Biology subjects

Yu, W.

Publications and source records attributed to Yu, W..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Targeted Protein Degradation by KLHDC2 Ligands Identified by High Throughput Screening

Proteolysis targeting chimeras (PROTACs) enable the selective and sub-stoichiometric elimination of pathological proteins, yet only two E3 ligases are routinely used for this purpose. Here, we expand the repertoire of PROTAC compatible E3 ligases by identifying a novel small molecule scaffold targeting the ubiquitin E3 ligase KLHDC2 using a fluorescence polarization-based high throughput screen. We highlight the utility of this ligand with the synthesis of PROTACs capable of potently degrading BRD4 in cells. This work affords additional chemical matter for targeting KLHDC2 and suggests a practical approach for identifying novel E3 binders by high throughput screening.

biochemistry↗

bioRxiv2025

A comprehensive benchmarking study of protein structure alignment tools based on downstream task performance

In this study, we investigate the performance of nine protein structure alignment tools by analyzing the influence of alignment results in accomplishing three downstream biological tasks: homology detection, phylogeny reconstruction, and function inference. These tools include (1) traditional sequential methods using both 3D and 2D structure representations, (2) non-sequential methods, (3) flexible methods, and (4) deep-learning methods. Canonical sequence alignment methods Needleman-Wunsch algorithm and BLASTp are used as baseline methods. We show that accuracies in downstream tasks can be uncorrelated with alignment quality metrics such as TM-score and RMSD, highlighting the discrepancy between the alignment results and the purposes of using them. We identify scenarios where structure alignment results outperform sequence alignment results. In homology detection, structure-based methods are much better than sequence alignment. In phylogeny reconstruction, structure-based methods generally outperform sequence-based methods on the filtered dataset with proteins sharing low sequence similarity. Moreover, we show that structure information improves the overall performance of these tools when used together with sequence information in phylogeny reconstruction and function inference. We also test the running time and CPU/GPU memory consumption of these tools for a large number of queries. Our study suggests that biological problems that were previously addressed with sequence-based methods using only sequence information could be further improved by using structure information alone or using both sequence and structure information. The trade-off between task accuracy and speed is the major consideration in developing new alignment tools for downstream tasks. We recommend both TMalign and KPAX for these tasks because of their good balance between running time and memory consumption, and relatively good and stable accuracy performance in downstream tasks. In tasks that require a large number of pairwise comparisons, such as homology detection and function inference, traditional methods outperform DL methods at the cost of long running time, and Foldseek is the best choice to achieve relatively high accuracy in a reasonable time. 1 Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=179 HEIGHT=200 SRC="FIGDIR/small/642719v1_fig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@9ba569org.highwire.dtl.DTLVardef@88cc4eorg.highwire.dtl.DTLVardef@11d2070org.highwire.dtl.DTLVardef@13cd20d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1:C_FLOATNO Graphical abstract. C_FIG

bioinformatics↗

bioRxiv2025

Sky islands of Southwest China. II: Unraveling hidden species diversity of talpid moles using phylogenomics and skull-based deep learning

The sky islands of Southwest China, characterized by dramatic topographical and climatic variations, are prominent hotspots of biodiversity and endemism. Organisms inhabiting middle-to-high elevation habitats in this region are geographically isolated within distinct mountain chains, which over geological time have been subjected to isolation-by-distance and isolation-by-environment. These processes have led to profound allopatric diversification and strong phylogeographic structuring, resulting in a plethora of genetically distinct cryptic species, as is becoming increasingly evident for many small mammal families. However, morphological conservatism can pose significant challenges in delineating these clades within species complexes. In this study, we leverage artificial intelligence technologies to unravel the hidden species diversity of moles (family Talpidae) in Southwest Chinas sky islands. We first employed ultraconserved elements (UCEs) to investigate the evolutionary history of talpid moles, conducted molecular species delimitation using mitochondrial and multi-locus genes, and utilized both traditional and geometric morphometrics to examine their morphological disparity. To address the challenges of morphology based cryptic species identification, we developed a deep learning Hierarchical Identification of Species NETwork (HIS-NET) to create an image-based model that analyzes four different views of the skull/mandible to distinguish genera and species hierarchically. HIS-NET not only achieved expert-level accuracy in species identification but also effectively distinguished between cryptic and known species, aiding in the identification of key morphological variation intervals. Our results support the recognition of allopatrically distributed taxa in Euroscaptor and Parascaptor as full species, thereby confirming that species diversity in this region remains underestimated. Beyond advancing our understanding of speciation in this unique and fragile ecosystem, our study serves as a proof-of-concept, demonstrating the power of deep learning in unraveling hidden biodiversity within this and other species complexes.

