Tumor Samples Research Articles

Predictive role of SLC1A5 in neuroblastoma prognosis and immunotherapy

BackgroundNeuroblastoma, a prevalent extracranial solid tumor in pediatric patients, demonstrates significant clinical heterogeneity, ranging from spontaneous regression to aggressive metastatic disease. Despite advances in treatment, high-risk neuroblastoma remains associated with poor survival. SLC1A5, a key glutamine transporter, plays a dual role in promoting tumor growth and immune modulation. However, its contributions to neuroblastoma biology remain largely unexplored.MethodsThis study utilized clinical neuroblastoma samples from 20 patients and 1310 cases from four public datasets to investigate SLC1A5 expression, biological function, and prognostic significance. Differential expression, Kaplan–Meier survival analysis, gene set enrichment analysis, and weighted correlation network analysis were conducted. Functional validation included qPCR, immunohistochemistry, Western blotting, and cell proliferation assays using the SLC1A5 inhibitor V-9302. A prognostic signature, SRPS, was constructed and validated using machine-learning approaches. Immune infiltration analysis was performed to evaluate the tumor immune microenvironment.ResultsSLC1A5 expression was significantly elevated in high-risk neuroblastoma and correlated with advanced stages and poor prognosis. GSEA revealed mTORC1 signaling enrichment in high SLC1A5 expression groups, validated by increased p-p70S6K levels in tumor samples and neuroblastoma cells. V-9302 treatment suppressed mTORC1 signaling and inhibited cell proliferation. Hub-genes were identified to form the SRPS model, which demonstrated superior prognostic performance compared to existing models. Immune infiltration analysis revealed a more immunosuppressive tumor microenvironment associated with high SLC1A5 expression. Additionally, SLC1A5 negatively regulated ST8SIA1, a gene crucial for GD2 biosynthesis, suggesting that SLC1A5 inhibition may enhance GD2-directed immunotherapies.ConclusionSLC1A5 plays a pivotal role in neuroblastoma by promoting tumor progression and shaping an immunosuppressive microenvironment. The SRPS model, incorporating SLC1A5-associated genes, offers robust prognostic utility. Targeting SLC1A5 through advanced drug delivery systems and combined metabolic-immunotherapeutic strategies may enhance treatment specificity and efficacy. These findings provide a foundation for novel therapeutic approaches to improve outcomes in high-risk neuroblastoma patients.

Epigenetic mechanisms underlying endometrial cancer (EC) outcomes: race-specific patterns of DNA methylation associated with molecular subtypes and survival.

Endometrial cancer [EC] is the fourth most common cancer in women in the United States. Stark racial disparities are present in EC outcomes in which Black women have significantly higher EC-related mortality than White women. The social and biologic factors that contribute to these disparities are complex, and may include racial differences in epigenetic landscapes. To investigate race-specific epigenetic differences in EC tumor characteristics and outcomes, we utilized the most recent data within the Cancer Genome Atlas (TCGA). Genome-wide CpG methylation data for more than 850 000 CpG sites were analyzed across 245 tumor samples, including 52 from Black women and 181 from White women. Race-adjusted and race-stratified associations among CpG methylation in ECs and molecular subtypes and disease-free survival (DFS) were examined. Race-specific analysis identified subtype-associated CpGs within 9572 genes in tumors from White women, and only 10 genes in tumors that were from Black women. Race-specific analyses also identified survival-associated CpGs with 1119 unique genes identified in tumors from White women, and none identified in tumors from Black women. Genes identified with differential methylation among subtypes included those involved in oxidative stress (HIF3A), and DNA repair (MLH1). Replication cohort data highlighted genes overlapping with those identified within the TCGA, such as G Protein Subunit Beta 1 (GNB1), involved in G-protein signaling, and Interleukin 37 (IL37), involved in cytokine signaling. Identification of these racial differences in EC tumor epigenetic landscapes and associated changes in gene expression may provide insight into strategies to improve outcomes and reduce disparities.

YAP/TEAD4/SP1-induced VISTA expression as a tumor cell-intrinsic mechanism of immunosuppression in colorectal cancer.

