Log2 Fold Change Research Articles

Similarities of metabolomic disturbances in prematurity-associated obstructive lung disease to chronic obstructive pulmonary disease

Prematurity-associated lung disease (PLD) is a long-term consequence of preterm-birth. Since the underlying mechanisms of PLD remain poorly characterised, we compared the urinary metabolome between recently described spirometry phenotypes of PLD. Preterm- and term-born children aged 7–12 years, from the Respiratory Health Outcomes in Neonates (RHiNO) cohort, underwent spirometry and urine collection. The urinary metabolome was analysed by gas chromatography time-of-flight mass spectrometry. Preterm-born children were classified into phenotypes of prematurity-associated obstructive lung disease (POLD, Forced expiratory volume in 1 s (FEV1) < lower limit of normal (LLN), FEV1/Forced Vital Capacity (FVC) < LLN), prematurity-associated preserved ratio impaired spirometry (pPRISm, FEV1 < LLN, FEV1/FVC ≥ LLN) and Preterm/Term controls (FEV1 ≥ LLN). Metabolite set enrichment analysis was used to link significantly altered metabolites between the groups with metabolic pathways. Univariable and multivariable linear regression models examined associations between early and current life factors and significantly altered metabolites of interest. Urine from 197 preterm- and 94 term-born children was analysed. 23 and 25 were classified into POLD and pPRISm groups respectively. Of 242 identified metabolites, 49 metabolites were significantly altered in the POLD group compared with Preterm controls. Decreased capric acid (log2 fold change − 0.23; p = 0.003), caprylic acid (− 0.18; 0.003) and ceratinic acid (− 0.64; 0.014) in the POLD group, when compared to preterm controls, were linked with reduced β-oxidation of very long chain fatty acids (p = 0.004). Reduced alanine (log2 fold change − 0.21; p = 0.046), glutamic acid (− 0.24; 0.023), and pyroglutamic acid (− 0.17; 0.035) were linked with decreased glutathione metabolism (p = 0.008). These metabolites remained significantly associated with POLD in multivariable models adjusting for early/current life factors. The pPRISm urinary metabolome was minimally changed when compared with preterm-born controls. When compared to term-born subjects, alterations in tryptophan metabolism were implicated (p = 0.01). The urinary metabolome in POLD showed significantly altered β-oxidation of fatty acids and glutathione metabolism, implying alterations in cellular metabolism and oxidative stress. Similar findings have been noted in adults with chronic obstructive pulmonary disease. Given the similarity of findings between the POLD group and those reported for COPD, the POLD group should be considered at future risk of developing COPD.

7248 Spliceosome component TCERG1 regulates the aggressiveness of somatotroph adenoma

Abstract Disclosure: K. Kim: None. The role of the spliceosome in the development of pituitary tumors is not well understood, despite preliminary studies indicating abnormal expression of oncogenic splicing variants in these neuroendocrine tumors. We aimed to identify differentially expressed spliceosome components in growth hormone (GH)-secreting pituitary tumors and investigate their roles in pathogenesis.We performed transcriptome analysis of 20 somatotroph adenomas and 6 normal pituitary tissues to select dysregulated spliceosome components. Clinical characteristics were analyzed based on gene expression in 64 patients with acromegaly. GH secreting pituitary adenomas were confirmed by 75 g oral glucose tolerance and immunohistochemical staining. Proliferation, invasion, and hormonal activity of GH secreting pituitary adenoma cells were investigated after modulating gene expression.TCERG1 expression was significantly higher in somatotroph adenomas than in normal cells (log2 fold change 0.59, adjusted P=0.0002*). Genotype-phenotype analysis revealed that patients with higher TCERG1 expression had lower surgical remission rates than those with lower expression (63.64% vs. 95.45%, P=0.009*). TCERG1 expression was significantly higher in groups with cavernous sinus (CS) invasion or Ki67 index over 1.5 (2.06 vs. 1.65, P=0.011*; 2.02 vs. 1.66, P=0.043*). TCERG1 overexpression led to a 16.91% increase in proliferation after 72 h (P&amp;lt;0.001*) and a 249.47% increase in invasion after 48 h in GH3 cells (P=0.026*). Conversely, TCERG1 silencing significantly decreased cell proliferation (10.15% at 72 h, P&amp;lt;0.001*) and invasion (96.87% at 48 h, P=0.029*). Vimentin was increased, but E-cadherin was decreased in both TCERG1 overexpressed GH3 cells and somatotroph adenomas. And TCERG1 silence reversed the expression of the genes (CDH2, SNAI1, ZEB2, and VIM) in GH3 cells. Additionally, GH secretion increased when TCERG1 was overexpressed in GH3 cells. Spliceosome machinery provide novel insights into the pathogenesis of GH-secreting pituitary tumor and highlight the potential role of TCERG1 as a therapeutic target. Presentation: 6/2/2024

8401 Genetic Characterization of a Case of Primary Aldosteronism in an 11-Year-Old Girl carrying a Germline VUS of CACNA1H and a Somatic Mutation of CTNNB1

