Significant Differential Expression Research Articles

Predicting prostate adenocarcinoma patients’ survival and immune signature: a novel risk model based on telomere-related genes

Alterations in telomeres constitute some of the earliest occurrences in the tumourigenesis of prostate adenocarcinoma (PRAD) and persist throughout the progression of the tumour. While the activity of telomerase and the length of telomeres have been demonstrated to correlate with the prognosis of PRAD, the prognostic potential of telomere-related genes (TRGs) in this disease remains unexplored. Utilising mRNA expression data from the Cancer Genome Atlas (TCGA), we devised a risk model and a nomogram to predict the survival outcomes of patients with PRAD. Subsequently, our investigations extended to the relationship between the risk model and immune cell infiltration, sensitivity to chemotherapeutic drugs, and specific signalling pathways. The risk model we developed is predicated on seven key TRGs, and immunohistochemistry results revealed significant differential expression of three TRGs in tumours and paracancerous tissues. Based on the risk scores, PRAD patients were stratified into high-risk and low-risk cohorts. The Receiver operating characteristics (ROC) and Kaplan–Meier survival analyses corroborated the exceptional predictive performance of our novel risk model. Multivariate Cox regression analysis indicated that the risk score was an independent risk factor associated with Overall Survival (OS) and was significantly associated with T and N stages of PRAD patients. Notably, the high-risk group exhibited a greater response to chemotherapy and immunosuppression compared to the low-risk group, offering potential guidance for treatment strategies for high-risk patients. In conclusion, our new risk model, based on TRGs, serves as a reliable prognostic indicator for PRAD. The model holds significant value in guiding the selection of immunotherapy and chemotherapy in the clinical management of PRAD patients.

COVID-19 severity gradient differentially dysregulates clinically relevant drug processing genes in nasopharyngeal swab samples.

Understanding how COVID-19 impacts the expression of clinically relevant drug metabolizing enzymes and membrane transporters (DMETs) is vital for addressing potential safety and efficacy concerns related to systemic and peripheral drug concentrations. This study investigates the impact of COVID-19 severity on DMETs expression and the underlying mechanisms to inform the design of precise clinical dosing regimens for affected patients. Transcriptomics analysis of 102 DMETs, 10 inflammatory markers, and 12 xenosensing regulatory genes was conducted on nasopharyngeal swabs from 50 SARS-CoV-2 positive (17 outpatients, 16 non-ICU, and 17 ICU) and 13 SARS-CoV-2 negative individuals, clinically tested through qPCR, in the Greater Toronto area from October 2020 to October 2021. We observed a significant differential gene expression for 42 DMETs, 6 inflammatory markers, and 9 xenosensing regulatory genes. COVID-19 severity was associated with the upregulation of AKR1C1, MGST1, and SULT1E1, and downregulation of ABCC10, CYP3A43, and SLC29A4 expressions. Altogether, SARS-CoV-2-positive patients showed an upregulation in CYP2C9, CYP2C19, AKR1C1, SULT1B1, SULT2B1, and SLCO4A1 and downregulation in FMO5, MGST3, ABCC5, and SLCO4C1 compared with SARS-CoV-2 negative individuals. These dysregulations were associated with significant changes in the expression of inflammatory and xenosensing regulatory genes driven by the disease. GSTM3, PPARA, and AKR1C1 are potential biomarkers of the observed DMETs dysregulation pattern in nasopharyngeal swabs of outpatients, non-ICU, and ICU patients, respectively. The severity of COVID-19 is associated with the dysregulation of DMETs involved in processing commonly prescribed drugs, suggesting potential disease-drug interactions, especially for narrow therapeutic index drugs.

Transcriptomic analysis reveals differential gene expression patterns of Lacticaseibacillus casei ATCC 393 in response to ultrasound stress

In recent years, there has been a growing interest in modulating the performance of probiotic, mainly Lactic Acid Bacteria (LAB), in the field of probiotic food. Attenuation, induced by sub-lethal stresses, delays the probiotic metabolism, and induces a metabolic shift as survival strategy. In this paper, RNA sequencing was used to uncover the transcriptional regulation in Lacticaseibacillus casei ATCC 393 after ultrasound-induced attenuation. Six (T) and 8 (ST) min of sonication induced a significant differential expression of 742 and 409 genes, respectively. We identified 198 up-regulated and 321 down-regulated genes in T, and similarly 321 up-regulated and 249 down-regulated in ST. These results revealed a strong defensive response at 6 min, followed by adaptation at 8 min. Ultrasound attenuation modified the expression of genes related to a series of crucial biomolecular processes including membrane transport, carbohydrate and purine metabolism, phage-related genes, and translation. Specifically, genes encoding PTS transporters and genes involved in the glycolytic pathway and pyruvate metabolism were up-regulated, indicating an increased need for energy supply, as also suggested by an increase in the transcription of purine biosynthetic genes. Instead, protein translation, a high-energy process, was inhibited with the down-regulation of ribosomal protein biosynthetic genes. Moreover, phage-related genes were down-regulated suggesting a tight transcriptional control on DNA structure. The observed phenomena highlight the cell need of ATP to cope with the multiple ultrasound stresses and the activation of processes to stabilize and preserve the DNA structure. Our work demonstrates that ultrasound has remarkable effects on the tested strain and elucidates the involvement of different pathways in its defensive stress-response and in the modification of its phenotype.

Proteomics of tumor and serum samples from isocitrate dehydrogenase-wildtype glioblastoma patients: is the detoxification of reactive oxygen species associated with shorter survival?