Hyperactivation of the YAP/TEAD transcriptional complex in cancers facilitates the development of an immunosuppressive tumor microenvironment. Herein, we observed that the transcription factor SP1 physically interacts with and stabilizes the YAP/TEAD complex at regulatory genomic loci in colorectal cancer (CRC). In response to serum stimulation, PKCζ (protein kinase C ζ) was found to phosphorylate SP1 and enhance its interaction with TEAD4. As a result, SP1 enhanced the transcriptional activity of YAP/TEAD and coregulated the expression of a group of YAP/TEAD target genes. The immune checkpoint V-domain Ig suppressor of T-cell activation (VISTA) was identified as a direct target of the SP1-YAP/TEAD4 complex and found to be widely expressed in CRC cells. Importantly, YAP-induced VISTA upregulation in human CRC cells was found to strongly suppress the antitumor function of CD8+ T cells. Consistently, elevated VISTA expression was found to be correlated with hyperactivation of the SP1-YAP/TEAD axis and associated with poor prognosis of CRC patients. In addition, we found by serendipity that enzymatic deglycosylation significantly improved the anti-VISTA antibody signal intensity, resulting in more accurate detection of VISTA in clinical tumor samples. Overall, our study identified SP1 as a positive modulator of YAP/TEAD for the transcriptional regulation of VISTA and developed a protein deglycosylation strategy to better detect VISTA expression in clinical samples. These findings revealed a new tumor cell-intrinsic mechanism of YAP/TAZ-mediated cancer immune evasion.

Uridine-cytidine kinase 2 is correlated with immune, DNA damage repair and promotion of cancer stemness in pan-cancer

BackgroundUCK2 (Uridine-Cytidine Kinase 2) is a promising prognostic marker for malignant tumors, but its association with immune infiltration and cancer stemness in pan-cancer remains to be fully understood. we find that gene UCK2 is closed related to RNA stemness scores (RNAss) and DNA stemness scores (DNAss), which is measured the tumor stemness. We also discover an association between UCK2 expression and immune cells by CIBERSORT algorithm, ESTIMATE algorithm and ssGSEA algorithm, especially, related to T cell, monocytes, mast cells, and macrophages. This study aims to shed light on the role and possible mechanism of UCK2 in pan-cancer.MethodsWe used the R programming language for pan-cancer bulk sequencing data analysis, which were obtained from the University of California, Santa Cruz (UCSC) datasets. UCSC database is a very useful for explore data from TCGA and other cancer genomics datasets, The data we explored at the UCK2 transcriptome level came from TCGA data in the UCSC database. We explored differential UCK2 expression between tumor and normal samples. Immunohistochemistry (IHC) was utilized to validate the expression of UCK2 in different types cancers using tumor tissue chips. The correlations of UCK2 with prognosis, genetic instability, DNA repair, cancer stem cell characteristics, and immune cell infiltration were investigated. Furthermore, single-cell datasets, acquired from the Gene Expression Omnibus (GEO) database, were used to validate the relationship between UCK2 and immune cells. GEO is a famous public genomics database supporting freely disseminates microarray data. Finally, we analyzed the correlation between UCK2 and drug sensitivity.ResultsUCK2 expression was observed to be high in most cancers and was remarkably related to the prognosis of pan-cancers. We found that the increased UCK2 expression was associated with higher genetic instability. Additionally, positive relationships were observed between UCK2 expression and mismatch repair genes, homologous recombination repair genes, and cancer stemness across different cancer types. There were significant correlations between UCK2 and T cells, monocytes, mast cells, and macrophages. Moreover, as expected, the immune checkpoint human leucocyte antigen (HLA) was found to be negatively related to UCK2. Similarly, UCK2 was also observed to have a negative association with major histocompatibility complex (MHC) genes. We noted that UCK2 had significant correlations with the sensitivity to various anti-cancer drug.ConclusionWe have observed that UCK2 plays pivotal roles in prognosis and tumor immunity, and it is associated with DNA repair and cancer stemness. The UCK2 gene exhibits a strong correlation with the immune checkpoints HLA. This study highlights its potential impact on drug sensitivity.

Cell signaling communication within papillary craniopharyngioma revealed by an integrated analysis of single-cell RNA sequencing and bulk RNA sequencing

ObjectiveThis study aims to elucidate the primary signaling communication among papillary craniopharyngioma (PCP) tumor cells.MethodsFive samples of PCP were utilized for single-cell RNA sequencing. The most relevant ligand and receptor interactions among different cells were calculated using the CellChat package in R software. Bulk RNA sequencing of 11 tumor samples and five normal controls was used to investigate the pair interactions detected by single-cell RNA sequencing.ResultsFibroblasts were not found in ACP, whereas they were detected in PCP. InferCNV revealed high CNV scores for the clusters of epithelial cells and fibroblasts using immune cells as a reference. Epithelial Mesenchymal Transition, Interferon Gamma Response, p53 Pathway, and Estrogen Response Early are pathways commonly shared by fibroblasts and epithelial cells, ranking high in priority. The Wnt signaling pathway and PI3K-Akt signaling pathway play a crucial role in facilitating communication between epithelial cells and fibroblasts. Neutrophils were recognized as the main receivers of incoming signals, with ANXA1-FPR1 and MIF-(CD74 + CXCR2) being identified as the primary signals transmitted from fibroblasts to neutrophils.ConclusionThrough analyzing the communication of essential signaling pathways, ligands, and receptors among epithelial cells, fibroblasts, and neutrophils in PCP tumor tissues, we have identified certain molecules with promising prognostic and therapeutic potential.

