Cancer Diagnostic Biomarkers Research Articles

UTRN as a potential biomarker in breast cancer: a comprehensive bioinformatics and in vitro study

Utrophin (UTRN), known as a tumor suppressor, potentially regulates tumor development and the immune microenvironment. However, its impact on breast cancer’s development and treatment remains unstudied. We conducted a thorough examination of UTRN using both bioinformatic and in vitro experiments in this study. We discovered UTRN expression decreased in breast cancer compared to standard samples. High UTRN expression correlated with better prognosis. Drug sensitivity tests and RT-qPCR assays revealed UTRN’s pivotal role in tamoxifen resistance. Furthermore, the Kruskal–Wallis rank test indicated UTRN’s potential as a valuable diagnostic biomarker for breast cancer and its utility in detecting T stage of breast cancer. Additionally, our results demonstrated UTRN’s close association with immune cells, inhibitors, stimulators, receptors, and chemokines in breast cancer (BRCA). This research provides a novel perspective on UTRN’s role in breast cancer’s prognostic and therapeutic value. Low UTRN expression may contribute to tamoxifen resistance and a poor prognosis. Specifically, UTRN can improve clinical decision-making and raise the diagnosis accuracy of breast cancer.

DNA Methylation Biomarkers in Cancer Diagnostics

Abstract Cancer development and progression are characterized by intricate genetic and epigenetic alternations, with DNA methylation playing a crucial role in this transformative process. Recent advancements in DNA methylation mapping technologies have significantly contributed to the identification of novel cancer biomarkers. We provide a short overview of Conformité Européenne-marked in vitro diagnostic tests designed to detect DNA methylation changes in oncology practice.

Estrogen receptor ER-α36: A diagnostic biomarker for endometrial cancer

Estrogen receptor ER-α36: A diagnostic biomarker for endometrial cancer

Evaluating Leukocyte Telomere Length and Myeloid-Derived Suppressor Cells as Biomarkers for Prostate Cancer.

Leukocyte telomere length (LTL) and myeloid-derived suppressor cells (MDSC) are associated with aging and the development and progression of cancer. However, the exact nature of this relationship remains unclear. Our study aimed to investigate the potential of LTL and MDSC as diagnostic biomarkers for prostate cancer while also seeking to deepen our understanding of the relationship of these potential biomarkers to each other. Our study involved patients undergoing a prostate biopsy. We analyzed the relative LTL in genomic DNA obtained from peripheral blood leukocytes as well as the percentage of MDSC and their subtypes in peripheral blood mononuclear cells (PBMC). Our evaluation focused on examining the relationship between LTL and MDSC and pathological diagnoses as well as investigating the correlation between LTL and MDSC levels. In our study of 102 participants, 56 were pathologically diagnosed with localized prostate cancer (cancer group), while 46 tested negative (control group). The cancer group exhibited significantly shorter LTL in comparison to the control group (p = 0.024). Additionally, the cancer group showed a tendency towards a higher percentage of monocytic MDSC (M-MDSC), although this difference did not reach statistical significance (p = 0.056). Our multivariate logistic regression analysis revealed that patients with shorter LTL and higher percentages of M-MDSC had a 2.98-fold (95% CI = 1.001-8.869, p = 0.049) and 3.03-fold (95% CI = 1.152-7.977, p = 0.025) increased risk of prostate cancer diagnosis, respectively. There was also a significant negative correlation between LTL and M-MDSC. (r = -0.347, p < 0.001). Our research has established a correlation between LTL and MDSC in patients undergoing biopsy for prostate cancer. Notably, we observed that individuals with localized prostate cancer tend to have shorter LTL and a higher percentage of M-MDSC prior to their diagnosis. These findings suggest that LTL and M-MDSC could potentially serve as adjunctive biomarkers for the early diagnosis of prostate cancer.

