Ubiquitin-mediated Proteolysis Pathway Research Articles

Comprehensive Proteomic Profiling ofHuman Myocardium Reveals SignalingPathways Dysregulated in Hypertrophic Cardiomyopathy.

Hypertrophic cardiomyopathy (HCM) is the most common genetic cardiac disease. Signaling pathways that link genetic sequence variants to clinically overt HCM and progression to severe forms of HCM remain unknown. The purpose of this study was to identify signaling pathways that are differentially regulated in HCM, using proteomic profiling of human myocardium, confirmed with transcriptomic profiling. In this multicenter case-control study, myocardial samples were obtained from cases with HCM and control subjects with nonfailing hearts. Proteomic profiling of 7,289 proteins from myocardial samples was performed using the SomaScan assay (SomaLogic). Pathway analysis of differentially expressed proteins was performed, using a false discovery rate<0.05. Pathway analysis of proteins whose concentrations correlated with clinical indicators of severe HCM (eg, reduced left ventricular ejection fraction, atrial fibrillation, and ventricular tachyarrhythmias) was also executed. Confirmatory analysis of differentially expressed genes was performed using myocardial transcriptomic profiling. The study included 99 HCM cases and 15 control subjects. Pathway analysis of differentially expressed proteins revealed dysregulation of the Ras-mitogen-activated protein kinase, ubiquitin-mediated proteolysis, angiogenesis-related (eg, hypoxia-inducible factor-1, vascular endothelial growth factor), and Hippo pathways. Pathways known to be dysregulated in HCM, including metabolic, inflammatory, and extracellular matrix pathways, were also dysregulated. Pathway analysis of proteins associated with clinical indicators of severe HCM and of differentially expressed genes supported these findings. The present study represents the most comprehensive (>7,000 proteins) and largest-scale (n=99 HCM cases) proteomic profiling of human HCM myocardium to date. Proteomic profiling and confirmatory transcriptomic profiling elucidate dysregulation of both newly recognized (eg, Ras-mitogen-activated protein kinase) and known pathways associated with pathogenesis and progression to severe forms of HCM.

Multi-Omics Exploration of the Mechanism of Curcumol to Reduce Invasion and Metastasis of Nasopharyngeal Carcinoma by Inhibiting NCL/EBNA1-Mediated UBE2C Upregulation.

Nasopharyngeal carcinoma (NPC) is closely linked to Epstein-Barr virus (EBV) infection. Curcumae Rhizoma, a traditional Chinese herb, has shown antitumor effects, primarily through its component curcumol (Cur), which has been shown to reduce NPC cell invasion and migration by targeting nucleolin (NCL) and Epstein-Barr Virus Nuclear Antigen 1 (EBNA1). We constructed an EBV-positive NPC cell model using C666-1 cells and performed transcriptomics studies after treatment with curcumol, which revealed a significant enrichment of ubiquitin-mediated proteolysis, the PI3K-AKT and mTOR signaling pathways, cell cycle and apoptosis involved in tumor invasion and migration. To investigate the importance of NCL and EBNA1 in curcumol-resistant EBV-positive NPC, we performed a multi-omics study using short hairpin NCL (shNCL) and shEBNA1 EBV-positive NPC cells, and the proteomics results showed enrichment in complement and coagulation cascades and ubiquitin-mediated proteolysis signaling pathways. Here, we focused on ubiquitin-conjugating enzyme E2C (UBE2C), which plays an important role in the ubiquitin-mediated proteolysis signaling pathway. In addition, metabolomics revealed that UBE2C is highly associated with 4-Aminobutanoic acid (GABA). In vitro studies further validated the function of the key targets, suggesting that UBE2C plays an important role in NCL and EBNA1-mediated curcumol resistance to nasopharyngeal carcinoma invasion and metastasis.

Sleep disturbances associated with DEAF1 pathogenic variants.

Neurodevelopmental disorders and sleep disturbances share genetic risk factors. DEAF1 genetic variants are associated with rare syndromes in which sleep disturbances are commonly reported, yet the specific sleep disorders in these patients, and the molecular mechanisms underlying this association, are unknown. We aimed to pinpoint specific biological processes that may be disrupted by pathogenic variants in this gene, comparing a list of DEAF1 regulatory target genes with a list of insomnia-associated genes, and using the intersect gene list as the input for pathway enrichment analysis. Thirty-nine DEAF1 regulatory targets were also identified as insomnia-associated genes, and the intersecting gene list was found to be strongly associated with immune processes, ubiquitin-mediated proteolysis pathways and regulation of the cell cycle. This preliminary study highlights pathways that may be disrupted by DEAF1 pathogenic mutations and might be putative factors underlying the manifestation of insomnia in patients harboring such variants.