Abstract B029: TWIST1 Associates with resistance to treatment and Twist1 drives tumor progression in vivo for small cell lung cancer

Abstract Purpose: Small cell lung cancer (SCLC) is a highly aggressive and deadly malignancy. Two major factors contributing to the high mortality of SCLC are early metastasis and rapid development of therapy resistance. Recent research suggests upregulation of the epithelial-mesenchymal transition (EMT) program and the EMT transcription factor Twist1 correlated with accelerated tumor progression and chemoradiation (CRT) resistance in SCLC. However, a causal relationship between Twist1 and these aspects of SCLC biology has not been rigorously studied. Here, we investigated whether Twist1 upregulation could promote SCLC tumorigenesis, metastasis, and resistance to CRT. Materials and Methods: We analyzed transcriptomic data from the IMpower133 phase 3 trial of extensive stage SCLC stratified by median TWIST1 levels using Kaplan-Meir statistic. To investigate the roles of Twist1 directly in SCLC biology, we have generated a novel genetically engineered mouse model (GEMM) termed RPGT (Rb1Flox; Trp53Flox; ROSA26LSL-rtTA-IRES-EGFP; Twist1-TetO7-Luc). The RPGT GEMM enables the generation of autochthonous SCLC tumors after induction with Cre recombinase adenovirus. By withdrawing or providing doxycycline to mice, we can control Twist1 expression to activate or inactivate EMT in tumors. By characterizing mouse tumor samples with histological, immunostaining, and transcriptomic profiling analyses, we evaluated the impact of Twist1 and EMT upregulation on SCLC tumor biology and plasticity as well as metastatic spread and outgrowth. To evaluate the impact of EMT activation on SCLC sensitivity to CRT, we performed in vitro viability assays on primary tumor cell lines established from RPGT tumors. We also treated RPGT mice with vs. without Twist1 overexpression with CRT to validate our in vitro data. Results: In the chemotherapy alone control arm of IMpower133 there was a trend towards a difference in overall survival (OS) between TWIST1-high or -low patients (p=025 by log-rank) and in the NMF1/NEUROD1 subtype, patients with TWIST1-high had statistically significantly inferior OS (p=0.01). We then observed that both control (no Twist1 overexpression) and Twist1-overexpressing RPGT mice developed neuroendocrine SCLC tumors. While SCLC-ASCL1 was the predominant subtype in both cohorts, RPGT tumors exhibited more plasticity, with features associated with SCLC-NEUROD1 subtype. Furthermore, Twist1 overexpression dramatically increased the metastatic incidence in RPGT compared to control animals, indicating an important role of EMT in SCLC dissemination. Transcriptomic profiling of primary tumors and matching metastases in RPGT mice also revealed downregulation of Twist1 and EMT in metastases, suggesting that EMT suppression was necessary for metastatic outgrowth. Furthermore, we found that repressing Twist1 expression enhanced SCLC susceptibility to CRT both in vitro and in vivo. Conclusions: Overall, our data suggest that TWIST1/Twist1 plays an important role in promoting SCLC plasticity, metastasis, and treatment resistance. Citation Format: Triet Nguyen, Jinhee Chang, Kathleen Gabrielson, Amol Shetty, Yang Song, Apaala Chatterjee, Audrey Lafargue, Yoo Sun Kim, Danielle Council, Aaron Chan, Dipanwita Dutta Chowdhury, Muhammad Ajmal Khan, Nick Connis, Daniel Sforza, Eric Gardner, Christopher McFarland, Mohammad Rezaee, Nitin Roper, Christine Hann, Phuoc T. Tran. TWIST1 Associates with resistance to treatment and Twist1 drives tumor progression in vivo for small cell lung cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Targeted Therapies in Combination with Radiotherapy; 2025 Jan 26-29; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(2_Suppl):Abstract nr B029.

CHAF1B promotes the progression of lung squamous-cell carcinoma by inhibiting SETD7 expression.

