Changes In Protein Expression Research Articles

Acrylamide-Aggravated Liver Injury by Activating Endoplasmic Reticulum Stress in Female Mice with Diabetes.

Acrylamide (ACR) is a common industrial contaminant with endocrine-disrupting toxicity. Numerous studies have indicated that females and diabetics are more sensitive to environmental contaminants. However, it remains unknown whether female diabetics are susceptible to ACR-induced toxicity and its potential mechanisms. Thus, the female ACR-exposure diabetic Balb/c mice model was established to address these issues. Results showed that ACR could induce liver injury in normal mice and cause more serious inflammatory cell infiltration, hepatocyte volume increase, and fusion in diabetic mice liver. Meanwhile, ACR could lead to exacerbation of diabetic symptoms in diabetic mice by disturbing the glucose and lipid metabolism in the liver, which mainly manifests as the accumulation of liver glycogen and liver lipids, the reduction of the activity/content of glycolytic and metabolizing enzyme as well as pentose phosphatase, upregulation of the gene expression in fatty acid transporter and gluconeogenesis, and downregulation of the gene expression in fatty acid synthesis and metabolism. Moreover, ACR exposure could induce oxidative stress, inflammation, and endoplasmic reticulum stress in the liver by a decrease in hepatic antioxidant enzyme activity and antioxidant content, an increase in inflammatory factor levels, and a change in the related protein expression of endoplasmic reticulum stress (ERS) and apoptosis-related pathways in diabetic mice. Statistical analysis results revealed that ACR-induced liver injury was highly correlated with inflammation and oxidative stress, and ERS and diabetic mice had a higher risk of liver injury than normal mice. Overall results suggested that female diabetic mice easily suffer from ACR-induced toxicity, and the reason was that ACR could induce further damage to the liver by worsening the condition of inflammation, oxidative stress, and ERS in the liver.

Disordered GPR43/NLRP3 expression in peripheral leukocytes of patients with atrial fibrillation is associated with intestinal short chain fatty acids levels

BackgroundAtrial fibrillation (AF) is associated with circulating inflammation. Short-chain fatty acids (SCFAs) derived from gut microbiota (GM) regulate leukocyte function and inhibit the release of inflammatory cytokines, which are partly mediated by the G-protein-coupled receptor 43 (GPR43) signaling. This study aimed to investigate the expression of GPR43/NOD-like receptors family pyrin domain containing 3 (NLRP3) in leukocytes and the interaction with intestinal SCFAs levels in AF patients.MethodsExpressions of GPR43 and NLRP3 mRNA in peripheral blood leukocytes from 23 AF patients and 25 non-AF controls were detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Expressions of leukocyte GPR43 and NLRP3 protein were evaluated by western blot analysis. The levels of plasma IL-1β were measured by enzyme-linked immunosorbent assay (ELISA). The fecal SCFAs levels based on GC/MS metabolome of corresponding 21 controls and 14 AF patients were acquired from our published dataset. To evaluate the expression of NLRP3 and GPR43 and the release of IL-1β, human THP-1 cells were stimulated with or without SCFAs (acetate, propionate, and butyrate), lipopolysaccharide (LPS), and nigericin in vitro, respectively.ResultsCompared to the controls, the mRNA expression in peripheral leukocytes was significantly reduced in AF patients (P = 0.011) coupled with the increase in downstream leukocyte NLRP3 mRNA expression (P = 0.007) and plasma IL-1β levels (P < 0.001), consistent with changes in GPR43 and NLRP3 protein expression. Furthermore, leukocyte GPR43 mRNA levels were positively correlated with fecal GM-derived acetic acid (P = 0.046) and negatively correlated with NLRP3 mRNA expression (P = 0.024). In contrast to the negative correlation between left atrial diameter (LAD) and GPR43 (P = 0.008), LAD was positively correlated with the leukocyte NLRP3 mRNA levels (P = 0.024). Subsequent mediation analysis showed that 68.88% of the total effect of intestinal acetic acid on AF might be mediated by leukocyte GPR43/NLRP3. The constructed GPR43–NLRP3 score might have a predictive potential for AF detection (AUC = 0.81, P < 0.001). Moreover, SCFAs treatment increased GPR43 expression and remarkably reduced LPS/nigericin-induced NLRP3 expression and IL-1β release in human THP-1 cells in vitro.ConclusionsDisrupted interactions between GPR43 and NLRP3 expression in peripheral blood leukocytes, associated with reduced intestinal GM-derived SCFAs, especially acetic acid, may be involved in AF development and left atrial enlargement by enhancing circulating inflammation.

Progressive changes in the protein expression profile of alveolar septa in early-stage lung adenocarcinoma.

