Primary Tumor Tissue Research Articles

Poređenje PD-L1 ekspresije u citološkom i histološkom materijalu seroznog high-grade karcinoma jajnika

Introduction: Neoplastic cells in peritoneal lavage express various proteins with significant prognostic and therapeutic potential. Such expression could differ from the expression in a primary tumor or in metastases. In this research, we compared PD-L1 (programmed cell death ligand-1) expression on ovarian cancer cells in cytological material with its expression on peritoneal metastases and a primary tumor. Materials and methods: The study included 30 patients who had been operated on for high-grade serous ovarian cancer (HGSC) in FIGO IIIC, over the period of one year. Cytoblocks, cytological and tissue microarrays were assembled and immunostained with PD-L1 antibody. For each tumor compartment we determined four PD-L1 expression categories: negative, low, moderate, and strong expression, according to the percentage of membrane positive tumor cells. Moderate and strong positivity together were considered as high PD-L1 expression. Results: Moderate PD-L1 expression was the most frequent pattern in primary HGSC (50%) and in peritoneal metastases (omentum) (60%). Cytological samples mostly showed low PD-L1 expression (57%). Statistical analysis did not show a significant difference in PD-L1 expression between the study groups. We found a positive correlation of PD-L1 expression between different, matched tumor samples in every patient, with statistical significance (p < 0.05) between all the analyzed samples. Conclusion: PD-L1 expression was similar in all three tumor compartments. This could point to similar peritumor regulatory mechanisms of HGSC in primary tumor tissue and cytology tumor samples. Immunohistochemical analysis of the assembled cytoblocks is sufficiently reliable in the assessment of PD-L1 expression on cancer ovarian cells from cytological material.

Comprehensive Mutation Profiling of Colorectal Cancer Patients With Lung or Liver Metastasis by Targeted Next-Generation Sequencing.

Primary tumor tissue is often analyzed to search for predictive biomarkers and DNA-guided personalized therapies, but there is an incomplete understanding of the discrepancies in the genomic profiles between primary tumors and metastases, such as liver and lung metastases. We performed in-depth targeted next-generation sequencing of 520 key cancer-associated genes for 47 matched primary and metastatic tumor samples which were retrospectively collected. A total of 699 mutations were detected in the 47 samples. The coincidence rate of primary tumors and metastases was 51.8% (n = 362), and compared to patients with liver metastases, patients with lung metastases had a significantly greater coincidence rate (P = .021). The number of specific mutations for the primary tumors and liver and lung metastases was 186 (26.6%), 122 (17.5%), and 29 (4.1%), respectively. Analysis of a patient with all three occurrences, including a primary tumor, liver metastasis, and lung metastasis, indicated a possible polyclonal seeding mechanism for liver metastases. Remarkably, multiple samples from patients with primary and metastatic tumors supported a mechanism of synchronous parallel dissemination from primary tumors to metastatic tumors that were not mediated through pre-metastatic tumors. We also found that the PI3K-Akt signaling pathway significantly altered lung metastases compared to matched primary tumors (P = .001). In addition, patients with mutations in CTCF, PIK3CA, or TP53 and LRP1B, AURKA, FGFR1, ATRX, DNMT3B, or GNAS had larger primary tumor sizes and metastases, especially patients with both LRP1B and AURKA mutations. Interestingly, CRC patients with TP53-disruptive mutations were more likely to have liver metastases (P = .016). In this study, we demonstrate significant differences in the genomic landscapes of colorectal cancer patients based on the site of metastasis. Notably, we observe a larger genomic variation between primary tumors and liver metastasis compared to primary tumors and lung metastasis. These findings can be used for tailoring treatments based on the specific metastatic site.

A pan-cancer analysis of the oncogenic role of polypyrimidine tract binding protein 1 (PTBP1) in human tumors

Polypyrimidine tract-binding protein 1 (PTBP1) is an RNA-binding protein that regulates several posttranscriptional events and is closely related to the development of multiple tumors. However, little is known about PTBP1. Thus, we carried out a systematic pan-cancer analysis to explore the relationship between PTBP1 and cancer. We used The Cancer Genome Atlas, Gene Expression Omnibus, and Human Protein Atlas datasets, as well as several bioinformatics tools, to explore the role of PTBP1 in 33 tumor types. The expression of PTBP1 in most tumor tissues was higher than that in normal tissues. Survival analysis indicated that overexpression of PTBP1 generally predicted poor overall survival in patients with tumors such as adrenocortical carcinoma, liver hepatocellular carcinoma, lung adenocarcinoma, and skin cutaneous melanoma. In addition, we compared the phosphorylation and immune infiltration of PTBP1 in cancer-associated fibroblasts between normal and primary tumor tissues and explored the putative functional mechanism of tumorigenesis mediated by PTBP1. These results provide clues to better understand PTBP1 from the perspective of bioinformatics and highlight its importance in various human cancers.