Proteomics has been little used for the identification of novel prognostic and/or therapeutic markers in isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GB). In this study, we analyzed 50 tumor and 30 serum samples from short- and long-term survivors of IDH-wildtype GB (STS and LTS, respectively) by data-independent acquisition mass spectrometry (DIA-MS)-based proteomics, with the aim of identifying such markers. DIA-MS identified 5422 and 826 normalized proteins in tumor and serum samples, respectively, with only three tumor proteins and 26 serum proteins displaying significant differential expression between the STS and LTS groups. These dysregulated proteins were principally associated with the detoxification of reactive oxygen species (ROS). In particular, GB patients in the STS group had high serum levels of malate dehydrogenase 1 (MDH1) and ribonuclease inhibitor 1 (RNH1) and low tumor levels of fatty acid-binding protein 7 (FABP7), which may have enabled them to maintain low ROS levels, counteracting the effects of the first-line treatment with radiotherapy plus concomitant and adjuvant temozolomide. A blood score built on the levels of MDH1 and RNH1 expression was found to be an independent prognostic factor for survival based on the serum proteome data for a cohort of 96 IDH-wildtype GB patients. This study highlights the utility of circulating MDH1 and RNH1 biomarkers for determining the prognosis of patients with IDH-wildtype GB. Furthermore, the pathways driven by these biomarkers, and the tumor FABP7 pathway, may constitute promising therapeutic targets for blocking ROS detoxification to overcome resistance to chemoradiotherapy in potential GB STS.

P.099 Transfer RNA fragments in patient plasma extracellular vesicles as biomarkers of high grade glioma

Background: High-grade gliomas (HGG) present challenges with short post-surgery survival and high progression rates. Extracellular vesicles (EVs) in the tumor microenvironment (TME) contribute to a pro-tumorigenic setting. Investigating Transfer RNA fragments (TfRNA) in HGG patient plasma EVs reveals potential biomarkers and therapeutic targets, shedding light on the molecular landscape for enhanced diagnostic and therapeutic strategies. This study examines TfRNA in 10 HGG patients at diagnosis, offering insights into the molecular landscape for improved management strategies. Methods: The study involved the collection of plasma samples from HGG patients and controls. EVs were isolated from these samples and subsequently analyzed for tfRNA. Results: Analysis of plasma EVs highlighted distinct differences in TfRNA fragments between High-Grade Glioma (HGG) and control samples. HGG EVs showed a global reduction in tRNA content, higher 5’ tfRNA proportions, and increased nuclear tfrna compared to controls. A notable biological marker, elevated in HGG, holds potential as a diagnostic indicator. Conclusions: Our study concludes that High-Grade Gliomas (HGG) demonstrate a global reduction in tfRNA content in plasma extracellular vesicles compared to non-cancer controls, echoing findings in other cancers. Despite this, specific tfRNA molecules in HGG show significant differential expression or sorting into EVs, indicating their potential as future biomarkers or therapeutic targets.

Proteomic identification of exosomes derived from psoriasis cells using data-independent acquisition mass spectrometry.

Psoriasis is renowned for its chronic nature and complex pathophysiology, with exosomes playing a crucial regulatory role within it. However, the proteomic composition of exosomes extracted from psoriasis cells remains largely unexplored. This study aimed to analyze the proteomic makeup of exosomes derived from psoriasis-model keratinocytes and compare it with that of normal controls, with the goal of identifying specific proteins that could aid in understanding the disease's pathology and potentially serve as biomarkers or therapeutic targets. The normal cultured keratinocyte line HaCaT served as the control group, while a concentration of 10 ng/mL of TNF-α was utilized to stimulate HaCaT cells and induce the formation of psoriasis model cells for the test group. Exosomes were extracted and prepared from the culture supernatant using the magnetic bead method, and their identity was confirmed through transmission electron microscopy, nanoparticle tracking analysis, and Western blotting. Data-independent acquisition (DIA) mass spectrometry was employed to detect the protein composition of exosomes, followed by GO, KEGG, Reactome, and PPI analyses. The analysis revealed a total of 2796 proteins within the exosomes, with 131 showing significant differential expression between the test and control groups. Notably, this study identified the proteins ADO, CBX1, and MIF within the exosomes derived from psoriasis model cells for the first time, highlighting their potential roles in angiogenesis, epigenetic regulation, and inflammatory responses in psoriasis. Several differentially expressed proteins identified in the KEGG enrichment analysis were implicated in immune infiltration pathways, keratinocyte-regulating pathways, angiogenesis pathways, and inflammation pathways. The identification of unique proteins within exosomes derived from psoriasis-model cells offers novel insights into the molecular mechanisms underlying psoriasis. These findings pave the way for further research into the biological functions of these exosomal proteins and their potential utility in diagnosing and treating psoriasis.

Development of a biomarker signature associated with anoikis to predict prognosis and immunotherapy response in melanoma.

Skin cutaneous melanoma (SKCM) is malignant cancer known for its high aggressiveness and unfavorable prognosis, particularly in advanced tumors. Anoikis is a specific pattern of programmed cell death associated with tumor regeneration, migration, and metastasis. Nevertheless, limited research has been conducted to investigate the function of anoikis in SKCM. Anoikis-related genes (ARGs) were extracted from Genecards to identify SKCM subtypes and to explore the immune microenvironment between the different subtypes. Prognostic models of SKCM were developed by LASSO COX regression analysis. Subsequently, the predictive value of risk scores in SKCM and the association with immunotherapy were further explored. Finally, the expression of 6 ARGs involved in the model construction was detected by immunohistochemistry and PCR. This study identified 20 ARGs significantly associated with SKCM prognosis and performed disease subtype analysis of samples based on these genes, different subtypes exhibited significantly different clinical features and tumor immune microenvironment (TIME) landscapes. The risk score prognostic model was generated by further screening and identification of the six ARGs. The model exhibited a high degree of sensitivity and specificity to predict the prognosis of individuals with SKCM. These high- and low-risk populations showed different immune statuses and drug sensitivity. Further immunohistochemical and PCR experiments identified significant differential expression of the six ARGs in tumor and normal samples. Anoikis-based features may serve as novel prognostic biomarkers for SKCM and may provide important new insights for survival prediction and individualized treatment development.