Adenocarcinomas show a stepwise progression from atypical adenomatous hyperplasia (AAH) through adenocarcinoma in situ (AIS) to invasive adenocarcinoma (IA). Immunoglobulin superfamily containing leucine-rich repeat (ISLR) is a marker of tumor-restraining cancer-associated fibroblasts (CAFs), which are distinct from conventional, strongly α-smooth muscle actin (αSMA)-positive CAFs. Fibroblastactivation protein (FAP) has been focused on as a potential therapeutic and diagnostic target of CAFs. We investigated the changes in protein expression during adenocarcinoma progression in the pre-existing alveolar septa by assessing ISLR, αSMA, and FAP expression in normallung, AAH, AIS, and IA. Fourteen AAH, seventeen AIS, and twenty IA lesions were identified and randomly sampled. Immunohistochemical analysis was performed to evaluate cancer-associated changes and FAP expression in the pre-existing alveolar structures. Normal alveolar septa expressed ISLR. The ISLR level in the alveolar septa decreased in AAH and AIS tissues when compared with that in normal lung tissue. The αSMA-positive area gradually increased from the adjacent lung tissue (13.3% ± 15%) to AIS (87.7% ± 14%), through AAH (70.2% ± 21%). Moreover, the FAP-positive area gradually increased from AAH (1.69% ± 1.4%) to IA (11.8% ± 7.1%), through AIS (6.11% ± 5.3%). Protein expression changes are a feature of CAFs in the pre-existing alveolar septa that begin in AAH. These changes gradually progressed from AAH to IA through AIS. FAP-positive fibroblasts may contribute to tumor stroma formation in early-stage lung adenocarcinoma, and this could influence the development of therapeutic strategies targeting FAP-positive CAFs for disrupting extracellular matrix formation.

M1-type microglia-derived exosomes contribute to blood–brain barrier damage

BackgroundAs a key substance for intercellular communication, exosomes could be a potential strategy for stroke treatment. Activated microglia disrupt the integrity of blood–brain barrier (BBB) to facilitate the stroke process. Hence, this study was designed to investigate the effect of microglia-derived exosomes on BBB cell model injury and to explore the underlying molecular mechanisms. MethodsM1 polarization of BV2 cells was induced with LPS and their derived exosomes were isolated. Astrocytes were cultured in primary culture and constructed with End3 cells as a BBB cell model. After co-culture with exosomes, the BBB cell model was examined for changes in TEER, permeability, and expression of BBB-related proteins (Claudin-1, Occludin, ZO-1 and JAM). Resting and M1-type BV2 cell-derived exosomes perform small RNA sequences and differentially expressed miRNAs (DE-miRNAs) are identified by bioinformatics. ResultsM1-type BV2 cell-derived exosomes decreased End3 cell viability, and increased their apoptotic ratio. Moreover, M1 type BV2 cell-derived exosomes dramatically enhanced the permeability of BBB cell model, and diminished the TEER and BBB-related protein (Claudin-1, Occludin, ZO-1) expression. Notably, resting BV2 cell-derived exosomes had no effect on the integrity of BBB cell model. Sequencing results indicated that 71 DE-miRNAs were present in M1 BV2 cell-derived exosomes, and their targets mediated neurological development and signaling pathways such as MAPK and cAMP. RT-qPCR confirmed the differential expression of mmu-miR-125a-5p, mmu-miR-122b-3p, mmu-miR-139-3p, mmu-miR-330-3p, mmu-miR-3057-5p and mmu-miR-342-3p consistent with the small RNA sequence. Furthermore, Creb1, Jun, Mtor, Frk, Pabpc1 and Sdc1 are the most well-connected proteins in the PPI network. ConclusionM1-type microglia-derived exosomes contribute to the injury of BBB cell model, which has the involvement of miRNAs. Our findings provide new perspectives and potential mechanisms for future M1 microglia-derived exosomes as therapeutic targets in stroke.

Abstract LB034: First-in-class compounds targeting the MIEN1 signaling pathway: A breakthrough approach for breast and prostate cancer therapy

Abstract We report the identification and complete characterization of first-in-class molecules targeting the MIEN1 signaling pathway in cancer. Migration and invasion enhancer 1 (MIEN1) overexpression characterizes several cancers and facilitates cancer cell migration and invasion. Leveraging conserved ITAM and prenylation motifs within MIEN1, we identified potent anti-cancer peptides. Among them, bioactive peptides LA3IK and RP-7 induced pronounced transcriptomic and protein expression changes at sub-IC50 concentrations. The peptides effectively inhibited genes and proteins driving cancer cell migration, invasion, and EMT pathways, concurrently suppressing EGF-induced NF-kB nuclear translocation in metastatic breast cancer cells. Specifically, peptides targeted the same signal transduction pathway initiated by MIEN1. Molecular docking and circular dichroism spectroscopy indicated the formation of MIEN1-peptide complexes. The third-positioned isoleucine in LA3IK and CVIL motif in RP-7 were crucial for inhibiting breast cancer cell migration. This is evident from the limited migration inhibition observed when MDA-MB-231 cells were treated with scrambled peptides LA3IK-SCR and RP-7-SCR. Additionally, LA3IK and RP-7 effectively suppressed tumor growth in an orthotopic breast cancer model. Notably, mice tolerated high peptide doses of up to 90 mg/Kg well, surpassing significantly lower doses of 5 mg/Kg intravenously (iv) and 30 mg/Kg intraperitoneally (ip) used in both in vivo pharmacokinetic studies and orthotopic mouse model assays. D-isomers of LA3IK and RP-7 showed enhanced anti-cancer activity compared to their L-isomers. D-LA3IK remained stable in mouse plasma for 24 h with 75% remaining, exhibiting superior pharmacokinetic properties over D/L-RP-7. In summary, our findings mark the first report of short peptides based on MIEN1 protein sequence capable of inhibiting cancer signaling pathways, effectively impeding cancer progression both in vitro and in vivo. Citation Format: Amit Kumar Tripathi, Jamboor K. Vishwanatha. First-in-class compounds targeting the MIEN1 signaling pathway: A breakthrough approach for breast and prostate cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB034.

