Differential Protein Expression Research Articles

Proteomics-driven discovery of LCAT as a novel biomarker for liver metastasis in colorectal cancer

BackgroundThis study aimed to identify molecular markers that influence liver metastasis in colorectal cancer (CRC) and assess their clinical relevance.MethodsProteomic analysis compared differential protein expression between CRC patients with liver metastasis (CRLM) and those without (CRNLM). Bioinformatics and survival analyses identified key proteins and validated them using the TCGA database for expression and clinical significance. Clinical and pathological data, along with tissue samples from our center, were used to create tissue microarrays for immunohistochemistry. Logistic regression assessed odds ratios (OR) for molecular markers linked to liver metastasis post-CRC surgery. Stable LCAT knockdown and overexpression CRC cell lines were constructed, and Transwell assays assessed the impact LCAT on cell migration. Nile red staining of these cells validated the effect LCAT on lipid metabolism in CRC cells.ResultsProteomic analysis identified 383 differentially expressed proteins between the CRLM and CRNLM groups (212 upregulated, 171 downregulated). Enrichment analysis linked these proteins to steroid and alcohol metabolism, inflammation, lipoproteins, and HDL particles, with key pathways in cholesterol and retinol metabolism. Lecithin cholesterol acyltransferase (LCAT), an important enzyme in this process, showed higher expression in CRC tissues, with increased LCAT linked to poorer 5-year OS, DSS, and PFI. LCAT expression also increased with tumor stage. Among 119 patients with CRC, preoperative complications, tumor staging, and LCAT scores differed significantly between patients with and without liver metastasis within 3 years post-surgery. LCAT and postoperative CEA levels were independent risk factors for liver metastasis (LCAT OR, 10.221; P = 0.002; CEA OR, 1.296; P = 0.014). Western blotting confirmed significantly higher LCAT expression in CRC tissues with liver metastasis. Transwell assays showed that LCAT overexpression enhanced migratory ability, while knockdown inhibited it. Nile red staining revealed increased lipid droplet accumulation in LCAT-overexpressing CRC cells, which was reduced by LCAT knockdown.ConclusionLCAT, which is involved in lipid metabolism, is an independent risk factor for liver metastasis following CRC surgery, suggesting its potential as a therapeutic target.

Myocardial Proteome in Human Heart Failure With Preserved Ejection Fraction.

Heart failure with preserved ejection fraction (HFpEF) constitutes more than half of all HF but has few effective therapies. Recent human myocardial transcriptomics and metabolomics have identified major differences between HFpEF and controls. How this translates at the protein level is unknown. Myocardial tissue from patients with HFpEF and nonfailing donor controls was analyzed by data-dependent acquisition (n=10 HFpEF, n=10 controls) and data-independent acquisition (n=44 HFpEF, n=5 controls) mass spectrometry-based proteomics. Differential protein expression analysis, pathway overrepresentation, weighted coexpression network analysis, and machine learning were integrated with clinical characteristics and previously reported transcriptomics. Principal component analysis (data-dependent acquisition-mass spectrometry) found HFpEF separated into 2 subgroups: one similar to controls and the other disparate. Downregulated proteins in HFpEF versus controls were enriched in mitochondrial transport/organization, translation, and metabolism including oxidative phosphorylation. Proteins upregulated in HFpEF were related to immune activation, reactive oxygen species, and inflammatory response. Ingenuity pathway analysis predicted downregulation of protein translation, mitochondrial function, and glucose and fat metabolism in HFpEF. Expression of oxidative phosphorylation and metabolism genes (higher) versus proteins (lower) was discordant in HFpEF versus controls. Data-independent acquisition-mass spectrometry proteomics also yielded 2 HFpEF subgroups; the one most different from controls had a higher proportion of patients with severe obesity and exhibited lower proteins related to fuel metabolism, oxidative phosphorylation, and protein translation. Three modules of correlated proteins in HFpEF that correlated with left ventricular hypertrophy and right ventricular load related to (1) proteasome; (2) fuel metabolism; and (3) protein translation, oxidative phosphorylation, and sarcomere organization. Integrative proteomics, transcriptomics, and pathway analysis supports a defect in both metabolism and translation in HFpEF. Patients with HFpEF with more distinct proteomic signatures from control more often had severe obesity, supporting therapeutic efforts targeting metabolism and translation, particularly in this subgroup.