The p60 subunit of the chromatin assembly factor-1 complex, that is, chromatin assembly factor-1 subunit B (CHAF1B), is a histone H3/H4 chaperone crucial for the transcriptional regulation of cell differentiation and self-renewal. CHAF1B is overexpressed in several cancers and may represent a potential target for cancer therapy. However, its expression and clinical significance in lung squamous-cell carcinoma (LUSC) remain unclear. In this study, we performed weighted gene correlation network analysis to analyze the Gene Expression Omnibus GSE68793 LUSC dataset and identified CHAF1B as one of the most important driver gene candidates. Immunohistochemical analysis of 126 LUSC tumor samples and 80 adjacent normal lung tissues showed the marked upregulation of CHAF1B in tumor tissues and the negative association of its expression level with patient survival outcomes. Silencing of CHAF1B suppressed LUSC proliferation in vitro and LUSC tumor growth in vivo. Furthermore, bulk RNA sequencing of CHAF1B knockdown cells indicated SET domain containing 7 (SETD7) as a significant CHAF1B target gene. In addition, CHAF1B competitively binds to the SETD7 promoter region and represses its transcription. Altogether, these results imply that CHAF1B plays a vital role in LUSC tumorigenesis and may represent a potential molecular target for this deadly disease.

Prognostic and clinical heterogeneity of PD1 and PD-L1- immunohistochemical scores in endometrial cancers.

PD1/PD-L1 inhibition (ICi) has recently become a new standard of care for patients with advanced MMR-deficient (MMRd) endometrial cancers. Nevertheless, response to immunotherapy is more complex than the presence of a single biomarker and therefore it remains challenging to predict patients response to ICi beyond MMRd tumors. Elevated PD-L1 expression (CPS ≥ 1) is often used as a prognostic marker as well as a predictive biomarker of response to ICi in different tumor types. In a retrospective, patient derived study, we analyzed PD1- and PD-L1 staining and correlated the results of different scores to clinical data to evaluate the prognostic impact of these scores. Immunohistochemical analysis of the receptor PD1 and the receptor ligand PD-L1 were performed on TMAs of primary paraffin‑embedded tumor samples. All patients were treated for primary endometrial cancer in the Department of Gynecology and Obstetrics, University Medical Center Schleswig-Holstein, Campus-Lübeck, Germany between the years 2006-2018. The evaluation and determination of the tumor proportion scoring (TPS), the combined positive score (CPS) and the immune cell scoring (IC) was automatically assessed semi-quantitatively, and results were correlated with clinicopathological characteristics and survival. 130 samples were evaluable and 64% showed a positivity (IC > 0) for the receptor PD1 and 56% for the receptor ligand PD-L1. Patients with a PD1 IC Score ≥ 1 showed a significant longer disease-free survival of 140months (95% confidence interval (CI): 124-158) compared to patients with a lower IC < 1 for PD1 of 89months (95% confidence interval (CI): 69-110); p = 0.017). Furthermore, the disease-free survival for patients with a CPS ≥ 5 for PD1 was longer (153.7months (95% confidence interval (CI): 134-173.6) vs. 98.6months (95% confidence interval (CI): 83-114); p = 0.036). Additionally, a PD1 CPS ≥ 5 showed a better overall survival but the result was not statistically significant. No difference in survival was found between patients with PD-L1 higher or lower than CPS 5. In this study we pointed out that there are significant clinical differences among several immunohistochemical scoring systems. In our trial, a PD1-positivity with CPS ≥ 5 and IC ≥ 1 were significantly associated to a better disease-free survival while there was no association with TPS. The PD1-IC scoring was associated with MMRd while the TPS scoring was not. Therefore, PD1-IC could be more appropriate for endometrial carcinomas compared to TPS and could also add prognostic information beside the more established PD-L1-staining. Further prospective studies are needed for a validation of these scores in combination with other biomarkers.

Brain Tumors and Beyond: Multi-Compartment Microbiome and Mycobiome Analysis

Brain tumors are frequently diagnosed diseases in which etiology and progression largely depend on mutations and genetic factors. Additionally, recent reports document that the microbiome may influence tumor growth, tumor microenvironment, and response to therapy. Our goal was to examine the extent to which the bacterial composition—microbiota—and fungal composition—mycobiota—characteristic of the tumor and its microenvironment correlate with the composition of the gut and blood microbiota and mycobiota in five randomly selected brain tumor patients. The bacterial composition of the tumor, tumor-adjacent tissue (TAT), blood, and gut samples of the five patients were analyzed by 16S rRNA and ITS-based sequencing in order to determine the bacterial and fungal composition. The gut microbiome and mycobiome composition showed individual and tissue-specific signatures in each patient. The microbiome composition of the blood, TAT, and tumor tissue was very similar in each patient, dominated by Klebsiella, Enterococcus, Blautia, and Lactobacillus spp. In contrast, the mycobiome composition of the blood, TAT, and tumor showed a diverse, individual picture. The most common fungal species in the blood and TAT were Tomentella, Didymosphaeria, Alternaria, Penicillium, Mycosphaerella, and Discosia. The blood and TAT mycobiome were similar to each other but unique and characteristic of the patients. In contrast, in the tumor tissues, Alternaria, Malassezia, Schizophyllum, and Tomentella genus were the most common fungi genus. Our results showed that the presence of fungi in tumors shows a unique pattern that is independent of the pattern observed in the gut, blood, and tumor environment and that the effects of the mycobiome are distinct and cannot be associated with those of the microbiome. Elucidating the role of fungi in tumors and exploring the relationship between fungi and brain tumor types may open up further therapeutic options.