Abstract LB012: Evaluating computational approaches for CPTAC pan-cancer cross-cohort protein expression comparison

Abstract Recently, the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) has generated harmonized genomic, transcriptomic, proteomic, and clinical data for &amp;gt;1000 tumors in 10 cohorts to facilitate pan-cancer discovery research. However, protein expression comparison across CPTAC cohorts remains challenging due to non-uniform missing data and protein expression distribution patterns across tumor types. Here we present our efforts to evaluate various missing data handling and normalization strategies to generate a normalized pan-cancer protein expression dataset. First, we developed a novel algorithm to select robustly expressed proteins in tumors in any of the CPTAC cohorts, 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 iBAQ using protein abundance value and applied global quantile normalization or smooth quantile normalization methods. To assess if our missing data imputation and normalization strategy affected downstream analyses, we compared the fold change in differential protein expression between tumor and matched normal for each cohort using non-normalized, global quantile normalized and smooth quantile normalized protein iBAQ values. Our results demonstrate a strong correlation in fold change between global quantile normalized data and non-normalized data (Pearson r = 0.97 (ccRCC), r = 0.96 (COAD), r = 0.99 (LUAD) and r = 0.99 (LSCC)). Similar results were observed comparing smooth quantile normalized data to non-normalized data (Pearson r = 1.00 for ccRCC, COAD, LUAD, and LSCC), indicating both normalization methods retained biological differences between tumor and matched normal tissues within cohorts. Lastly, we identified several proteins (ERAP2, CA9, GSTM3, MX1, STAT1) whose protein and RNA expression were highly correlated across eight CPTAC cohorts (r &amp;gt; 0.7 for COAD, BRCA, LUAD, ccRCC, PDAC, UCEC, HNSCC, and LSCC). We then compared their protein expression rank across CPTAC cohorts with their RNA expression rank across corresponding TCGA cohorts. Specifically, median log2(iBAQ) of CPTAC and median log2(TPM) of TCGA are calculated for those proteins within indications, then indications are ranked by median log2(iBAQ) and median log2(TPM) in CPTAC and TCGA, respectively. Weighted rank correlation was used to measure rank agreement. Global quantile normalization has the highest rank correlation (weighted rank correlation between 0.597 to 0.931) compared to smooth quantile normalization or without normalization. These results suggest that combination of cohort hybrid imputation and global quantile normalization is a reasonable approach to generate a normalized CPTAC pan-cancer protein dataset that could be leveraged to interrogate protein expression across different cancer types. Citation Format: Jixin Wang, Xiaowen Tian, Wen Yu, John Bullen, Elaine Hurt, Wenyan Zhong. Evaluating computational approaches for CPTAC pan-cancer cross-cohort protein expression comparison [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB012.

Biofilm-producing Escherichia coli O104:H4 overcomes bile salts toxicity by expressing virulence and resistance proteins.

We investigated bile salts' ability to induce phenotypic changes in biofilm production and protein expression of pathogenic Escherichia coli strains. For this purpose, 82 pathogenic E. coli strains isolated from humans (n=70), and animals (n=12), were examined for their ability to form biofilms in the presence or absence of bile salts. We also identified bacterial proteins expressed in response to bile salts using sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-electrophoresis) and liquid chromatography-mass spectrometry (LC-MS/MS). Lastly, we evaluated the ability of these strains to adhere to Caco-2 epithelial cells in the presence of bile salts. Regarding biofilm formation, two strains isolated from an outbreak in Republic of Georgia in 2009 were the only ones that showed a high and moderate capacity to form biofilm in the presence of bile salts. Further, we observed that those isolates, when in the presence of bile salts, expressed different proteins identified as outer membrane proteins (i.e. OmpC), and resistance to adverse growth conditions (i.e. F0F1, HN-S, and L7/L12). We also found that these isolates exhibited high adhesion to epithelial cells in the presence of bile salts. Together, these results contribute to the phenotypic characterization of E. coli O104: H4 strains.

Uncovering the health implications of abandoned mines through protein profiling of local residents

Residents in areas with abandoned mines risk significant exposure to abundant heavy metals in the environment. However, current clinical indicators cannot fully reflect the health changes associated with abandoned mine exposure. The aim of this study was to identify biological changes in the residents of abandoned mine areas via proteomic analysis of their blood. Blood samples were collected from abandoned mine and control areas, and mass spectrometry was used for protein profiling. A total of 138 unique or common proteins that were differentially expressed in low-exposure abandoned mine area (LoAMA) or high-exposure abandoned mine area (HiAMA) compared to non-exposure control area (NEA) were analyzed, and identified 4 clusters based on functional similarity. Among the 10 proteins that showed specific change in LoAMA, 4 proteins(Apolipoprotein M, Apolipoprotein E, Apolipoprotein L1, and Cholesteryl ester transfer protein) were cluded in cluster 1(plasma lipoprotein remodeling), and linked to proteins that showed specific change in protein expression in HiAMA. Therefore, it is suggested that 4 proteins are changed at low exposure to an abandoned mine (or initial exposure), and then at high exposure, changes in various proteins involved in linked plasma lipoprotein remodeling are induced, which might triggered by the 4 proteins. Interestingly, in addition to plasma lipoprotein remodeling, proteins involved in other functional networks were changed in the high exposure group. These were all directly or indirectly linked to the 4 biomarkers(Apolipoprotein M, Apolipoprotein E, Apolipoprotein L1, and Cholesteryl ester transfer protein) that changed during low exposure. This suggests their potential utility in identifying areas impacted by abandoned mines. Especially, proteins involved in lipid metabolism and renal function-related diseases in individuals exposed to heavy metals in abandoned mine areas were correlated. Chronic kidney disease is predominantly instigated by cardiovascular disease and is commonly accompanied by dyslipidemia.