#1320 Differential microRNA expression profile in obesity-induced kidney disease driven by high-fat diet in mice

Abstract Background and Aims Obesity is one of the main causes of chronic kidney disease; however, the precise molecular mechanisms leading to the onset of kidney dysfunction in obesity-induced kidney disease (OIKD) remain unclear. MicroRNAs (miRNAs) have been implicated in the development and progression of obesity, and several candidates have been identified as critical regulators of adipogenesis and lipid metabolism, while their dysregulation contribute to obesity-related metabolic abnormalities. The aim of the present study was to decipher the kidney microRNA (miRNA) expression profile in a mouse model of obesity-induced kidney disease characterized by systemic metabolic disturbances and kidney injury that closely resemble those observed in human disease. Method Male C57BL/6J mice were randomly divided and placed either a standard diet (STD) or a high fat diet (HFD) for 10 weeks. Serum triglycerides and total, HDL and LDL cholesterol were determined by standard clinical methods. In the kidney sections, histopathological assessments were done by using PAS and Oil-Red-O staining's. Expression of renal MCP1, TNFα, α-SMA, Fibronectin, miR-146a, miR-551b and miR-5099 was assessed by real time PCR. In order to elucidate the role of differentially expressed miRNAs, a search for target genes was done using an online computational resource DIANA-miRPath v4.0. Results High fat diet (HFD)-induced obesity led to evident structural alterations in tubular and glomerular regions of the kidney, increased renal expression of adiposity-related proinflammatory and profibrotic genes, as well as an elevated renal expression of genes involved in cellular lipid metabolism. The miRNA sequencing analysis identified a set of 9 miRNAs differentially expressed in the kidney upon HFD feeding, with miR-5099, miR-551b-3p, miR-223-3p, miR-146a-3p and miR-21a-3p showing most significant differential expression between standard diet (STD) and HFD mice. Consistently, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses revealed that 3 validated miRNAs (miR-5099, miR-551b-3p and miR-146a-3p) modulated target genes involved in metabolic and adipocytokine pathways, fatty acid and lipid metabolism, inflammatory, senescence and profibrotic pathways. Conclusion Our results propose that differentially expressed miRNAs play pivotal roles in the intricated pathophysiology of obesity-associated kidney disease and could potentially create novel treatment strategies to counteract the deleterious effects of obesity on kidney function.

Exosomes enriched by miR-429-3p derived from ITGB1 modified Telocytes alleviates hypoxia-induced pulmonary arterial hypertension through regulating Rac1 expression

BackgroundRecent studies have emphasized the critical role of Telocytes (TCs)-derived exosomes in organ tissue injury and repair. Our previous research showed a significant increase in ITGB1 within TCs. Pulmonary Arterial Hypertension (PAH) is marked by a loss of microvessel regeneration and progressive vascular remodeling. This study aims to investigate whether exosomes derived from ITGB1-modified TCs (ITGB1-Exo) could mitigate PAH.MethodsWe analyzed differentially expressed microRNAs (DEmiRs) in TCs using Affymetrix Genechip miRNA 4.0 arrays. Exosomes isolated from TC culture supernatants were verified through transmission electron microscopy and Nanoparticle Tracking Analysis. The impact of miR-429-3p-enriched exosomes (Exo-ITGB1) on hypoxia-induced pulmonary arterial smooth muscle cells (PASMCs) was evaluated using CCK-8, transwell assay, and inflammatory factor analysis. A four-week hypoxia-induced mouse model of PAH was constructed, and H&E staining, along with Immunofluorescence staining, were employed to assess PAH progression.ResultsForty-five miRNAs exhibited significant differential expression in TCs following ITGB1 knockdown. Mus-miR-429-3p, significantly upregulated in ITGB1-overexpressing TCs and in ITGB1-modified TC-derived exosomes, was selected for further investigation. Exo-ITGB1 notably inhibited the migration, proliferation, and inflammation of PASMCs by targeting Rac1. Overexpressing Rac1 partly counteracted Exo-ITGB1’s effects. In vivo administration of Exo-ITGB1 effectively reduced pulmonary vascular remodeling and inflammation.ConclusionsOur findings reveal that ITGB1-modified TC-derived exosomes exert anti-inflammatory effects and reverse vascular remodeling through the miR-429-3p/Rac1 axis. This provides potential therapeutic strategies for PAH treatment.Graphical 1. Identification of Differentially Expressed microRNAs (DEmiRs) in ITGB1 overexpressed TCs.2. Effects of Exo-ITGB1 or miR-429-3p on Hypoxia-Induced PASMCs in vitro.3. Exo-ITGB1 inhibits the hyper-proliferation and migration of PASMCs through regulating miR-429-3p/Rac1 axis in vitro.4. The therapeutic potential of Exo-ITGB1 in hypoxia-induced PAH model in vivo.

Effect of Obstructive Sleep Apnea during Pregnancy on Fetal Development: Gene Expression Profile of Cord Blood.

