Tumor Samples Research Articles

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.

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.

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.

Plasma Matrix Metalloproteinase-9 Predicts Intraoperative Experience and Extent of Resection in Vestibular Schwannoma Surgery.

To evaluate the predictive value of plasma matrix metalloproteinase-9 (MMP-9) level in determining the extent of tumor resection (EOR) and tumor adherence in vestibular schwannoma (VS) surgery. Prospective cohort study. Academic referral center. Plasma and tumor samples were prospectively collected from patients with nonradiated, sporadic VS undergoing microsurgical resection from July 2022 to June 2023. Plasma MMP-9 levels were measured by enzyme-linked immunosorbent assay, and their association with tumor adherence and postoperative outcomes were evaluated. Thirty-three patients undergoing microsurgical resection agreed to participate (15 females, median age 54 years old, median tumor size 26.7 mm). A gross total resection (GTR) was performed in 18 patients (55%), and a near-total (NTR)/subtotal resection (STR) in 15 (45%). Tumor size was not significantly different between the GTR and NTR/STR groups (20.7 vs 24.8 mm, P= .185). Intraoperatively, a larger fraction of NTR/STR tumors were highly adherent to the brainstem and/or cranial nerves (93% vs 56%, P = .015). Preoperative plasma MMP-9 was higher in patients who underwent an NTR/STR compared to a GTR (229.9 vs 131.2ng/mL, P = .007). On multivariable logistic regression, preoperative plasma MMP-9 strongly predicted EOR by receiver operating characteristic analysis (area under the curve [AUC] = 0.77 P = .008). Combining plasma MMP-9 and age was an excellent predictor of EOR (AUC = 0.91, P = .0001). Plasma MMP-9 levels strongly predicted intraoperative tumor adherence and postoperative extent of resection. This could provide crucial preoperative insights into surgical difficulty, potential complications, and the likelihood of gross total tumor removal, enhancing informed decision-making for both physicians/surgeons and patients.

Long-term safety of lentiviral or gammaretroviral gene-modified T cell therapies.

Long-term risks of gene therapy are not fully understood. In this study, we evaluated safety outcomes in 783 patients over more than 2,200 total patient-years of observation from 38 T cell therapy trials. The trials employed integrating gammaretroviral or lentiviral vectors to deliver engineered receptors to target HIV-1 infection or cancer. Eighteen patients (2.3%) developed secondary malignancies after treatment, with a median onset of 1.94 years (range: 51 d to 14 years). Where possible, incident tumor samples were analyzed for vector copy number, revealing no evidence of high-level marking or other indications of insertional mutagenesis. One T cell lymphoma was detected, but malignant T cells were not marked by vector integration. Analysis of vector integration sites in 176 patients revealed no pathological insertions linked to secondary malignancies, although, in some cases, integration in or near specific genes, including tumor suppressor genes, was associated with modest clonal expansion and sustained T cell persistence. These findings highlight the safety of engineered T cell therapies.

Comparison of genetic mutations of gastric cancer diagnosed before or after H. pylori eradication and between differentiated and undifferentiated types using next-generation sequencing.

Genetic abnormalities specific to post-H. pylori eradication gastric cancer (GC), especially those associated with undifferentiated post-eradication GC, are unknown. We conducted next-generation sequencing of GC diagnosed either before or after eradication to investigate the carcinogenesis of post-eradication GC. Five cases of post-eradication differentiated GC [HP(-)-D group], five cases of H. pylori-positive differentiated GC [HP(+)-D group], four cases of post-eradication undifferentiated GC [HP(-)-U group)], and six cases of H. pylori-positive undifferentiated GC [HP(+)-U group)] underwent analysis. DNA was extracted from tumor samples, and non-tumor samples of all subjects. Next-generation target sequencing was conducted using the Ion AmpliSeq Library Kit 2.0 with the Ion AmpliSeq Cancer Hotspot Panel v2. Next-generation targeted sequencing results of the cancer part were subtracted from the results of the non-cancer part. The HP (-)-D group displayed significantly fewer SNPs in hotspot than the other groups (P < 0.01). Definitive DNA mutations were identified by sequencing of cancerous and non-cancerous tissues. 5 of 20 patients had specific somatic mutations, with different TP53 mutations in the HP(+)-D and HP(-)-U groups, CTNNB1 mutations in the HP(+)-U group, and ATM mutations in the HP(+)-U group, but no mutations in the HP(-)-D group. Several definite genetic mutations involved in GC were observed. Mutations were less frequent in post-eradication differentiated GC. However, because of small number of cases analyzed to identify carcinogenic differences, further analysis with a large number of cases and with strictly grading GC samples is needed.