Endothelial knockdown of the tumor suppressor, WWOX, increases inflammation in ventilator-induced lung injury.

Chronic cigarette smoke exposure decreases lung expression of WWOX which is known to protect the endothelial barrier during infectious models of acute respiratory distress syndrome (ARDS). Proteomic analysis of WWOX-silenced endothelial cells (ECs) was done using tandem mass tag mass spectrometry (TMT-MS). WWOX-silenced ECs as well as those isolated from endothelial cell Wwox knockout (EC Wwox KO) mice were subjected to cyclic stretch (18% elongation, 0.5 Hz, 4 h). Cellular lysates and media supernatant were harvested for assays of cellular signaling, protein expression, and cytokine release. These were repeated with dual silencing of WWOX and zyxin. Control and EC Wwox KO mice were subjected to high tidal volume ventilation. Bronchoalveolar lavage fluid and mouse lung tissue were harvested for cellular signaling, cytokine secretion, and histological assays. TMT-MS revealed upregulation of zyxin expression during WWOX knockdown which predicted a heightened inflammatory response to mechanical stretch. WWOX-silenced ECs and ECs isolated from EC Wwox mice displayed significantly increased cyclic stretch-mediated secretion of various cytokines (IL-6, KC/IL-8, IL-1β, and MCP-1) relative to controls. This was associated with increased ERK and JNK phosphorylation but decreased p38 mitogen-activated kinases (MAPK) phosphorylation. EC Wwox KO mice subjected to VILI sustained a greater degree of injury than corresponding controls. Silencing of zyxin during WWOX knockdown abrogated stretch-induced increases in IL-8 secretion but not in IL-6. Loss of WWOX function in ECs is associated with a heightened inflammatory response during mechanical stretch that is associated with increased MAPK phosphorylation and appears, in part, to be dependent on the upregulation of zyxin.NEW & NOTEWORTHY Prior tobacco smoke exposure is associated with an increased risk of acute respiratory distress syndrome (ARDS) during critical illness. Our laboratory is investigating one of the gene expression changes that occurs in the lung following smoke exposure: WWOX downregulation. Here we describe changes in protein expression associated with WWOX knockdown and its influence on ventilator-induced ARDS in a mouse model.

Introducing a Possible Proteomic and Genomic Biomarker Panel Related to Methanol Poisoning: A Review

Context: Methanol is one of the simplest organic compounds widely used in industry. It is highly toxic and unfit for human consumption. The abuse of methanol-containing beverages is becoming a severe health problem. This review discusses new clinical and pathological manifestations alongside proteomic and genomic changes based on methanol's toxic effects. Evidence Acquisition: Medical literature was reviewed in Google Scholar, Scopus, and PubMed to examine the effect of methanol intoxication on proteomic and genomic changes in the human body. Results: The results revealed the rapid direct absorption of methanol and its spread in body tissues. Various side effects, from digestive problems to neurological disorders, blindness, and death, could occur depending on the consumed dosage. Methanol poisoning causes extensive changes at the protein level, affecting blood coagulation, vitamin metabolism, immune response, and lipid transport processes. Methanol could alter the gene expression profile pattern by increasing the production of free radical species, which cause changes in DNA nucleotides. Conclusions: In conclusion, since methanol poisoning is associated with serious adverse effects (protein expression changes) and mortality, it should be managed seriously and promptly.

Chronic villitis as a distinctive feature of placental injury in maternal SARS-CoV-2 infection