Obstructive sleep apnea (OSA) is quite prevalent during pregnancy and is associated with adverse perinatal outcomes, but its potential influence on fetal development remains unclear. This study investigated maternal OSA impact on the fetus by analyzing gene expression profiles in whole cord blood (WCB). Ten women in the third trimester of pregnancy were included, five OSA and five non-OSA cases. WCB RNA expression was analyzed by microarray technology to identify differentially expressed genes (DEGs) under OSA conditions. After data normalization, 3238 genes showed significant differential expression under OSA conditions, with 2690 upregulated genes and 548 downregulated genes. Functional enrichment was conducted using gene set enrichment analysis (GSEA) applied to Gene Ontology annotations. Key biological processes involved in OSA were identified, including response to oxidative stress and hypoxia, apoptosis, insulin response and secretion, and placental development. Moreover, DEGs were confirmed through qPCR analyses in additional WCB samples (7 with OSA and 13 without OSA). This highlighted differential expression of several genes in OSA (EGR1, PFN1 and PRKAR1A), with distinct gene expression profiles observed during rapid eye movement (REM)-OSA in pregnancy (PFN1, UBA52, EGR1, STX4, MYC, JUNB, and MAPKAP). These findings suggest that OSA, particularly during REM sleep, may negatively impact various biological processes during fetal development.

MiRNA-27b-3p, let-7f-5p and miRNA-142-5p can be Used in a Novel Serum Diagnostic Panel for Clear Cell Renal Cell Carcinoma.

Clear cell renal cell carcinoma (ccRCC) is a prevalent malignant tumor affecting the urinary system. Due to its unfavorable prognosis, there is a pressing need to discover effective approaches for early diagnosis and treatment of ccRCC. Extensive research has consistently demonstrated the presence of stable microRNAs (miRNAs) in human serum. Accordingly, the objective of this study was to identify a specific panel of miRNAs in serum that can serve as a reliable and non-invasive biomarker for the early detection of ccRCC. The study comprised of training and validation phases to identify potential biomarkers. In the training phase, a total of 10 miRNAs exhibiting the most significant differential expression among 28 ccRCC patients and 28 healthy controls (HCs) were identified using quantitative reverse transcription polymerase chain reaction (qRT-PCR). In the subsequent validation phase, these 10 miRNAs were assessed in serum samples obtained from an additional 80 ccRCC patients and 84 HCs using RT-qPCR. To construct a panel with optimal diagnostic capability, backward stepwise logistic regression analysis was conducted. Furthermore, bioinformatics analysis was performed on this selected miRNA panel. In ccRCC patients, the serum expression level of miRNA-142-5p was found to be significantly elevated compared to healthy controls (HCs), whereas the expression levels of let-7f-5p, miRNA-27b-3p, miRNA-212-3p, and miRNA-216-5p were significantly reduced. To assess their diagnostic potential for ccRCC, receiver operating characteristic (ROC) curve analysis was performed. The analysis revealed that miRNA-27b-3p, let-7f-5p, and miRNA-142-5p exhibited moderate diagnostic capabilities for ccRCC, with area under the curve (AUC) values of 0.826, 0.828, and 0.643, respectively. To further enhance diagnostic accuracy, a final diagnostic panel consisting of these three miRNAs was constructed, demonstrating good diagnostic value with an AUC of 0.952. The miRNA serum biomarker panel (miRNA-27b-3p, let-7f-5p, and miRNA-142-5p) identified in this study holds promise for early, non-invasive, and accurate diagnosis of ccRCC. This panel could potentially provide a valuable tool in clinical settings to aid in the timely detection and management of ccRCC.

Differential expression of angiogenesis-related genes ‘VEGF’ and ‘angiopoietin-1’ in metastatic and EMAST-positive colorectal cancer patients

Abnormal angiogenesis leads to tumor progression and metastasis in colorectal cancer (CRC). This study aimed to elucidate the association between angiogenesis-related genes, including VEGF-A, ANGPT-1, and ANGPT-2 with both metastatic and microsatellite alterations at selected tetranucleotide repeats (EMAST) subtypes of CRC. We conducted a thorough assessment of the ANGPT-1, ANGPT-2, and VEGF-A gene expression utilizing publicly available RNA sequencing and microarray datasets. Then, the experimental validation was performed in 122 CRC patients, considering their disease metastasis and EMAST+/− profile by using reverse transcription polymerase chain reaction (RT-PCR). Subsequently, a competing endogenous RNA (ceRNA) network associated with these angiogenesis-related genes was constructed and analyzed. The expression level of VEGF-A and ANGPT-2 genes were significantly higher in tumor tissues as compared with normal adjacent tissues (P-value < 0.001). Nevertheless, ANGPT-1 had a significantly lower expression in tumor samples than in normal colon tissue (P-value < 0.01). We identified a significantly increased VEGF-A (P-value = 0.002) and decreased ANGPT-1 (P-value = 0.04) expression in EMAST+ colorectal tumors. Regarding metastasis, a significantly increased VEGF-A and ANGPT-2 expression (P-value = 0.001) and decreased ANGPT-1 expression (P-value < 0.05) were established in metastatic CRC patients. Remarkably, co-expression analysis also showed a strong correlation between ANGPT-2 and VEGF-A gene expressions. The ceRNA network was constructed by ANGPT-1, ANGPT-2, VEGF-A, and experimentally validated miRNAs (hsa-miR-190a-3p, hsa-miR-374c-5p, hsa-miR-452-5p, and hsa-miR-889-3p), lncRNAs (AFAP1-AS1, KCNQ1OT1 and MALAT1), and TFs (Sp1, E2F1, and STAT3). Network analysis revealed that colorectal cancer is amongst the 82 significant pathways. We demonstrated a significant differential expression of VEGF-A and ANGPT-1 in colorectal cancer patients exhibiting the EMAST+ phenotype. This finding provides novel insights into the molecular pathogenesis of colorectal cancer, specifically in EMAST subtypes. Yet, the generalization of in silico findings to EMAST+ colorectal cancer warrants future experimental investigations. In the end, this study proposes that the EMAST biomarker could serve as an additional perspective on CMS4 biology which is well-defined by activated angiogenesis and worse overall survival.