Abstract Disclosure: S. Parisien-La Salle: None. G. Van Vliet: None. G. Corbeil: None. M. Labrecque: None. M. Tétreault: None. I. Bourdeau: None. Introduction: Primary aldosteronism is a frequent cause of secondary hypertension in adults but is rare in children. We report the case and genetic studies of an 11 yo girl presenting with primary aldosteronism at puberty. Case presentation: An 11-year-old female patient was referred to the pediatric endocrinology clinic for hypertension (166/118). Her past medical history and family history were unremarkable. She reported polyuria, polydipsia and occasional headaches and abdominal pain. Her Tanner stage indicated that puberty was initiated (P2M2). An abdominal CT revealed a 9x10x11cm right adrenal mass with calcifications and a necrotic zone. On [1]8F-FDG PET/CT, the mass had an uptake of 2.9 SUVmax. Laboratory results revealed hypokalemia (K: 2.6 mmol/L [N: 3.5-4.5]) and elevated aldosterone (1712.8 pmol/L [N: 110-1330]) with suppressed renin (0.2 ng/ml/h [N: &amp;lt;5.3]). Her urinary aldosterone level was elevated (114 nmol/day [N: &amp;lt;67]). The rest of the biochemical adrenal panel was normal. Patient underwent a right adrenalectomy by laparotomy. The pathology report showed an adrenal tumor without capsular or vascular invasion. The only malignancy criterion was an area of necrosis and the ki-67% proliferation index was &amp;lt; 1%. Genetic investigations: After informed consent, the patient underwent germline analysis for the chimeric gene CYP11B2/CYP11B1 (Ruhr University Bochum, Germany) and a multigene panel including KCNJ5, CACNA1D, CACNA1H and CLCN2 genes (Fulgent, CA), which were both negative except for a variant of unknown significance (VUS) that was identified in CACNA1H (c.3868G&amp;gt;A, p.Val1290Ile) with a minor allele frequency of 3.291E-5 (GnomAD). Tumor DNA was extracted after adrenalectomy from fresh frozen tissues. Somatic genetic analysis of GNAS, CTNNB1, KCNJ5, ATP1A1, ATP2B3 and CACNA1D was performed using direct Sanger Sequencing (Genome Quebec Innovation Centre) and revealed a heterozygous missence pathogenic variant in the CTNNB1 gene (c.121 A&amp;gt;G p.Thr41Ala). This mutation was absent in leukocyte DNA of the patient. Immunohistochemistry of the adrenal tumor disclosed strong cytoplasmic β-catenin staining in most tumor cells (monoclonal anti-β-catenin antibody; BD Transduction Laboratories). RNA-sequencing of patient tumor RNA was performed (Research Center CHU Québec) and compared to human adrenal total RNA (Clontech, Mountain View, CA). Pathway enrichment analysis showed activation of the Wnt signaling pathway. No variant was identified in GNAQ or GNA11 genes. However, GNRHR was upregulated compared to the control sample with a log2 fold change of 3.96 (p=0.000074). Conclusion: We present a rare pediatric case of an aldosterone producing adenoma harbouring a somatic β-catenin pathogenic variant with upregulation of GNRHR. The implication of the germline CACNA1H VUS still needs to be clarified. Presentation: 6/3/2024

6828 Exploring Metabolomic Clues in Diabetic Retinopathy

Abstract Disclosure: M.W. Simonson: None. Y. Li: None. J.J. McAnany: None. B. Prasad: None. E.C. Hanlon: None. S. Pannain: None. B.T. Layden: None. E. Van Cauter: None. J.C. Park: None. S.J. Crowley: None. F.Y. Chau: None. K.K. Danielson: None. H. Chen: None. G.E. Chlipala: None. C. Martinez: None. S. Reutrakul: Speaker; Self; Eli Lilly &amp; Company. Background: Diabetic retinopathy (DR) is a common microvascular complication of diabetes. Metabolomics offers the possibility for novel biomarker discovery. The purpose of this study was to determine metabolomic differences that characterized patients with versus without DR. Methods: A total of 62 serum samples were collected from 36 type 2 diabetes (T2D) patients with DR and 26 T2D patients without DR, and analyzed via UPLC-MS. The metabolite data were normalized using median normalization. The differential expression of metabolites was compared among the groups using the limma package in R. The covariates (age, sex, BMI and sleep apnea severity) were accounted for by using a generalized linear model fitted to the data. Significantly different metabolites were filtered by an absolute log2 Fold Change (FC) of 1.5 or greater and Q values &amp;lt; 0.05. Results: Mean (SD) age for DR and no-DR group was 55 (±5.9) versus 54 (±6.7) years, while BMI was 33 (±5.8) versus 33 (±6.3) kg/m2 respectively. Both DR and no-DR groups were 58% female. A1C levels in DR group was marginally higher than in no-DR group (p=0.09). There were significant differences in metabolomic changes between DR versus no-DR, with 166 total differential metabolites after adjusting for covariates and filtering by FC. Notable metabolites included those involved in fatty acid metabolism, acyl carnitines, prostaglandins, and phospholipids. There was an overall upregulation of serum acyl carnitines in DR as compared to no-DR, including 2,6 dimethylheptanoyl carnitine (FC = 3.0) and cis-5-Tetradecenoylcarnitine (FC = 2.0). Additionally, there was a decrease in long chain fatty acids in DR as compared to no-DR, which included 6-hydroxypentadecanedioic acid (FC = -6.6), 10,16-dihydroxy-palmitic acid (FC = -6.0), and tetracosatetraenoyl CoA (FC = -6.1). The 11-beta prostaglandin F2 (11-PGF2) was increased in DR (FC = 1.9). Circulating phospholipids including lysophosphatidylcholine (22:2) (lysoPC) (FC = 1.8) and phosphatidylcholine (24:1/24:1) (PC) (FC = 5.9) were also significantly dysregulated. Conclusions: We identified a subset of metabolites that discriminate T2D patients with or without DR. The changes in acyl carnitines and long chain fatty acids may reflect mitochondrial dysfunction in DR. The presence of certain prostaglandins highlights the inflammatory environment which may facilitate DR progression. Increases in phospholipids such as lysoPC suggest an atherogenic state and higher LDL oxidation, while increases in PC may indicate altered lipogenesis in DR. These findings may serve as new potential serum biomarkers to promote efficient preventive care and provide mechanistic insight into understanding DR pathophysiology. Presentation: 6/2/2024

Spliceosome component TCERG1 regulates the aggressiveness of somatotroph adenoma.