Genome-wide identification and transcriptome profiling expression analysis of the U-box E3 ubiquitin ligase gene family related to abiotic stress in maize (Zea mays L.)

BackgroundThe U-box gene family encodes E3 ubiquitin ligases involved in plant hormone signaling pathways and abiotic stress responses. However, there has yet to be a comprehensive analysis of the U-box gene family in maize (Zea mays L.) and its responses to abiotic stress.ResultsIn this study, 85 U-box family proteins were identified in maize and were classified into four subfamilies based on phylogenetic analysis. In addition to the conserved U-box domain, we identified additional functional domains, including Pkinase, ARM, KAP and Tyr domains, by analyzing the conserved motifs and gene structures. Chromosomal localization and collinearity analysis revealed that gene duplications may have contributed to the expansion and evolution of the U-box gene family. GO annotation and KEGG pathway enrichment analysis identified a total of 105 GO terms and 21 KEGG pathways that were notably enriched, including ubiquitin-protein transferase activity, ubiquitin conjugating enzyme activity and ubiquitin-mediated proteolysis pathway. Tissue expression analysis showed that some ZmPUB genes were specifically expressed in certain tissues and that this could be due to their functions. In addition, RNA-seq data for maize seedlings under salt stress revealed 16 stress-inducible plant U-box genes, of which 10 genes were upregulated and 6 genes were downregulated. The qRT-PCR results for genes responding to abiotic stress were consistent with the transcriptome analysis. Among them, ZmPUB13, ZmPUB18, ZmPUB19 and ZmPUB68 were upregulated under all three abiotic stress conditions. Subcellular localization analysis showed that ZmPUB19 and ZmPUB59 were located in the nucleus.ConclusionsOverall, our study provides a comprehensive analysis of the U-box gene family in maize and its responses to abiotic stress, suggesting that U-box genes play an important role in the stress response and providing insights into the regulatory mechanisms underlying the response to abiotic stress in maize.

MicroRNA expression profile of chicken jejunum in different time points Eimeria maxima infection.

Coccidiosis stands as a protozoan disease of notable economic impact, characterized by an intracellular parasite that exerts substantial influence over poultry production. This invasion disrupts the integrity of the enteric mucosa, leading to the emergence of severe lesions and diminishing the efficiency of feed utilization in chickens. MicroRNA (miRNA) are short, non-coding RNA molecules with approximately 21-24 nucleotides long in size that play essential roles in various infectious diseases and inflammatory responses. However, the miRNA's expression patterns and roles in the context of Eimeria maxima infection of chicken intestines remain unclear. miRNA sequencing was employed to assess the miRNA expression profile in chicken jejunum during E. maxima infection. In this study, we analyzed miRNA expression profiles related to the host's immune response in the chicken jejunum during E. maxima infection. At 4 days infection and control (J4I versus J4C), 21 differentially expressed miRNAs in the jejunum were identified, comprising 9 upregulated and 12 downregulated miRNAs. Furthermore, in the jejunum, at 7 days infection and control (J7I versus J7C) groups, a total of 35 significantly differentially expressed miRNAs were observed, with 13 upregulated and 22 downregulated miRNAs. The regulatory networks were constructed between differentially expressed miRNA and mRNAs to offer insight into the interaction mechanisms between chickens and E. maxima coccidian infection. Furthermore, within the comparison group, we obtained 946, 897, and 281 GO terms that exhibited significant enrichment associated with host immunity in the following scenarios, J4I vs. J4C, J7I vs. J7C, and J4I vs. J7I, respectively. The KEGG pathway analysis indicated notable enrichment of differentially expressed miRNAs in the jejunum, particularly in J4I vs. J4C; enriched pathways included metabolic pathways, endocytosis, MAPK signaling pathway, regulation of actin cytoskeleton, and cytokine-cytokine receptor interaction. Moreover, in J7I vs. J7C, the KEGG pathway was significantly enriched, including metabolic pathways, protein processing in the endoplasmic reticulum, ubiquitin-mediated proteolysis, and FoxO signaling pathway. A comprehensive understanding of the host genetic basis of resistance with a combination of time-dependent infection to the Eimeria parasite is crucial for pinpointing resistance biomarkers for poultry production.

Network Analysis of Metabolome and Transcriptome Revealed Regulation of Different Nitrogen Concentrations on Hybrid Poplar Cambium Development.