BackgroundSARS-CoV-2 infection during pregnancy is associated with increased risk of stillbirth, preeclampsia and preterm birth. However, this does not appear to be due to intrauterine fetal infection, as vertical transmission is rarely reported. There is a paucity of data regarding associated placental SARS-CoV-2 histopathology and their relationship to timing and severity of infection. ObjectiveTo determine if maternal SARS-CoV-2 infection is associated with specific patterns of placental injury and whether these findings differ by gestational age at time of infection or disease severity. Study DesignA retrospective cohort study was performed at University of California San Diego between 03/2020 to 02/2021. Placentas from pregnancies with a positive SARS-CoV-2 test were matched to two sets of controls: one set was time-matched by delivery date and sent to pathology for routine clinical indications, and the other was chosen from a cohort of placentas previously collected for research purposes without clinical indications for pathologic examination prior to the SARS-CoV-2 outbreak. Placental pathologic lesions were defined based on standard criteria and included maternal and fetal vascular malperfusion, and acute and chronic inflammatory lesions. Bivariate analysis was performed with independent Student’s T test and Pearson’s chi-square. Logistic regression was used to control for relevant covariates. Regions of SARS-CoV-2-associated villitis were further investigated using protein-based digital spatial profiling (DSP) assays on the GeoMx platform, validated by immunohistochemistry, and compared to cases of infectious villitis and villitis of unknown etiology. Differential expression analysis was performed to identify protein expression differences between these groups of villitis. ResultsWe included 272 SARS-CoV-2 positive cases, 272 time-matched controls, and 272 historical controls. The mean age of SARS-CoV-2 affected subjects was 30.1 ± 5.5 years and the majority were Hispanic (53.7%) and parous (65.7%). SARS-CoV-2 placentas demonstrated a higher frequency of the four major patterns of placental injury (all p<.001), compared to historical controls. SARS-CoV-2 placentas also showed a higher frequency of chronic villitis (CV) and severe CV (p=.03 for both) compared to time-matched controls, which remained significant after controlling for gestational age at delivery (aOR 1.52, 95% CI 1.01-2.28; aOR 2.12, 95% CI 1.16-3.88, respectively). DSP revealed programmed death-ligand 1 (PD-L1) to be increased in villitis-positive regions of the SARS-CoV-2 (logFC 0.47, adj p-value=0.002) and VUE (logFC 0.58, adj p-value=0.003) cases, but conversely decreased in villitis-positive regions of the infectious villitis group (log FC -1.40, adj p-value<0.001). ConclusionsCV appears to the most specific histopathological finding associated with SARS-CoV-2 maternal infection. CV involves damage to the vasculosyncytial membrane of the chorionic villi, involved in gas/nutrient exchange, suggesting potential mechanisms of placental (and perhaps neonatal) injury, even in the absence of vertical transmission. Surprisingly, changes in protein expression in SARS-CoV-2-associated villitis appear to be more similar to VUE rather than infectious villitis.

504 Dihydroxyacetone, a combustion of electronic cigarettes, promotes cardiac-specific injury through metabolic and mitochondrial imbalances

OBJECTIVES/GOALS: Electronic cigarettes have become increasingly popular, with various combustion products generated in the process. Dihydroxyacetone (DHA), a carbohydrate made during the heating process. Exposures may reach high micromolar to low millimolar doses of DHA per day and no studies have been done to understand the effects of DHA in the heart. METHODS/STUDY POPULATION: Here, we examine if DHA contributes to these using rat cardiomyocytes, H9c2 cells, and rat cardiac tissues to DHA evaluating metabolic and mitochondrial effects. Using the cells, we will investigate metabolic and mitochondrial pathways using Seahorse, protein expression changes in nutrient sensing pathways, and understand dose-dependent effects of DHA in the heart. Metabolite pools will also be evaluated to understand the changes promoted by DHA. Oxidative stress as previously observed in other cell models will also be measured. Key findings in the cardiac cells will be investigated in the cardiac tissues exposed to DHA. RESULTS/ANTICIPATED RESULTS: We have previously shown DHA induces oxidative stress, metabolic changes, and mitochondrial dysfunction in various cell line models. Interestingly, these effects are highly cell-type dependent. E-cigarettes are known to have toxic cardiac effects, including arterial stiffness, endothelial dysfunction, vascular injury, and oxidative stress. Changes in glycolytic, fatty acid synthesis, and the citric acid cycle enzymes and metabolites were found in the H9c2 cells. We also observed increased mitochondrial ROS and fuel changes due to DHA exposure. In DHA exposed cardiac tissues, we observed oxidative stress and mitochondrial fission and fusion dynamics altered. DISCUSSION/SIGNIFICANCE: These data suggest further study at physiologically relevant doses is warranted to understand how DHA inhaled impacts the long-term health of vapers. As well as the regulation of DHA in e-cigarettes as it has been deemed as safe for topical applications and warned against inhalation.

High-dose ascorbate exerts anti-tumor activities and improves inhibitory effect of carboplatin through the pro-oxidant function pathway in uterine serous carcinoma cell lines

ObjectiveUterine serous carcinoma is a highly aggressive non-endometrioid subtype of endometrial cancer with poor survival rates overall, creating a strong need for new therapeutic strategies to improve outcomes. High-dose ascorbate (vitamin C) has been shown to inhibit cell proliferation and tumor growth in multiple preclinical models and has shown promising anti-tumor activity in combination with chemotherapy, with a favorable safety profile. We aimed to study the anti-tumor effects of ascorbate and its synergistic effect with carboplatin on uterine serous carcinoma cells. MethodsCell proliferation was evaluated by MTT and colony formation assays in ARK1, ARK2 and SPEC2 cells. Cellular stress, antioxidant ability, cleaved caspase 3 activity and adhesion were measured by ELISA assays. Cell cycle was detected by Cellometer. Invasion was measured using a wound healing assay. Changes in protein expression were determined by Western immunoblotting. ResultsHigh-dose ascorbate significantly inhibited cell proliferation, caused cell cycle arrest, induced cellular stress, and apoptosis, increased DNA damage, and suppressed cell invasion in ARK1 and SPEC2 cells. Treatment of both cells with 1 mM N-acetylcysteine reversed ascorbate-induced apoptosis and inhibition of cell proliferation. The combination of ascorbate and carboplatin produced significant synergistic effects in inhibiting cell proliferation and invasion, inducing cellular stress, causing DNA damage, and enhancing cleaved caspase 3 levels compared to each compound alone in both cells. ConclusionsAscorbate has potent antitumor activity and acts synergistically with carboplatin through its pro-oxidant effects. Clinical trials of ascorbate combined with carboplatin as adjuvant treatment of uterine serous carcinoma are worth exploring.