Auxiliary diagnosis and prognosis evaluation of KIF4A, RAD51AP1 and CDKN3 in esophageal cancer

To investigate the expression of mRNA in esophageal cancer (ESCA) tissues and its potential and diagnostic and prognostic value by high-throughput sequencing data. Using the Cancer Genome Atlas Program (TCGA) database in USA by integrative bioinformatics analysis methods, the gene expression profiles and clinical data of 173 patients with ECSA were collected. The mRNA expression levels in ESCA tissue and para-cancerous tissue samples were analyzed using DESeq2, edgeR and limma to screen the differentially expressed genes (DEGs). DEGs-related protein network diagrams were drawn. GO and KEGG function enrichment analysis were performed and the hub genes were screened and the survival analysis of hub genes was analyzed. Genes related to the prognosis of ESCA were selected and their prognostic value in ESCA was analyzed. Finally, the receiver operating characteristic curve was drawn to evaluate its diagnostic value. The results showed that using TCGA cancer data, a total of 620 up-regulated DEGs and 668 down-regulated DEGs with significant differential expression between ESCA and para-cancerous tissues were screened. DEGs were mainly involved in receptor complexes, ubiquitin ligase complexes, etc., playing GTPase activity, phospholipid binding, and other molecular functions, and participating in the regulation of intracellular substance transport, small molecule metabolism, and other biological processes. Protein functional enrichment analysis showed that these proteins were mainly enriched in the IL-17 signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway, Epstein-Barr virus infection, neutrophil extracellular trap formation, and other pathways involved in the formation and development process of ESCA. Survival analysis showed that the overall survival rate of ESCA patients with high expression of KIF4A, RAD51AP1, and CDKN3 was significantly shortened, and the difference was statistically significant (P<0.05). Furthermore, the areas under the curve (AUC) of KIF4A, RAD51AP1, and CDKN3 for diagnosing esophageal cancer were 0.956, 0.951 and 0.979, respectively, with sensitivities and specificities both exceeding 80%. Additionally, ROC results of the combined diagnostic model of these three genes showed an AUC of 0.979, with sensitivities and specificities of 0.914 and 1, respectively. This indicates that KIF4A, RAD51AP1 and CDKN3 have individual or combined auxiliary diagnostic value for ESCA. In conclusion, KIF4A, RAD51AP1 and CDKN3 have high diagnostic efficiency for ESCA, and their increased expression is closely related to the prognosis, suggesting that these three genes could be used as auxiliary diagnostic and prognostic factors for ESCA.

Abstract PS16-03: Intratumoral dosing of INT230-6 in Early-Stage Breast Cancer Patients Induces Tumor Cell Necrosis and Immunomodulatory Effects: A Phase II Randomized Window-Of-Opportunity Study – the INVINCIBLE Trial

Abstract Background: Larger tumors pose an increased risk for breast cancer (BC) recurrence post-surgery. In addition, most BC outside of the triple negative subtype are considered immunological quiescent and minimally responsive to immunotherapies. One potential method to combat disease recurrence risk and induce immune activation pre-surgery is through a local therapy that could cause cell death to expose tumor antigens, provide adjuvants for anti-tumor immune priming, and thus potentially increase responsiveness to immunotherapies or rates of pathological complete response in combination with chemotherapy. We have conducted a randomized, Phase 2 presurgical Window-Of-Opportunity trial for intratumoral (IT) INT230-6 comprising vinblastine, cisplatin and a diffusion enhancer (SHAO) in patients with early-stage operable BC, the INVINCIBLE trial (NCT04781725). Previous in vivo and clinical studies demonstrated that INT230-6 induces cancer cell death and halts replication while maturing dendritic cells and recruiting T-cells into the tumor. In this trial, IT injections of INT230-6 were conducted to 1) evaluate the safety of regional cytotoxic use on BC, 2) assess the drug’s ability to cause necrosis, 3) assess immune response within the tumor, microenvironment and systemically prior to surgical resection, and 4) understand the genetic pathways involved in immune activity. Methods: Women awaiting surgery for newly diagnosed early-stage intermediate or high-grade T1-T2 invasive BC were recruited to the trial. The study has two parts. Part I was a randomized (2:1) open label trial comparing 1-3 doses of INT230-6 injected weekly versus no treatment prior to surgery to evaluate safety, feasibility, and optimal drug dosing. Part II was a double-blinded randomized (2:1) trial where patients received one IT dose of INT230-6 vs saline injection IT. Results: We successfully recruited 91 patients with age ranges of 40-77 yrs (mean of 60 yrs) with tumor size ranging from 1.1 - 4.8 cm (mean 2.5 cm; SD 0.9 cm). The most common (&amp;gt;10%) AEs were injection site pain, injection site reaction and nausea/vomiting. Approximately 90% of AEs were grade 1. In the study INT230-6 induced necrosis in 64% of subjects (37 out of 58, range 0 to 100%); whereas saline induced partial necrosis in 25% of patients (5 out of 20, range 0 to 10%). The table below shows the results of necrosis for INT230-6 use in the entire study compared to saline injection for all subjects and those with tumors of size T2. A single injection of INT230-6 caused necrosis in various histologies, including invasive lobular carcinoma. Gene expression analysis showed significant differential gene expression between the baseline biopsy and surgical specimens using INT230-6. Pathway analysis identified genes associated with TCR signaling, B cells and T cell activation that were significantly upregulated in the post INT230-6 treatment samples. There was a relative increase in CD4 and CD8 T cells and B and mast cells. Conclusion: Preliminary evidence shows that a single dose of INT230-6 can cause significant intratumoral necrosis compared to saline especially in tumors &amp;gt;2. cm. INT230-6 stimulates an immune response in breast cancers prior to surgery with minimal adverse effects and good tolerability. Given its immune activation properties, INT230-6 shows promising potential in future breast cancer neoadjuvant studies. Table 1: INVINCIBLE Study Tumor Necrosis Results Intratumoral INT230-6 injection compared to IT saline injection Citation Format: Angel Arnaout, Lewis Bender, Megan Hopkins, Vanessa Lopez Ozuna, Linda Liao, Susan Robertson, Vida Talebian, Kianoosh Keyhanian, Arif Awan, Franco Abbate, Ian Walters, Gregory Pond, John Bartlett, Lazlo Radvanyi, Melanie Spears. Intratumoral dosing of INT230-6 in Early-Stage Breast Cancer Patients Induces Tumor Cell Necrosis and Immunomodulatory Effects: A Phase II Randomized Window-Of-Opportunity Study – the INVINCIBLE Trial [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS16-03.