Integrated proteome and phosphoproteome analysis of gastric adenocarcinoma reveals molecular signatures capable of stratifying patient outcome.

Metastasis is one of the main causes of low survival rate of gastric cancer patients. Exploring key proteins in the progression of gastric adenocarcinoma (GAC) may provide new candidates for prognostic biomarker development and therapeutic intervention. We applied quantitative mass spectrometry to compare the proteome and phosphoproteome of primary tumor tissues between GAC patients with and without lymph node metastasis (LNM). We then performed an integrated analysis of the proteomic and transcriptomic data to reveal the molecular features. We quantified a total of 5536 proteins, and we found 218 upregulated and 49 downregulated proteins in tumor samples from patients with LNM compared to those without LNM. Clustering analysis identified a number of hub proteins that have been previously shown to play important roles in gastric cancer progression. We also found that two extracellular proteins, TNXB and SPON1, are overexpressed in patients with LNM, which correlates with poor survival of GAC patients. Overexpression of TNXB and SPON1 was validated by western blotting and immunohistochemistry. Furthermore, treating gastric cancer cells with anti-TNXB antibody significantly reduced cell migration. Finally, quantitative phosphoproteomic analysis combined with activity-based kinase capture revealed a number of activated kinases in primary tumor tissues from patients with LNM, among which GSK3 might be a new target that warrants further study. Our study provides a snapshot of the proteome and phosphoproteome of GAC tumor tissues that have metastatic potential, and identifies potential biomarkers for GAC progression.

Activin B and Activin C Have Opposing Effects on Prostate Cancer Progression and Cell Growth

Current prognostic and diagnostic tests for prostate cancer are not able to accurately distinguish between aggressive and latent cancer. Members of the transforming growth factor-β (TGFB) family are known to be important in regulating prostate cell growth and some have been shown to be dysregulated in prostate cancer. Therefore, the aims of this study were to examine expression of TGFB family members in primary prostate tumour tissue and the phenotypic effect of activins on prostate cell growth. Tissue cores of prostate adenocarcinoma and normal prostate were immuno-stained and protein expression was compared between samples with different Gleason grades. The effect of exogenous treatment with, or overexpression of, activins on prostate cell line growth and migration was examined. Activin B expression was increased in cores containing higher Gleason patterns and overexpression of activin B inhibited growth of PNT1A cells but increased growth and migration of the metastatic PC3 cells compared to empty vector controls. In contrast, activin C expression decreased in higher Gleason grades and overexpression increased growth of PNT1A cells and decreased growth of PC3 cells. In conclusion, increased activin B and decreased activin C expression is associated with increasing prostate tumor grade and therefore have potential as prognostic markers of aggressive prostate cancer.

The valuable role of dynamic 18F FDG PET/CT-derived kinetic parameter [formula omitted] in patients with nasopharyngeal carcinoma prior to radiotherapy: A prospective study

Background and PurposeDynamic positron emission tomography/computed tomography (PET/CT) served the potential role of characterizing malignant foci. The main objective of this prospective study was to explore the advantage of dynamic PET/CT imaging in characterizing nasopharyngeal carcinoma (NPC). Methods and MaterialsPatients with probable head and neck disease underwent a local dynamic PET/CT scan followed by a whole-body static scan. Patlak analysis was used to generate parametric influx rate constant (Ki) images from 48 frames obtained from a dynamic PET/CT scan. By delineating the volumes-of-interest (VOIs) of: primary tumor (PT), lymph node (LN), and normal nasopharyngeal tissues (N), we acquired the corresponding Ki mean and SUVmean of each site respectively to perform the quantitative statistical analysis. ResultsQualified images of 71 patients with newly diagnosed NPC and 8 without nasopharyngeal malignant lesions were finally included. We found the correlations between Ki mean-PT and critical clinical features, including clinical stage (r = 0.368), T category (r = 0.643) and EBV-DNA copy status (r = 0.351), and Ki mean-PT differed within the group. SUVmean-PT showed correlations with clinical stage (r = 0.280) and T category (r = 0.472), but could hardly differ systematically within group of clinical features except T category. Ki mean-LN offered the positive correlations with N category (r = 0.294), M category (r = 0.238) and EBV-DNA copy status (r = 0.446), and differed within the group. In addition, Ki mean represented a sensitivity of 94.4 % and a specificity of 100 %, in distinguishing NPC from the non-NPC, when the cut-off was defined as 0.0106. When the cut-off of SUV being defined as 2.03, the sensitivity and specificity were both 100 %. ConclusionOur research confirmed Ki compared favorably to SUV in characterizing NPC and found that Ki can serve as an effective imaging marker of NPC.