How plants respond to heavy metal contamination: a narrative review of proteomic studies and phytoremediation applications.

Heavy metal pollution caused by human activities is a serious threat to the environment and human health. Plants have evolved sophisticated defence systems to deal with heavy metal stress, with proteins and enzymes serving as critical intercepting agents for heavy metal toxicity reduction. Proteomics continues to be effective in identifying markers associated with stress response and metabolic processes. This review explores the complex interactions between heavy metal pollution and plant physiology, with an emphasis on proteomic and biotechnological perspectives. Over the last century, accelerated industrialization, agriculture activities, energy production, and urbanization have established a constant need for natural resources, resulting in environmental degradation. The widespread buildup of heavy metals in ecosystems as a result of human activity is especially concerning. Although some heavy metals are required by organisms in trace amounts, high concentrations pose serious risks to the ecosystem and human health. As immobile organisms, plants are directly exposed to heavy metal contamination, prompting the development of robust defence mechanisms. Proteomics has been used to understand how plants react to heavy metal stress. The development of proteomic techniques offers promising opportunities to improve plant tolerance to toxicity from heavy metals. Additionally, there is substantial scope for phytoremediation, a sustainable method that uses plants to extract, sequester, or eliminate contaminants in the context of changes in protein expression and total protein behaviour. Changes in proteins and enzymatic activities have been highlighted to illuminate the complex effects of heavy metal pollution on plant metabolism, and how proteomic research has revealed the plant's ability to mitigate heavy metal toxicity by intercepting vital nutrients, organic substances, and/or microorganisms.

Myelin-Specific microRNA-23a/b Cluster Deletion Inhibits Myelination in the Central Nervous System during Postnatal Growth and Aging.

Microribonucleic acids (miRNAs) comprising miR-23a/b clusters, specifically miR-23a and miR-27a, are recognized for their divergent roles in myelination within the central nervous system. However, cluster-specific miRNA functions remain controversial as miRNAs within the same cluster have been suggested to function complementarily. This study aims to clarify the role of miR-23a/b clusters in myelination using mice with a miR-23a/b cluster deletion (KO mice), specifically in myelin expressing proteolipid protein (PLP). Inducible conditional KO mice were generated by crossing miR-23a/b clusterflox/flox mice with PlpCre-ERT2 mice; the offspring were injected with tamoxifen at 10 days or 10 weeks of age to induce a myelin-specific miR-23a/b cluster deletion. Evaluation was performed at 10 weeks or 12 months of age and compared with control mice that were not treated with tamoxifen. KO mice exhibit impaired motor function and hypoplastic myelin sheaths in the brain and spinal cord at 10 weeks and 12 months of age. Simultaneously, significant decreases in myelin basic protein (MBP) and PLP expression occur in KO mice. The percentages of oligodendrocyte precursors and mature oligodendrocytes are consistent between the KO and control mice. However, the proportion of oligodendrocytes expressing MBP is significantly lower in KO mice. Moreover, changes in protein expression occur in KO mice, with increased leucine zipper-like transcriptional regulator 1 expression, decreased R-RAS expression, and decreased phosphorylation of extracellular signal-regulated kinases. These findings highlight the significant influence of miR-23a/b clusters on myelination during postnatal growth and aging.

Age-related changes after intracerebral hemorrhage: a comparative proteomics analysis of perihematomal tissue.

The risk factors and causes of intracerebral hemorrhage (ICH) and the degree of functional recovery after ICH are distinct between young and elderly patients. The increasing incidence of ICH in young adults has become a concern; however, research on the molecules and pathways involved ICH in subjects of different ages is lacking. In this study, tandem mass tag (TMT)-based proteomics was utilized to examine the protein expression profiles of perihematomal tissue from young and aged mice 24h after collagenase-induced ICH. Among the 5,129 quantified proteins, ICH induced 108 and 143 differentially expressed proteins (DEPs) in young and aged mice, respectively; specifically, there were 54 common DEPs, 54 unique DEPs in young mice and 89 unique DEPs in aged mice. In contrast, aging altered the expression of 58 proteins in the brain, resulting in 39 upregulated DEPs and 19 downregulated DEPs. Bioinformatics analysis indicated that ICH activated different proteins in complement pathways, coagulation cascades, the acute phase response, and the iron homeostasis signaling pathway in mice of both age groups. Protein-protein interaction (PPI) analysis and ingenuity pathway analysis (IPA) demonstrated that the unique DEPs in the young and aged mice were related to lipid metabolism and carbohydrate metabolism, respectively. Deeper paired-comparison analysis demonstrated that apolipoprotein M exhibited the most significant change in expression as a result of both aging and ICH. These results help illustrate age-related protein expression changes in the acute phase of ICH.