Unbiased CSF Proteomics in Patients With Idiopathic Normal Pressure Hydrocephalus to Identify Molecular Signatures and Candidate Biomarkers.

Idiopathic normal pressure hydrocephalus (iNPH) is a reversible neurologic disorder that remains poorly understood. Accurate differential diagnosis of iNPH and Alzheimer disease (AD) is complicated by overlapping clinical manifestations. Beyond neuroimaging, there are currently no biomarkers available for iNPH leading to frequent misdiagnosis, and proteomic studies into iNPH have been limited by low sample sizes and inadequate analytical depth. In this study, we report the results of a large-scale proteomic analysis of CSF from patients with iNPH to elucidate pathogenesis and identify potential disease biomarkers. CSF samples were collected through lumbar puncture during diagnostic visits to the Mass General Brigham neurology clinic. Samples were analyzed using mass spectrometry. Differential expression of proteins was studied using linear regression models. Results were integrated with publicly available single-nucleus transcriptomic data to explore potential cellular origins. Biological process enrichment was analyzed using gene-set enrichment analyses. To identify potential diagnostic biomarkers, decision tree-based machine learning algorithms were applied. Participants were classified as cognitively unimpaired (N = 53, mean age: 66.5 years, 58.5% female), AD (N = 124, mean age: 71.2 years, 46.0% female), or iNPH (N = 44, mean age: 74.6 years, 34.1% female) based on clinical diagnosis and AD biomarker status. Gene Ontology analyses indicated upregulation of the immune system and coagulation processes and downregulation of neuronal signaling processes in iNPH. Differential expression analysis showed a general downregulation of proteins in iNPH. Integration of differentially expressed proteins with transcriptomic data indicated that changes likely originated from neuronal, endothelial, and glial origins. Using machine learning algorithms, a panel of 12 markers with high diagnostic potential for iNPH were identified, which were not all detected using univariate linear regression models. These markers spanned the various molecular processes found to be affected in iNPH, such as LTBP2, neuronal pentraxin receptor (NPTXR), and coagulation factor 5. Leveraging the etiologic insights from a typical neurologic clinical cohort, our results indicate that processes of immune response, coagulation, and neuronal signaling are affected in iNPH. We highlight specific markers of potential diagnostic interest. Together, our findings provide novel insights into the pathophysiology of iNPH and may facilitate improved diagnosis of this poorly understood disorder.

Network Pharmacology-Based Elucidation of the Hypoglycemic Mechanism of Grifola frondosa GF5000 Polysaccharides via GCK modulation in Diabetic Rats

Background/Objectives: Our lab has previously reported that Grifola frondosa (maitake mushroom) GF5000 has antidiabetic potential owing to its ability to improve insulin resistance. This study aimed to gain insight into the system-level hypoglycemic mechanisms of GF5000 using transcriptomics, proteomics, and network pharmacology. This study provides new insights into the hypoglycemic mechanisms of GF5000, identifying key molecular targets involved in mitigating insulin resistance in T2DM. Methods: Liver protein and gene expression in normal control (NC), diabetic control (DC), and GF5000-treated (GF5000) rats were analyzed via iTRAQ and RNA-seq. The relationships between differentially expressed genes (DEGs), differentially expressed proteins (DEPs), and type 2 diabetes (T2DM) disease targets were studied using Metascape and the Cytoscape GeneMANIA plug-in. Results: One hundred and fifty-two DEGs and sixty-two DEPs were identified; twenty DEGs/DEPs exhibited the same trend in mRNA and protein expression levels when comparing the GF5000 vs. DC groups. The Metascape analysis revealed that the T2DM disease targets included four DEGs—Gck, Scd, Abcb4, and Cyp3a9—and two DEPs—glucokinase and acetyl-CoA carboxylase 2. A Cytoscape–GeneMANIA analysis of thirteen DEGs/DEPs related to T2DM showed that Apoa1/Apolipoprotein A-I, Gckr/glucokinase regulatory protein, and Gck/glucokinase had the highest connectivity and centrality in the topological network. The qPCR results confirmed that GF5000 increased the mRNA expression of GCK in GCK-knockdown HepG2 cells. Conclusions: These results provide theoretical evidence for the use of GF5000 as a potential active nutritional ingredient for the prevention and treatment of T2DM. Our findings suggest that GF5000 targets multiple pathways implicated in T2DM, offering a multi-faceted approach to disease management and prevention.