The role of positron emission tomography combined with computed tomography with 18F-fluorodeoxyglucose in the diagnosis of soft tissue sarcomas

Soft tissue sarcoma are here, heterogeneous malignant neoplasms that present difficulties in diagnosis, treatment and follow-up. High-quality diagnostic planning allows timely decision-making on further tactics of patient management in a particular case. Positron emission tomography with a biological analogue of glucose – 18F-fluorodeoxyglucose, combined with computed tomography, is an imaging tool that measures the metabolic activity of a tumor and is increasingly used in clinical practice to assess primary tumor tissue, staging, monitoring the effectiveness of treatment and as a method of early detection of relapses. This literature review is aimed at evaluating the usefulness of positron emission tomography combined with computed tomography at different stages of diagnostic control in patients with soft tissue sarcomas.

Association between Intratumoral CD8+ T Cells with FoxP3+ and CD163+ Cells: A Potential Immune Intrinsic Negative Feedback Mechanism for Acquired Immune Resistance.

Acquired immune resistance (AIR) describes a situation in which cancer patients who initially responded clinically to immunotherapies, after a certain period of time, progress with their disease. Considering that AIR represents a feedback response of the tumor against the immune attack generated during the course of immunotherapies, it is conceivable that AIR may also occur before treatment initiation as a mechanism to escape endogenous adaptive antitumor immunity (EAAI). In the present study, we assessed the EAAI in paraffin-embedded breast primary tumor tissue samples and drew correlations with the clinical outcomes. In particular, we analyzed densities of CD8+ cells as elements mediating antitumor cytotoxicity, and of CD163+ and FoxP3+ cells as suppressor elements. We found a direct correlation between the densities of CD8+ cells and of CD163+ and/or FoxP3+ cells in the vast majority of patients' tumors. Importantly, the vast majority of patients whose tumors were overpopulated by CD8+ cells developed AIR, which was characterized by high intratumoral CD163+ and/or FoxP3+ cell densities and reduced overall survival (OS). We also showed that AIR depends on the levels of CD8+ cell-ratios in the tumor center to the invasive margin. Our data suggest that tumors develop AIR only when under a robust endogenous immune pressure.

Overrepresentation of human epidermal growth factor receptor 2 positive- and Luminal B breast cancer metastases in the eyes and orbit

BackgroundBreast cancer is the most common cancer to spread to the choroid and orbit. Depending on a set of prognostic and predictive biomarkers, breast cancer can be divided into at least four distinct subtypes with separate treatment and clinical course.SubjectsThirty-two patients with metastases to the eye and periocular area diagnosed between 2005 and 2020, of which 11 also had primary tumour tissue available. Expression levels of oestrogen- (ER) and progesterone receptors (PR), Human epidermal growth factor receptor 2 (HER2) and the proliferation marker Ki67 were analysed.ResultsTwenty-five of 32 patients (78%) had a history of primary breast cancer, whereas the remaining 7 (22%) presented with metastatic disease. Of available metastases, 83% were positive for ER, 37% for PR, 54% for HER2, and 50% for Ki67. Metastases had significantly lower proportions of PR-positive cells than primary tumours, and the distribution of the Luminal A, Luminal B, HER2 enriched and triple-negative subtypes differed between primary tumours and metastases (P = 0.012): Six of 9 patients with a full set of biomarkers on both primary tumours and metastases switched subtype (67%), and 23 of 32 metastases (77%) were of the Luminal B subtype.ConclusionsNearly 4 in 5 breast cancer metastases in the eyes and orbit are of the Luminal B subtype, and a majority are HER2 positive. The breast cancer subtype frequently switches between primary tumours and metastases. Future studies should evaluate these results in larger cohorts.