Abstract 6222: Exposing the heterogeneity of the lipidome in the TME of cutaneous melanoma following treatment with NUC-7738 in combination with anti-PD-1 therapy

Abstract Background. Malignant melanoma exhibits distinct lipid profiles compared to normal tissue and changes in the lipidome influence multiple aspects of tumor biology. Lipidomic alterations within the tumor microenvironment (TME) may influence the efficacy of anti-PD-1 therapy. In combination with anti-PD-1 agent pembrolizumab, NUC-7738 (3'-deoxyadenosine [3’-dA] which is phosphorylated and protected with a phosphoramidate moiety attached at the 5’-position) has shown promising activity in anti-PD-1 refractory melanoma (Phase 2; NCT03829254). NUC-7738 generates sustained intracellular levels of 3’-dATP, which profoundly alters RNA regulatory processes in tumor cells, resulting in impaired cellular responses and changes in expression of proteins related to lipid biosynthesis. To interrogate components of the TME before and after NUC-7738 + pembrolizumab treatment, we developed a novel workflow incorporating Mass Spectrometry Imaging (MSI) to co-register lipidomic changes with molecular markers. Machine learning accelerated the interpretation of complex data obtained from paired patient biopsies. Methods. Snap frozen paired biopsies from patients with advanced cutaneous melanoma treated with NUC-7738 ±pembrolizumab were analyzed by desorption electrospray ionization (DESI)-MSI. Specific metabolic (e.g., ASAH1) and immune (e.g., CD8, CD20) markers were investigated by multiplex immunofluorescence (mIF) post DESI-MSI. Target selection was guided by bulk RNA-seq data. Raw MSI data was visualized using Waters HDI® software. Data extracted from selected regions of interest was exported into MetaboAnalyst 5.0 for statistical analysis. LIPID MAPS® Structure Database was used to assign lipid species. mIF/mIHC images were analyzed by HALO® AI. Results. Single 10 µm tissue sections allowed co-registered DESI-MSI and mIF, suitable for further informatic and AI-enabled image analysis. This facilitated direct comparison of lipids, cells, and protein expression in the TME, before and after treatment with NUC-7738, a compound known to cause profound changes in poly(A) tail regulation. MSI data analyses of the TME uncovered intra-tumoral heterogeneity of the lipidome and demonstrated changes following treatment. Conclusion. This platform provides a powerful investigative tool to simultaneously explore the myriad of factors in the TME that contribute to tumorigenesis and therapeutic response. Further analyses of the role of the lipidome in the TME and intra-tumoral heterogeneity will be explored in paired biopsies from patients with PD-1 inhibitor refractory melanoma. Citation Format: Alison L. Dickson, Greice M. Zickuhr, In Hwa Um, Ying Zhang, Ruth Plummer, Sarah P. Blagden, Stefan N. Symeonides, Natalie Cook, T.R. Jeffry Evans, Mustafa Elshani, David J. Harrison. Exposing the heterogeneity of the lipidome in the TME of cutaneous melanoma following treatment with NUC-7738 in combination with anti-PD-1 therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6222.

Abstract 5634: Tristetraprolin induces an antitumorigenic phenotype in triple negative breast cancer via a novel non-canonical mechanism

Abstract The ultimate cause of death for most triple negative breast cancer (TNBC) patients is metastatic disease, which has a five-year survival rate of 12.8%. This low survival rate is partly due to the lack of targeted treatments for metastatic TNBC, resulting from the heterogeneity of the disease. As such, further research is needed to identify novel molecular mechanisms that can be targeted to suppress TNBC malignancy. Tristetraprolin (TTP) is an RNA-binding protein that binds to AU-rich elements (AREs) in the 3’ UTRs of select mRNAs, including many that encode proteins involved in cancer-related processes, and targets these mRNAs for degradation. Loss of TTP in tumors correlates with increased disease severity and decreased survival, suggesting a role as a tumor suppressor in multiple cancers, including breast cancer. While previous research has shown that TTP can suppress proliferation in breast cancer, the mechanism remains weakly defined. To elucidate how TTP impacts tumorigenic phenotypes in advanced breast cancer, we stably transfected a FLAG-TTP-expressing construct into three aggressive and metastatic TNBC cell lines. We analyzed TTP-induced changes in gene expression patterns among these cell lines using RNA-sequencing and observed that TTP alters the expression levels of many genes. Gene Set Enrichment Analysis (GSEA) of our datasets revealed that TTP affects multiple pathways, including significant suppression of pathways that promote cell growth, various metabolic processes contributing to tumor growth, and the response to hypoxia. As these pathways highly associated with tumorigenesis, we hypothesized that TTP would attenuate multiple tumor phenotypes. Our subsequent functional analyses revealed that TTP potently suppressed four tumor phenotypes in these cell models: cell proliferation, stem cell frequency, migration, and invasiveness. We hypothesized that inhibition of proliferation was mediated by cell cycle alterations, however, flow cytometry analysis revealed no substantial cell cycle perturbations between TTP-expressing cells and controls. Further analysis of cell cycle regulators revealed minimal changes in expression of proteins encoded by known or suspected TTP target mRNAs. Actinomycin D assays surprisingly revealed that TTP had no effect on the decay kinetics of several known TTP targets, suggesting that TTP’s antitumorigenic properties observed in TNBC cells are independent of its RNA-destabilizing function. To confirm this finding, we constructed cell models expressing an RNA-binding defective mutant of TTP, C147R, which recapitulated suppression of the four tumorigenic phenotypes seen with the wild-type protein. Collectively, these findings reveal that expression of TTP can potently suppress several oncogenic phenotypes in TNBC cells via a mechanism independent of its canonical RNA-binding/destabilizing functions. Citation Format: Julia L. Rutherford, Megan B. Stemberger, Rohaan Mahmud, Christina R. Ross, Elizabeth J. White, Gerald M. Wilson. Tristetraprolin induces an antitumorigenic phenotype in triple negative breast cancer via a novel non-canonical mechanism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5634.