Histone lactylation stimulated upregulation of PSMD14 alleviates neuron PANoptosis through deubiquitinating PKM2 to activate PINK1-mediated mitophagy after traumatic brain injury

ABSTRACT Alleviating the multiple types of programmed neuronal death caused by mechanical injury has been an impetus for designing neuro-therapeutical approaches after traumatic brain injury (TBI). The aim of this study was to elucidate the potential role of PSMD14 (proteasome 26S subunit, non-ATPase 14) in neuron death and the specific mechanism through which it improves prognosis of TBI patients. Here, we identified differential expression of the PSMD14 protein between the controlled cortical impact (CCI) and sham mouse groups by LC-MS proteomic analysis and found that PSMD14 was significantly upregulated in neurons after brain injury by qPCR and western blot. PSMD14 suppressed stretch-induced neuron PANoptosis and improved motor ability and learning performance after CCI in vivo. Mechanistically, PSMD14 improved PINK1 phosphorylation levels at Thr257 and activated PINK1-mediated mitophagy by deubiquitinating PKM/PKM2 (pyruvate kinase M1/2) to maintain PKM protein stability. PSMD14-induced mitophagy promoted mitochondrial homeostasis to reduced ROS production, and ultimately inhibited the neuron PANoptosis. The upregulation of neuronal PSMD14 after TBI was due to the increase of histone lactation modification level and lactate treatment alleviated neuron PANoptosis via increasing PSMD14 expression. Our findings suggest that PSMD14 could be a potential therapeutic approach for improving the prognosis of TBI patients. Abbreviations: CCI: controlled cortical impact; CQ: chloroquine; DUBs: deubiquitinating enzymes; H3K18la: H3 lysine 18 lactylation; IB: immunoblot; IHC: immunohistochemistry; IP: immunoprecipitation; MLKL: mixed lineage kinase domain like pseudokinase; PI3K: phosphoinositide 3-kinase; PINK1: PTEN induced kinase 1; PKM/PKM2: pyruvate kinase M1/2; PSMD14: proteasome 26S subunit, non-ATPase 14; ROS: reactive oxygen species; RIPK1: receptor interacting serine/threonine kinase 1; RIPK3: receptor interacting serine/threonine kinase 3; TBI: traumatic brain injury.

Multi-omics analysis of synovial tissue and fluid reveals differentially expressed proteins and metabolites in osteoarthritis.

Knee osteoarthritis is a common degenerative joint disease involving multiple pathological processes, including energy metabolism, cartilage repair, and osteogenesis. To investigate the alterations in critical metabolic pathways and differential proteins in osteoarthritis patients through metabolomic and proteomic analyses and to explore the potential mechanisms underlying synovial osteogenesis during osteoarthritis progression. Metabolomics was used to analyze metabolites in the synovial fluid and synovium of osteoarthritis patients (osteoarthritis group: 10; control group: 10), whereas proteomics was used to examine differential protein expression. Alkaline phosphatase activity was assessed to evaluate osteogenesis. Upregulation of the tricarboxylic acid cycle: Significant upregulation of the tricarboxylic acid cycle in the synovial fluid and synovium of osteoarthritis patients indicated increased energy metabolism and cartilage repair activity. Arginine metabolism and collagen degradation: Elevated levels of ornithine, proline, and hydroxyproline in the synovial fluid reflect active collagen degradation and metabolism, contributing to joint cartilage breakdown. Abnormal Phenylalanine Metabolism: Increased phenylalanine and tyrosine metabolite levels in osteoarthritis patients suggest their involvement in cartilage destruction and osteoarthritis progression. Synovial osteogenesis: Increased expression of type I collagen in the synovium and elevated alkaline phosphatase activity confirmed the occurrence of osteogenesis, potentially driven by the differentiation of synovial fibroblasts, mesenchymal stem cells, and hypertrophic chondrocytes. Relationships between differential proteins and osteogenesis: FN1 and TGFBI are closely associated with synovial osteogenesis, while the upregulation of energy metabolism pathways provides the energy source for osteogenic transformation. Alterations in energy metabolism, cartilage repair, and osteogenic mechanisms are critical. The related metabolites and proteins have potential as diagnostic and therapeutic targets for osteoarthritis.