Novel CSF1R-positive tenosynovial giant cell tumor cell lines and their pexidartinib (PLX3397) and sotuletinib (BLZ945)-induced apoptosis

Tenosynovial giant cell tumor (TGCT) is a mesenchymal tumor derived from the synovium of the tendon sheath and joints, most frequently in the large joints. The standard of care for TGCTs is surgical resection. A new targeting approach for treating TGCTs has emerged from studies on the role of the CSF1/CSF1 receptor (CSF1R) in controlling cell survival and proliferation during the pathogenesis of TGCTs. We established four novel cell lines isolated from the primary tumor tissues of patients with TGCTs. The cell lines were designated Si-TGCT-1, Si-TGCT-2, Si-TGCT-3, and Si-TGCT-4, and the TGCT cells were characterized by CSF1R and CD68. These TGCT cells were then checked for cell proliferation using an MTT assay and three-dimensional spheroid. The responses to pexidartinib (PLX3397) and sotuletinib (BLZ945) were evaluated by two-dimensional MTT assays. All cells were positive for α‑smooth muscle actin (α‑SMA), fibroblast activation protein (FAP), CSF1R, and CD68. Except for Si-TGCT-4, all TGCT cells had high CSF1R expressions. The cells exhibited continuous growth as three-dimensional spheroids formed. Treatment with pexidartinib and sotuletinib inhibited TGCT cell growth and induced cell apoptosis correlated with the CSF1R level. Only Si-TGCT-4 cells demonstrated resistance to the drugs. In addition, the BAX/BCL-2 ratio increased in cells treated with pexidartinib and sotuletinib. With the four novel TGCT cell lines, we have an excellent model for further in vitro and in vivo studies.

Abstract A029: Investigating primary colorectal cancer tumor and liver metastasis clonality through whole exome sequencing of synchronous biopsies

Abstract Advanced-stage liver metastatic Colorectal Cancer (CRC) disease remission rates are markedly low, often with less time for life-saving but challenging medical procedures and physically demanding regimens of neoadjuvant chemotherapies. Medical decisions supported by patient-specific genomic information may improve cancer prognosis, long-term remission rates, and overall patient health. Understanding the genomic landscape of liver metastasis with respect to primary tumors can help clinical decision-making that may result in added life years for patients with advanced disease. For unresectable metastatic disease, prediction of the possible targetable mutations of both primary colon tumors and liver metastasis could have an impact on treatment decisions and survival rates. In this study 16 samples were collected from five different CRC patients with cooccurring liver metastases. Whole exome sequencing (WES) was performed on an Illumina Hi-Seq 2000. Samples included primary tumor, tumor micro-environment and metastasis (with one patient undergoing a polypectomy). At the biopsy date, treatment naïve samples allowed observation of the natural genomic makeup. Analysis confirmed 70x average coverage. Data were processed with multiple mapping and variant discovery algorithms. In these samples, a putative driver variant, FAM25C was identified, in addition to observing canonic driver mutations for colorectal cancer such as TP53, APC, KRAS. After variant discovery, microsatellite instability and tumor mutation burden (TMB) analyses were conducted. One patient showed high TMB with almost 10-fold more mutations observed, when compared to other samples. All samples of the High-TMB patient share almost half of the same variants, which can be indicative of early expansion of the major clone. Average probabilistic Jaccard similarity coefficient percentages of somatic variants of only primary CRC tumor and liver metastasis tissues were 41.08% with a standard deviation of 4.05% across all patients. Whole exome sequencing of samples with subsequent analysis of clonal variation between CRC tumors and liver metastasis show different mutational composition trends in dissimilarity to the primary tumor. To understand tumor evolution, phylogenetic analysis was conducted for each patient sample. Although different studies were conducted on understanding the genomic properties of metastasis through pairwise comparison, detailed studies which investigate the genomic patterns of tumor expansion through detailed sampling are crucial for effective therapy development. We believe our results in combination with other multi-sample sequencing studies will help the CRC community to better understand this deadly disease, leading to better treatment strategies. These authors hypothesize that investigating clonal diversity via synchronous biopsy in primary and metastatic tumors may be one facet in a larger conversation of treatment decisions and responses of patients who will undergo neoadjuvant chemotherapies for nonresectable liver metastatic CRC disease. Citation Format: Duygu Altinok Dindar, Batuhan Kısakol, Sahin Sarihan, Mehmet Arif Ergun, John Cheney, Emel Ergul, Nihal Uren, Ender Dulundu, Emine Bozkurtlar, Nihat Zafer Utkan, Mehmet Baysan. Investigating primary colorectal cancer tumor and liver metastasis clonality through whole exome sequencing of synchronous biopsies [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr A029.

