spondylitis (AS) have been observed in multiple studies, but the common etiology of UC and AS remain unknown. Thus, the current research was conducted to investigate the shared genes and relevant mechanisms in UC and AS. GSE87466 and GSE25101 datasets were used to identify DEGs involved in UC and AS, respectively. The clusterProfiler R package was utilized to detect the biological processes of DEGs in UC and AS. The performance of common DEGs in distinguishing UC or AS samples from control ones were evaluated by ROC curves. The miRWalk, Cistrome and TransmiR database were utilized to construct the network of TF-miRNA-diagnostic biomarker. GSEA method and CTD database were used to investigate the common KEGG pathways shared by UC and AS. In addition, CTD database was also used to detect the interaction score between diagnostic biomarkers and diseases associated with UC or AS. Moreover, prospective diagnostic biomarker-targeting drugs were identified using the DGIdb database. A total of 20 common DEGs were obtained by analyzing data in GSE97466 and GSE25101 datasets. ROC curves revealed that GMFG, GNG11, CLEC4D, CMTM2, VAMP5, S100A8, S100A12 and DGKQ may serve as diagnostic biomarkers for the individuals with AS and UC. A network of TF-miRNA-diagnostic biomarker, composed of 212 nodes and 721 edges, was constructed and visualized by Cytoscape software. Toll-like receptor signaling pathway, antigen processing and presentation, allograft rejection, viral myocarditis, pathways in cancer, graft versus host disease and natural killer cell mediated cytotoxicity were identified as common pathways in UC and AS. For the first time, our study identified 8 common key genes and 7 common pathways in UC and AS. These findings may help to clarify the relationship between UC and AS, and provide guidance in the diagnosis and treatment of UC and AS patients. Author SummaryAnkylosing spondylitis (AS) and Ulcerative colitis (UC) are two types of autoimmune diseases that often co-occur. The simultaneous onset of both diseases often results in severe clinical manifestations and limited therapeutic efficacy. So there is an urgent need to gain a deeper understanding of the causes of UC and AS in order to develop more effective treatment strategies. In this study, we explored the genes and pathways commonly involved in two diseases, constructed a transcriptional network, and further investigated potential drugs. The discoveries could potentially offer insights into the connection between UC and AS, and assist in identifying and managing patients with UC and AS.

bioinformatics↗

bioRxiv2023

exFINDER: identify external communication signals using single-cell transcriptomics data

Cells make decisions through their communication with other cells and receiving signals from their environment. Using single-cell transcriptomics, computational tools have been developed to infer cell-cell communication through ligands and receptors. However, the existing methods only deal with signals sent by the measured cells in the data, the received signals from the external system are missing in the inference. Here, we present exFINDER, a method that identifies such external signals received by the cells in the single-cell transcriptomics datasets by utilizing the prior knowledge of signaling pathways. In particular, exFINDER can uncover external signals that activate the given target genes, infer the external signal-target signaling network (exSigNet), and perform quantitative analysis on exSigNets. The applications of exFINDER to scRNA-seq datasets from different species demonstrate the accuracy and robustness of identifying external signals, revealing critical transition-related signaling activities, inferring critical external signals and targets, clustering signal-target paths, and evaluating relevant biological events. Overall, exFINDER can be applied to scRNA-seq data to reveal the external signal-associated activities and maybe novel cells that send such signals.

bioinformatics↗

bioRxiv2023

A HicA toxin-based counter-selection marker for allelic exchange mutations in Fusobacterium nucleatum

The study of fusobacterial virulence factors has dramatically benefited from the creation of various genetic tools for DNA manipulation, including the galK-based counterselection for in-frame deletion mutagenesis in Fusobacterium nucleatum that was recently developed. However, this method requires a host lacking the galK gene, which is an inherent limitation. To circumvent this limitation, we explored the possibility of using the hicA gene that encodes a toxin consisting of a HicAB toxin-antitoxin module in Fusobacterium periodonticum as a new counter-selective marker. Interestingly, the full-length hicA gene is not toxic in F. nucleatum, but a truncated hicA gene version lacking the first six amino acids is functional as a toxin. The toxin expression is driven by an rpsJ promoter and is controlled at its translational level using a theophylline-responsive riboswitch unit. As a proof of concept, we created markerless in-frame deletions in the fusobacterial adhesin RadD gene within the F. nucleatum rad operon and the tnaA gene that encodes the tryptophanase for indole production. After vector integration, plasmid excision after counterselection appeared to have occurred in 100% of colonies grown on theophylline-added plates and resulted in in-frame deletions in 50% of the screened isolates. This hicA-based counterselection system provides a robust and reliable counterselection in wild-type background F. nucleatum and should also be adapted for use in other bacteria. IMPORTANCEFusobacterium nucleatum is an indole-producing human oral anaerobe associated with periodontal diseases, preterm birth, and several cancers. Little is known about the mechanisms of fusobacterial pathogenesis and associated factors mainly due to the lack of robust genetic tools for this organism. Here we showed that a mutated hicA gene from Fuosbacterium periodonticum expresses an active toxin and was used as a counterselection marker. This hicA-based in-frame deletion system efficiently creates in-frame deletion mutations in the wild-type background of F. nucleatum. This is the first report to use the hicA gene as a counterselection marker in a bacterial genetic study.