zoology↗

bioRxiv2025

YTHDF3 promotes the progression of gastric cancer by activating Wnt/β-catenin signaling pathway via targeting NEK7

Gastric cancer (GC) is a widespread and deadly malignancy among global digestive tract tumors, alarmingly ranked the fifth most common cancer in terms of incidence and mortality. This study used immunohistochemistry and RT-qPCR to reveal a significant upregulation of YTHDF3 expression in GC tissues compared with that of adjacent normal tissues. This increased expression of YTHDF3 was closely associated with the incidence of lymph node metastasis and the progression to more advanced TNM stages. In vitro experiments demonstrated that YTHDF3 was crucial in promoting the aggressive characteristics of GC cells by enhancing their ability to proliferate, migrate, and invade, while simultaneously inhibiting apoptosis. The role of YTHDF3 in the progression of GC was further confirmed using the BALB/c nude mice subcutaneous tumor model, which showed a slowed tumor growth after YTHDF3 knockdown. This study further confirmed through Co-IF RIP-qPCR, western blotting, and rescue studies that YTHDF3 promotes GC progression by targeting NEK7 to regulate the Wnt/{beta}-catenin signaling pathway. In conclusion, our pivotal findings highlight the YTHDF3/NEK7/Wnt/{beta}-catenin axis as a promising and accessible therapeutic target for the development of new treatments aimed at improving clinical outcome of patients with GC.

cancer biology↗

bioRxiv2025

The N-terminal order-disorder transition is a critical determinant for a metamorphosis of IscU

IscU, a key scaffold protein mediating the biogenesis of iron-sulfur (Fe-S) clusters, exhibits metamorphic characteristics crucial for its versatile and efficient function. Previous studies have demonstrated that IscU has two interconverting conformations: the structured state (S-state) and the disordered state (D-state), each contributing to its distinct functionality and interaction network. Despite its physiological importance, the precise mechanism underpinning the maintenance of IscUs unique structural heterogeneity has remained elusive. In this study, we used computational and experimental approaches to reveal that the N-terminal order-disorder plays a critical role in the metamorphic modulation of IscU. We found that the N-terminal region displays greater structural plasticity, which is linked to other regions of IscU through coevolutionary relationships. Moreover, we demonstrated that the degree of orderliness in the N-terminal region correlates positively with the stabilization of IscUs S-state and negatively with its affinity for HscA. This indicates that the flexibility in the N-terminal region is finely tuned to optimize IscUs physiological efficiency and efficacy. Finally, our data suggest that a peptide mimicking the N-terminal motif can modulate IscUs metamorphic properties, suggesting a novel therapeutic potential for related pathogenic processes.

biochemistry↗

bioRxiv2024

ITGB4 promotes the progression of colorectal cancer by activating Wnt/β-catenin signaling pathway via targeting EZR

ObjectivesColorectal cancer (CRC) is a major cause of cancer-related mortality worldwide. Integrin beta 4 (ITGB4) has been previously identified as being overexpressed in CRC; however, its precise oncogenic mechanism remains unclear. The present study aimed to elucidate the functional role of ITGB4 in CRC progression and identify its downstream molecular effectors to provide new insights for targeted therapy. MethodsThe biological functions of ITGB4 were investigated in CRC cell lines (SW480 and HCT116) using a series of in vitro assays, including CCK-8, colony formation, Transwell migration and invasion, and flow cytometry for apoptosis following ITGB4 knockdown. An in vivo xenograft mouse model was used to evaluate the effect of ITGB4 on tumor growth. Downstream targets were screened using RNA sequencing (RNA-seq) and validated by co-immunoprecipitation and co-immunofluorescence. The underlying signaling pathway was investigated by Western blotting and functional rescue experiments. ResultsKnockdown of ITGB4 significantly suppressed CRC cell proliferation, migration, and invasion, while promoting apoptosis in vitro. Similarly, silencing ITGB4 markedly inhibited tumor growth in the in vivo xenograft model. RNA-seq analysis identified Ezrin (EZR) as a key downstream target of ITGB4, and a direct protein-protein interaction was confirmed between them. Mechanistically, ITGB4 knockdown decreased the expression of EZR at both the mRNA and protein levels. ITGB4 was demonstrated to exert its pro-tumorigenic effects through the regulation of EZR, which subsequently activated the Wnt/{beta}-catenin signaling pathway. Interestingly, EZR overexpression partially restored ITGB4 levels, suggesting a potential positive feedback loop via Wnt/{beta}-catenin signaling that further amplifies this oncogenic axis. Notably, the malignant phenotypes suppressed by ITGB4 silencing were significantly rescued by the overexpression of EZR. ConclusionThe present study identified a novel ITGB4/EZR/Wnt/{beta}-catenin signaling axis in colorectal cancer. ITGB4 promotes CRC progression by modulating EZR expression and subsequently activating the Wnt/{beta}-catenin pathway. These findings highlight ITGB4 as a potential prognostic biomarker and a promising therapeutic target for CRC.