We aimed to identify differentially expressed spliceosome components in growth hormone (GH)-secreting pituitary tumors and investigate their roles in pathogenesis. We performed transcriptome analysis of 20 somatotroph adenomas and 6 normal pituitary tissues to select dysregulated spliceosome components. Clinical characteristics were analyzed based on gene expression in 64 patients with acromegaly. Proliferation, invasion, and hormonal activity of GH secreting pituitary adenoma cells were investigated. TCERG1 expression was significantly higher in somatotroph adenomas than in normal pituitaries (log2 fold change 0.59, adjusted P = 0.0002*). Genotype-phenotype analysis revealed that patients with higher TCERG1 expression had lower surgical remission rates than those with lower expression (63.64% vs. 95.45%, P = 0.009*). TCERG1 expression was significantly higher in groups with cavernous sinus (CS) invasion or Ki67 index over 3 (all P>0.05*). TCERG1 overexpression led to a 29.60% increase in proliferation (P<0.001*) and a 249.47% increase in invasion after 48h in GH3 cells (P = 0.026*). Conversely, TCERG1 silencing significantly decreased cell proliferation (25.76% at 72h, P<0.001*) and invasion (96.87% at 48h, P = 0.029*). E-cadherin was decreased, but vimentin was increased in both TCERG1 overexpressed GH3 cells and somatotroph adenomas. And TCERG1 silence reversed the expression of the genes (CDH2, SNAI1, ZEB2, and VIM) in GH3 cells. Spliceosome machinery provide novel insights into the pathogenesis of GH-secreting pituitary tumor and highlight the potential role of TCERG1 as a biomarker for tumor aggressiveness.

Metabolomic insights into idiopathic xerostomia: The central role of caffeine metabolism in salivary biochemistry

ObjectiveThis study aims to delineate the salivary metabolomic profile of patients with idiopathic xerostomia using untargeted metabolomics techniques, with the goal of addressing the lack of clear diagnostic markers and providing insights into the pathophysiological mechanisms of the condition. DesignIn this observational, cross-sectional study, saliva samples from 33 patients with idiopathic xerostomia and 34 healthy controls were analyzed using Ultra Performance Liquid Chromatography Quadrupole Time of Flight Mass Spectrometry (UPLC-QTOF MS). Metabolomic profiling was complemented by multivariate statistical analysis to differentiate between affected individuals and controls. ResultsMetabolomic analysis delineated a pronounced differentiation between patients with idiopathic xerostomia and healthy controls. A total of 195 metabolites displayed significant differential expression, each with a variable importance in projection (VIP) greater than 1 and a P-value less than 0.05. Pathway enrichment analysis, according to the Kyoto Encyclopedia of Genes and Genomes (KEGG), identified 22 metabolites that participated in 18 distinct metabolic pathways. Among these, the caffeine metabolism pathway, characterized by notable alterations in impact values (VIP, P-value, Log2-fold change, Rich factor), emerged as the most significantly disrupted, underscoring its potential role in the pathophysiology of idiopathic xerostomia (P = 0.0000395). ConclusionsThe salivary metabolomic profiling revealed distinct alterations in idiopathic xerostomia, with a significant reduction in caffeine metabolism pathways, underscoring potential neuropathic involvement. This study advances our understanding of the metabolic alterations in xerostomia, suggesting that salivary metabolomics may offer viable biomarkers for diagnosing and understanding the etiology of idiopathic xerostomia. Future research should focus on therapeutic targeting of these metabolic disturbances and evaluating their reversibility with treatment.

Characterization of the oral mycobiome of Portuguese with allergic rhinitis and asthma

Allergic rhinitis and asthma are two prevailing chronic airway diseases and serious public health concerns. Previous research has already described the role of the airway bacteriome in these two diseases, but almost no study so far has explored the mycobiome and its possible association to airway inflammation. Here we sequenced the internal transcribed spacers (ITS) 1 and 2 to characterize the oral mycobiome of 349 Portuguese children and young adults with allergic rhinitis alone (AR) or with asthma (ARAS), asthmatics (AS) and healthy controls (HC). Our genomic analyses showed that the two most abundant fungal phyla (Ascomycota and Basidiomycota) and 3-5 of the 14 most abundant fungal genera (Cladosporium, Aspergillus, Aleurina, Candida and Rhodotorula) in the mouth differed significantly (P≤0.04) between both rhinitic groups and HC. However, none of the same taxa varied significantly between the three respiratory disease groups (AR, ARAS and AS). The oral mycobiomes of respiratory ill patients showed the highest intra-group diversity (microbial richness and evenness), while HC showed the lowest, with all alpha-diversity indices varying significantly (P≤0.0424) between them. Similarly, all disease groups showed significant differences (P≤ 0.0052) in microbial structure (i.e., beta-diversity indices) when compared to HC samples. Thirty metabolic pathways (PICRUSt2) were differentially abundant (Wald's test) between AR or ARAS and HC patients, but only one of them (D-galactose degradation I) was over abundant (log2 Fold Change >0.75) in the ARAS group. Spiec-Easi fungal networks varied greatly among groups, which suggests chronic respiratory allergic diseases may alter fungal connectivity in the mouth. This study increases our comprehension of the role of the oral mycobiome in allergy-related conditions. It shows for the first time that the oral mycobiota changes during health and allergic rhinitis (with and without asthma comorbidity) and highlights specific taxa, metabolic pathways and fungal interactions that may relate to chronic airway disease.