Comparative Hypothalamic Proteomic Analysis Between Diet-Induced Obesity and Diet-Resistant Rats

Obesity arises from a complex interplay of genetic and environmental factors. Even among individuals with the same genetic predisposition, diet-induced obesity (DIO) exhibits varying degrees of susceptibility, which are categorized as DIO and diet-induced obesity resistance (DR). The hypothalamus plays a pivotal role in regulating energy homeostasis. This study performed a comparative hypothalamic proteomic analysis in DIO and DR rats to identify differentially expressed proteins (DEPs) associated with alterations in body weight. Male Sprague Dawley rats were fed either a standard chow diet or a high-fat diet for 12 weeks. DIO rats exhibited the most rapid weight gain compared to both the control and DR rats. Despite consuming similar caloric intake, DR rats exhibited less weight gain relative to DIO rats. Proteomic analysis revealed 31 DEPs in the hypothalamus of DR rats compared to DIO rats (with a false discovery rate (FDR) < 1%). Notably, 14 proteins were upregulated and 17 proteins were downregulated in DR rats. Gene ontology analysis revealed an enrichment of ion-binding proteins, such as those binding to Fe2+, Zn2+, Ca2+, and Se, as well as proteins involved in neuronal activity and function, potentially enhancing neuronal development and cognition in DR rats. The DEPs pathway analysis via the Kyoto Encyclopedia of Genes and Genomes (KEGG) implicated starch and sucrose metabolism, antigen processing and presentation, and the regulation of inflammatory mediator affecting TRP channels. Western blotting confirmed the proteomic findings for TRPV4, CaMKV, RSBN1, and BASP1, which were consistent with those obtained from Tandem Mass tag (TMT) proteomic analysis. In conclusion, our study highlights the hypothalamic proteome as a critical determinant in the susceptibility to DIO and provides novel targets for obesity prevention and treatment.

Changes in the Proteomic Profile After Audiogenic Kindling in the Inferior Colliculus of the GASH/Sal Model of Epilepsy

Epilepsy is a multifaceted neurological disorder characterized by recurrent seizures and associated with molecular and immune alterations in key brain regions. The GASH/Sal (Genetic Audiogenic Seizure Hamster, Salamanca), a genetic model for audiogenic epilepsy, provides a powerful tool to study seizure mechanisms and resistance in predisposed individuals. This study investigates the proteomic and immune responses triggered by audiogenic kindling in the inferior colliculus, comparing non-responder animals exhibiting reduced seizure severity following repeated stimulation versus GASH/Sal naïve hamsters. To assess auditory pathway functionality, Auditory Brainstem Responses (ABRs) were recorded, revealing reduced neuronal activity in the auditory nerve of non-responders, while central auditory processing remained unaffected. Cytokine profiling demonstrated increased levels of proinflammatory markers, including IL-1 alpha (Interleukin-1 alpha), IL-10 (Interleukin-10), and TGF-beta (Transforming Growth Factor beta), alongside decreased IGF-1 (Insulin-like Growth Factor 1) levels, highlighting systemic inflammation and its interplay with neuroprotection. Building on these findings, a proteomic analysis identified 159 differentially expressed proteins (DEPs). Additionally, bioinformatic approaches, including Gene Set Enrichment Analysis (GSEA) and Weighted Gene Co-expression Network Analysis (WGCNA), revealed disrupted pathways related to metabolic and inflammatory epileptic processes and a module potentially linked to a rise in the threshold of seizures, respectively. Differentially expressed genes, identified through bioinformatic and statistical analyses, were validated by RT-qPCR. This confirmed the upregulation of six genes (Gpc1—Glypican-1; Sdc3—Syndecan-3; Vgf—Nerve Growth Factor Inducible; Cpne5—Copine 5; Agap2—Arf-GAP with GTPase domain, ANK repeat, and PH domain-containing protein 2; and Dpp8—Dipeptidyl Peptidase 8) and the downregulation of two (Ralb—RAS-like proto-oncogene B—and S100b—S100 calcium-binding protein B), aligning with reduced seizure severity. This study may uncover key proteomic and immune mechanisms underlying seizure susceptibility, providing possible novel therapeutic targets for refractory epilepsy.

Novel De Novo BRCA2 Variant in an Early-Onset Ovarian Cancer Reveals a Unique Tumor Evolution Pathway.