Secondary development is a key biological characteristic of woody plants and the basis of wood formation. Exogenous nitrogen can affect the secondary growth of poplar, and some regulatory mechanisms have been found in the secondary xylem. However, the effect of nitrogen on cambium has not been reported. Herein, we investigated the effects of different nitrogen concentrations on cambium development using combined transcriptome and metabolome analysis. The results show that, compared with 1 mM NH4NO3 (M), the layers of hybrid poplar cambium cells decreased under the 0.15 mM NH4NO3 (L) and 0.3 mM NH4NO3 (LM) treatments. However, there was no difference in the layers of hybrid poplar cambium cells under the 3 mM NH4NO3 (HM) and 5 mM NH4NO3 (H) treatments. Totals of 2365, 824, 649 and 398 DEGs were identified in the M versus (vs.) L, M vs. LM, M vs. HM and M vs. H groups, respectively. Expression profile analysis of the DEGs showed that exogenous nitrogen affected the gene expression involved in plant hormone signal transduction, phenylpropanoid biosynthesis, the starch and sucrose metabolism pathway and the ubiquitin-mediated proteolysis pathway. In M vs. L, M vs. LM, M vs. HM and M vs. H, differential metabolites were enriched in flavonoids, lignans, coumarins and saccharides. The combined analysis of the transcriptome and metabolome showed that some genes and metabolites in plant hormone signal transduction, phenylpropanoid biosynthesis and starch and sucrose metabolism pathways may be involved in nitrogen regulation in cambium development, whose functions need to be verified. In this study, from the point of view that nitrogen influences cambium development to regulate wood formation, the network analysis of the transcriptome and metabolomics of cambium under different nitrogen supply levels was studied for the first time, revealing the potential regulatory and metabolic mechanisms involved in this process and providing new insights into the effects of nitrogen on wood development.

Identification of the hub genes linked to zearalenone-induced hepatotoxicity in broiler chickens

Zearalenone (ZEN) is a mycotoxin found in food and feed that impairs the function of multiple organs, especially the liver. However, the specific mechanisms through which ZEN induces liver damage in broiler chickens are not well understood. Therefore, this study aimed to identify the key genes linked to the hepatotoxicity induced by ZEN exposure in broiler chickens. Gene expression data from ZEN-treated and control chicken embryo primary hepatocytes (CEPHs) were used to implement differential expression analysis. Totally, 436 differentially expressed genes (DEGs) were detected, in which 223 and 213 genes were up- and down-regulated in ZEN-treated CEPHs, respectively. Gene ontology analysis suggested that these DEGs were involved in various biological processes, including chromosome segregation, mitotic cytokinesis, mitotic cell cycle, cell division, and mitotic spindle organization. Pathway analysis showed that the DEGs were associated with p53, FoxO, ubiquitin-mediated proteolysis, cell cycle, and mismatch repair signaling pathways. Furthermore, the hub genes, including BRCA1, CDC45, CDCA3, CDKN3, CENPE, CENPF, CENPI, CENPM, CENPU, and CEP55, potentially contributed to ZEN-induced hepatotoxicity. In conclusion, our study provides the valuable insight into the mechanism underlying ZEN-induced hepatotoxicity in broiler chickens.

Blood RNA-sequencing analysis in acrylamide-induced neurotoxicity and depressive symptoms in rats.

Acrylamide (ACR) is a by-product of the Maillard reaction, which occurs when food reacts at high temperatures. Occupational exposure is a risk factor for chronic ACR toxicity. ACR may cause neurotoxicity and depressive symptoms with high concentration in the blood; however, the underlying mechanism remains unknown. We showed the rats developed neurotoxic symptoms after being fed with ACR for 28 days, such as reduced activity and hind limb muscle weakness. We investigated whether ACR exposure causes gene expression differences by blood RNA sequencing and analyzed the differential expression of depressive symptoms-associated genes. The result indicated that IFN-γ the key regulator of neurotoxicity and depressive symptoms was induced by ACR. ACR induced the ubiquitin-mediated proteolysis pathway and JAK/STAT pathways gene expression. ACR upregulated the expression of IFN-γ, inducing neuroinflammation and neurotoxicity. ACR also upregulated the expression of JAK2, STAT1, PI3K, AKT, IκBα, UBE2D4, NF-κB, TNF-α, and iNOS in rat brain tissues and Neuro-2a cells. Thus, IFN-γ induction by ACR may induce depressive symptoms, and the ubiquitin-mediated proteolysis pathway and JAK/STAT pathways may involve in ACR neurotoxicity and depressive symptoms.

TICRR serves as a prognostic biomarker in lung adenocarcinoma with implications in RNA epigenetic modification, DDR pathway, and RNA metabolism.