Stromal PDGFR-beta expression is a prognostic factor in high-grade serous ovarian cancer patients but is it also predictive for response to antiangiogenic treatment?

ObjectiveIn advanced ovarian cancer, the majority of patients receive anti-angiogenic treatment with bevacizumab. However, its use is often associated with severe side effects, and not all patients benefit from the therapy. Currently, there are no reliable biomarkers to predict response to treatment. Given their role as key regulators of angiogenesis, platelet-derived growth factor receptor-beta (PDGFR-beta) and vascular endothelial growth factor receptor-2 (VEGFR-2) are promising candidates for predictive biomarkers. This study evaluates their potential.MethodsPDGFR-beta and VEGFR-2 expression was evaluated using immunohistochemistry in a tissue microarray assay including 391 ovarian tissue samples. Correlation analyses with clinical and histopathological parameters were performed in a homogeneous cohort of 199 high grade serous ovarian cancer samples (HGSOC).ResultsIn HGSOC, strong stromal PDGFR-beta expression was associated with significantly shorter overall survival compared to weak/moderate expression. The impact of stromal PDGFR-beta expression on patient survival was however not restricted to the subgroup of patients receiving therapy with bevacizumab, and therefore cannot be considered as a predictive factor. For VEGFR-2, no or weak protein expression was found in the majority of the tumor samples. Survival analyses showed a more favorable prognosis with no or weak VEGFR-2 expression.ConclusionsHigh stromal expression levels of PDGFR-beta correlate with shorter overall survival in HGSOC. Thus, stromal PDGFR-beta might serve as a prognostic biomarker. No predictive effect in response to bevacizumab therapy could be attributed.

Spatial transcriptome reveals histology-correlated immune signature learnt by deep learning attention mechanism on H&E-stained images for ovarian cancer prognosis

BackgroundThe ability to predict the prognosis of patients with ovarian cancer can greatly improve disease management. However, the knowledge on the mechanism of the prediction is limited. We sought to deconvolute the attention feature learnt by a deep learning convolutional neural networks trained with whole-slide images (WSIs) of hematoxylin-and-eosin (H&E)–stained tumor samples using spatial transcriptomic data.MethodsIn this study, 773 WSIs of H&E-stained tumor sections from 335 patients with treatment naïve high-grade serous ovarian cancer who were included in The Cancer Genome Atlas (TCGA) Pan-Cancer study were used to train, and validate, and to test a ResNet101 CNN model modified with attention mechanism. WSIs from patients in an independent cohort were used to further evaluate the model.ResultsThe prognostic value of the predicted H&E-based survival scores from the trained model on patient survival was evaluated. The attention signals learnt by the model were then examined their correlation with immune signatures using spatial transcriptome. After validating the model with the testing datasets, pathway enrichment analysis showed that the H&E—based survival score significantly correlated with certain immune signatures and this was validated spatially using spatial transcriptome data generated from ovarian cancer FFPE samples by correlating the selected signature and attention signal.ConclusionsIn conclusion, attention mechanism might be useful to identify regions for their specific immune activities. This could guide future pathological study for the useful immunological features that are important in modulating the prognosis of ovarian cancer patients.

Patient-derived xenograft models of gastrointestinal stromal tumors: a ready-to-use platform for translational research.

Gastrointestinal stromal tumors (GIST) are the most common mesenchymal malignancy of the gastrointestinal tract. Most GIST harbor mutations in oncogenes, such as KIT, and are treated with tyrosine kinase inhibitors (TKI), such as imatinib. Most tumors develop secondary mutations inducing drug resistance against the available TKI, which requires novel therapies. We established a GIST patient-derived xenograft (PDX) platform of GIST that can be used for preclinical drug testing. Tumor tissue from consenting GIST patients was transplanted subcutaneously to NMRI nu/nu mice. Once tumor growth was observed, the tumor was re-transplanted to a next generation of mice. Tumors were characterized histopathologically and molecularly at every re-transplantation and compared with the original patient tumor. We transplanted 112 tumor samples from 99 GIST patients, resulting in 12 established and well-characterized GIST models with different mutations and TKI sensitivity. Three models harbor secondary KIT mutations. One model is characterized by a primary, imatinib-resistant PDGFRA exon 18 p.D842V mutation. Our established platform of well-characterized GIST PDX models, covering the most relevant driver mutations, serves as an excellent tool for preclinical drug testing and tumor biology studies.