Abstract PO3-16-03: Investigating HER2DX genomic assay concordance within HER2-positive breast cancer

Abstract Background: The HER2DX genomic assay, encompassing a 27-gene panel, provides prognostic (risk-score) and predictive (pathological complete response [pCR]-score) information while quantifying ERBB2 mRNA expression (ERBB2-score). This study aims to explore the variability of HER2DX scores within tumor samples and between paired diagnostic biopsies and surgical specimens. Methods: The standardized HER2DX assay was conducted on pretreatment FFPE biopsies from two distinct geographical areas within tumors (i.e., two different core biopsies) of patients enrolled in the 14-409 phase II study. This study assessed the impact of HER2 heterogeneity on treatment response in stage II-III HER2+ breast cancer patients treated with neoadjuvant T-DM1 and pertuzumab. Additionally, HER2DX was evaluated on paired biopsy-surgery FFPE samples from 6 patients who underwent primary surgery without pre-operative treatment. Variability and concordance of the three HER2DX groups scores were calculated, and Pearson's correlation coefficient determined the correlation between scores at different sites/time points. Paired t-tests were performed between tumor samples for the HER2DX scores. Results: The HER2DX assay was evaluated in two different diagnostic pre-treatment core biopsies from 106 patients (n=212 HER2DX assays). Intra-tumor concordance rates of the three HER2DX groups (risk-score, pCR-score, and ERBB2-score) were 94.3%, 87.7%, and 91.5%, respectively. No significant differential expression of HER2DX scores was observed across paired core biopsies (p-values=0.327 [risk-score], 0.415 [pCR-score], and 0.451 [ERBB2-score]). The average score differences (core 1 - core 2 [scale from 0 to 100]) were 0.57 (risk-score), 0.63 (pCR score), and -0.63 (ERBB2-score). Correlation coefficients across paired core biopsies were 0.96 (risk-score), 0.91 (pCR-score), and 0.90 (ERBB2-score). Additionally, intra-patient variability of the HER2DX scores was evaluated. Average variability in risk-score was 3.38% (95% CI: 2.76-4.01), in pCR-score was 3.53% (95% CI: 2.84-4.23) and in ERBB2 was 3.87% (95% CI: 2.97-4.77). In 6 patients with cT1-2 cN0 disease, HER2DX was evaluated in a diagnostic core biopsy and a surgical specimen, with an average time interval of 8.5 weeks (range 4 to 12 weeks) between time points. The intra-patient concordance rates of the three HER2DX groups were 83.3%, 83.3%, and 100% for risk-score, pCR-score, and ERBB2-score, respectively. No significant differential expression of HER2DX scores was found across paired biopsy-surgery samples (p-values=0.814 [risk-score], 0.128 [pCR-score], and 0.607 [ERBB2-score]). The average score differences (core biopsy - surgical specimen [scale from 0 to 100]) were -0.67 (risk-score), -11.5 (pCR score), and 2 (ERBB2-score). Correlation coefficients across paired HER2DX assays were 0.97 (risk-score), 0.87 (pCR-score), and 0.94 (ERBB2-score). Conclusion: The HER2DX genomic assay demonstrates low variability within HER2+ breast cancer, supporting its reliability as a consistent tool for assessing prognosis, the probability of pCR and ERBB2 quantitative expression. Citation Format: Fara Brasó-Maristany, Laia Paré, Guillermo Villacampa, Mercedes Marín-Aguilera, Paul Spellman, Adrienne Waks, Ian Krop, Esther Sanfeliu, Zhequi Li, Patricia Galván, Eva Hernández-Illán, Pedro Jares, Joan Antón Puig-Butillé, Ana Vivancos, Patricia Villagrasa, Joel S. Parker, Charles M. Perou, Sara Tolaney, Otto Metzger, Kornelia Polyak, Aleix Prat. Investigating HER2DX genomic assay concordance within HER2-positive breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-16-03.