Abstract 4635: RNF208: A novel diagnostic and prognostic biomarker for colorectal cancer and key regulator of malignant behavior

Abstract Background: RNF208, a member of the RING finger protein family, has been implicated in ubiquitin-mediated degradation of Vimentin, regulating invasion in breast cancer, and serves as a prognostic factor in uveal melanoma. However, its diagnostic and prognostic value in colorectal cancer (CRC), as well as its role in regulating malignant behavior in CRC, remains unclear. This study aims to reveal the potential of RNF208 as a diagnostic and prognostic marker for CRC and its function in regulating malignant behavior in CRC through bioinformatics analysis and experimental validation. Methods: In this study, based on the ExoRbase2.0 human plasma exosome database (CRC=35; Healthy=118) and TCGA-COAD dataset (CRC=478; Healthy=41), we conducted bioinformatics analysis of the transcriptomic differences in plasma exosomes between CRC patients and normal individuals using ExoRbase2.0. Survival data from the TCGA-COAD dataset were integrated to select key molecules for CRC diagnosis and prognosis. Plasma samples from 39 CRC patients and 16 normal individuals were collected from hospital, and exosomes were isolated and purified using a reagent kit. qPCR was employed to validate the levels of RNF208 in plasma exosomes, confirming the results of bioinformatics analysis. Biological behavior was assessed through CCK-8 proliferation assays, flow cytometry experiments, and Transwell migration assays to investigate the relationship between RNF208 and malignant behavior in the HCT116 colorectal cancer cell line. Results: Bioinformatics analysis revealed a significant correlation between elevated RNF208 expression in plasma exosomes and the incidence of CRC, as well as poor prognosis. The qPCR results from clinical samples further confirmed this correlation, and ROC curves demonstrated high sensitivity and accuracy, suggesting RNF208's potential as a diagnostic and independent prognostic factor for CRC. CCK-8 experiments showed that RNF208 knockdown suppressed proliferation activity in HCT116 cells, flow cytometry indicated that RNF208 knockdown promoted apoptosis in HCT116 cells, and Transwell migration assays demonstrated that RNF208 knockdown inhibited the migration of HCT116 cells. Conclusion: RNF208 serves as a novel diagnostic and prognostic biomarker for colorectal cancer, promoting the proliferation and migration of colorectal cancer cells and contributing to the further deterioration of the disease. Citation Format: Fangyue Guo, Shanfeng Zhang, Pei Li. RNF208: A novel diagnostic and prognostic biomarker for colorectal cancer and key regulator of malignant behavior [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4635.

Abstract 5214: HYAL4 splice variant induces treatment-resistance in advanced bladder cancer

Abstract Introduction and Objective: Precision-based treatment approaches could improve the prognosis of patients with bladder cancer (BC). We recently discovered a first-in-class human Chondroitinase (Chase) that degrades chondroitin sulfate. This Chase is a splice variant of HYAL4 (V1) and promotes a malignant phenotype and chemoresistance in BC cells. We evaluated V1/Chase expression and functions in BC and inhibitors to overcome V1/Chase-mediated Gemcitabine (Gem) resistance. Methods: Cohort 1: 653 voided urine specimens (BC, 160; non-BC, 493); cohort 2: 40 cystectomy specimens from MIBC patients who received adjuvant Gemcitabine plus cisplatin (G+C) treatment. Gene expression was measured by q-PCR and urine was assayed by the Chase test. V1 was expressed in BC cell lines or silenced and the transfectants were analyzed for sensitivity to Gem and Cisplatin. The mechanism of Gem resistance was evaluated in preclinical in vitro and in vivo models. Results: In cohort 1, Chase levels were 7-10-fold elevated in patients with BC compared to patients with benign genitourinary conditions, history of BC, or other cancers. Chase test detected BC with 94.4% and 87.4% specificity. Chase test had 84% accuracy in correctly diagnosing the cases with atypical cytology inference. Stem cell marker CD44 was the major substrate of Chase in BC cells. V1’s Chase activity induced CD44 cleavage and shedding. Intracellularly, CD44 cleavage induced JAK2/Stat3 pathway and subsequently upregulation of cytidine deaminase. CDA induces Gem metabolism and efflux of dFdU, an inactive Gem metabolite. HPLC analysis showed, V1 transfectants have increased levels of dFdU and higher efflux. STAT3 and CDA inhibitors synergistically re-sensitized V1-expressing cells to Gem. In cohort 2, V1, p-JAK2 and CDA expression predicted failure to G+C treatment (P&amp;lt;0.0001). JAK2, STAT3 and CDA inhibitors synergistically re-sensitized V1-expressing cells to Gem. V1-induced muscle invasive tumors that were metastatic. While V1-expressing tumors were resistant, combination of Gem with a CDA or JAK-2 inhibitor abrogated V1 tumor growth with minimal toxicity. Conclusion: V1/Chase is a potential diagnostic and prognostic biomarker for bladder cancer and drives muscle-invasion, metastasis, and Gem resistance in BC. Inhibitors of the Chase signaling pathway overcome V1-induced Gem resistance, suggesting a precision-based treatment approach to improve treatment response. Support: 1R01CA227277-05A1; 1R01CA283699-01 Citation Format: Karina Aguilar, Sunita Panda, Joshua Van Der Eerden, Luis Lopez, Martha Terris, Pablo Santamaria, Bal Lokeshwar, Vinata B. Lokeshwar. HYAL4 splice variant induces treatment-resistance in advanced bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5214.