PD-L1 monoclonal antibody alleviated MI injury of left ventricular function via modulating CD47/SHP2/SIRPα/SYK/FcγR signalings in tumor associated macrophages

To investigate how PD-L1 monoclonal antibodies (mAbs) affect the left ventricular function in mice with myocardial infarction (MI) and through what mechanisms they exert their effects. In vivo experiments were conducted using 27 female BALB/c mice, which were divided equally into 3 groups. Cardiac function was assessed by ultrasound. Heart tissue and breast cancer tumor samples were isolated, and the content of cGAMP was measured using LC-MS/MS. The extent of myocardial infarction was evaluated by Masson staining. In vitro experiments involved dividing macrophages, treated with different inducers, into 8 groups. Protein expression levels in each group were analyzed by Western blotting, and the macrophages were transplanted into experimental mice for observation. In the in vivo experiments, ultrasound examination showed that PD-L1 mAb improved cardiac function in mice with breast cancer and MI. Both cGAMP content measurement and Masson staining results indicated that PD-L1 mAb had a therapeutic effect on mice with breast cancer and MI, improving the infarct condition and slowing tumor progression. In vitro Western blotting analysis revealed that PD-L1 mAb can modulate the CD47/SHP2/SIRPα/SYK/FcγR signaling pathway, thereby affecting breast cancer. Treatment with a STING inhibitor significantly reduced the cGAMP effect, leading to improved left ventricular function in mice with MI. PD-L1 monoclonal antibodies improve left ventricular function in mice with myocardial infarction by modulating the CD47/SHP2/SIRPα/SYK/FcγR signaling pathway in tumor-associated macrophages and inhibiting the expression of cGAMP.

Loss of O6-Methylguanine-DNA Methyltransferase Protein Expression by Immunohistochemistry Is Associated With Response to Capecitabine and Temozolomide in Neuroendocrine Neoplasms.

A recent prospective phase II study (ECOG-ACRIN E2211) demonstrated that MGMT deficiency was associated with a significant response to capecitabine and temozolomide (CAPTEM) in pancreatic neuroendocrine neoplasms (NENs); however, routine MGMT analysis in NENs was not recommended. Our study sought to demonstrate whether loss of MGMT protein expression is associated with improved overall survival (OS) in patients receiving CAPTEM for NENs from various tumor sites. Paraffin-embedded tumor samples were evaluated by immunohistochemistry (IHC) using an MGMT monoclonal antibody. Intact MGMT protein expression (i.e., IHC positivity) was defined as any staining intensity (>1+) in ≥36% of neoplastic cells according to an internal validation study. IHC and pyrosequencing for MGMT promotor methylation was performed in an independent cohort of 58 NENs. Real-world OS was extrapolated from insurance claims data with Kaplan-Meier estimates from the date of first CAPTEM administration to the last date of contact. The study cohort included 80 patients (42 men and 38 women) with a median age of 57years (range: 19-89). They had various NENs (33 pancreatic, 17 intestinal, 7 pulmonary, 8 other, and 15 of unknown origin) treated with CAPTEM. The median OS for the 48 patients with MGMT negative tumors was 31months compared to 17.5months for the 32 patients whose tumors were MGMT positive by IHC (HR: 1.75 [95% CI: 1.066-2.87] and p=0.025). IHC results from the independent cohort of 58 NENs showed only 57% concordance with pyrosequencing results. MGMT promotor status by IHC may be a clinically useful indicator that predicts improved OS for NENs treated with CAPTEM, but IHC does not reliably correlate with the findings of MGMT promoter methylation by pyrosequencing.