The ctDNA-based postoperative molecular residual disease status in different subtypes of early-stage breast cancer.

Breast cancer is a highly heterogeneous disease. Early-stage, non-metastatic breast cancer is considered curable after definitive treatment. Early detection of tumor recurrence and metastasis through sensitive biomarkers is helpful for guiding clinical decision-making and early intervention in second-line treatment, which could improve patient prognosis and survival. In this real-world study, we retrospectively analyzed 82 patients with stages I to III breast cancer who had been analyzed by molecular residual disease (MRD) assay. A total of 82 tumor tissues and 224 peripheral blood samples were collected and detected by next-generation sequencing (NGS) based on a 1,021-gene panel in this study. MRD positivity was detected in 18 of 82 patients (22.0%). The hormone receptor-/human epidermal growth factor receptor 2+ (HR-/HER2+) subgroup had the highest postoperative MRD detection rate at 30.8% (4/13). The BRCA2 and SLX4 genes were significantly enriched in all patients in the MRD positive group and FGFR1 amplification was significantly enriched in the MRD negative group with HR+/HER2-. The number of single nucleotide variants (SNVs) in tissue samples of MRD-positive patients was higher than that of MRD-negative patients (11.94 vs. 8.50 SNVs/sample). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that there was a similar biological function of the tumor-mutated genes in the 2 MRD status groups. This real-world study confirmed that patient samples of primary tumor tissue with different MRD status and molecular subtypes had differential genetic features, which may be used to predict patients at high risk for recurrence.

Establishment of the Dutch Nationwide, Interdisciplinary Infrastructure and Biobank for Fundamental and Translational Ovarian Cancer Research: Archipelago of Ovarian Cancer Research

Objectives: Ovarian cancer has the worst overall survival rate of all gynecologic malignancies. For the majority of patients, the 5-year overall survival rate of less than 50% has hardly improved over the last decades. To improve the outcome of patients with all subtypes of ovarian cancer, large-scale fundamental and translational research is needed. To accommodate these types of ovarian cancer research, we have established a Dutch nationwide, interdisciplinary infrastructure and biobank: the Archipelago of Ovarian Cancer Research (AOCR). The AOCR will facilitate fundamental and translational ovarian cancer research and enhance interdisciplinary, national, and international collaboration. Design: The AOCR biobank is a prospective ovarian cancer biobank in which biomaterials are collected, processed, and stored in a uniform matter for future (genetic) scientific research. All 19 Dutch hospitals in which ovarian cancer surgery is performed participate and collaborate in the AOCR biobank. Participants/Materials, Setting, Methods: Patients of 16 years and older with suspected or diagnosed ovarian, fallopian tube, or primary peritoneal cancer are recruited for participation. Patients who agree to participate give written informed consent for collection, storage, and issue of their biomaterials for future studies. After inclusion, different blood samples are taken at various predefined time points both before and during treatment. In case of a diagnostic paracentesis or biopsy, the residual biomaterials of these procedures are stored in the biobank. During surgery, primary tumor tissue and, if applicable, tissue from metastatic sites are collected and stored. From each patient, a representative histological hematoxylin and eosin stained slide is digitalized for research purposes, including reassessment by a panel of gynecologic pathologists. Clinical and pathological data are obtained on a per-study basis from Dutch registries. Research proposals for the issue of biomaterials and data are evaluated by both the Archipelago Scientific Committee and the Steering Committee. Researchers using the biomaterials from the AOCR biobank are encouraged to enrich the biobank with data and materials resulting from their analyses and experiments. Limitations: The implementation and first 4 years of collection are financed by an infrastructural grant from the Dutch Cancer Society. Therefore, the main limitation is that the costs for sustaining the biobank after the funding period will have to be covered. This coverage will come from incorporation of budget for biobanking in future grant applications and from fees from external researchers and commercial parties using the biomaterials stored in the AOCR biobank. Moreover, we will apply for grants aimed at sustaining and improving research infrastructures and biobanks. Conclusions: With the establishment of the Dutch nationwide, interdisciplinary Archipelago of Ovarian Cancer Research infrastructure and biobank, fundamental and translational research on ovarian cancer can be greatly improved. The ultimate aim of this infrastructure is that it will lead to improved diagnostics, treatment, and survival of patients with ovarian cancer.