Abstract 2629: N6AMT1-mediated DNA 6mA modification in DNA repetitive elements LINE-1 dynamically regulates the IFN signal pathway in colorectal cancer

Abstract Background: DNA N6-methyldeoxyadenosine (6mA) modification is the most prevalent DNA modification in prokaryotes, like bacteria, which participates in the host defense system. However, the presence and function of DNA 6mA in eukaryotes remains elusive. Many studies have reported that DNA 6mA modification is distributed across the genome and regulates transcription and the activity of transposable elements, in which the DNA 6mA methyltransferases and demethylases are involved, including the methyltransferase N6AMT1. LINE-1 is a genome-wide DNA repetitive element that acts as a diagnostic and prognostic biomarker for colorectal cancer. Therefore, we aimed to map the DNA 6mA in LINE-1 and investigate its role in the colorectal cancer (CRC) development. Methods: The restriction-enzyme-digestion assay followed by quantitative PCR (6mA-RE-qPCR) was used to evaluate the LINE-1 DNA 6mA levels in the tumor and normal tissues. The DNA Nanopore sequencing was utilized to determine DNA 6mA and 5mC modifications. After the knockdown of N6AMT1, the dynamic changes of LINE-1 DNA 6mA methylation and RNA transcription under various stresses were determined by 6mA-RE-qPCR and qPCR, and the subsequent RNA-seq was performed to explore the downstream regulated pathways. Results: The DNA 6mA methylation in LINE-1 is highly variant in the tumor and normal tissues, and it was significantly less prevalent in tumor tissues. The genomic distribution of LINE-1 DNA 6mA is significantly different from that of LINE-1 5mC. The LINE-1 DNA 6mA methylation and RNA transcription levels were dynamically changed in response to various stimuli, including 5-FU and H2O2. Knockdown of N6AMT1 downregulated LINE-1 DNA 6mA methylation and RNA transcription, promoted the proliferation, migration and invasion of CRC cells in vitro, and suppressed the IFN-gamma pathway. The co-culture assay showed N6AMT1 facilitated chemotaxis of macrophages and cytotoxicity of T cells via the IFN-gamma signal pathway. Conclusions: The heterogeneity of DNA 6mA methylation in LINE-1 and its dynamic change in response to stimuli indicate a biological role of LINE-1 6mA methylation in the primary and adaptive tumor heterogeneities, which provides a novel insight into cancer development. The N6AMT1-mediated DNA 6mA modification in LINE-1 regulates CRC development through the IFN-gamma pathway. Keywords: N6AMT1, LINE-1, DNA 6mA methylation, colorectal cancer Citation Format: Ze Yuan, Xiaoxia Liu, Xiaolin Wang, Yanxin Luo, Huichuan Yu. N6AMT1-mediated DNA 6mA modification in DNA repetitive elements LINE-1 dynamically regulates the IFN signal pathway in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2629.