TOPBP1 interacting checkpoint and replication regulator (TICRR), a hub gene of the Cdk2-mediated initiation step of DNA replication, has been shown an essential role in tumorigenesis by accelerating the DNA replication of tumor cells. RT-qPCR was used to detect the mRNA expression of TICRR in LUAD tumors and adjacent normal tissues. The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database of LUAD were acquired to analyze the critical role of TICRR expression in survival prognosis and clinicopathology characters in LUAD. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were performed using the R package. The correlation of TICRR expression with immune cellinfiltration, RNA epigenetic modification, DNA damage repair (DDR) pathway, and cell metabolism of LUAD was further explored to verify significant conclusions. TICRR was significantly upregulated in most cancer types, including LUAD, lung squamous cell carcinoma (LUSC), and others. Cox regression analysis indicated the overexpression of TICRR was associated with poor survival in several cancers. In LUAD, TICRR expression was positively correlated with tumor stage and was increased in smoking, male, and high tumor mutational burden (TMB) patients. Enrichment analysis revealed that TICRR could influence tumor proliferation and prognosis via activating pathways involving cell cycle, DNA repair, DNA replication, cysteine metabolism, oxidative phosphorylation, and ubiquitin-mediated proteolysis pathways. Interestingly, high TICRR expression correlated with DDR pathway signature (34 genes), 37 m6A/m5C regulated genes, and some metabolism-regulated genes. Silencing the TICRR gene affects cysteine metabolism and modifies cancer-related pathways, with decreased cell cycle and increased B/T cell receptor signaling. Our TICRR risk model accurately predicts LUAD patient prognosis, validated across GEO datasets, and is integrated with clinical characteristics via a nomogram, facilitating personalized treatment strategies and enhancing patient management. Taken together, TICRR has emerged as a promising prognostic biomarker in lung adenocarcinoma (LUAD), with implications in immune activation, cell cycle regulation, RNA modification, and tumor energy metabolism. These findings suggest that TICRR could serve as a viable therapeutic target and a reliable prognostic indicator for LUAD.

Proteogenomic Features Define Novel Subtypes of Mantle Cell Lymphoma

Introductions Recent advancements in mass spectrometry-based proteomics have unveiled novel translational and post-translational aspects of tumor biology. The joint characterization of tumor proteomics with genomics and transcriptomics enables proteogenomic analysis, improving our understanding of the molecular mechanisms, identifying new proteome-specific markers associated with clinical outcomes, and discovering novel treatment approaches. However, proteogenomic features remain largely uncharted due to a scarcity of information on MCL proteome. Methods We conducted a proteogenomic profiling study with 4 normal and 27 MCL B cells derived from healthy donors and MCL patients, integrating whole-exon sequencing (WES), transcriptome sequencing and mass spectrometry-based proteomics with data-independent acquisition (DIA) mode. We assessed the relationship among genetic lesions, RNA and protein expression, and further classified MCL based on omics information using k-means clustering. Results To this end, we first identified 1107 differentially expressed proteins between MCL and normal B cells (FDR&amp;lt;0.05) (329 upregulated and 778 downregulated in MCLs). The up-regulated proteins are highly enriched for RNA splicing and DNA repair pathway while the down-regulated proteins are primarily involved in cytoskeleton and endosomal transport. When integrated with 33 recurrent genetic lesions we previously reported, we found that mutations in CCND1 and NOTCH1 had significant impact on protein expression. Key genes including ATM and BCL10 were differentially expressed between samples with and without NOTCH1 mutation. Next, we computed Pearson correlation coefficients between RNA and protein levels for each gene to define the relationships between them. RB1 (0.88), PML (0.81) and CDK2 (0.81) showed high correlation efficiency, however, the overall correlation between RNA and protein abundance was low (0.26), suggesting that proteome abundance profiles may provide unseen information not previously discovered from WES and transcriptome data. Last, we evaluated protein expression level and their associations with progress free survival and overall survival to identify proteins potentially influencing clinical outcomes. Our comprehensive analysis led us to identify 40 proteins that could play a crucial role in disease progression. To assess the prognostic value of the omics data, we performed multi-omics clustering by incorporating genomics, transcriptomics and proteomics. This enabled us to identify four distinct clusters, each characterized by key driver genetic lesions as well as RNA and protein signatures. Notably, patients in these four clusters exhibited significantly different median overall survival (C1 to C4: not reach, 28.9, 15.8 and 7.9 months; log-rank test, P&amp;lt;0.001). Importantly, the protein signature remained significant even when considering the MIPI stage as a covariate (P&amp;lt;0.001), suggesting its potential as an independent prognostic factor. We then conducted an in-depth protein feature analysis and found that cluster 1 exhibited a significant enrichment of genes involved in ubiquitin-mediated proteolysis pathway. Cluster 2 showed a remarkable upregulation in DNA replication and cell cycle pathways. C3 displayed a significant upregulation of genes associated with BCR pathway and oxidative phosphorylation. Cluster 4 had an upregulation of RNA polymerase, pyrimidine metabolism, and RNA splicing, along with a notable downregulation in the BCR pathway. Our cluster analysis not only stratified MCL patients but also uncovered critical cellular pathways that could serve as potential therapeutic targets. Conclusions In this study, we investigated proteome changes and identified protein signatures associated with overall survival in MCL. Our integrative analysis unveiled four clusters, each characterized with unique genetic features, distinct gene and protein signatures, and different clinical outcomes. This study emphasizes the significance of protein abundance data as a nonredundant layer of information in MCL biology. Moreover, we have provided a protein expression reference map for MCL, offering valuable insights for future research and clinical applications.