Pir-hsa-216911 inhibit pyroptosis in hepatocellular carcinoma by suppressing TLR4 initiated GSDMD activation

Hepatocellular carcinoma (HCC) is a global health concern, ranking as the fourth leading cause of cancer-related deaths worldwide. However, the role of piwi-interacting RNAs (piRNAs) in HCC processes has not been extensively explored. Through small RNA sequencing, our study identified a specific piRNA, pir-hsa-216911, which is highly expressed in HCC cells. This overexpression of pir-hsa-216911 promotes HCC cell invasion and inhibits cell death, particularly pyroptosis. Knocking out pir-hsa-216911 led to increased cell pyroptosis activity, resulting in the activation of caspase-1 and GSDMD. Further analysis revealed that pir-hsa-216911 targets and suppresses TLR4, a key gene associated with pyroptosis in HCC. In the Huh7 cell line, pir-hsa-216911 knockout confirmed its role in suppressing the TLR4/NFκB/NLRP3 pathway by silencing TLR4. Knocking out pir-hsa-216911 significantly inhibited the formation of Huh7 xenograft tumor. In HCC patients, pir-hsa-216911 was highly expressed in HCC tumor samples with steatosis, suppressing TLR4 expression and inhibiting GSDMD activation. This study introduces pir-hsa-216911 as a new high-expressing piRNA in HCC, which inhibits pyroptosis by silencing TLR4 to suppress GSDMD activation. These findings have significant implications for HCC molecular subtyping and as a potential target for cancer therapy.

Expression level of miR-548aa in tissue samples of patients with colorectal cancer.

The pathogenesis of colorectal cancer (CRC) is influenced by various risk factors, and genetic alterations in progression of colon polyps. The expression patterns of microRNA-548 (miR-548) in colorectal tissues have been sufficiently characterized. The aim of this study is to clarify the role of miR-548aa in tumorigenesis, gene targeting, predictive value and its expression levels in tumoral versus adjacent marginal tissues in CRC patients. This study included 35 CRC patients who underwent surgery to remove their tumor tissue. Tumor samples and adjacent marginal tissue were collected and gene expression was analyzed through real-time PCR. The correlation between miR-548aa expression levels and clinical parameters were investigated. Our findings showed a significant increase in the expression of miR-548aa in tumoral tissues compared to marginal tissues (p < 0.05). The upregulation of miR-548aa was significantly detected in CRC samples, showing an area under the curve of 0.89 (p = 0.002), indicating strong sensitivity and specificity for CRC diagnosis. To prediction of miRNA target genes and construction of regulatory networks of miR-548aa, we used bioinformatics tools including TargetScan and miRDB. Protein-protein interaction (PPI) network was constructed through STRING database and visualized using Cytoscape software. Dysregulation of miR-548aa is closely related to tumorigenesis in colorectal tissues, which affects disease progression and clinical outcomes. The miR-548aa can be introduced as a proposed biomolecule involved in mechanism of tumorigenesis, gene targeting and predictive value for CRC diagnosis and a target for therapeutic intervention.

Molecular and immune landscape of tumours in geriatric patients with non-small cell lung cancer, melanoma and renal cell carcinoma

ObjectiveCancer patients aged ≥80 years present unique characteristics affecting response to immune checkpoint inhibitors (ICIs), with unidentified molecular differences. This study aimed to explore potential biomarkers of response to ICI...

Necroptosis-Related Gene Signature Predicts Prognosis in Patients with Advanced Ovarian Cancer.

Background/Objectives: This study aimed to construct a risk score (RS) based on necroptosis-associated genes to predict the prognosis of patients with advanced epithelial ovarian cancer (EOC). Methods: EOC data from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) series 140082 (GSE140082) were used. Based on known necroptosis-associated genes, clustering was performed to identify molecular subtypes of EOC. A least absolute shrinkage and selection operator (LASSO)-Cox regression analysis identified key genes related to prognosis. The expression of one of them, RIPK3, was analyzed via immunohistochemistry in an EOC cohort. Results: An RS made from ten genes (IDH2, RIPK3, FASLG, BRAF, ITPK1, TNFSF10, ID1, PLK1, MLKL and HSPA4) was developed. Tumor samples were divided into a high-risk group (HRG) and low-risk group (LRG) using the RS. The model is able to predict the overall survival (OS) of EOC and distinguish the prognosis of different clinical subgroups. Immunohistochemical verification of the receptor-interacting serine/threonine-protein kinase (RIPK) 3 confirmed that high nuclear expression is correlated with a longer OS. In addition, the score can predict the response to a programmed death ligand 1 (PD-L1) blockade treatment in selected solid malignancies. Patients from the LRG seem to benefit more from it than patients from the HRG. Conclusions: Our RS based on necroptosis-associated genes might help to predict the prognosis of patients with advanced EOC and gives an idea on how the use of immunotherapy can potentially be guided.