Heterogeneity and Clinical Effect of Epidermal Growth Factor Receptor in Primary Lung and Brain Metastases of Nonsmall Cell Lung Cancer

IntroductionThis study aimed to analyze the heterogeneity in epidermal growth factor receptor (EGFR) gene mutation and its impact on clinical outcomes in primary tumor and corresponding brain metastasis (BM) in nonsmall cell lung cancer (NSCLC). Materials and methodsPrimary pulmonary tumors and paired BMs of 27 NSCLC patients were surgically removed. All brain lesions were histologically confirmed as metastatic NSCLC. EGFR gene mutation status was detected by using amplification refraction mutation system. McNemar test was performed to compare EGFR mutation status between lung primary tumors and metastatic brain tumors and Kappa test was performed to quantify the agreement between the two. ResultsOf the 27 patients, nine cases were found to have EGFR mutations in BMs and 10 had a positive EGFR mutation status in primary lung tumor tissue. The rate of consistency of the matched tumor was 24/27 (88.9%). Among the three cases presenting EGFR mutational heterogeneity, two patients harbored an EGFR mutation in the primary tumor but not in the BMs; meanwhile, the last patient demonstrated the opposite pattern. Compared to patients with consistent EGFR mutations, patients with inconsistent mutations showed better outcomes. Further analysis revealed that the two patients whose EGFR mutant-type primary tumor progressed to wild-type cerebral metastatic tumor had longer overall survival than the patient whose EGFR wild-type primary tumor progressed to mutant-type brain metastatic tumor. ConclusionsHeterogeneity of EGFR mutation status was observed between primary NSCLC and paired BM. Patients possessing a wild-type EGFR mutation in BM might have better outcomes, especially those with transition from mutant to wild-type.

Ectopic expression of lncRNA MVIH as a potential diagnostic biomarker in cervical cancer.

Cervical cancer (CC) is one of the most common cancers in women. Recent advances in screening and vaccination against the papilloma virus (HPV) have increased protection against CC. However, there is no effective diagnostic biomarker and treatment approach during the course of the disease. The current study is thus aimed to evaluate the changes in the expression of lncRNA associated with microvascular invasion in hepatocellular carcinoma (lncRNA MVIH) and its diagnostic value as a biomarker in CC patients. One-hundred and fifteen (n = 115) pairs of CC primary tumor and marginal non-tumor tissue samples were obtained from Tabriz Valiasr International Hospital (Tabriz, Iran). RNA extraction and cDNA synthesis followed by quantitative reverse transcriptase PCR (qRT-PCR) were considered to investigate alterations in the expression levels of MVIH in patients with CC. The associations between MVIH expression changes and clinicopathological features as well as its potential as a diagnostic biomarker were assessed using SPSS and GraphPad prism software and the receiver operating characteristic (ROC). The expression levels of MVIH were significantly higher in CC tumors as compared to marginal non-tumor samples (p < 0.0001). Overexpression of MVIH was significantly associated with younger age (p = 0.033), lymph node metastasis (p = 0.031), tumor invasion depth (p = 0.035), and squamous cell type of CC (p = 0.019). The ROC analysis for MVIH as a diagnostic biomarker revealed the respective sensitivity and specificity of 67.83 and 80. Overexpression of MVIH in CC tumors suggests its oncogenic role during tumorigenesis. Thus, it may serve as a potential diagnostic biomarker.

Activated Eosinophils Predict Longer Progression-Free Survival under Immune Checkpoint Inhibition in Melanoma.