microbiology↗

bioRxiv2023

A human iPSC-based in vitro neural network formation assay to investigate neurodevelopmental toxicity of pesticides

Proper brain development is based on the orchestration of key neurodevelopmental processes, including the formation and function of neural networks. If at least one key neurodevelopmental process is affected by a chemical, an adverse outcome is expected. To allow a higher testing throughput than the guideline animal experiments, a developmental neurotoxicity (DNT) in vitro testing battery (DNT IVB) has been set up that includes a variety of assays, which model several key neurodevelopmental processes. Gap analyses of the DNT IVB revealed the need of a human-based assay to assess neural network formation and function (NNF). Therefore, here we established the human NNF (hNNF) assay. A co-culture comprised of human-induced pluripotent stem cell (hiPSC)- derived excitatory and inhibitory neurons, as well as primary human astroglia, was differentiated for 35 days on micro-electrode arrays (MEA) and spontaneous electrical activity, together with cytotoxicity, was assessed on a weekly basis after washout of the compounds 24 h prior to measurements. In addition to the characterization of the test system, the assay was challenged with 28 compounds, mainly pesticides, identifying their DNT potential by evaluation of specific spike-, burst- and network parameters. This approach confirmed the suitability of the assay for screening environmental chemicals. Comparison of benchmark concentrations (BMC) with an NNF in vitro assay (rNNF) based on primary rat cortical cells, revealed differences in sensitivity. Together with the successful implementation of hNNF data into a postulated stressor-specific adverse outcome pathway (AOP) network associated with a plausible molecular initiating event for deltamethrin, this study suggests the hNNF assay as a useful complement to the current DNT IVB.

pharmacology and toxicology↗

bioRxiv2022

Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD

Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. One Sentence SummaryC9orf72-associated ALS and FTD showed a distinct pattern of transcriptome changes, with the largest number of affected genes in C9-ALS in astrocytes and excitatory neurons in upper and deep layers.

neuroscience↗

bioRxiv2022

A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike

A major challenge in understanding SARS-CoV-2 evolution is interpreting the antigenic and functional effects of emerging mutations in the viral spike protein. Here we describe a new deep mutational scanning platform based on non-replicative pseudotyped lentiviruses that directly quantifies how large numbers of spike mutations impact antibody neutralization and pseudovirus infection. We demonstrate this new platform by making libraries of the Omicron BA.1 and Delta spikes. These libraries each contain ~7000 distinct amino-acid mutations in the context of up to ~135,000 unique mutation combinations. We use these libraries to map escape mutations from neutralizing antibodies targeting the receptor binding domain, N-terminal domain, and S2 subunit of spike. Overall, this work establishes a high-throughput and safe approach to measure how ~105 combinations of mutations affect antibody neutralization and spike-mediated infection. Notably, the platform described here can be extended to the entry proteins of many other viruses.

microbiology↗

bioRxiv2022

Proteomics Characteristics Reveal the Risk of T1 Colorectal Cancer Metastasis to Lymph Nodes

BackgroundThe presence of lymph node metastasis (LNM) affects treatment strategy decisions in T1NxM0 colorectal cancer (CRC), but the currently used clinicopathological-based risk stratification cannot predict LNM accurately. In this study, we established a classifier for predicting LNM in T1 CRC. MethodsWe detected proteins in formalin-fixed paraffin-embedded (FFPE) tumor samples from 143 LNM-negative and 78 LNM-positive patients with T1 CRC and revealed changes in molecular and biological pathways by label-free LC-MS/MS. An effective prediction model was built and validated in a training cohort (N=132) and two validation cohorts (VC1, N=42; VC2, N=47) by machine learning. We further built a simplified classifier with 9 proteins. The expression patterns of 13 proteins were confirmed by immunohistochemistry, and the IHC score of 5 proteins were used to build a IHC predict model. ResultPatients with or without LNM have different molecular signatures. The 55-proteins prediction model achieved an impressive AUC of 1.00 in the training cohort, 0.96 in VC1 and 0.93 in VC2. The 9-protein classifier achieved an AUC of 0.824, and the calibration plot was excellent. We found that 5 biomarkers could predict LNM by the IHC score, with an AUC of 0.825. RHOT2 silence significantly enhanced migration and invasion of colon cancer cells. ConclusionsOur study explored the mechanism of metastasis in T1 CRC and can be used to facilitate the individualized prediction of LNM in patients with T1 CRC, which may provide a guidance for clinical practice in T1 CRC.

cancer biology↗