Abstract 5106: Pharmacological targeting of LSD1 prolongs animal survival times in patient derived orthotopic xenograft models of posterior fossa ependymoma in combination with fractionated radiation

Abstract Background: Posterior Fossa Group A Ependymoma (PFA EPN) constitute one of the most aggressive and highly recurrent molecular subtypes of childhood Ependymomas. We recently performed a comprehensive genome-wide DNA methylation analysis in recurrent pediatric EPN tumors from patients that were followed up for over 13 years. Integrative analysis between tumor DNA methylation and histone modification identified LSD1 as a druggable driver of PFA EPN recurrence. In this study, we examined the therapeutic efficacy of our newly developed LSD1 inhibitor SYC-836 in PDOX models of recurrent PFA EPN. Methodology: To determine the in vitro anti-tumor activities of SYC-836, paired PFA EPN xenograft cell cultures (monolayer and 3D neurospheres) were treated with SYC-836 at 8 concentrations (0.02-25 µM) and examined for changes of cell proliferation every 3-4 days through day 14. To validate the drug’s in vivo efficacy, two established posterior fossa EPN PDOX models, ICb-4423EPN and ICb-2002EPN, were utilized. Forty 8-week old SCID mice of both genders received intra-cerebellar tumor cell implantation and were divided into 4 treatment groups (n=10 per group): 1) control, 2) radiation (2 Gy/day x 5 days), 3) SYC-836 (15 mg/kg, daily intra-peritoneal injection for 28 days), and 4) combination (radiation + SYC-836). Animal survival times were analyzed using log-rank analysis. Changes in LSD1 protein expression and histone lysine methylation were examined through western hybridization. Results: SYC-836 strongly suppressed PFA EPN cell growth in vitro, in both, a time- and dose-dependent manner. While there was no survival benefit with either SYC-836 only (P=0.186) or XRT only (P=0.205); combining SYC-836 with XRT significantly (P=0.04) prolonged the median survival time of ICb-4423EPN, from 46 days in the untreated group to 59 days; and in ICb-2002EPN, even more prominent, from 136 days to 180 days (P=0.007). SYC-836 was well tolerated in mice with no loss of body weight or other toxicities. Changes in LSD1 protein expression and H3K4me2 were detected through western hybridization during and after SYC-836 treatment. Conclusion: Our data support LSD1 as a druggable driver of PFA recurrence and highlights strong anti-tumor activities of SYC-836 in combination with radiation, a standard therapy of pediatric EPN. SYC-836 may have a role in the clinical setting by either reducing radiation dosages or be an adjuvant agent to other chemotherapy drugs in our treatment approach for ependymoma. Citation Format: Milagros M. Suarez Palacios, Sibo Zhao, Huiyuan Zhang, Lin Qi, Holly Lindsay, Mari Kogiso, Frank Braun, Adekunle M. Adesina, Yuchen Du, Yongcheng Song, Xiao-Nan Li. Pharmacological targeting of LSD1 prolongs animal survival times in patient derived orthotopic xenograft models of posterior fossa ependymoma in combination with fractionated radiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5106.

Abstract 1851: Comprehensive multi-level proteomics characterization of gastric cancer

Abstract Gastric cancer is the leading cause of cancer related deaths worldwide, accounts for over 700,000 deaths each year. There is an urgent need for advancing therapeutic strategies for patients with gastric cancer. Addressing this need, the Clinical Proteomics Tumor Analysis Consortium (CPTAC) has conducted a comprehensive characterization of gastric cancer, aiming to elucidate the complex molecular mechanisms driving this cancer type, and to discover underlying cancer biology that will form the basis for developing new approaches for precision medicine. This comprehensive study includes an integrated multi-level proteomics analysis of 165 surgically resected gastric cancer and 41 normal adjacent tissues. We employed a multi-faceted approach, analyzing the proteome, phosphoproteome and glycoproteome, along with other protein modifications including ubiquitination, acetylation, and tyrosine phosphorylation. Furthermore, we extended our research to include 74 pairs of early-onset gastric cancer and normal adjacent tissues, analyzed using a proteomic approach. We can totally identify more than 12,000 protein groups with median identification of 9750 protein groups per sample. This expansive dataset helps constructing a comprehensive multi-omics atlas of gastric cancer, offering a deep understanding into the disease's molecular landscape. The depth of this study was enhanced by incorporating multi-level proteomics data across 6 tiers, facilitating an unprecedented multi-level proteomics analysis. Our integrated approach allows us to illustrate the changes in protein expression, protein modifications, signaling pathways, and protein networks during tumorigeneis. This analysis uncovers potential therapeutic targets for personalized treatments. Overall, our study provides a multi-omics atlas for gastric cancer, a profound insight into gastric cancer biology, contributing significantly to the understanding of its pathogenesis. It could pave the way for precise treatments for gastric cancer, underscoring the potential of multi-level proteomics analyses in advancing personalized medicine. Citation Format: Yuefan Wang, Clinical Proteomic Tumor Analysis Consortium (CPTAC). Comprehensive multi-level proteomics characterization of gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1851.