Immune checkpoint inhibition (ICI) has yielded remarkable results in prolonging survival of metastatic melanoma patients but only a subset of individuals treated respond to therapy. Success of ICI treatment appears to depend on the number of tumor-infiltrating effector T-cells, which are known to be influenced by activated eosinophils. To verify the co-occurrence of activated eosinophils and T-cells in melanoma, immunofluorescence was performed in 285 primary or metastatic tumor tissue specimens from 118 patients. Moreover, eosinophil counts and activity markers such as eosinophil cationic protein (ECP) and eosinophil peroxidase (EPX) were measured in the serum before therapy start and before the 4th infusion of ICI in 45 metastatic unresected melanoma patients. We observed a positive correlation between increased tumor-infiltrating eosinophils and T-cells associated with delayed melanoma progression. High baseline levels of eosinophil count, serum ECP and EPX were linked to prolonged progression-free survival in metastatic melanoma. Our data provide first indications that activated eosinophils are related to the T-cell-inflamed tumor microenvironment and could be considered as potential future prognostic biomarkers in melanoma.

EPCO-44. HOXD13 GENE PLAYS A ROLE AS A PUTATIVE MASTER EPIGENETIC REGULATOR IN GLIOMA RECURRENCE AND PROGRESSION

Abstract BACKGROUND Adult diffuse glioma is a heterogenous brain tumor group that has malignant potential and recurring properties. Glioma CpG island methylator phenotype (G-CIMP) associated with chromatin remodeling encompasses two different methylation degrees: G-CIMP-high and G-CIMP-low that have high levels of DNA methylation and loss of DNA methylation, respectively. G-CIMP-high confers a more favorable prognosis and better predictive values by altering transcriptional dynamics and the gene expression. METHODS We have performed Chromatin Immunoprecipitation Sequencing (ChIP-Seq) on DNA extracted from fresh frozen primary tumor tissues (G-CIMP-high and G-CIMP-low). We have processed the sequencing data by using FastQC (v.:0.11.5), bwa-mem (v.:0.7.15) and picard tool (v.:2.7.1). The ChIP-seq peaks and the differentially bound peaks were obtained using MACS2 (v.:2.1.1) and DiffBind (v.:3.4.11), respectively. We have also integrated transcriptomic, epigenomic and genomic data. RESULTS Initial results showed that the differentially bound H3K27ac and H3K4me3 peak gains and losses are located mainly in intronic and intergenic regions. The integration between epigenetic and transcriptomic data revealed that the promoter of the HOXD13 gene upregulated in GCIMP-low presents an active regulatory region and is enriched by H3K27ac and H3K4me3 sites. We were able to identify that GCIMP-low, in addition to presenting more downregulated genes than GCIMP-high, also has greater affinity to the H3K27ac peaks. In GCIMP-low, we identified that regions enriched by H3K27ac are highly associated with the presence H3K4me3 marks. CONCLUSION We mapped the enrichment of histone modifications in the TSS of differentially expressed genes in G-CIMP-high and G-CIMP-low identifying both the susceptibility of GIMP-low to interact with H3K27ac and the fact that the progression of GCIMP-high to G-CIMP-low can be explained by the association between H3K27ac gain and gene downregulation. Also, we predicted the HOXD13 gene as a putative master epigenetic regulator of the G-CIMP demethylation process and, consequently, of tumor recurrence and progression, over time.

Single-Vesicle Infrared Nanoscopy for Noninvasive Tumor Malignancy Diagnosis.

Protein heterogeneity in molecular expression and structures determines tumorigenesis and is the diagnostic and therapeutic cancer biomarker. Small extracellular vesicles (sEVs) are cell-released nanoscaled membrane-bound vesicles transferring bioactive molecules for intercellular communication and playing essential roles in tumor progression and metastasis. Therefore, protein heterogeneity in tumor-derived sEVs indicates the degree of malignant transformation, providing a noninvasive biomarker for cancer diagnosis and malignancy evaluation. We employ near-field infrared (nano-FTIR) spectroscopy to investigate malignancy-related protein heterogeneity in a single sEV and demonstrate the discriminability of sEV protein heterogeneity to evaluate tumor malignancy and metastasis. We found that the amide I/II adsorption ratio of the sEVs increases with tumor malignancy, the proportion of α-helix + random coil (α-helix and random coil) in sEV proteins decreases with tumor malignancy, and the proportion of β-sheet + β-turn (β-sheet and β-turn) increases with tumor malignancy. These nano-FTIR spectral signatures of the sEVs from the primary tumor tissue of breast cancer patients show high sensitivity and specificity in evaluating tumor metastasis. This study shows the advantages of nano-FTIR in single sEV characterization and demonstrates the significance of sEV protein heterogeneity in cancer diagnosis. It provides a noninvasive solution to elucidate cancer development and facilitates the exploitation of potential cancer biomarkers.