molecular biology↗

bioRxiv2024

Plant-induced transcriptional plasticity diverges between generalist and specialist herbivores

Most herbivores are specialized on particular host plants but some are generalists that can exploit distinct hosts. Generalists may have evolved adaptive transcriptional plasticity to cope with the defenses of the different hosts. However, the fundamental differences in plant-induced transcriptional plasticity between generalists and specialists remain poorly understood. Here, we investigated transcriptional plasticity of the generalist aphid Myzus persicae and two specialist aphids, Brevicoryne brassicae and Rhopalosiphum padi, by transferring them between Brassica napus (a host for B. brassicae but not for R. padi) and Zea mays (a host for R. padi but not for B. brassicae), both suitable hosts for M. persicae. Generalist and specialist aphids exhibited transcriptional plasticity coordinately in response to different plant species, but their gene expression patterns often diverged. Generalists suppressed plant-defense salicylic acid (SA) signaling in the host plants, while specialist aphids provoked it in nonhost plants. SA signaling had limited effects on gene expression in the generalist aphids, but significantly shaped transcriptional responses of the specialists. These findings underscore the fundamental differences in plant-induced transcriptional plasticity between generalists and specialists and highlight the critical role of plasticity directionality in insect adaptation. Significance statementMost insects specialize in feeding on just a few specific plants, but some generalists can thrive on many plant species. This study compares the gene expression of green peach aphid Myzus persicae, a generalist, with two specialist aphids in response to different types of plants. Generalists showed adaptive plasticity in their gene responses, while specialists often exhibited opposite gene expression changes. Interestingly, generalists appeared to suppress plant defense signals like salicylic acid, while specialists tended to trigger them. These findings highlight how gene expression plasticity enables generalists to adapt and survive, providing new insights into the evolution of insect-plant interactions.

plant biology↗

bioRxiv2024

Convincing Evidence of Carnivorous Diet in Alvarezsaurian Dinosaur

A dietary shift from carnivory to insectivore has been proposed to explain the dramatic morphological evolution of alvarezsaurians, particularly the adaptation related to the manual digital reduction and body size miniaturization. However, based solely on morphological shifts, this hypothesis lacked direct dietary evidence to support either carnivory or insectivore. Here, we present the first convincing dietary evidence for alvarezsaurians, derived from the intestinal contents of the Early Cretaceous Bannykus wulatensis. Our analysis revealed significantly higher levels of calcium and phosphorus in the intestinal contents compared to the surrounding sandstone. Scanning electron microscopy identified hard tissue debris and possible soft tissues surrounding by phosphatized bacteria and tightly packed hollow microspheres, suggesting that the intestinal contents were strongly pseudomorphed by phosphatized microbes during fossilization. Raman spectroscopy showed characteristic peaks indicative of bone-derived material, consistent with the hard tissue debris appeared in the intestinal contents. Our results suggest that Bannykus had a carnivorous diet with strong chemical digestion, which likely compensated for its delicate cranial structures and small teeth. These results imply that if a dietary shift to insectivore occurred, it likely took place later in alvarezsaurian evolution, probably coinciding with a reduction in body size.

paleontology↗

bioRxiv2024

Functional, Biotinylproteomic and Bioinformatic Analysis of Both Cytoskeletal and Plastoskeletal Proteins in Plant Mechanoresponse