Abstract 7092: Cancer biomarker discovery with scalable biofluid proteomics

Abstract Biofluid proteomics opens opportunities for the discovery of early detection, diagnostic, and prognostic cancer biomarkers through non-invasive or minimally invasive screening. Plasma and serum are accessible sample types, however, the high dynamic range of proteins creates analytical challenges for the sensitive detection of potential biomarkers. In this work, we compare two proteomic approaches for large-scale cancer biomarker discovery: the Olink Proximity Extension Assay and the Seer Proteograph Product Suite. Olink Explore 3072 is an immunoassay that gains specificity by using dual antibody recognition to measure approx. 3,000 proteins in each sample. Antibody pairs are tagged with oligonucleotides, which hybridize and are amplified before measurement by next generation sequencing. Seer Proteograph is an enrichment strategy that uses a proprietary mix of functionalized magnetic nanoparticles with affinity for certain amino acids and functional groups in native state proteins. The resulting peptides are measured using untargeted mass spectrometry to identify proteins at the peptide level, paving the way for the identification of proteoforms and peptide variants. Aliquots of human plasma from 78 samples representing a range of cancer indications were obtained through the Discovery Life Sciences biobank and used for analysis by both the Olink and Proteograph workflows. Olink analysis achieved Pearson correlation scores of greater than or equal to 0.8 when correlating each of seven process controls to each other for all approx. 3000 proteins. On average, greater than or equal to 75% of the proteins were detected across all panels in all sample groups except for Normal and Benign groups (64% and 74% respectively). After stringent FDR filtering to ensure only high-quality data was analyzed, the Seer Proteograph workflow quantified 4,323 proteins across all 78 samples. Pearson correlation scores of greater than or equal to 0.96 were achieved when comparing digestion controls, process controls, and sample cleanup controls. Both platforms achieved detection of proteins across the dynamic range of plasma, including low abundance proteins. The Olink Explore 3072 and Seer Proteograph platforms were found to be complementary, with approx. 15% overlap in measured proteins. Cancer biomarker discovery at the proteomic level is bolstered by recent advances in analytical capabilities, as revealed by the Olink Explore and Seer Proteograph platforms. Importantly, complementary implementation of these two workflows will enable comprehensive biomarker analysis. Citation Format: Danielle B. Gutierrez, Jessica L. Moore, Jaison Arivalagan, Tiffany Louie, Leslie Wilkinson, Ray Clemens. Cancer biomarker discovery with scalable biofluid proteomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7092.

Abstract 7419: Seq2Karyotype (S2K): A method for deconvoluting heterogeneity of copy number alterations using single-sample whole-genome sequencing data

Abstract Broad copy number alterations (CNAs) at chromosomal band resolution have been used as cancer diagnostic and prognostic biomarkers for decades. These events have been characterized by cytogenetic imaging, an approach which is powerful for assessing heterogeneity but limited for locus fine mapping. While CNA detection by next-generation sequencing has become a standard analysis, existing methods rarely model CNA heterogeneity in bulk tumor samples and often require a paired normal sample for control. To overcome these limitations, we developed Seq2Karyotype (S2K, https://github.com/chenlab-sj/Seq2Karyotype), a new algorithm for in-silico karyotyping using single-sample whole-genome sequencing (WGS) data. S2K performs joint modeling of read-depth and allelic imbalance (AI) of high-quality heterozygous SNPs to identify reference diploid regions, followed by modeling and segmenting the deviation from the reference. Empirical coverage and AI of segmented regions are fitted to models of single and admixed CNAs to estimate clonality. The final karyotyping considers both the model fitness and minimization of evolution steps.To evaluate S2K’s performance, we analyzed two cell lines commonly used for benchmark test: COLO829 (melanoma) and HCT1395 (breast cancer); both had single-cell (sc) WGS for validation. For COLO829, S2K replicated the four populations detected by scWGS but derived a different clonality estimate. The predominant clone, defined by loss of 1p, 10p, and chr18, was estimated to have 67% cellular fraction (CF) by bulk sample analysis of S2K in contrast to the 10% CF by scWGS analysis. In HCT1395, S2K identified three new CNAs present in &amp;gt;50% of the cells of the matching germline sample which were subsequently validated by FISH, karyotyping and SKY mapping.To demonstrate S2K’s utility, we analyzed three diverse data sets: 17 neuroblastoma cell lines, 24 pediatric AML samples with karyotyping data, and two blood samples from children with myelodysplastic syndromes (MDS) known to harbor mosaic uniparental disomy (UPD). CNA-based intra-tumor heterogeneity was detected in 88% (15/17) of the neuroblastoma cell lines, comprised of 2-4 distinct populations with diverse ranges of CF (~10%-90%) and varying CNA patterns (e.g. admixture of tetraploid and diploid cells), which were validated by cytogenetics or scWGS. In the patient AML samples, S2K detected &amp;gt;95% of the previously reported cytogenetic events and 30% of additional copy-neutral loss-of-heterozygosity events. The mosaic UPD events in MDS patients were detected with projected clonality of 60% and 25%, respectively. These results not only demonstrate the accuracy of in-silico karyotyping performed by S2K but also reveal the dynamic intra-tumor heterogeneity in cancer cell lines, which may impact the design and interpretation of future experiments using these cell lines. Citation Format: Limeng Pu, Karol Szlachta, Virginia Valentine, Xiaolong Chen, Jian Wang, Dennis Kennetz, Daniel Putnam, Sivaraman Natarajan, Li Dong, Thomas Look, Marcin Wlodarski, Lu Wang, Steven Burden, John Easton, Xiang Chen, Jinghui Zhang. Seq2Karyotype (S2K): A method for deconvoluting heterogeneity of copy number alterations using single-sample whole-genome sequencing data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7419.