Ovarian cancer (OC) is a highly heterogeneous malignancy, often characterized by complex genomic alterations that drive tumor progression and therapy resistance. In this paper, we report a novel de novo BRCA2 germline variant NM_000059.3:c.(8693_8695delinsGT) associated with early-onset OC that featured two regions with differential MMR (Mismatch Repair) gene expression. To date, only six cases of de novo BRCA2 variants have been reported, none of which were associated with early-onset high-grade serous OC. The immunohistochemical analysis of MMR genes revealed two distinct tumor areas, separated by a clear topographic boundary, with the heterogeneous expression of MLH1 and PMS2 proteins. Seventy-five percent of the tumor tissue showed positivity, while the remaining 25% exhibited a complete absence of expression, underscoring the spatial variability in MMR gene expression within the tumor. Integrated comparative spatial genomic profiling identified several tumor features associated with the genetic variant as regions of loss of heterozygosity (LOH) that involved BRCA2 and MLH1 genes, along with a significantly higher mutational tumor burden in the tumor area that lacked MLH1 and PMS2 expression, indicating its further molecular evolution. The following variants were acquired: c.6572C>T in NOTCH2, c.1852C>T in BCL6, c.191A>T in INHBA, c.749C>T in CUX1, c.898C>A in FANCG, and c.1712G>C in KDM6A. Integrated comparative spatial proteomic profiles revealed defects in the DNA repair pathways, as well as significant alterations in the extracellular matrix (ECM). The differential expression of proteins involved in DNA repair, particularly those associated with MMR and Base Excision Repair (BER), highlights the critical role of defective repair mechanisms in driving genomic instability. Furthermore, ECM components, such as collagen isoforms, Fibrillin-1, EMILIN-1, Prolargin, and Lumican, were found to be highly expressed in the MLH1/PMS2-deficient tumor area, suggesting a connection between DNA repair deficiencies, ECM remodeling, and tumor progression. Thus, the identification of the BRCA2 variant sheds light on the poorly understood interplay between DNA repair deficiencies and ECM remodeling in OC, providing new insights into their dual role in shaping tumor evolution and suggesting potential targets for novel therapeutic strategies.

Targeting the Galectin-7/TRPM2/Zn2+/DRP-1 Signaling Pathway: A Potential Therapeutic Intervention in the Pathogenesis of SJS/TEN.

Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) represent a spectrum of severe drug-induced cutaneous reactions. These conditions are characterized by widespread and confluent keratinocyte apoptosis, which differentiates them from erythema multiforme (EM). Mounting evidence has implicated the mitochondrial-dependent apoptosis pathway in the pathogenesis of SJS/TEN, but the potential roles and specific mechanisms of these pathways in SJS/TEN remain largely unexplored. Proteomic analyses were conducted to investigate differential protein expression in blister fluid (BF)-derived exosomes from suction surgery in healthy individuals (Con Exo) or patients with EM (EM Exo) or SJS/TEN (TEN Exo). Further analysis involved glutathione S-transferase (GST) pull-down assay, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, and validation of MS results through proximity ligation assay (PLA) and coimmunoprecipitation (co-IP). Phenotypic and mechanistic analyses were performed using immunohistochemistry (IHC) staining, enzyme-linked immunosorbent assay (ELISA), western blotting, reverse transcription-polymerase chain reaction (RT-PCR), co-IP, CCK-8 assay, adenosine triphosphate (ATP) level measurements, and flow cytometry. Galectin-7 was markedly upregulated in BF-derived exosomes from SJS/TEN patients and showed a correlation with disease severity. Further analysis confirmed the interaction between galectin-7 and transient receptor potential (melastatin) 2 (TRPM2). BF-derived exosomes from SJS/TEN patients induced an imbalance in mitochondrial dynamics via galectin-7/TRPM2 upregulation. Activation of TRPM2 led to an elevation in mitochondrial Zn2+, which facilitated the recruitment of the fission factor dynamin-related protein-1 (DRP-1) to mitochondria to trigger mitochondrial fission in the keratinocyte. In addition, the recruitment of DRP-1-dependent mitochondrial fission via the voltage-dependent anion channel 1 (VDAC1)/hexokinase 2 (HK2)-mediated opening of the mitochondrial permeability transition pore (mPTP)-triggered cytochrome c release. These effects ultimately induce activation of the intrinsic mitochondrial apoptotic pathway and contribute to the pathogenesis of SJS/TEN. Targeting the galectin-7/TRPM2/Zn2+/DRP-1 signaling pathway in keratinocytes presents a prospective therapeutic strategy for mitigating SJS/TEN in the future.