Efficacy of ramucirumab combined with erlotinib or osimertinib in untreated EGFR-mutated NSCLC patients with asymptomatic brain metastases: insights from molecular biomarkers in the RELAY-brain trial.

The RELAY-Brain trial examined the clinical utility and survival impacts of ramucirumab (RAM) combined with epidermal growth factor receptor (EGFR)-TKI in patients with EGFR-mutated non-small-cell lung cancer (NSCLC) with brain metastases. Although RAM combined with erlotinib (ERL) is known to have clinical benefits, the benefits in patients with baseline brain metastases remain unclear. This report examined the long-term follow-up data (Japan Registry of Clinical Trials: jRCTs2051190027) of the same patients, analyzing relevant biomarkers from tumor and plasma samples. The six patients enrolled in the RELAY-Brain trial received RAM plus ERL or osimertinib (OSM). Our long-term follow-up observational study assessed patient survival, treatment status, and genetic biomarkers. Tumor and plasma samples were analyzed at baseline, during treatment, and at disease progression using next-generation sequencing and droplet digital PCR, to identify gene alterations and EGFR-TKI-resistant mutations. After median follow-up of 44.2months, the first site of disease progression in three of the patients was the brain metastases. In the RAM + ERL group, two patients with the T790M mutation subsequently received OSM. Progression-free survival (PFS) and overall survival ranged from 10.46 to 42.07months and from 30.14 to 52.25months, respectively. Gene alterations included TP53 mutations in three patients and ERBB2 and PIK3CA mutations in two. TP53 mutations were associated with shorter PFS. RAM with ERL or OSM achieved significant clinical benefits for patients with EGFR-mutated NSCLC with asymptomatic brain metastases. These positive outcomes and the identification of related biomarkers support the therapeutic potential of these combinations.

Dynamine 3 as a Diagnostic and Prognostic Biomarker in Pancreatic Cancer: Implications for Early Detection and Targeted Therapy

ABSTRACT Background Dynamins are defined as a group of molecules with GTPase activity that play a role in the formation of endocytic vesicles and Golgi apparatus. Among them, DNM3 has gained recognition in oncology for its tumor suppressor role. Based on this, the aim of this study is to investigate the effects of the DNM3 gene in patients diagnosed with pancreatic cancer using bioinformatics databases. Materials and Methods For differential gene expression analysis, TCGA TARGET GTEx study on the UCSC Xena, GSE196009, GSE211398, GSE151580 datasets on The Gene Expression Omnibus (GEO) were utilized; for the analysis of changes in gene expression according to stages GEPIA2 were utilized; for the analysis of changes in gene expression according to clinical and pathological characteristics, UALCAN was employed; for Overall Survival (OS) analysis, Kaplan-Meier Plotter was used; for gene alteration analysis, cBioPortal was utilized; for immune cell infiltration analysis, Tumor Immune Estimation Resource (TIMER) and TIMER2.0 were employed; for protein-protein interaction and gene enrichment analyses, STRING was used; for enrichment analyses Enrichr was used; for Gene Set Correlation Enrichment Analysis Gscore was used on GSE15471; for essentiality of DNM3 gene in pancratic cancer cell lines DepMap was used; and for the detection of miRNAs, miRDB was utilized; ENCORI was used for gene-miRNA correlation and miRNA prognosis analyses. Results In the pancreatic adenocarcinoma (PAAD) cohort, DNM3 gene expression was higher in tumor samples, and there was no significant difference in expression among cancer stages. High levels of DNM3 gene expression were associated with longer OS in PAAD. A weak positive correlation was observed between DNM3 gene expression and B-Cell and CD + T Cell infiltrations, while a moderate positive correlation was found with CD8+ T Cell, Macrophage, Neutrophil, and Dendritic Cell infiltrations in TIMER. NK cell by QUANTISEQ, CD 4+ T Cell by TIMER, T cell regulatory (Tregs) by CIBERSORT-ABS infiltrations were positively associated with DNM3 gene expression and decreased risk in prognosis. Common lymphoid progenitor by XCELL and MDSC by TIDE infiltrations were negatively associated with DNM3 gene expression and increased risk of prognosis. Macrophage M1 by QUANTISEQ was positively associated with DNM3 gene expression and increased risk in prognosis. DNM3 gene appears to be associated with various pathways related to inflammation and the immune system. Amplification of the DNM3 gene was detected in 5 out of 175 patients. Enrichment was observed in pathways such as bacterial invasion of epithelial cells, endocytosis, endocrine and other factor-regulated calcium reabsorption, synaptic vesicle cycle, and phospholipase D signaling pathway. According to Gscore, DNM3 gene was associated with Fc epsilon RI signaling pathway, HALLMARK MTORC1 SIGNALING, HALLMARK EPITHELIAL MESENCHYMAL TRANSITION gene sets. According to ENCORI, DNM3 gene was negatively correlated with hsa-miR-203a-3p and increased expression of this miRNA was associated with adverse prognosis in PAAD. Conclusions The DNM3 gene may play a tumor suppressor role in pancreatic cancer, similar to its role in other malignancies. The contribution of immune cells may also be significant in this effect. However, in vitro studies are needed to elucidate the mechanisms triggered in pancreatic cancer.