Integrative profiling of metabolome and transcriptome of skeletal muscle after acute exercise intervention in mice.

This study aims to explore the molecular regulatory mechanisms of acute exercise in the skeletal muscle of mice. Male C57BL/6 mice were randomly assigned to the control group, and the exercise group, which were sacrificed immediately after an acute bout of exercise. The study was conducted to investigate the metabolic and transcriptional profiling in the quadriceps muscles of mice. The results demonstrated the identification of 34 differentially expressed metabolites (DEMs), with 28 upregulated and 6 downregulated, between the two groups. Metabolic pathway analysis revealed that these DEMs were primarily enriched in several, including the citrate cycle, propanoate metabolism, and lysine degradation pathways. In addition, the results showed a total of 245 differentially expressed genes (DEGs), with 155 genes upregulated and 90 genes downregulated. KEGG analysis indicated that these DEGs were mainly enriched in various pathways such as ubiquitin mediated proteolysis and FoxO signaling pathway. Furthermore, the analysis revealed significant enrichment of DEMs and DEGs in signaling pathways such as protein digestion and absorption, ferroptosis signaling pathway. In summary, the identified multiple metabolic pathways and signaling pathways were involved in the exercise-induced physiological regulation of skeletal muscle, such as the TCA cycle, oxidative phosphorylation, protein digestion and absorption, the FoxO signaling pathway, ubiquitin mediated proteolysis, ferroptosis signaling pathway, and the upregulation of KLF-15, FoxO1, MAFbx, and MuRF1 expression could play a critical role in enhancing skeletal muscle proteolysis.

Circulatory extracellular vesicle derived miR-195-5p promotes cellular apoptosis and suppresses cell proliferation in the buffalo endometrial primary cell culture

In pregnant animals, communication between the mother and conceptus occurs via extracellular vesicles (EVs) that carry several biomolecules such as nucleic acids (miRNAs, mRNAs), proteins, and lipids. At the time of implantation, the endometrium undergoes several morphological and physiological changes, such as angiogenesis, apoptosis, and cell proliferation regulation at the implantation site, to attain a receptive state. This study was conducted to detect pregnancy-specific miRNAs derived from extracellular vesicles in the systemic circulation of Bubalus bubalis (water buffalo) and to assess their functional significance in the modulation of endometrial primary cells. The extracellular vesicles were isolated from the blood plasma using a precipitation-based method and further characterized by various methods such as Differential light scattering, Nanoparticle tracking assay, Western blot, and transmission electron microscopy. The relative expression of the selected extracellular vesicles associated miRNAs (EV-miRNA) at different intervals (days 15, 19, 25, and 30) post artificial insemination (AI) was analyzed using RT-qPCR, and expression of miR-195-5p was found to be significantly higher (P < 0.01) in pregnant animals on day 19 post AI (implantation window) as compared to day 15 post AI. The elevated expression might indicate the involvement of this miRNA in the maternal-conceptus cross-talk occurring during the implantation period. The KEGG pathway enrichment and Gene Ontology analyses of the miR-195-5p target genes revealed that these were mostly involved in the PI3-Akt, MAPK, cell cycle, ubiquitin-mediated proteolysis, and mTOR signaling pathways, which are related to the regulation of cell proliferation. Transfecting the in vitro cultured cells with miR-195-5p mimic significantly suppressed (P < 0.05) the expression of its target genes such as YWHAQ, CDC27, AKT-3, FGF-7, MAPK8, SGK1, VEGFA, CACAND1, CUL2, MKNK1, and CACAN2D1. Furthermore, the downregulation of the miR-195-5p target genes was positively correlated with a significant increase in the apoptotic rate and a decrease in the proliferation. In conclusion, the current findings provide vital information on the presence of EV miR-195-5p in maternal circulation during the implantation window indicating its important role in the modulation of buffalo endometrium epithelial cells via promoting cell death. Altogether, the milieu of miR-195-5p may serve as a novel and potential molecular factor facilitating the implantation of the early embryo during the establishment of pregnancy in buffaloes. Thus, miR-195-5p may be identified as a unique circulatory EV biomarker related to establishing pregnancy in buffaloes as early as day 19 post-AI.