Pre-eclampsia intronic polyadenylation enriched in VEGFA-VEGFR2 signaling pathway

AimsThis study aims to reveal transcriptome-wide intronic polyadenylation (IPA) events associated with Pre-eclampsia (PE). BackgroundPre-eclampsia (PE) is a potentially life-threatening complication of pregnancy, affecting both maternal and fetal health. However, our understanding of the underlying molecular mechanisms of PE remains limited. ObjectiveIn this study, we conducted a transcriptome-wide analysis of gene expression levels and intronic polyadenylation (IPA) events in samples of patients with PE. We also conducted motif analysis and scanned the microRNA targeting IPA network. MethodWe collected 90 PE-related samples from GEO database. IPA events were analyzed using IPAfinder software from hg38 alignment files from STAR. Miranda software was used to perform miRNA target gene prediction. Differentially expressed genes (DEG) were evaluated using edgeR with log2 fold change >1 and adjusted p-value <0.05. Function enrichment was performed through Clusterprofiler. ResultOur analysis revealed that genes in the VEGFA-VEGFR2 signaling pathway were functionally enriched with IPA events related to PE. We observed a negative correlation between gene expression levels and IPA events in VEGFA-VEGFR2 pathway. We identified LIN28B and AGO2 as the most significantly binding motifs to IPA sites. Furthermore, our analysis of miRNA binding sites associated with these IPA events revealed the central regulatory roles of miR-193b and miR-365a in IPA genes. ConclusionOur findings suggest that transcriptome data-mining might be a useful approach in future studies aimed at identifying potential biomarkers for PE.

Biodegradation and high-value utilization of waste cooking oil: Strategies and mechanisms for producing lipopeptide biosurfactants using Bacillus subtilis YZQ-2

This study explored the strategies and mechanisms of Bacillus subtilis YZQ-2 in producing lipopeptide biosurfactants using waste cooking oil (WCO) as a raw material. The optimal conditions achieved a WCO utilization rate of 75.88% and a biosurfactant yield of 0.30g/L at pH 6.0, 30°C, with 20g/L WCO and 5g/L yeast extract. GC-MS analysis of degradation products at different intervals elucidated the mechanism of WCO degradation. After 72hours of fermentation, a reduction in linoleic and palmitic acid levels indicated the completion of lipid hydrolysis and the continuation of β-oxidation. The biosurfactants, identified as lipopeptides (surfactin and fengycin), exhibited stability in alkaline environments (pH 7.0-11.0) and high-salt concentration (5-45g/L). Genomic and transcriptomic analyses of Bacillus subtilis YZQ-2 revealed genes associated with biosurfactant production, which were upregulated in the presence of WCO. The differential expression values (log2 fold change) were SrfAA 3.30, SrfAB 3.31, SrfAC 3.63, FenA 2.42, FenB 2.55, FenC 1.99, FenD 2.03 and FenE 2.29, respectively. The proposed biosynthesis pathway of lipopeptides begins with the hydrolysis of WCO by lipase into glycerol and fatty acids. The glycerol is then transformed into pyruvate through glycolysis, entering the Tricarboxylic Acid cycle. Additionally, pyruvate contributes to synthesizing amino acids and branched-chain fatty acids, which serve as precursors for lipopeptide synthesis. These findings underscore the potential of WCO as a sustainable feedstock for biosurfactant production.

Exploring Differentially Expressed Genes and Immune Modulation in Diffuse Large B-Cell Lymphoma through RNA Sequencing Analysis.

Diffuse large B-cell lymphoma (DLBCL) is globally recognized as the most prevalent and aggressive subtype of non-Hodgkin lymphoma. While conventional treatments are effective initially, the disease can become resistant or relapse over time. This study aimed to examine the differentially expressed genes at the transcriptome level and molecular pathways in DLBCL patients. This investigation utilized RNA sequencing analysis to compare differentially expressed gene samples from five diffuse large B-cell lymphoma patients with two healthy volunteers. These participants were admitted to UKM Medical Center, Kuala Lumpur between 2019 and 2020. The differentially expressed genes were identified using the DESeq2 R package (version 1.10.1) using a negative binomial distribution model. The obtained P values were corrected with the Benjamin and Hochberg method and identified using a False Discovery Rate threshold of <0.05, with log2 fold change (FC) of ≥2 or ≤-2. Results showed 73 differentially expressed genes between the two groups, among which 70 genes were downregulated, and three genes were upregulated. The differentially expressed genes analyzed with the Reactome pathway were significantly associated with the downregulation of antimicrobial humoral response (P<0.001), neutrophil degranulation (P<0.001), chemokine receptors bind chemokines (P=0.028), defensins (P=0.028) and metabolism of angiotensinogen (P=0.040). These findings suggest that the identified pathways may contribute to cancer progression and weaken the immune response in diffuse large B-cell lymphoma patients. This study offers fresh insights into previously undiscovered downstream targets and pathways modulated by diffuse large B-cell lymphoma.

Development and validation of a recurrence risk assessment model for high-grade bladder cancer based on TCGA and GEO.

Bladder cancer is one of the most commonly diagnosed urinary cancers worldwide. Although muscle-invasive bladder cancer (MIBC) accounts for only 25% of bladder cancer cases, it has a high recurrence rate and poor prognosis, especially among high-grade cases. Despite the existence of some molecular markers, there is a clear clinical need for a robust recurrence prediction model that can assist in patient management and therapeutic decision-making. Therefore, we aimed to use public databases to develop such an effective assessment model. We developed a recurrence risk assessment model for high-grade bladder cancer based on the clinical information of 217 cases from The Cancer Genome Atlas (TCGA) and profiles of 87 samples from GSE31684 in the Gene Expression Omnibus (GEO) database. Edge R was used to analyze differences between RNAs of bladder cancer in the TCGA database, with thresholds of P<0.05 and |log2(fold change)| >1; least absolute shrinkage and selection operator (LASSO) Cox regression models were used to screen the RNAs significantly related to recurrence with minimum λ. Survival receiver operating characteristic (ROC) and area under the curve (AUC) was used to assess the predictive accuracy of the model in the training and validation sets of GSE31684. There were 2,876 differential RNAs obtained from TCGA data. Among a total of 284 RNAs identified as significantly related to recurrence of bladder cancer, 49 were obtained by LASSO regression, and 30 were finally obtained by multifactor risk regression to construct a risk assessment model. The model was found to predict the prognosis of bladder cancer recurrence well, with an AUC of 0.911 in the TCGA training set and an adjusted AUC value of 0.839 in the GEO validation set. The recurrence assessment model is a relatively accurate recurrence prediction tool for high-grade bladder cancer and could provide a guidance for the treatment of bladder cancer.