Abstract PO1-14-03: Discovery of proliferation essential gene signature and ACTL6A as potential biomarker for predicting prognosis and neoadjuvant therapy response in triple-positive breast cancer

Abstract Background: Based on the expression of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2), a special subtype of breast cancer which expresses all three receptors can be distinguished, namely triple-positive breast cancer (TPBC). TPBC patients has a higher risk of recurrence and lower survival rate compared to other luminal breast cancers. However, there are few studies on predicting molecules of prognosis and treatment response for TPBC. Methods: Proliferation essential genes (PEGs) were identified using CRISPR-Cas9 dataset of DepMap. The expression profiles and clinical data of TPBC were obtained from the TCGA database, GEO datasets and our center cohort. To develop a TPBC-PEG prognostic signature, cox regression and Lasso (Least absolute shrinkage and selection operator) regression analysis were applied. Functional analysis was performed using Gene Set Enrichment analysis. Finally, the relationship between candidate genes and neoadjuvant therapy (NAT) sensitivity was explored using real-time qPCR (RT-qPCR) and immunohistochemistry (IHC) based on clinical samples. Results: Among 900 TPBC-PEGs, 437 genes showed significant differential expression between TPBC and normal tissues. Subsequently, we identified 3 prognostic PEGs (ACTL6A, CCT2, TARS) and used them to construct a PEG signature. Patients with high PEG signature scores exhibited worse overall survival and lower sensitivity to NAT compared to those with low PEG signature scores. RT-qPCR indicated that in patients who lacked sensitivity to NAT, ACTL6A and CCT2 were significantly upregulated. The IHC results showed that ACTL6A protein was highly expressed in the NAT-insensitive group and non-pathological complete response patients. Conclusion: In this study, we developed an efficient PEG prognostic model that can predict the outcome for TPBC. Furthermore, we found that the expression of ACTL6A is associated with neoadjuvant therapy sensitivity in TPBC patients and can serve as an important factor in predicting patient prognosis and drug sensitivity. Figure 3. Construction and validation of a PEG signature for TPBC patients. Figure 6. The predictive value of ACTL6A on NAT efficacy and its correlation with clinical characteristics. Citation Format: Xiaofen Li, Wenfen Fu, Shiping Luo, Jie Zhang, Qingshui Wang, Chuangui Song. Discovery of proliferation essential gene signature and ACTL6A as potential biomarker for predicting prognosis and neoadjuvant therapy response in triple-positive breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-14-03.

Transcriptomic profiling of Rana [Lithobates] catesbeiana back skin during natural and thyroid hormone-induced metamorphosis under different temperature regimes with particular emphasis on innate immune system components

As amphibians undergo thyroid hormone (TH)-dependent metamorphosis from an aquatic tadpole to the terrestrial frog, their innate immune system must adapt to the new environment. Skin is a primary line of defense, yet this organ undergoes extensive remodelling during metamorphosis and how it responds to TH is poorly understood. Temperature modulation, which regulates metamorphic timing, is a unique way to uncover early TH-induced transcriptomic events. Metamorphosis of premetamorphic tadpoles is induced by exogenous TH administration at 24 °C but is paused at 5 °C. However, at 5 °C a “molecular memory” of TH exposure is retained that results in an accelerated metamorphosis upon shifting to 24 °C. We used RNA-sequencing to identify changes in Rana (Lithobates) catesbeiana back skin gene expression during natural and TH-induced metamorphosis. During natural metamorphosis, significant differential expression (DE) was observed in >6500 transcripts including classic TH-responsive transcripts (thrb and thibz), heat shock proteins, and innate immune system components: keratins, mucins, and antimicrobial peptides (AMPs). Premetamorphic tadpoles maintained at 5 °C showed 83 DE transcripts within 48 h after TH administration, including thibz which has previously been identified as a molecular memory component in other tissues. Over 3600 DE transcripts were detected in TH-treated tadpoles at 24 °C or when tadpoles held at 5 °C were shifted to 24 °C. Gene ontology (GO) terms related to transcription, RNA metabolic processes, and translation were enriched in both datasets and immune related GO terms were observed in the temperature-modulated experiment. Our findings have implications on survival as climate change affects amphibia worldwide.

Mechanism of Apoptosis in Porcine Ovarian Granulosa Cells Triggered by T-2 Toxin.

T-2 toxin (T-2), an A-type mono mycotoxin produced by various Fusarium species, disrupts DNA/RNA and protein synthesis upon entering the body, resulting in pathological conditions in various tissues/organs and posing a significant threat to human and animal health. However, the mechanisms underlying its toxicity remain unclear. With the goal of learning how T-2 affects reproduction in animals, we utilized primary porcine ovarian granulosa cells (pGCs) as a carrier in vitro and constructed concentration models for analyzing cell morphology and RNA-sequencing (RNA-seq). Our findings showed that T-2 could influence pGCs morphology, induce cell cycle arrest, and promote apoptosis in a dose-dependent manner. The results of RNA-seq analyses indicated that a total of 8216 genes exhibited significant differential expression (DEG) following T-2 treatment, of which 4812 were observed to be down-regulated and 3404 were up-regulated. The DEGs following T-2 toxin treatment of pGCs had a notable impact on many metabolic pathways such as PI3K-Akt, Ras, MAPK, and apoptosis, which in turn altered important physiological processes. Gene set enrichment analysis (GSEA) indicated that the differences in the harmful effects of T-2 might be caused by the varying control of cellular processes and the pathway responsible for steroid metabolism. These results present further insights regarding the mechanism of T-2 action on sow reproductive toxicity, enhance our understanding of T-2 reproductive toxicological effects, and lay a theoretical foundation for the judicious prevention of T-2-induced reproductive toxicity.