Establishment of gastric cancer organoid and its application in individualized therapy.

The application of cancer organoids is of great value in individualized therapy as an embodiment of the tumor of a patient, a gastric cancer organoid model was established and its application in individualized drug screening was explored. The primary tumor tissues of 3 patients with gastric cancer who underwent primary surgery at the Fourth Department of General Surgery of the First Hospital of Lanzhou University (Lanzhou, China) between July and August 2021 were selected and digested with mixed enzymes to prepare cell suspensions. Of these, two were cultured by mixing with Matrigel, while the cells from the third patient were placed in a 24-well ultra-low adhesion plate for suspension organoid culture. After intensive organoid growth, they were digested, passaged, cryopreserved and thawed for further analyses. The formation of gastric cancer organoids was observed under an inverted microscope. One case was selected, and organoids were compared with the original tumor tissue via H&E and immunohistochemical staining to evaluate the consistency of the two. Finally, paclitaxel, oxaliplatin and fluorouracil were administered to the organoids to verify the value of screening individualized drugs. It was indicated that the passage and cryopreservation of gastric cancer organoids were successfully established in all three cases. The H&E and immunohistochemical staining results suggested that the structure and protein expression of the organoids were highly similar to those of the source tumor tissue. The use of established gastric cancer organoids for individualized chemotherapy drug screening is of high clinical value. Gastric cancer organoids with high similarity to the original tissue may be successfully constructed by the suspension growth culture method. The established organoids may serve as an effective model for individualized drug screening.

Prognostic value of lncRNAs related to fatty acid metabolism in lung adenocarcinoma and their correlation with tumor microenvironment based on bioinformatics analysis.

BackgroundAs a key regulator of metabolic pathways, long non-coding RNA (lncRNA) has received much attention for its relationship with reprogrammed fatty acid metabolism (FAM). This study aimed to investigate the role of the FAM-related lncRNAs in the prognostic management of patients with lung adenocarcinoma (LUAD) using bioinformatics analysis techniques.MethodsWe obtained LUAD-related transcriptomic data and clinical information from The Cancer Genome Atlas (TCGA) database. The lncRNA risk models associated with FMA were constructed by single-sample gene set enrichment analysis (ssGSEA), weighted gene co-expression network (WGCNA), differential expression analysis, overlap analysis, and Cox regression analysis. Kaplan-Meier (K-M) and receiver operating characteristic (ROC) curves were utilized to assess the predictive validity of the risk model. Gene set variation analysis (GSVA) revealed molecular mechanisms associated with the risk model. ssGSEA and microenvironment cell populations-counter (MCP-counter) demonstrated the immune landscape of LUAD patients. The relationships between lncRNAs, miRNAs, and mRNAs were predicted by using LncBase v.2 and miRTarBase. The lncRNA-miRNA-mRNA regulatory network was visualized with Cytoscape v3.4.0. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was performed using DAVID v6.8. Quantitative real-time fluorescence PCR (qRT-PCR) was performed to verify the expression levels of the prognostic lncRNAs.ResultsWe identified 249 differentially expressed FMA-related lncRNAs in TCGA-LUAD, six of which were used to construct a risk model with appreciable predictive power. GSVA results suggested that the risk model may be involved in regulating fatty acid synthesis/metabolism, gene repair, and immune/inflammatory responses in the LUAD process. Immune landscape analysis demonstrated a lower abundance of immune cells in the high-risk group of patients associated with poor prognosis. Moreover, we predicted 279 competing endogenous RNA (ceRNA) mechanisms for 6 prognostic lncRNAs with 39 miRNAs and 201 mRNAs. Functional enrichment analysis indicated that the ceRNA network may be involved in the process of LUAD by participating in genomic transcription, influencing the cell cycle, and regulating tissue and organogenesis. In vitro experiments showed that prognostic lncRNA CTA-384D8.35, lncRNA RP5-1059L7.1, and lncRNA Z83851.4 were significantly upregulated in LUAD primary tumor tissues, while lncRNA RP11-401P9.4, lncRNA CTA-384D8.35, and lncRNA RP11-259K15.2 were expressed at higher levels in paraneoplastic tissues.ConclusionIn summary, the prognostic factors identified in this study can be used as potential biomarkers for clinical applications. ceRNA network construction provides a new vision for the study of LUAD pathogenesis.