Exploring the potential of BOLA3-DT as a diagnostic biomarker in prostate cancer.

Exploring the potential of BOLA3-DT as a diagnostic biomarker in prostate cancer. Expression of the lncRNA BOLA3-DT was analyzed between normal and tumor samples in the GDC TCGA PRAD (Genomic Data Commons: The Cancer Genome Atlas Prostate Adenocarcinoma Collection) dataset. Disease progression-related clinicopathological parameters such as serum PSA level (ng/ml) and Gleason score were associated with the expression of BOLA3-DT using the same GDC TCGA PRAD dataset. To validate these findings, the expression of BOLA3-DT was checked in our sample set of 15 PCa (prostate cancer) and 15 BPH (benign hypertrophy of the prostate) patients. In the GDC TCGA PRAD dataset, the expression of the lncRNA BOLA3-DT was significantly downregulated in prostate cancer tissue samples (n = 492) compared to adjacent normal (n = 52; p < 0.0001), and, there was a significant negative correlation between the expression of the lncRNA BOLA3-DT and the serum PSA level (p < 0.01). However, no significant association was found between the lncRNA BOLA3-DT expression and the Gleason score (p > 0.05). In this study, it was found that BOLA3-DT was downregulated in PCa tissue samples compared to BPH samples (p > 0.05). In the GDC TCGA PRAD dataset, it was revealed that BOLA3-DT could serve as an excellent diagnostic marker with a sensitivity of 86.9% and a specificity of 84.6% (AUC-0.916). LncRNA BOLA3-DT, a novel long non-coding RNA, was found to be downregulated in prostate cancer. The expression of the lncRNA BOLA3-DT can serve as a diagnostic marker in prostate cancer.

Early Detection of the Pathogenetic Variants of Homologous Recombination Repair Genes in Prostate Cancer: Critical Analysis and Experimental Design

It has been shown that the pathogenic variants (PVs) of the DNA Damage Response (DDR) genes, whether of a germinal or somatic nature, represent a predictive biomarker of high sensitivity to treatment with inhibitors of the enzyme poly-ADP-ribose polymerase (PARP) in patients with hormone-resistant metastatic prostate cancer (HRPCa). Moreover, the detection of PVs of the Homologous Recombination Repair (HRR) genes in PCa patients can help to define the patient’s prognosis and the choice of the therapeutic procedure. Among men with metastatic PCa, the frequency of PVs in HRR genes ranges from 11% to 33%, which is a significantly higher rate compared to non-metastatic PCa, where the incidence is between 5% and 10%. Next-Generation Sequencing (NGS) results were more commonly obtained from newly acquired somatic samples compared to archived samples (prostate biopsy or prostatectomy). We developed an experimental multidisciplinary prospective study in patients with a new diagnosis of high-risk PCa at biopsy. The aim was to evaluate the presence of PVs of different HRR genes in patients with the first diagnosis of PCa in relation to a metastatic or non-metastatic stage, tumor aggressiveness, and early risk of progression. Among 43 initial tumor samples from 22 patients, 25 samples from 12 patients were selected for library preparation based on their DNA concentration and quality. After the NGS, 14 different DNA variants were prioritized. Oncogenetic and likely oncogenetic variants were found in the ATM, BRCA1, PTEN, KMT2D, and CDH1 genes. Moreover, variants of uncertain significance were found in ATM, DDR2, FANCA, FOXA1, PLCB4, PTCH1, and RB1.