Dysfunction of an Anaphase-Promoting Complex Subunit 8 Homolog Leads to Super-Short Petioles and Enlarged Petiole Angles in Soybean

Plant height, petiole length, and the angle of the leaf petiole and branch angles are crucial traits determining plant architecture and yield in soybean (Glycine max L.). Here, we characterized a soybean mutant with super-short petioles (SSP) and enlarged petiole angles (named Gmssp) through phenotypic observation, anatomical structure analysis, and bulk sequencing analysis. To identify the gene responsible for the Gmssp mutant phenotype, we established a pipeline involving bulk sequencing, variant calling, functional annotation by SnpEFF (v4.0e) software, and Integrative Genomics Viewer analysis, and we initially identified Glyma.11G026400, encoding a homolog of Anaphase-promoting complex subunit 8 (APC8). Another mutant, t7, with a large deletion of many genes including Glyma.11G026400, has super-short petioles and an enlarged petiole angle, similar to the Gmssp phenotype. Characterization of the t7 mutant together with quantitative trait locus mapping and allelic variation analysis confirmed Glyma.11G026400 as the gene involved in the Gmssp phenotype. In Gmssp, a 4 bp deletion in Glyma.11G026400 leads to a 380 aa truncated protein due to a premature stop codon. The dysfunction or absence of Glyma.11G026400 caused severe defects in morphology, anatomical structure, and physiological traits. Transcriptome analysis and weighted gene co-expression network analysis revealed multiple pathways likely involved in these phenotypes, including ubiquitin-mediated proteolysis and gibberellin-mediated pathways. Our results demonstrate that dysfunction of Glyma.11G026400 leads to diverse functional consequences in different tissues, indicating that this APC8 homolog plays key roles in cell differentiation and elongation in a tissue-specific manner. Deciphering the molecular control of petiole length and angle enriches our knowledge of the molecular network regulating plant architecture in soybean and should facilitate the breeding of high-yielding soybean cultivars with compact plant architecture.

Identification and dimorphic expression of sex-related genes in Pacific abalone (Haliotis discus hannai)

Sex determination is a hot topic in evolutionary biology. The mechanism of sex determination is complex and diverse in shellfish, while no sex chromosomes have been found in mollusks. The Pacific abalone (Haliotis discus hannai) is one of the most economically important cultured shellfish species in China, and its sex determination mechanism is still unclear. Here, we identified the sex-determination region (SDR) of Pacific abalone and developed five stable sex-specific markers through genome-wide association studies (GWAS) based on re-sequencing data from 803 abalones. These markers can be used for sex discrimination in polyploid and sexually immature individuals in abalone breeding projects. In addition, haplotype analysis and quantitative expression of candidate sex-related genes showed that RhoGAPp190, Skp1, Cul2, and Otulin were potentially involved in the sex determination of Pacific abalone by the ubiquitin-mediated proteolysis pathway. Our study could help to better understand the molecular mechanisms that underpin sex determination and reproductive regulation in mollusks.

Transcriptome profiling provides insight into root development at low temperature by chimeric metacaspase for directing Pep1 formation

Plant elicitor peptides (Peps) and low temperatures have both emerged as important regulators of root development. The intracellular formation of Pep1 by metacaspase 4 at low temperature is expectedly linked to root-growth regulation. Here, we engineered a chimeric metacaspase 4 (cMC4) protein with altered structure by substituting linker of MC4 with linker of MC7 to efficiently direct Pep1 generation at low temperature (15 °C). Arabidopsis seedlings exhibited significantly root length inhibition at low temperature by incubating with in vitro Pep1 producing solution from cMC4-mediated cleavage, which was simulated as intracellular Pep1 of damaged root cell. Further investigation of root transcriptomic profiling for these treated seedlings indicated that low-temperature-responsive genes involving in cellular ion/cation homeostasis, response to karrikin, plant-type vacuole and cell wall, along with metabolic networks of protein processing in endoplasmic reticulum and phenylpropanoid biosynthesis potentially contributed to low-temperature resistance of Arabidopsis root. Root-developmental-response genes of pollen tube growth, meristem growth, root hair cell development, and cell projection, along with ubiquitin mediated proteolysis pathways and defense-related genes were positively correlated with Pep1 generation pattern for triggering defense response. To the best of our knowledge, this is the first time to engineer chimeric protein to strengthen Pep1-triggered immunity for root development at low temperature, which could provide a potential clue for controlling root growth against stress.