The diagnostic and prognostic value of exosomal microRNAs in lung cancer: a systematic review.

Studies have shown that many exosomal microRNAs (miRNAs) can be used as non-invasive biomarkers of lung cancer, but their diagnostic and prognostic values need to be further clarified. We conducted a systematic literature search in Web of Science, PubMed, and ScienceDirect databases, obtained relevant articles and extracted data, and used statistical methods and statistical software to comprehensively evaluate the diagnostic and prognostic value of exosomal miRNAs in lung cancer. PROSPERO CRD42023447398. In terms of diagnosis, two exosomal miRNAs (miR-486-5p and miR-451a) were reported with the highest frequency in lung cancer patients, both of which had good diagnostic value. Compared with the control group, the pooled sensitivities of miR-486-5p and miR-451a were 0.80 (95% CI: 0.73-0.86) and 0.76 (95% CI: 0.60-0.87), specificities: 0.93 (95% CI: 0.63-0.99) and 0.85 (95% CI: 0.72-0.92), and AUCs: 0.85 (95% CI: 0.81-0.88) and 0.88 (95% CI: 0.84-0.90), for the respective miRNAs. For prognosis, in lung cancer patients with abnormally expressed exosomal miRNAs, miR-1290 was associated with PFS outcome; miR-382, miR-1246, miR-23b-3p, miR-21-5p, and miR-10b-5p were associated with OS outcome; miR-21 and miR-4257 were associated with DFS outcome; miR-125a-3p and miR-625-5p were associated with PFS and OS outcomes; miR-216b and miR-451a were associated with OS and DFS outcomes. Exosomal miRNAs are valuable biomarkers in lung cancer patients. Exosomal miR-486-5p and miR-451a can be used as new diagnostic biomarkers for lung cancer. Dysregulated exosomal miRNAs could serve as indicators of survival outcomes in lung cancer patients.

Plasma Thioredoxin Reductase as a Potential Diagnostic Biomarker for Breast Cancer