To investigate the early signaling components of skeletal proteins in mediating Arabidopsis thigmomorphogenesis, both microscopic and proximity labeling (PL)-based quantitative biotinylproteomics were applied to investigate the subcellular location and putative interactors of a touch-responsive WPRa4 protein. These experiments have demonstrated that the cytoskeletal protein WPRa4 is localized nearby the plastid. Several cytosolic Plastid Movement-Impaired (PMI) proteins and a member of the plastidic translocon were identified as putative interactors of WPRa4, suggesting an integrated network of skeletal proteins linking the cytoskeleton with the plastid membrane. Further bioinformatic analysis of both Proximity Labeling- and XL-MS-based proteomic results suggested that Plastid Movement-Impaired 4 (PMI4) protein may serve as a candidate in mediating the plant touch response. The loss-of-function pmi4 mutant showed neither the touch-induced bolting delay nor the rosette size reduction upon repetitive touches, suggesting that pmi4 is a unique type of mutant of Arabidopsis thigmomorphogenesis. Moreover, the null mutant pmi4 displayed a severe defect in the touch-induced Ca2+ oscillation. Further transcriptomic analysis performed on both the wild-type Arabidopsis and pmi4 mutant indicated that the mutated pmi4 gene suppressed the expression of a number of touch rapidly induced transcripts and a JA-responsive gene, LOX2. These findings led us to propose a revised touch force-sensing theory, in which the interconnected cytosolic and plastidic skeletal proteins serve as the early mechano-sensing components mediating Arabidopsis thigmomorphogenesis and the retrograde calcium signaling in response to touch.

plant biology↗

bioRxiv2024

Profiling amino acid substitution on proteomic scale unveils novel protein regulation in cancer diseases

Amino acid (AA) substitutions play a critical role in regulating cellular activities, including complex signaling and cell cycle processes. Recent research on AA substitutions has primarily relied on genomic and transcriptomic data. The identification at the proteomic scale remains underexplored, despite evidence suggesting that DNA and RNA biosynthesis are not the sole sources of these substitutions. This gap persists due to challenges in analyzing large-scale proteomic data. In this study, we address this limitation by analyzing multiple independent datasets across five cancer types using PIPI-C, a novel mass spectrometry data analysis tool. And we propose AA substitutomics, a pipeline for characterizing AA substitutions arising after protein translation and dissecting the regulatory functions of key proteins with AA substitutions. Among our identified AA substitutions, 87% are novel findings and not recorded in genomic/transcriptomic databases, which indicates that the post-translational AA substitutions are prevalent. Our findings reveal biologically significant AA substitutions linked to cancer, such as F43S and E91D in hemoglobin subunit beta, P584T in filamin A, and A175N in fructose-bisphosphate aldolase B. Furthermore, our pipeline enables direct investigation of drug resistance and immune escape. By capturing functional protein-level alterations beyond genomic and transcriptomic profiling, it establishes a robust framework to advance cancer research.

cancer biology↗

bioRxiv2024

Adiponectin Signaling Regulates Urinary Bladder Function by Blunting Smooth Muscle Purinergic Contractility

Lower urinary tract symptoms (LUTS) affect [~] 50% of the population aged >40 years and are strongly associated with obesity and metabolic syndrome. Adipose tissue plays a key role in obesity/metabolic syndrome by releasing adipokines that regulate systemic energy/lipid metabolism, insulin resistance, and inflammation. Adiponectin (ADPN), the most abundant adipokine, modulates energy/metabolism homeostasis through its insulin-sensitizing and anti-inflammatory effects. Human plasma ADPN levels are inversely associated with obesity and diabetes. The role of adipokines such as ADPN in the LUTS associated with obesity/metabolic syndrome remains unknown. We have tested such a possible role in a global ADPN knockout mouse model (Adpn-/-). Adpn-/- mice exhibited increased voiding frequency, small voids, and reduced bladder smooth muscle (BSM) contractility with absence of purinergic contraction. Molecular examination indicated significantly altered metabolic and purinergic pathways. The ADPN receptor agonist AdipoRon was found to abolish acute BSM contraction. Intriguingly, both AMPK activators and inhibitors also abolished BSM purinergic contraction. These data indicate the important contribution of a novel ADPN signaling pathway to the regulation of BSM contractility. Dysregulation of this ADPN signaling pathway might be an important mechanism leading to LUTS associated with obesity/metabolic syndrome. ARTICLE HIGHLIGHTSLower urinary tract symptom (LUTS) is strongly associated with obesity and metabolic syndrome, however, the underlying molecular mechanisms are missing. Dysregulation of adipokine signaling could be the link for this association. Whether adiponectin, the most abundant adipokine, plays a role in regulating bladder function and dysfunction. Mice null for adiponectin exhibited increased voiding frequency, small voids, and reduced bladder smooth muscle contractility, with corresponding metabolic and purinergic pathway changes. Dysregulation of adiponectin signaling might be an important mechanism leading to LUTS associated with obesity/metabolic syndrome.