Metabolome and Transcriptome Joint Analysis Reveals That Different Sucrose Levels Regulate the Production of Flavonoids and Stilbenes in Grape Callus Culture.

To reveal the effect of sucrose concentration on the production of secondary metabolites, a metabolome and transcriptome joint analysis was carried out using callus induced from grape variety Mio Red cambial meristematic cells. We identified 559 metabolites-mainly flavonoids, phenolic acids, and stilbenoids-as differential content metabolites (fold change ≥2 or ≤0.5) in at least one pairwise comparison of treatments with 7.5, 15, or 30 g/L sucrose in the growing media for 15 or 30 days (d). Resveratrol, viniferin, and amurensin contents were highest at 15 d of subculture; piceid, ampelopsin, and pterostilbene had higher contents at 30 d. A transcriptome analysis identified 1310 and 498 (at 15 d) and 1696 and 2211 (at 30 d) differentially expressed genes (DEGs; log2(fold change) ≥ 1, p < 0.05) in 7.5 vs. 15 g/L and 15 vs. 30 g/L sucrose treatments, respectively. In phenylpropane and isoflavone pathways, DEGs encoding cinnamic acid 4-hydroxylase, chalcone synthase, chalcone isomerase, and flavanone 3-hydroxylase were more highly expressed at 15 d than at 30 d, while other DEGs showed different regulation patterns corresponding to sucrose concentrations and cultivation times. For all three sucrose concentrations, the stilbene synthase (STS) gene exhibited significantly higher expression at 15 vs. 30 d, while two resveratrol O-methyltransferase (ROMT) genes related to pterostilbene synthesis showed significantly higher expression at 30 vs. 15 d. In addition, a total of 481 DEGs were annotated as transcription factors in pairwise comparisons; an integrative analysis suggested MYB59, WRKY20, and MADS8 as potential regulators responding to sucrose levels in flavonoid and stilbene biosynthesis in grape callus. Our results provide valuable information for high-efficiency production of flavonoids and stilbenes using grape callus.

Proteomic Profiling Identifies Predictive Signatures for Progression Risk in Patients with Advanced-Stage Follicular Lymphoma.

Background: Follicular lymphoma (FL) is characterized by an indolent nature and generally favorable prognosis, yet poses a particular clinical challenge, since disease progression is observed in a notable subset of patients. Currently, it is not possible to anticipate which patients will be at risk of progression, highlighting the need for reliable predictive biomarkers that can be detected early in the disease. Methods: We applied tandem-mass-tag labelled nano-liquid chromatography tandem mass spectrometry (nLC-MS/MS) on 48 diagnostic formalin-fixed, paraffin-embedded tumor samples from patients with advanced-stage FL. Of these, 17 experienced subsequent progression (subsequently-progressing, sp-FL) while 31 did not (non-progressing, np-FL). Results: We identified 99 proteins that were significantly differentially expressed between sp-FL samples and np-FL samples (p < 0.05; log2-fold changes between 0.2 and -1.3). Based on this subset of proteins, we classified patients into high-risk and low-risk subgroups using unsupervised machine learning techniques. Pathway analyses of the identified proteins revealed aberrancies within the immune system and cellular energy metabolism. In addition, two proteins were selected for immunohistochemical evaluation, namely stimulator of interferon genes 1 (STING1) and isocitrate dehydrogenase 2 (IDH2). Notably, IDH2 retained significantly lower expression levels in sp-FL samples compared with np-FL samples (p = 0.034). Low IDH2 expression correlated with shorter progression-free survival (PFS, p = 0.020). Conclusions: This study provides evidence for some of the biological mechanisms likely to be involved in FL progression and, importantly, identifies potential predictive biomarkers for improvement of risk stratification up-front at time of FL diagnosis.

Abstract C097: PVT1 exon 9-dependent overexpression of RSAD2 is a characteristic of prostate cancer in males of African ancestry

Abstract Aggressive prostate cancer (PCa), including castrate-resistant and neuroendocrine subtypes, is projected to increase in incidence 5% each year. Aggressive PCa disproportionally impacts African American men, has limited effective treatment options and high mortality rates. Although racial disparities are established in PCa development, attributed to multiple contributory factors including systemic racism, differences in socioeconomic status and distrust in the medical system, work is still needed to understand the contribution of biological factors. We found the exon 9 region of plasmacytoma variant translocation 1 (PVT1) overexpressed in aggressive PCa cell lines derived from African American (AA) men. We found PVT1 exon 9 overexpression induced phenotypic changes to normal prostate epithelial cells in vitro and led to tumor formation in vivo. RNA-sequencing analysis revealed 156 significantly differentially expressed genes influenced by PVT1 exon 9 overexpression and radical S-adenosyl methionine domain containing 2 (RSAD2) was the top significantly overexpressed gene (log2Fold change 1.71, p-value &amp;lt; 0.05). We utilized the GSE223405 publicly available dataset to identify whether our identified PVT1 exon 9 downstream genes were enriched in AA prostate cancer cells. RSAD2 was significantly overexpressed in AA prostate cancer cells compared to prostate cancer cells from men of European ancestry (moEA) (log2Fold change 6.18, p-value &amp;lt; 0.05). Comparing normal cells to prostate cancer cells between these groups, we found that normal AA prostate cells had significantly higher expression of RSAD2 (log2fold change 4.25, p-value &amp;lt; 0.001) whereas moEA samples did not (log2fold change 0.837, p-value=0.150). From analysis of data obtained from cBioPortal, we found RSAD2 alteration significantly correlates (p-value &amp;lt; 0.001) with self-identified race and copy number overexpression of RSAD2 was found to be enriched in AA patients (18.16% moEA versus 24% AA). Finally, we found 88.6% of the significantly differentially expressed genes within our PVT1 exon 9 RNA-sequencing dataset were significantly differentially expressed in GSE223405 AA samples and of those, 51.7% of genes exhibited a similar differential expression pattern suggesting that the PVT1 exon 9/RSAD2 dependent pathway may be more prominent in AA men. Mechanistically, we found two differing pathways of RSAD2 overexpression in aggressive prostate cancer cell models, one dependent and one independent of PVT1 exon 9 overexpression, with similar but differing biological functions related to epigenetic processes and metabolism. Ongoing work is investigating the RSAD2 and PVT1 exon 9 expression axis in a diverse set of human prostate cancer tissues and investigating their utilization as a therapeutic target in prostate cancer. Citation Format: Rachel E. Sexton-Bonacci1, Murtaza Barkarar1, Chindeum Udekwu1, Olorunseun O. Ogunwobi1. PVT1 exon 9-dependent overexpression of RSAD2 is a characteristic of prostate cancer in males of African ancestry [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C097.