Investigation of targets and anticancer mechanisms of covalently acting natural products by functional proteomics.

Eriocalyxin B (EB), 17-hydroxy-jolkinolide B (HJB), parthenolide (PN), xanthatin (XT) and andrographolide (AG) are terpenoid natural products with a variety of promising antitumor activities, which commonly bear electrophilic groups (α,β-unsaturated carbonyl groups and/or epoxides) capable of covalently modifying protein cysteine residues. However, their direct targets and underlying molecular mechanisms are still largely unclear, which limits the development of these compounds. In this study, we integrated activity-based protein profiling (ABPP) and quantitative proteomics approach to systematically characterize the covalent targets of these natural products and their involved cellular pathways. We first demonstrated the anti-proliferation activities of these five compounds in triple-negative breast cancer cell MDA-MB-231. Tandem mass tag (TMT)-based quantitative proteomics showed all five compounds commonly affected the ubiquitin mediated proteolysis pathways. ABPP platform identified the preferentially modified targets of EB and PN, two natural products with high anti-proliferation activity. Biochemical experiments showed that PN inhibited the cell proliferation through targeting ubiquitin carboxyl-terminal hydrolase 10 (USP10). Together, this study uncovered the covalently modified targets of these natural products and potential molecular mechanisms of their antitumor activities.

Abstract P2-03-20: Clinical profiling and comprehensive analysis of candidate genes related to breast cancer estrogen receptor intratumour heterogeneity

Abstract 1. Background and Aim Breast cancer has the highest incidence among the world’s population. One third of patients diagnosed with early breast cancer progressed into metastatic outcomes due to the inherent heterogeneity and evolutionary features of tumors. The main clinical manifestation is the discordance of receptor expression in metastases. ESR1 the estrogen receptor (ER) encoding gene, has been proved affected ER expression. Nevertheless, the correlation between ER transformation and the somatic mutation profiles in breast cancer metastatic lesions remains unclear. Availability of advanced high-throughput technologies, and the development of bioinformatics tools has greatly accelerated our cognition of the molecular basis of cancer. In this study, we aimed to evaluate the frequency, clinical characteristics and prognostic value of ER receptor conversion between primary and first metastatic lesions in 115 patients whose primary ER status are positive. We also compared the results of NGS of 42 patients and explored latent genes related to ER discordance in expression. 2. Method Qualified metastatic tumor tissue sequencing information was available for 42 patients. Samples were accessed using the FoundationOne CDx assay (Foundation Medicine, Cambridge, MA, USA) panel including 733 tumor related genes. High frequency mutant genes were defined as the genes count more than 4 times in each group. All data were analyzed using SPSS 25.0 software (Chicago, IL, USA). Pearson’s chi-squared (χ2) test, Fisher’s exact test, were used to test the associations between different variables. The Cox proportional hazard models was used to evaluate the relationship between KMT2C mutation and Disease free survival (DFS) in the patients cohorts. The results with p &amp;lt; 0.05 were considered statistically significant. 3. Results and Conclusions All 115 patients (primary ER status is positive) were divided into two groups, 70(60.87%) patients ER status remained positive while 45(39.14%) patients ER status transformed into negative. The histological type (p=0.008) and DFS (p=0.004) were significantly different in two subgroups. There were no significant correlations between the age at the time of diagnosis, BMI classification, menopausal status, surgery, histological grade, tumor size, lymph node status, metastasis, Ki67, adjuvant radiotherapy, neoadjuvant, metastasis site before second biopsy, first treatment after recurrent and first PFS after rebiopsy. Univariable analysis of DFS proved metastasis to be distinct risk factor for poor survival (hazard ratio [HR] &amp;gt; 1, p = 0.001). By contrast, neoadjuvant proved to be protective factor for better survival (hazard ratio [HR] &amp;lt; 1, p &amp;lt; 0.001). The surgery, histological type, histological grade, tumorsize, metastasis, neoadjuvant, first treatment after recurrent, first PFS after rebiopsy were subsequently analyzed with the multivariable Cox analysis. Metastasis (HR&amp;gt;1, p=0.007) and neoadjuvant (HR&amp;lt;1, p&amp;lt;0.001) remained independent prognostic factors of DFS. We compared the differentially mutated genes in the ER differential expression BC patient groups. Mutations in TP53 (n=24) and PIK3CA (n=19) occurred most frequently in both groups and account for 57.14% and 49.23% separately. Notably, mutations in KMT2C (n=6) was detected in ER+ to – subgroup and accounted for 37.5%. According to the results of NGS, the distribution of KMT2C mutations was different among the two cohorts. We identified the mutation in codon 321 was the hot spot of KMT2C in our patient cohort. Next, we used the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to analyze the enriched pathways of KMT2C. KEGG pathway analysis revealed that patients with KMT2C mutations harbored significantly more mutations in genes involved in the Ubiquitin mediated proteolysis and Lysine degradation signaling pathway. Table 1. Patients’ basic clinicopathological characteristics among two groups Table 2. Univariate and Multivariate Analysis Between Clinicopathological Characteristics and DFS of 115 BC patients Table 3. Mutated Genes Rank and patients number Citation Format: Xi Wang, Yongmei Yin, Ziyi Fu. Clinical profiling and comprehensive analysis of candidate genes related to breast cancer estrogen receptor intratumour heterogeneity [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-03-20.