P073 Functional investigation of Osteoarthritis-associated non-coding variants using CRISPR/Cas9-mediated perturbation of active enhancer regions

Abstract Background/Aims OA is a common, complex disease, affecting millions of people worldwide with no effective treatments. Recent studies have implicated over 100 regions of the genome that carry DNA changes that increase the risk of developing OA. Although these findings have advanced our understanding of the disease, implicating biological pathways and cell types as being important in disease, there is still much work required to understand the mechanism by which risk variants cause OA and fully translate the findings. This is primarily due to the nature of these DNA risk variants, often located outside gene coding regions, in regions that control gene activity. Here we use CRISPR technology to investigate two DNA regions implicated in OA risk to determine the target genes that are regulated and the likely cell types in which they operate. Methods We annotated OA associated SNPs utilising in-house ATAC-seq for open chromatin regions and CUT&amp;Tag for H3K27ac marks generated for the first time here in two chondrocyte cell lines (TC28a2 and SW1353), along with H3K27ac marks from primary chondrocytes derived from the ENCODE database. Additionally we focused on regions which had genes expressed in chondrocytes within 1Mb of the lead SNP. Together this information guided prioritisation of OA regions and residing SNPs for functional validation. The two chondrocyte cell lines were engineered to constitutively express either CRISPR activation (dCas9-VPR) or CRISPR inhibition (dCas9-MeCP2-KRAB) machinery and subsequently designed guide RNAs targeted the prioritised SNPs. This enabled the activation or repression of regulatory regions, with the resultant effect on gene expression of potential target genes measured through qPCR. Results Through functional annotation of OA-associated regions, we focused on two SNPs prioritised across two distinct regions: rs1149611 in the TSKU region and rs3795159 in the UQCC1 region. These SNPs coincided with active chromatin marks in the chondrocyte cell lines and were targeted by CRISPR activation or inhibition systems in both chondrocyte cell lines. Both activation and inhibition of rs3795159 in the SW1353 chondrocyte cell line resulted in significant differential expression of the UQCC1 gene. Similarly, activation of rs1149611 upregulated TSKU in this cell line, whilst deletion of the SNP region downregulated TSKU expression in the Tc28a cell line. UQCC1 is a fibroblast growth factor, and TSKU is an inhibitor of TGFB1, and has been implicated in bone growth. Conclusion Although these results should be replicated in primary chondrocytes, here we determine firm evidence that DNA regions containing OA risk SNPs can regulate UQCC1 and TSKU in cell lines. This implicates these genes, and biological pathways, being perturbed prior to disease onset, and as such constitute novel targets for OA intervention. Disclosure A. Frantzeskos: None. J. Srinivasan: None. S. Morris: None. C. Shi: None. A. McGovern: None. E. Richards: None. S. Rossi: None. S. Eyre: None. G. Orozco: None.

P096 Pathway directionality across different immune cell lineages contributes to methotrexate response in juvenile idiopathic arthritis

Abstract Background/Aims Juvenile idiopathic arthritis (JIA) is the most common autoimmune rheumatic disease in children with methotrexate (MTX) as the first line treatment. However, about 50% of JIA patients will not respond well to MTX yet still experience drug side effects. Early prediction to MTX treatment response would be beneficial for patients and families to avoid incurring unnecessary MTX side effects and ongoing uncontrolled inflammation: such validated tools or biomarkers are currently not available. Methods Transcriptional analysis was performed on peripheral blood mononuclear cells (PBMC) from pre-MTX-treated JIA patients (n = 97) of all ILAR JIA subtypes, excluding systemic JIA. RNAseq was performed on total PBMC and sorted immune cell populations: CD4+ T cells, CD8+ T cells, CD19+ B cells, and CD14+ monocytes. Clinical data collected at the time of sampling (baseline) and at the follow-up time (between 3-12 months) were used to define outcomes, measured as change in active joint count (AJC), change in Physician VAS (PhysVAS), and change in cJADAS10. After batch normalisation with ComBat-seq, differential gene expression (DGE) analysis was performed using limma-voom with age, sex, ethnicity, and steroid status included as covariates. Log2 fold changes were utilised to rank genes to implement gene set enrichment analysis (GSEA) by fgsea. Results DGE analysis showed minimal significant differentially expressed (DE) genes that passed 5% false discovery rate (FDR). The greatest number of significant DE genes were observed in CD14+ monocytes, where baseline expression of 13 genes were significantly associated with change in PhysVAS. As alterations of gene expression for a heterogeneous disease such as JIA can be subtle and correlated between genes, GSEA was performed to investigate expression changes at pathway level. Using MSigDb Hallmark pathways, GSEA showed interferon-related and tumor-necrosis-factor pathways as significantly associated with MTX response in all cell types (5% FDR). However, the directionality (up/down regulation) differed between cell lineages, suggesting pathways divergence between T cell and non-T cell lineages. For example, in interferon gamma pathway, up-regulation associated with poor treatment response in T-cells and down-regulation in non-T cells. Preliminary analysis of the leading edge genes of the interferon gamma pathway in the non-T cell lineages showed that many of the genes are driven by interferon alpha, whilst within CD4+ and CD8+ T cells the majority of the leading edge genes are specific to interferon gamma. Conclusion Different directionality of pathways that might be relevant to JIA response to treatment with MTX is observed in different mononuclear cell lineages. This could potentially explain the difficulties of finding biomarkers which correlate with response to treatment from whole blood or PBMC. Shared genes across different interferon-related pathways also suggest that interaction between interferon pathways might be driving the different direction of interferon pathway expression in different cell lineages. Disclosure M. Kartawinata: None. W. Lin: None. B. Jebson: None. K. O'Brien: None. E. Ralph: None. R. Restuadi: None. G.T. Hall: None. S. Castellano: None. C. Wallace: None. L.R. Wedderburn: Grants/research support; LRW Declares in kind contributions to CLUSTER by AbbVie, GSK, UCB, Sobi and Pfizer inc and non renumerated collaborations with Lilly and Novartis.