P0179 Spatial immune profiling of Crohn’s Disease fistula carcinomas - Defining a distinct cancer subtype

Abstract Background Fistula formation is a common and debilitating complication of Crohn’s disease (CD). Although rare, CD-associated fistula carcinomas present significant diagnostic and prognostic challenges. This study aims to identify disease-specific immune cell subsets in CD-associated fistula carcinomas. Methods The study analyzed tissue samples from 10 CD patients with fistula carcinomas, 7 patients with CD-associated fistulas, and 6 patients with sporadic colorectal cancer (CRC). In the tumor samples, the main tumor, infiltration front, and non-involved areas were included. Using a 36-marker panel, the immune landscape was characterized through imaging mass cytometry. The samples were processed, stained, and analyzed for immune cell compositions, cell-cell interactions, and spatial microenvironments. Results The immune infiltrate observed in fistula carcinomas displayed similarities to both CD fistulas and CRC. Fistula-carcinoma samples exhibited elevated levels of neutrophils, B cells, and CD163high macrophages. CRC main tumor samples exhibited a higher presence of intraepithelial CD8+ lymphocytes and CD163low macrophages. The highest levels of Cleaved Caspase-3 were observed in CRC main tumor samples, which exhibited a positive correlation with CD163low macrophages and cytotoxic T cells. Conversely, a negative correlation was observed between cleaved Caspase-3 and cytotoxic T cells in fistula-carcinoma main tumor samples. The analysis of cellular microenvironments and dimensionality reduction clustering based on immune cell frequencies revealed that fistula carcinomas exhibit a unique combination of immune cell characteristics derived from both CD fistulas and CRC. Conclusion The immune landscape of CD-associated fistula carcinomas exhibits characteristics of both CD fistulas and CRC, indicating a complex pathogenesis driven by chronic inflammation. These findings suggest that fistula carcinomas constitute a distinct cancer subtype, necessitating further research to develop targeted therapeutic strategies.

Like, share, and spike: Glioblastoma progenitors influence neuronal excitability at the glioma-neural interface.

Writing in Neuron, Zhang etal. identify a subpopulation of glioblastoma cells from patient tumor samples with progenitor-like features that expresses the potassium ion channel KCND2.1 In mouse and organoid models, these cells enhance neural activity at the glioma-neural interface.

Functional genomic imaging (FGI), a virtual tool for visualization of functional gene expression modules in heterogeneous tumor samples

Advances in sequencing technologies are reshaping clinical diagnostics, prompting the development of new software tools to decipher big data. To this end, we developed functional genomic imaging (FGI), a visualization tool designed to assist clinicians in interpreting RNA-Seq results from patient samples. FGI uses weighted gene co-expression network analysis (WGCNA), followed by a modified Phenograph clustering algorithm to identify co-expression gene clusters. These gene modules were annotated and projected onto a t-SNE map for visualization. Annotation of FGI gene clusters revealed three categories: tissue-specific, functional, and positional. These clusters may be used to build tumor subtypes with pre-annotated functions. At the multi-cancer cohort level, tissue-specific clusters are enriched, whereas at the single cancer level, such as in lung cancer or ovarian cancer, positional clusters can be more prominent. Moreover, FGI analysis could also reveal molecular tumor subtypes not documented in clinical records and generated a more detailed co-expression gene cluster map. Based on different levels of FGI modeling, each individual tumor sample can be customized to display various types of information such as tissue origin, molecular subtypes, immune activation status, stromal signaling pathways, cell cycle activity, and potential amplicon regions which can aid in diagnosis and guide treatment decisions. Our results highlight the potential of FGI as a robust visualization tool for personalized medicine in molecular diagnosis.

Development of a microvessel density gene signature and its application in precision medicine.

Combination therapy with anti-angiogenic drugs and immune checkpoint inhibitors has shown enhanced clinical activity and has been approved for the treatment of multiple tumor types. Despite extensive research, predictive biomarkers for combination therapy remain poorly understood. Microvessel density (MVD), a surrogate marker for aberrant angiogenesis measured by immunohistochemistry (IHC), has been associated with response to monotherapy with anti-angiogenesis inhibitors. However, obtaining tumor tissue with a sufficient mass for IHC analysis is not always practical, and IHC-based MVD measurements are unavailable in large public datasets. In this study, we developed an MVD gene score based on RNA-sequencing data that reflects MVD by using RNA-seq and MVD measured by IHC in 12 mouse syngeneic tumor models. We explored the relationship between the MVD gene score and a gene signature predicting the response to anti-PD-1 therapy in mouse and human tumor datasets. The MVD gene score correlated with the antitumor activity of lenvatinib, a multiple tyrosine kinase inhibitor mainly targeting VEGFRs and FGFRs, in mouse tumor models and MVD measured by IHC in commercially available human formalin-fixed, paraffin-embedded tumor samples. Tumor types in The Cancer Genome Atlas were classified into four subgroups based on the MVD gene score and T-cell inflamed gene expression profile (TcellinfGEP), which were correlated with clinical indications for treatment. In conclusion, the newly developed MVD gene score enables the estimation of MVD in large public datasets where IHC data are unavailable and has potential clinical utility together with the TcellinfGEP to characterize patients' tumors for precision medicine.