Transcriptome analysis and identification of genes associated with leaf crude protein content in foxtail millet [Setaria italica (L.) P. Beauv.

Introduction: Spruce spider mite is a primary insect pest of Chinese chestnut in China and seriously influences its yield and quality. However, the current management against this mite is costly and poorly effective. In previous research, we bred several foxtail millet materials for interplanting with chestnut tree, and found that they had high levels of crude protein (CP) in leaves and attracted spruce spider mite to feed on the leaves, thereby reducing chestnut damage. Methods: In this study, four foxtail millet varieties with significant differences in leaf crude protein content were used for high-throughput sequencing and identification of genes associated with leaf crude protein content. Gene enrichment analyses were carried out to comprehend the functions of these genes and the biological processes in which they are involved. In addition, transcription factors (TFs) were evaluated. Results: 435 differentially expressed genes (DEGs) were identified, suggesting their potential role in crude protein accumulation. Some differentially expressed genes were found to be associated with nitrogen metabolism and ubiquitin-mediated proteolysis pathways. Moreover, we identified 40 TF genes categorized into 11 transcription factor families. Discussion: Our findings represent an important resource that clarifies the mechanisms of accumulation and control of leaf crude protein in foxtail millet, and provide an opportunity for suppression of spruce spider mite attack on Chinese chestnut by interplanting with foxtail millet varieties with high concentrations of leaf crude protein.

CircRNA-miRNA-mRNA network targets ubiquitin-mediated proteolysis pathway in coronary artery disease

The convoluted crosstalk of non-coding RNA (ncRNA) and mRNA results in the regulation of pathogenic processes in coronary artery disease (CAD). We utilized an in silico approach to assess circular RNA (circRNA), microRNA (miRNA), and mRNA, as potential biomarkers for CAD. CircRNA pertaining to CAD, atherosclerosis, and myocardial infarction were extracted from two databases namely Circad and circR2Disease. miRNA target sites & RNA-binding protein interactions were predicted using the circRNAinteractome database. miRNA gene targets were predicted using TargetScan, DIANA, and miRDIP. Gene enrichment analysis revealed that circRNA-miRNA distinctively targets ubiquitin-mediated proteolysis pathways (p = 0.02). Dysregulated ubiquitin pathway is known to play a role in atherosclerotic plaque progression and instability.

Involvement of Small Non-Coding RNA and Cell Antigens in Pathogenesis of Extramedullary Multiple Myeloma

Extramedullary multiple myeloma (EMD) is an aggressive disease; malignant plasma cells lose their dependence in the bone marrow microenvironment and migrate into tissues. EMD is a negative prognostic factor of survival. Using flow cytometry and next-generation sequencing, we aimed to identify antigens and microRNAs (miRNAs) involved in EMD pathogenesis. Flow cytometry analysis revealed significant differences in the level of clonal plasma cells between MM and EMD patients, while the expression of CD markers was comparable between these two groups. Further, miR-26a-5p and miR-30e-5p were found to be significantly down-regulated in EMD compared to MM. Based on the expression of miR-26a-5p, we were able to distinguish these two groups of patients with high sensitivity and specificity. In addition, the involvement of deregulated miRNAs in cell cycle regulation, ubiquitin-mediated proteolysis and signaling pathways associated with infections or neurological disorders was observed using GO and KEGG pathways enrichment analysis. Subsequently, a correlation between the expression of analyzed miRNAs and the levels of CD molecules was observed. Finally, clinicopathological characteristics as well as CD antigens associated with the prognosis of MM and EMD patients were identified. Altogether, we identified several molecules possibly involved in the transformation of MM into EMD.