physiology↗

bioRxiv2024

Capturing the Hierarchically Assorted Protein-protein Interaction Modules of Mammalian Cell

Proteins are organized into modules by both functions and physical interactions within compartments of an eukaryotic cell. The in vivo chemical crosslinking mass spectrometry (XL-MS) data collected from organelles, the whole cells and tissues are able to provide unique information about both protein-protein interaction (PPI) and the intensity of PPI. In the present study, we have retrieved 55,982 crosslinked peptides (XL-peptides) from the XL-MS databases, out of which 6,356 in vivo PPIs were identified. Introduction of the MONET software into analysis of 4,526 hetero PPIs revealed a total of 402 protein modules, including 15, 58 and 163 stable protein complex(s), condensate-forming protein module(s) and intrinsically disordered region (IDR)-containing protein module(s), respectively. The application of ChatGPT in analysis of these modules unexpectedly identified 4 vesicle-related modules. Together, these modules were assorted into 6 communities (module of modules) and 3 systems (module of communities) hierarchically. The bioinformatic analysis found that the three systems are corresponding to three compartments of eukaryotic cell: nuclei, mitochondria, endoplasmic reticulum (ER), respectively. This study presents a novel and comprehensive biomolecular modulome of a mammalian cell, which captures putative protein compositions of protein complexes, protein condensates and vesicles and provides a hierarchical protein organization and function within compartments of mammalian cell.

bioinformatics↗

bioRxiv2024

A persistent bacterial Regiella transinfection in the bird cherry-oat aphid Rhopalosiphum padi increasing host fitness and decreasing plant virus transmission

The bird cherry-oat aphid, Rhopalosiphum padi, is a major pest of agriculture due to its ability to directly damage crops and transmit plant viruses. As industries move away from chemical pest control, there is interest in exploring new options to suppress the impact of this pest. Here we describe the production of a transinfected line of R. padi carrying the bacterial endosymbiont, Regiella insecticola, originating from the green peach aphid, Myzus persicae. We show that Regiella increases the fitness of its novel host despite decreasing fitness in its native host. Regiella also shows a low level of horizontal transmission. Importantly the infection suppresses the ability of R. padi to transmit the barley yellow dwarf virus which damages wheat plants. This transinfection could be released to suppress virus transmission by aphids with its ability to persist and spread, making it potentially suitable for wide area release.

microbiology↗

bioRxiv2024

Single-cell Landscape of Immune Cells in Blood and Skin in Psoriasis

BackgroundPsoriasis is a systemic inflammatory disease for which there is currently no cure, in part due to an incomplete understanding of its pathophysiology. MethodsTo better understand the immune response in psoriasis, we performed single-cell RNA sequencing (scRNA-seq) on peripheral blood mononuclear cells (PBMCs) and on lesional and non-lesional skin samples from a cohort of 11 psoriasis patients and 8 healthy controls. Additionally, we conducted flow cytometry on PBMCs from a separate cohort of 13 psoriasis patients and 11 ankylosing spondylitis. FindingsOur study revealed altered immune signatures of specific myeloid and lymphocyte subsets in blood and skin, both in terms of cell numbers and gene expression. Specifically, we discovered elevated proportions of circulating CD14++ monocytes, increased expression of major histocompatibility complex (MHC) class II molecule by circulating CD16+ monocytes, as well as increased expression of genes related to skin homing and to pro-inflammatory responses in psoriasis by circulating plasmacytoid dendritic cells (pDCs). Circulating CD8+ T effector memory cells in psoriasis patients exhibited reduced abundance but increased skin-homing potential. In psoriatic lesions, we observed a hyperinflammatory myeloid-cell state and enrichment of IL17-producing cells with a tissue-resident memory T-cell signature. InterpretationThe changes in immune cell numbers and gene expression indicate a significant alteration in the immune landscape of psoriasis patients. This suggests that the immune system in psoriasis is reprogrammed, affecting both innate and adaptive branches. These findings provide new insights into the aberrant immune-cell signatures in the circulation and skin lesions in psoriasis, and thereby help to understand its pathophysiology. FundingThis study was financially supported by the National Natural Science Foundation of China (U23A6012), Science and Technology Planning Project of Guangzhou (2024A03J0055, 202206080005), Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine (ZYYCXTD-C-202204).