Suppression of MCP-1, IFN-γ and IL-6 production of HNSCC ex vivo by pembrolizumab added to docetaxel and cisplatin (TP) exceeding those of TP alone is linked to improved survival

BackgroundAdding pembrolizumab, an anti-PD-1 antibody approved for treatment of head and neck squamous cell carcinoma (HNSCC) to neoadjuvant (induction-) chemotherapy utilizing docetaxel and cisplatin (TP) followed by radiotherapy may improve outcome in larynx organ-preservation (LOP) that is investigated in the European Larynx-Organ preservation Study (ELOS). As biomarkers for response to TP and pembrolizumab +TP are missing but may include cytokines, this work aims on determining cytokines potentially linked to outcome as prognostic markers sufficient to predict and/or monitor response to successful LOP.MethodsCollagenase IV digests were generated from 47 histopathological confirmed HNSCC tumor samples and seeded in 96-well plates containing pembrolizumab, docetaxel, cisplatin either solely or in binary or ternary combination. According to the FLAVINO protocol, supernatants were collected after 3 days, adherent cells fixed using ethanol, air-dried and pan-cytokeratin positive epithelial cells counted using fluorescence microscopy. The cytokines IL-6, IL-8, IFN-γ, IP-10, MCP-1, TNF-α, and VEGF in the supernatant were quantified by sandwich ELISA.ResultsThe mode of interaction between pembrolizumab and TP was assessed and correlated to outcome (overall, disease-specific and progression-free survival of patients). Suppression of MCP-1, IFN-γ and IL-6 production by pembrolizumab + TP exceeding the suppressive effect of TP was detected in the majority of samples and linked to improved survival. Multivariate Cox proportional hazard regression modeling revealed MCP-1, IFN-γ and IL-6 as independent outcome predictors.ConclusionsComparing response to TP vs. pembrolizumab vs. TP + pembrolizumab may allow for identification of patients with superior outcome independent from treatment applied.

Genetic Risk Profiling Reveals Altered Glycosyltransferase Expression as a Predictor for Patient Outcome in Neuroblastoma.

Background/Objectives: Neuroblastoma is a highly aggressive pediatric cancer that arises from immature nerve cells and exhibits a broad spectrum of clinical presentations. While low- and intermediate-risk neuroblastomas often have favorable outcomes, high-risk neuroblastomas are associated with poor prognosis and significant treatment challenges. The complex genetic networks driving these high-risk cases remain poorly understood. This study aims to investigate differences in gene expression patterns that may contribute to disease outcomes. Methods: We employed an in silico approach to analyze a cohort of 493 neuroblastoma tumor samples that underwent mRNA sequencing (GSE49711). This dataset was reanalyzed in depth with a non-hypothesis-driven approach to identify the expression patterns and regulatory mechanisms associated with a poor prognosis. Results: By exploring global gene expression and the integration of clinical parameters, we stratified the samples into two groups with highly distinct gene expression profiles. MYCN amplification emerged as a major driver not only of poor prognosis but also of specific gene regulatory patterns. Notably, tumors with MYCN amplification exhibited the strong regulation of immune response genes and less immune infiltration, suggesting potential immune evasion. However, while we observed only minor changes in immune checkpoint expression, there was a strong modulation of glycosyltransferase genes in MYCN-amplified tumors. Using this information, we were able to construct a risk profile based on 12 glycosylation-related genes, which correlates with the survival outcomes of neuroblastoma patients. Conclusions: This study highlights the role of MYCN amplification in driving a poor prognosis in neuroblastoma through the regulation of immune response and glycosylation-related genes. Based on this finding, we developed a genetic risk profile that correlates with survival outcomes in neuroblastoma patients.