Leukocyte-specific protein 1 is associated with the stage and tumor immune infiltration of cervical cancer

Cervical cancer (CC) is a leading cause of cancer-related mortality among women and is strongly associated with persistent infection by high-risk human papillomavirus (HR-HPV), particularly the HPV16 subtype. Existing detection methods have limitations in meeting clinical requirements. This study aims to identify biomarkers that can aid in the staging and prognosis of cervical cancer. Cervical epithelial exfoliated cell samples were collected from three groups: HPV16-negative normal cervix, HPV16-positive normal cervix, and HPV16-positive cervical cancer. Differential expression proteins (DEPs) were identified using TMT-LC–MS/MS technology, and their associations with tumor-infiltrating lymphocytes (TILs) and immune regulatory molecules were analyzed. Leukocyte-specific protein 1 (LSP1), an intracellular F-actin-binding protein predominantly expressed in macrophages, neutrophils, B cells, and T cells, was identified as a potential biomarker. The expression levels of LSP1 were evaluated and validated using the Human Protein Atlas (HPA) database, immunohistochemistry (IHC), Western blotting (WB), and real-time quantitative PCR (RT-qPCR). Multiplex fluorescence immunohistochemistry (mIHC) was employed to assess the co-localization of LSP1 with CD4+ and CD8+ T cells. Results indicated that both protein and mRNA levels of LSP1 were significantly elevated in cervical cancer tissues compared to adjacent non-tumor tissues. Notably, LSP1 expression was higher in early-stage cervical cancer (Stage IB) than in advanced-stage disease (Stage IIIC). Furthermore, LSP1 was predominantly localized in CD4+ and CD8+ T cells with low TIM-3 expression. Analysis of public databases (GEPIA, TIMER2.0, and TISIDB) revealed that higher LSP1 mRNA levels correlated with better patient outcomes. LSP1 expression was positively associated with the abundance of major TILs and immune regulatory molecules, particularly activated B cells, CD8+ T cells, and CD4+ T cells, while negatively correlated with M2 macrophages and myeloid-derived suppressor cells. These findings indicate that the expression levels of LSP1 in cervical tissues are correlated with cancer staging and patient prognosis, potentially reflecting both tumor immune infiltration and T-cell exhaustion within the tumor microenvironment (TME).

Utilizing Multi-Omics Analysis to Elucidate the Molecular Mechanisms of Oat Responses to Drought Stress.

The oat is a crop and forage species with rich nutritional value, capable of adapting to various harsh growing environments, including dry and poor soils. It plays an important role in agricultural production and sustainable development. However, the molecular mechanisms underlying the responses of oat to drought stress remain unclear, warranting further research. In this study, we conducted a pot experiment with the drought-resistant cultivar JiaYan 2 (JIA2) and water-sensitive cultivar BaYou 9 (BA9) during the booting stage under three water gradient treatment conditions: 30% field capacity (severe stress), 45% field capacity (moderate stress), and 70% field capacity (normal water supply). After 7 days of stress, root samples were collected for transcriptome and proteome analyses. Transcriptome analysis revealed that under moderate stress, JIA2 upregulated 1086 differential genes and downregulated 2919 differential genes, while under severe stress, it upregulated 1792 differential genes and downregulated 4729 differential genes. Under moderate stress, BA9 exhibited an upregulation of 395 differential genes, a downregulation of 669, and an upregulation of 886 differential genes, and it exhibited 439 downregulations under severe stress. Under drought stress, most of the differentially expressed genes (DEGs) specific to JIA2 were downregulated, mainly involving redox reactions, carbohydrate metabolism, plant hormone signal regulation, and secondary metabolism. Proteomic analysis revealed that in JIA2, under moderate stress, 489 differential proteins were upregulated and 394 were downregulated, while 493 differential proteins were upregulated and 701 were downregulated under severe stress. In BA9, 590 and 397 differential proteins were upregulated under moderate stress, with 126 and 75 upregulated differential proteins under severe stress. Correlation analysis between transcriptomics and proteomics demonstrated that compared with no drought stress, four types of differentially expressed proteins (DEPs) were identified in the JIA2 differential gene-protein interaction network analysis under severe stress. These included 13 key cor DEGs and DEPs related to plant hormone signal transduction, biosynthesis of secondary metabolites, carbohydrate metabolism processes, and metabolic pathways. The consistency of gene and protein expression was validated using qRT-PCR, indicating their key roles in the strong drought resistance of JIA2.