systems biology↗

bioRxiv2024

YTHDF1 Facilitates Lung Adenocarcinoma Progression via Promotion of EEF1G Translation in a m6A-Dependent Manner

Lung adenocarcinoma (LUAD) is a malignant tumor with high morbidity and mortality worldwide, and overall survival rates for LUAD patients remain unimproved. RNA modification is a key process in post-transcriptional gene regulation in epigenetics, with N6-methyladenosine (m6A) being a common RNA modification. The molecular mechanisms of LUAD are unclear, but evidence suggests that m6A RNA methylation plays a significant role. This study aimed to clarify the role of YTHDF1 in LUAD development and pathogenesis. These findings confirmed that YTHDF1, a m6A reader protein, is highly expressed in LUAD tissues and is correlated with tumor differentiation and TNM stage. The results of functional loss experiments in LUAD cell lines revealed that downregulating YTHDF1 inhibits proliferation, migration, and invasion and induces apoptosis, with opposite effects observed upon YTHDF1 upregulation. In vivo, YTHDF1 knockout suppressed LUAD xenograft growth. RNA-seq, MeRIP-seq, RIP-seq, and bioinformatics analyses identified EEF1G as a downstream target of YTHDF1 in LUAD, and high expression of EEF1G was confirmed. The interaction between YTHDF1 and EEF1G was validated through RIP-qPCR, Co-IP and Co-IF assays. The overexpression of EEF1G in LUAD cells partially counteracts the tumor suppression induced by YTHDF1 silencing, and the knockdown of EEF1G has the opposite effect, further confirming the regulatory relationship. In summary, this study describes a novel YTHDF1/EEF1G regulatory pathway in which YTHDF1 promotes LUAD progression by recognizing and binding to the m6A-modified mRNA of EEF1G, accelerating its translation, suggesting that YTHDF1 may be a potential biomarker and therapeutic target.

cancer biology↗

bioRxiv2024

Evaluating computational approaches for comparison of protein expression across cancer indications

BackgroundThe National Cancer Institutes Clinical Proteomic Tumor Analysis Consortium (CPTAC) recently generated harmonized genomic, transcriptomic, proteomic, and clinical data for over 1,000 tumors across 10 cohorts to facilitate pan-cancer discovery research. However, protein expression comparison across CPTAC cohorts remains challenging due to non-uniform missing data and varying protein expression distribution patterns across tumor types. Here, we present our efforts to evaluate various missing data handling and normalization strategies to create a normalized pan-cancer protein expression dataset. ResultsFirst, we developed a novel algorithm to select robustly expressed proteins in tumors within any CPTAC cohort. Second, we applied a cohort hybrid imputation approach to protein abundance values from FragPipe within each cohort based on protein expression distribution patterns. Third, we calculated intensity-based absolute quantification using protein abundance values and applied both global and smooth quantile normalization methods. Our results indicate that global quantile normalization ensured identical distribution across cohorts for both tumor and normal tissues, while smooth quantile normalization preserved distribution differences between biological conditions. We assessed our method by comparing differential protein expression analysis results with and without normalization. Additionally, we examined the ranks of protein expression in the normalized CPTAC dataset for selected proteins with high protein-to-RNA expression correlation across CPTAC cohorts. We then compared these protein expression ranks with their RNA expression ranks across corresponding cohorts in The Cancer Genome Atlas (TCGA). Differential protein expression analysis revealed a high level of agreement in the fold change of tumor versus normal tissue within cohorts before and after normalization. Furthermore, our results indicate that global quantile normalization resulted in the highest cohort rank correlation between CPTAC and TCGA for selected proteins. ConclusionsIn summary, our thorough analysis demonstrates that global quantile normalization surpasses both smooth quantile normalization and no normalization, as evidenced by its higher rank correlation across cancer cohorts between CPTAC and TCGA for selected proteins. The findings suggest that combining cohort hybrid imputation with global quantile normalization is an effective method for creating a normalized CPTAC pan-cancer protein dataset, which can facilitate the study of protein expression across different cancer types.