BackgroundEarly diagnosis of breast cancer is critical to the treatment and prognosis of breast cancer patients. Our aim is to explore more practical and effective diagnostic methods to facilitate early treatment and improve prognosis for breast cancer patients. Materials and MethodsThe Mann–Whitney U test, receiver operating characteristic curve, Youden index, Chi-square test, and Fisher's exact test were used to determine whether plasma thioredoxin reductase (TrxR) could be used for the clinical diagnosis of breast cancer. The Wilcoxon signed-rank test was used to validate the prognostic potential of plasma TrxR activity assessment. ResultsA total of 761 patients were included, including 537 cases of breast cancer and 224 cases of benign breast diseases. Plasma TrxR activity in the breast cancer group [8.0 (6.0, 9.45) U/mL] was significantly higher than that in the benign group [3.05 (1.20, 6.275) U/mL]. The diagnostic efficiency of TrxR for breast cancer was higher than that of other conventional breast cancer biomarkers, with an area under the curve of 0.821 (95% CI = 0.791-0.852). In addition, TrxR can be used in combination with conventional tumor markers to further improve the diagnostic efficiency. The optimal TrxR threshold for identifying benign and malignant diseases is 7.45 U/mL. We detected plasma TrxR activity and serum tumor markers before and after antitumor therapies in 333 breast cancer patients and found that their trends were basically the same, with a significant decrease in plasma TrxR activity after treatment. ConclusionPlasma TrxR activity can be used as a suitable biomarker for breast cancer diagnosis and efficacy assessment.

N-glycan biosignatures as a potential diagnostic biomarker for early-stage pancreatic cancer.

Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis, with a 5-year survival rate of less than 10%, owing to its late-stage diagnosis. Early detection of pancreatic cancer (PC) can significantly increase survival rates. To identify the serum biomarker signatures associated with early-stage PDAC by serum N-glycan analysis. An extensive patient cohort was used to determine a biomarker signature, including patients with PDAC that was well-defined at an early stage (stages I and II). The biomarker signature was derived from a case-control study using a case-cohort design consisting of 29 patients with stage I, 22 with stage II, 4 with stage III, 16 with stage IV PDAC, and 88 controls. We used multiparametric analysis to identify early-stage PDAC N-glycan signatures and developed an N-glycan signature-based diagnosis model called the "Glyco-model". The biomarker signature was created to discriminate samples derived from patients with PC from those of controls, with a receiver operating characteristic area under the curve of 0.86. In addition, the biomarker signature combined with cancer antigen 19-9 could discriminate patients with PDAC from controls, with a receiver operating characteristic area under the curve of 0.919. Glyco-model demonstrated favorable diagnostic performance in all stages of PC. The diagnostic sensitivity for stage I PDAC was 89.66%. In a prospective validation study, this serum biomarker signature may offer a viable method for detecting early-stage PDAC.

N6-methyladenosine levels in peripheral blood RNA: a potential diagnostic biomarker for colorectal cancer

BackgroundN6-methyladenosine (m6A) is dysregulated in various cancers, including colorectal cancer (CRC). Herein, we assess the diagnostic potential of peripheral blood (PB) m6A levels in CRC.MethodsWe collected PB from healthy controls (HCs) and patients with CRC, analyzed PB RNA m6A levels and the expression of m6A-related demethylase genes FTO and ALKBH5, cocultured CRC cells with PB mononuclear cells (PBMCs), and constructed an MC38 cancer model.ResultsPB RNA m6A levels were higher in the CRC than that in HCs. The area under the curve (AUC) of m6A levels (0.886) in the CRC was significantly larger compared with carbohydrate antigen 199 (CA199; 0.666) and carcinoembryonic antigen (CEA; 0.834). The combination of CEA and CA199 with PB RNA m6A led to an increase in the AUC (0.935). Compared with HCs, the expression of FTO and ALKBH5 was decreased in the CRC. After coculturing with CRC cells, the PBMCs RNA m6A were significantly increased, whereas the expression of FTO and ALKBH5 decreased. Furthermore, m6A RNA levels in the PB of MC38 cancer models were upregulated, whereas the expression of FTO and ALKBH5 decreased.ConclusionsPB RNA m6A levels are a potential diagnostic biomarker for patients with CRC.

Abstract B048: Evaluating the impact of pulmonary diseases on the use of microRNAs as biomarkers for early detection of ovarian cancer

Abstract B048: Evaluating the impact of pulmonary diseases on the use of microRNAs as biomarkers for early detection of ovarian cancer

COL10A1 as a Prognostic Biomarker in Association with Immune Infiltration in Prostate Cancer.