The TCF4 Gene Regulates Apoptosis of Corneal Endothelial Cells in Fuchs Endothelial Corneal Dystrophy.

Fuchs endothelial corneal dystrophy (FECD) is a progressive corneal disorder characterized by excessive extracellular matrix (ECM) accumulation and corneal endothelial cell death. CTG trinucleotide repeat expansion in the transcription factor 4 (TCF4) gene represents the most significant genetic risk factor. This study aimed to elucidate the role of TCF4 in FECD pathogenesis through comprehensive proteomic analysis. Corneal endothelial cells isolated from patients with FECD harboring TCF4 trinucleotide repeat expansion were immortalized to establish an FECD cell model (iFECD). CRISPR/Cas9-mediated genome editing was employed to generate TCF4-knockout iFECD cells. Whole-cell proteome analysis was performed using liquid chromatography-mass spectrometry, followed by pathway enrichment analysis of differentially expressed proteins (DEPs). The effects of TCF4 deletion on TGF-β-mediated protein aggregation and cell death were evaluated using Western blot analysis, flow cytometry, and aggresome detection assays. Proteomic analysis identified 88 DEPs among 6510 detected proteins. Pathway analysis revealed significant enrichment in ECM-associated pathways, oxidative stress responses, and cellular motility. TCF4 deletion attenuated TGF-β-induced cell death in iFECD cells. Concordantly, Western blot analysis demonstrated that TCF4 deletion suppressed TGF-β2-mediated cleavage of caspase-3 and poly (ADP-ribose) polymerase. Flow cytometric analysis of Annexin V-positive cells confirmed reduced apoptosis in TCF4-deleted cells following TGF-β2 treatment. Additionally, aggresome detection assays revealed that TCF4 deletion diminished TGF-β2-induced protein aggregation. This study demonstrates a crucial role for TCF4 in FECD pathogenesis, particularly in ECM regulation and protein aggregation-induced cell death.

Differential cellular origins of the extracellular matrix of tumor and normal tissues according to colorectal cancer subtypes.

Understanding the proteomic-level heterogeneity of the tumor microenvironment (TME) in colorectal cancer (CRC) is crucial due to its well-known heterogeneity. While heterogenous CRC has been extensively characterized at the molecular subtype level, research into the functional heterogeneity of fibroblasts, particularly their relationship with extracellular matrix (ECM) alterations, remains limited. Addressing this gap is essential for a comprehensive understanding of CRC progression and the development of targeted therapies. 24 tissue samples from 21 CRC patients, along with adjacent normal tissues (NAT), were collected and decellularized using a detergent-based method to enrich the ECM component. Proteomic analysis of ECM-enriched samples was performed using tandem mass tag (TMT) spectrometry, followed by statistical analysis including differential expression protein (DEP) analysis. Single-cell RNA sequencing (scRNA-Seq) data from public datasets were integrated and analyzed to delineate cell states within the TME. Bulk tissue RNA-Seq and bioinformatics analysis, including consensus molecular subtype (CMS) classification and single-cell level deconvolution of TCGA bulk RNA-seq data, were conducted to further explore gene expression patterns and TME composition. Differential cellular origin of the NAT and tumorous ECM proteins were identified, revealing 110 ECM proteins enriched in NAT and 28 ECM proteins in tumor tissues. Desmoplastic and WNT5A+ inflammatory fibroblasts were indicated as the sources of tumor-enriched ECM proteins, while ADAMDEC1+ expressing fibroblasts and PI16+ expressing fibroblast were identified as the sources of NAT-enriched ECM proteins. Deconvolution of bulk RNA-seq of CRC tissues discriminated CMS-specific fibroblast state, reflecting the biological traits of each CMS subtype. Specially, seven ECM genes specific to mesenchymal subtype (CMS4), including PI16+ fibroblast-related 4 genes (SFRP2, PRELP, OGN, SRPX) and desmoplastic fibroblast-related 3 genes (THBS2, CTHRC1, BGN), showed a significant association with poorer survival in patient with CRC. We conducted an extracellular matrix (ECM)-focused profiling of the TME by integrating quantitative proteomics with single-cell RNA sequencing (scRNA-seq) data from CRC patients. We identified the ECM proteins of NAT and tumor tissue, and established a cell-matrisome database. We defined mesenchymal subtype-specific molecules associated with specific fibroblast subtypes showing a significant association with poorer survival in patients with CRC. Our ECM-focused profiling of tumor stroma provides new insights as indicators for biological processes and clinical endpoints.