bioinformatics↗

bioRxiv2024

Signal peptidase SpsB coordinates staphylococcal cell cycle, surface protein septal trafficking and LTA synthesis

Many cell wall anchored surface proteins of Gram-positive bacteria harbor a highly conserved YSIRK/G-S signal peptide (SPYSIRK+), which deposits surface protein precursors at the cell division septum where they are subsequently anchored to septal peptidoglycan. Previously we identified that LtaS-mediated lipoteichoic acid (LTA) synthesis regulates septal trafficking of YSIRK+ proteins in S. aureus. Interestingly, both LtaS and SPYSIRK+ are cleaved by the signal peptidase SpsB, but the biological implications remain unclear. Here we show that SpsB is required for cleaving SPSpA(YSIRK+) of staphylococcal surface protein A (SpA). Depletion of spsB not only diminished SPSpA processing but also abolished SpA septal localization. The mis-localization is attributed to the cleavage activity of SpsB, as an A37P mutation of SPSpA that disrupted SpsB cleavage also abrogated SpA septal localization. Strikingly, depletion of spsB led to aberrant cell morphology, cell cycle arrest and daughter cell separation defects. Localization studies showed that SpsB predominantly localized at the septum of dividing staphylococcal cells. Finally, we show that SpsB spatially regulates LtaS as spsB depletion enriched LtaS at the septum. Collectively, the data suggest a new dual-mechanism model mediated by SpsB: the abundant YSIRK+ proteins are efficiently processed by septal localized SpsB; SpsB cleaves LtaS at the septum, which spatially regulates LtaS activity contributing to YSIRK+ proteins septal trafficking. The study identifies SpsB as a novel and key regulator orchestrating protein secretion, cell cycle and cell envelope biogenesis. ImportanceSurface proteins containing a YSIRK/G-S positive signal peptide are widely distributed in Gram-positive bacteria and play essential roles in bacterial pathogenesis. They are highly expressed proteins that are enriched at the septum during cell division. The biogenesis of these proteins is coordinated with cell cycle and LTA synthesis. The current study identified the staphylococcal signal peptidase SpsB as a key determinant in regulating surface protein septal trafficking. Furthermore, this study highlights the novel functions of SpsB in coordinating LtaS-mediated LTA production and regulating staphylococcal cell cycle. As SpsB, YSIRK+ proteins and LTA synthesis are widely distributed and conserved, the mechanisms identified here may be shared across Gram-positive bacteria.

microbiology↗

bioRxiv2024

Identifying crosstalks among post-translational modifications in lung cancer proteomic data

Post-translational modifications (PTMs) are pivotal in cellular regulations, and their crosstalk is related to various diseases such as cancer. Given the prevalence of PTM crosstalk within close amino acid ranges, identifying peptides with multiple PTMs is essential. However, this task is an NP-hard combinatorial problem with exponential complexity, posing significant challenges for existing analysis methods. Here, we introduce PIPI-C (PTM-Invariant Peptide Identification with a Combinatorial model), a novel search engine that addresses this challenge through a mixed-integer linear programming (MILP) model, thereby overcoming the limitations of existing approaches that struggle with high-order PTM combinations. Rigorous validation across diverse datasets confirms PIPI-Cs superior performance in detecting PTM crosstalks. When applied to over 72 million mass spectra of three human cancers--lung squamous cell carcinoma (LSCC), colorectal adenocarcinoma (COAD), and glioblastoma (GBM)--PIPI-C reveals significantly upregulated PTM crosstalks. In LSCC, 50% of 860 upregulated unique PTM site patterns (UPSPs) (when comparing cancer vs. normal samples) carried at least two PTMs, including literature-supported crosstalks such as di-methylation with trifluoroleucine substitution and amidation with proline-to-valine substitution. Similar findings in COAD and GBM highlight PIPI-Cs utility in uncovering cancer-relevant PTM crosstalk landscapes. Overall, PIPI-C provides a robust mathematical framework for decoding complex PTM patterns, advancing our understanding of PTM-driven cellular processes in diseases.

bioinformatics↗