Abstract C103: Exploring ethnicity-specific molecular mechanism of cholesterol and fatty acid synthesis pathway in Hispanic colorectal cancer

Abstract Colorectal cancer (CRC) is the most prevalent gastrointestinal cancer, the third most common malignancy and the second leading cause of cancer-related mortality worldwide. The American Cancer Society (ACS) estimates 152,810 new cases of colorectal cancer, with an estimated 53,010 deaths in 2024. Typically diagnosed in older adults, CRC incidence is rising among younger individuals, particularly in Hispanics (16.5%) compared to non-Hispanic whites (8.7%). Due to the lack of timely screenings in this ethnic group, further research is crucial to identify novel biomarkers and therapeutic targets for improved early detection and intervention. To accomplish this goal, we performed RNA-sequencing of Hispanic and non-Hispanic White (NHW) CRC tissues. The transcriptomic analysis revealed differential gene expression patterns in Hispanic and NHW populations when compared to respective normal adjacent tissues (NATs). We identified 3577 differentially expressed genes (DEGs) in Hispanic CRC samples and 2971 DEGs in NHW CRC samples, of which 1831 DEGs were unique to Hispanic. Based on the preliminary analysis we hypothesized that unique DEGs from the Hispanic population could help identify potential pathways contributing to CRC progression. Among these 1831 unique DEGs, many of the genes are associated with cholesterol and fatty acid synthesis pathway. The cholesterol biosynthesis pathway is a highly diverse and interconnected signaling pathway, playing essential roles in cellular function and systemic homeostasis. Its complexity and regulatory mechanisms make it a critical area of study in cancer. Studies indicate that Hispanics and African Americans with high cholesterol tend to have higher Body mass index (BMI) levels compared to Whites which has an increased risk of colorectal cancer. However, the role of cholesterol metabolism and fatty acid metabolism in CRC have not been studied from the Hispanic health disparities perspective. From the 1831 DEGs, we selected those in the cholesterol and fatty acid synthesis pathways with significant log2 fold changes (≤ -2 or ≥ +2) and adjusted p-values (FDR ≤ 0.05). Our bioinformatics analysis identified four key DEGs: LCN2, DHCR7, PCSK9 and SQLE. The expression levels of these genes were examined in Hispanic CRC vs. NHW CRC tissue samples using qRT-PCR. Elevated expression of LCN2 and SQLE was observed in late-stage Hispanic CRC tissues compared to NHW CRC tissues, while DHCR7 exhibited high expression in early-stage Hispanic CRC. On the other hand, PCSK9 showed low expression in both early and late stages of Hispanic CRC, suggesting potential ethnicity-specific molecular signatures in CRC progression. Moving forward, protein level studies and functional analysis of these DEGs in Hispanic CRC tissues and organoids will enhance our understanding of the role of cholesterol and fatty acid synthesis pathway proteins. Thus, elucidating novel molecular mechanisms underlying CRC progression could lead to identification of potential Hispanic specific biomarkers and therapeutic targets for early diagnosis and intervention. Citation Format: Somrita Roy, Soumya Nair, MD Zahirul Islam Khan, Sourav Roy. Exploring ethnicity-specific molecular mechanism of cholesterol and fatty acid synthesis pathway in Hispanic colorectal cancer [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C103.

Abstract C094: Differential expression analysis with transcriptome data in FFPE samples from Colombian patients with colorectal cancer

Abstract Introduction: Colorectal cancer (CRC) is a significant public health issue in Colombia, It occupies third place in incidence and ranking as the fifth leading cause of cancer-related deaths. Understanding the sociodemographic, clinicopathological, and molecular characteristics of CRC patients is crucial for prognosis, effective management, and treatment. Several molecular alterations and clinicopathological variables have been associated with the prognosis of the disease in different populations; However, we do not know if there are differentially expressed genes specific to Colombian population that are associated with CRC prognosis. Objective: Perform differential expression analysis using RNA-seq data obtained from formalin-fixed paraffin-embedded (FFPE) tissue samples from Colombian patients with CRC. Methodology: For this preliminary analysis were included 5 patients diagnosed with CRC between 2010-2014 at Instituto Nacional de Cancerologia from Colombia. From each patient, formalin-fixed and paraffin-embedded (FFPE) samples of tumor tissue and non-tumor tissue from the surgical remnant were obtained. Extracted RNA was used to perform whole-genome RNA sequencing (RNA-seq) at a depth of 100X. Bioinformatic analysis was performed using Fastqc, Cutadapt, Ribodetector, and STAR on a Linux server. The DESeq2 package in RStudio was used to perform the differential expression analysis between tumor samples vs. non-tumorous. A significant differential expression was considered using an FDR-adjusted p ≤0.05 and a log fold change of 2. Results and discussion: A list of 18 differentially expressed genes was obtained which 5 underexpressed stand out: B3GNT6 (LFC:-10.66; padj=0.0093), ITLN1 (LFC:-6.23; padj=0.0231), NR3C2 (LFC:-3.34; padj=0.0231), NLGN1 (LFC:- 0.46; padj=0.0301), CEACAM7 (LFC:-5.91; padj= 0.0301); and one overexpressed gene: RPL9 (LFC:5.44; padj=0.0267). These genes have been previously characterized and associated with the progression and prognosis of this disease in other populations. Conclusions: 6 differentially expressed genes were found using RNA-seq in FFPE samples. These genes have been associated with CRC progression and prognosis in previous studies, but have not been evaluated in the Colombian population. From this perspective, we propose to continue with the analysis by increasing the number of samples and evaluating their association with the different clinicopathological variables and their impact on the prognosis of the disease. Citation Format: Wendy J. Montero Ovalle, Silvia J Serrano Gómez, Diego F Ballen Lozano. Differential expression analysis with transcriptome data in FFPE samples from Colombian patients with colorectal cancer [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C094.