Implications of CYP1B1 in the treatment and prognosis of breast cancer

BackgroundCytochrome P450 1B1 (CYP1B1) enzyme plays an important metabolic role, especially in the metabolism of xenobiotics, endogenous substances, and procarcinogens. It may be involved in tumor initiation and progression. High levels of CYP1B1 have been identified in aggressive breast cancer cell lineages. The aim of the present study was to identify the expression and role of this enzyme in progression, prognosis, and clinical features of breast cancer patients.MethodsMicroarray paraffin-embedded tumor samples from 166 women with breast cancer were analyzed by immunohistochemical for CYP1B1. Statistical analyses were performed to correlate CYP1B1 expression with various clinical parameters among breast cancer patients. Bioinformatic tools were used to determine differential CYP1B1 mRNA and protein expression from patients in databases compared with our cohort.ResultsThe CYP1B1 enzyme was overexpressed in 75% of breast cancer tissues. This result remained consistent regardless of the treatment regimen. Furthermore, although it was not negatively associated with overall survival, its expression was notably higher in patients who died and in patients with ER- (estrogen receptor negative) and PR- (progesterone receptor negative) tumors and p53 (protein 53) mutation carriers. These findings align with the consulted databases, which indicated a relationship between CYP1B1 expression, tumor progression, and malignancy, suggesting its potential role as a biomarker for tumor aggressiveness.ConclusionsIn conclusion, CYP1B1 showed a positive correlation with breast cancer malignancy, tumor progression, and toxicity effects in breast cancer patients. These findings emphasize the importance of CYP1B1 as a potential treatment target and its significance in the clinical management of breast cancer.

A Preliminary Exploration of Transcriptome and Proteomic Changes During the Young and Harvest Periods in Morchella sextelata

Based on transcriptome and proteome sequencing technologies, this study aims to preliminarily reveal the molecular mechanisms of growth and development and related metabolic regulation in Morchella sextelat. A total of 42.31 GB of Clean Data was acquired from the transcriptome sequencing (RNA-seq) of six samples in two development phases (n = 3) of M. sextelata. In the young phase (YP) and harvest phase (HP), there were 2887 differentially expressed genes (DEGs), including 1910 up-regulated genes and 977 down-regulated genes. In YP and HP, there were 987 differentially expressed proteins (DEPs), including 417 up-regulated ones and 570 down-regulated ones. Based on GO and KEGG analysis, significant differences in the transcriptomes and proteins in metabolic pathways are disclosed. Glycometabolism, especially starch, saccharose, and polysaccharide metabolism, plays a crucial role in the growth of M. sextelata. In addition, expression changes in the genes related to selenium metabolism are here recognized. These research results not only offer strong support for further exploration of the biological significance and functional differences of M. sextelata, but are also conducive to discovering key genes and understanding their regulation network during growth.

Mechanistic insights into retinoic-acid treatment for autism in the improvement of social behavior: evidence from a multi omics study in rats

Mechanistic insights into retinoic-acid treatment for autism in the improvement of social behavior: evidence from a multi omics study in rats

Multi-omics analyses reveal that sirtuin 5 promotes the development of pre-recruitment follicles by inhibiting the autophagy-lysosome pathway in chicken granulosa cells.

Multi-omics analyses reveal that sirtuin 5 promotes the development of pre-recruitment follicles by inhibiting the autophagy-lysosome pathway in chicken granulosa cells.

Identification of voltage-dependent anion-selective channel protein 1 as a freezability biomarker in chicken spermatozoa.

Identification of voltage-dependent anion-selective channel protein 1 as a freezability biomarker in chicken spermatozoa.

Tas2r123-associated mitochondrial organization and neuroplasticity underlying the antidepressant effect of resveratrol.

Tas2r123-associated mitochondrial organization and neuroplasticity underlying the antidepressant effect of resveratrol.