Abstract C084: Genetic polymorphism rs3820282 and WNT4-mediated metabolic plasticity contributes to differential therapy response in ovarian cancer clear carcinoma

Abstract Purpose of research: Ovarian clear cell carcinoma (OCCC) is a rare and notoriously chemoresistant gynecologic malignancy that is more likely to affect patients of Asian race. Unlike the more common tubo-ovarian high-grade serous carcinoma, OCCC is rising in incidence. Previous work highlights the increased risk of reproductive pathology associated with single nucleotide polymorphism (SNP) rs3820282, a genetic variant that is also overrepresented in people of Asian race. In particular, rs3820282 results in increased WNT4 expression and is associated with metabolic reprogramming and elevated phospho-AMPK as demonstrated in murine models and primary human tumors. We hypothesize the WNT4/rs3820282 regulatory axis in OCCC mediates the response to chemotherapy via metabolic plasticity. Methods: Using SNP-variant genotype (OVTOKO) and wild-type (TOV-21G) OCCC cell lines, we manipulated the expression of WNT4 via short interfering RNA knockdown and lentiviral overexpression. We evaluated the proliferation and survival of cells in nutrient deprivation conditions. We used Agilent Seahorse to evaluate metabolic outputs of oxidative phosphorylation in the presence of cytotoxic stress conditions (platinum chemotherapy [cisplatin]), antimetabolic agents [metformin and dimethyl malonate], lipid- and glucose-deprived media, and fatty acid oxidation and glycolysis inhibition). We used immunoblotting to measure total AMPK and phospho-AMPK as signals of cellular response to metabolic stress. To evaluate the effect of WNT4 on response to chemotherapy, we measured changes in the half-maximal inhibitory concentration (IC50) of cisplatin. Results: Knockdown and overexpression of WNT4 in variant and wild-type OCCC cells altered cellular proliferation and survival in nutrient deprivation conditions. Seahorse cellular energetics conducted in variant OCCC cells demonstrated that WNT4 knockdown mitigates the metabolic detriment of cytotoxic and metabolic stress conditions with the opposite trend observed in wild-type WNT4 overexpressing OCCC cells. The variant phenotype is consistent with models of high-grade serous carcinoma. Over five experiments, WNT4 knockdown reduced the IC50 of cisplatin in variant cells (mean log fold change -0.29, range -0.91 to 0.07). While WNT4 knockdown led to a modest increase in total AMPK protein expression, in lipid- and glucose-deprived conditions WNT4 loss significantly attenuated phospho-AMPK levels. Conclusions: Genetically variant OCCC cells exposed to metabolic and antineoplastic stressors demonstrate metabolic plasticity which is regulated by WNT4. Knockdown of WNT4 induces metabolic rigidity that may convey increased susceptibility to chemotherapy, as indicated by the WNT4-induced reduction in cisplatin IC50. The SNP is highly prevalent in people of Asian race, and further investigation of this axis of metabolic reprogramming represents an opportunity to further understand an established cancer disparity and improve chemotherapeutic response in ovarian clear cell carcinoma. Citation Format: Julia Dexter, Madeleine Shackleford, Sydney Robinson, Matthew Sikora, Benjamine Bitler. Genetic polymorphism rs3820282 and WNT4-mediated metabolic plasticity contributes to differential therapy response in ovarian cancer clear carcinoma [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C084.

Abstract C110: The role of the S100 family signaling pathway proteins in Hispanic colorectal cancer disparities

Abstract Colorectal cancer (CRC) is a global health concern, ranking as the second deadliest and third most diagnosed cancer. In the United States alone, it is estimated that there will be 152,810 new cases of CRC in 2024. CRC has an overall survival rate of 90% when detected in its early stages (Stage I/II). However, due to low screening rates, only 39% of CRC patients in the U.S. are diagnosed during the early stage, particularly among the minority groups like Hispanics. This disparity can be attributed to various factors, including limited access to health care facilities and socio-economic barriers. Among Hispanics, CRC diagnosis and screening rate are lower, resulting in a higher incidence of late-stage (Stage III/IV) diagnosis compared to Non-Hispanic Whites (NHW). Only 33% of Hispanics receive timely diagnosis, and merely 49% undergo recommended screening protocols, in comparison to a diagnosis rate of 35% and screening rate of 58% in NHW. Addressing this health disparity emphasizes the urgent need for targeted interventions to improve early screening and diagnosis within the Hispanic population. We hypothesize that genetic factors across different ethnicities/races may influence gene expression patterns during various stages, thereby contributing to CRC tumorigenesis and progression. To enhance the chances of identifying markers for early detection and diagnosis among Hispanics, we aim to identify new ethnicity-specific transcriptomic profiles. RNA sequencing of Hispanic CRC, NHW CRC and their respective normal tissues adjacent to the tumor (NAT), revealed unique sets of differentially expressed genes (DEGs) with a log2 foldchange of ≥ 2.0 and ≤ -2.0 and p-adjusted value ≤ 0.05 in Hispanic (1831) and NHW (1225) CRC populations compared to their respective NATs. Further analysis identified DEGs specific to early (1012) and late (765) stages of CRC within the Hispanic population, as compared to the respective stages in the NHW. Ingenuity Pathway Analysis (IPA) was used to uncover significant DEGs associated with the S100 family signaling pathway in Hispanic CRC samples. Previous studies have indicated the involvement of the S100 family proteins and their signaling pathways in CRC development, progression, metastasis, and drug resistance through interactions with WNT/β-catenin, RAGE, MAPK and NF-κβ signaling pathways. Our investigation of DEGs within the S100 signaling pathway and their interaction with downstream effectors suggests differential expression of genes crucial in cellular processes, including matrix metallopeptidases (MMP), mitogen-activated protein kinases (MAP2K) and Wingless-related integration site (WNT) family proteins. Exploring these proteins and their downstream effectors in Hispanic CRC tissues and organoids would elucidate specific functional attributes influencing CRC progression. Understanding the interaction of proteins identified in this study may serve as potential ethnicity-specific biomarkers or targets for the development of novel therapeutic interventions for early-stage CRC diagnosis in Hispanics. Citation Format: Soumya Nair, Brian I Grajeda, Sourav Roy. The role of the S100 family signaling pathway proteins in Hispanic colorectal cancer disparities [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C110.

Identification of potential characteristic genes in chronic skin infections through RNA sequencing and immunohistochemical analysis.

The objective of the present study was to perform RNA sequencing and immunohistochemical analysis on skin specimens obtained from healthy individuals and individuals afflicted with prolonged skin infections. Bioinformatics methodologies were used to scrutinize the RNA sequencing data with the intention of pinpointing distinctive gene signatures associated with chronic skin infections. Skin tissue samples were collected from 11 individuals (4 subjects healthy and 7 patients with chronic skin infections) at the Affiliated Hospital of Southwest Medical University (Luzhou, China). The iDEP tool identified differentially expressed genes (DEGs) with log2 (fold change) ≥2 and q-value ≤0.01. Functional enrichment analysis using Gene Ontology and KEGG databases via the oebiotech online tool was then performed to determine the biological functions and pathways related to these DEGs. A protein-protein interaction network of DEGs identified HIF1A as a potential key gene. Subsequent immunohistochemistry analyses were performed on the samples to assess any variations in HIF1A expression. A total of 900 DEGs, 365 upregulated and 535 downregulated, were observed between the normal and chronic infection groups. The identified DEGs were found to serve a role in various biological processes, including 'hypoxia adaptation', 'angiogenesis', 'cell adhesion' and 'regulation of positive cell migration'. Additionally, these genes were revealed to be involved in the 'TGF-β', 'PI3K-Akt' and 'IL-17' signaling pathways. HIF1A and nine other genes were identified as central nodes in the PPI network. HIF1A expression was higher in chronically infected skin samples than in healthy samples, indicating its potential as a novel research target.

Impact of smoking habit on the subgingival proteome in patients with periodontitis.

Few investigations evaluated smoking's impact on the periodontal proteome. Therefore, this study aimed to analyse the influence of tobacco on the overall periodontal proteome and the differential expression of gingival crevicular fluid (GCF) proteins using sequential window acquisition of all theoretical mass spectra (SWATH-MS). GCF samples were collected from 40 periodontitis subjects (stages III-IV). These were separated based on smoking status into smokers (17), ex-smokers (10), and non-smokers (13). Samples were analysed using SWATH-MS, and proteins were identified using the UniProt human-specific database. Data are available via ProteomeXchange with the identifier PXD043474. Principal component analysis (PCA) was employed to examine the spectral mass distribution of the proteome. Protein expression was different for a p-value<0.05 and a log2 fold change ≥0.3 (upregulated) or ≤-0.3 (downregulated). The distribution of overall proteome did not differ between non-smokers, smokers, and ex-smokers. Considering protein expression, 23 were differentially expressed in smokers vs. non-smokers (16 upregulated and 7 downregulated), 17 in ex-smokers vs. non-smokers (2 upregulated and 15 downregulated), and only 8 in smokers vs. ex-smokers (7 upregulated and 1 downregulated). Smoking increased the expression of proteins related to epithelial hyperkeratinization (keratins type II cytoskeletal 4, type I cytoskeletal 13 and type I cytoskeletal 19, cornulin, and fatty acid-binding protein 5). However, multiple immunoglobulins were underexpressed when comparing smokers and ex-smokers to non-smokers. Although smoking does not significantly modify the overall GCF proteome associated with periodontitis, it alters the expression of several proteins compared to never-smokers and ex-smokers. Smoking is a critical risk factor for the development and progression of periodontitis. However, evidence of the effect of smoking on the subgingival proteome is scarce. Therefore, this study aimed to determine the impact of smoking on the overall proteome and differential expression of gingival crevicular fluid (GCF) proteins using the sequential window acquisition of all theoretical mass spectra (SWATH-MS) proteomic technique. For this purpose, GCF samples were collected from 40 subjects with periodontitis, of which 17 were smokers, 10 were ex-smokers, and 13 were non-smokers. These samples were analysed by SWATH-MS, and proteins were identified using the UniProt human-specific database. Analysis of the overall proteome showed that its distribution was not significantly different between smokers, ex-smokers, and non-smokers. However, several proteins were found to be differentially expressed according to the smoking status. Smoking can increase the expression of several keratins and proteins related to hyperkeratinization of the epithelium. However, in ex-smokers, these proteins return to similar levels to those of non-smokers. Moreover, smoking may induce a lower expression of proteins related to adaptive immunity, such as immunoglobulins. This immunosuppressive effect may persist in ex-smokers.