The collagen type X alpha 1 (COL10A1) has recently been found to play an important role in the development and progression of cancer. However, the link between COL10A1 and the tumor immune microenvironment remains understood scantily. In the current study, the pan-cancer data of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were used to investigate the expression mode, the clinical prognostic and diagnostic value of COL10A1 in different tumors. We used TCGA data to assess the correlations between COL10A1 and clinical symptoms of prostate cancer. The R packages "edgR" and "clusterProfiler" were used for differential expression gene and enrichment analysis of COL10A1. Immunohistochemistry was further employed to corroborate the expression of COL10A1 gene in prostate cancer. After that, we used TIMER to evaluate the pertinence of COL10A1 expression to immune infiltration level in prostate cancer. On the whole, COL10A1 was expressed at significantly higher levels in a variety of tumor tissues than in the corresponding normal tissues. Besides, significant correlations with tumor prognosis and relative exactitude in predicting tumors show that COL10A1 may be a probable prognostic and diagnostic biomarker of prostate cancer. In addition, the evidence indicates a significant correlation between COL10A1 and clinical symptoms of prostate cancer. Furthermore, the main molecular functions of COL10A1 included humoral immune response, complement activation, immunoglobulin, regulation of complement activation, and regulation of humoral immune response. Finally, we found that COL10A1 expression is positively correlated with enhanced macrophage and M2 macrophage infiltration in prostate cancer. The study indicates that COL10A1 might participate in M2 macrophage polarization in prostate cancer. COL10A1 might be an innovative biomarker to evaluate tumor microenvironment immune cell infiltration and prognosis in prostate cancer.

Serum miR-16 and CA15.3 combination as early diagnostic biomarkers for breast cancer in Egyptian females

Serum miR-16 and CA15.3 combination as early diagnostic biomarkers for breast cancer in Egyptian females

Abstract A023: Assessing the reproducibility crisis in vaginal microbiome studies for clinical applications in endometrial cancer

Abstract Recent associations between vaginal microbiota and gynecological cancer have led to high-throughput sequencing datasets identifying diagnostic biomarkers for Endometrial Cancer (EC). However, lack of bioinformatics standards results in inconsistent independent studies with poor reproducibility, making them clinically inapplicable. This study leverages publicly available amplicon sequence data to address the reproducibility of EC microbiome studies. We implemented bioinformatics pipelines from five studies to reproduce and measure the replicability of published results across cohorts using metrics such as alpha diversity, beta diversity and differentially expressed taxa. We further evaluated separability between benign and cancer patients at different taxonomic levels (phylum, class, order, family, and genus) within and across datasets using boosted tree classifiers and Area Under the Curve (AUC) as the performance metric. While we reproduced the general trend of observing higher microbial diversity in EC compared to healthy controls, we found irregularities in two cohorts. Using beta diversity distance metrics, we identified that histology alone explains less than 3% of the variance in all cohorts. Three microbiome differential abundance methods were used in the five studies. While they all agree on a decrease in the Lactobacillus genus in EC patients, there is no consensus on other taxa associated with EC. We also found that separability between benign and cancerous conditions is highest at the class level, having an AUC score of 0.86. In subsequent steps, we will perform an integrative analysis to identify an EC vaginal microbiome predictive signature that is preserved across all five cohorts, benefiting screening programs. Citation Format: Dollina D. Dodani, Aline Talhouk. Assessing the reproducibility crisis in vaginal microbiome studies for clinical applications in endometrial cancer [abstract]. In: Proceedings of the AACR Special Conference on Endometrial Cancer: Transforming Care through Science; 2023 Nov 16-18; Boston, Massachusetts. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(5_Suppl):Abstract nr A023.

Integrative Bioinformatics Analysis Reveals Potential Target Genes and PTEN Signaling in Breast Cancer and Effect of Zingiber officinale (Ginger) and Allium sativum (Garlic) extract on It.

Breast cancer is the most common type of cancer in women. The construction of a competing gene network is an important step in the identification of the role of hub genes in breast cancers. In the current research, we used a number of bioinformatics tools to construct this network in breast cancer and investigated the combined effect of garlic and ginger on mice model of breast cancer. We chose female mice weighing 18-20 g that were divided into 7 groups including; the cancer group receiving normal saline, different doses of ginger extract (100 and 500 mg/kg), different doses of garlic (50 and 100 mg/kg), tamoxifen (10 mg/ kg) and simultaneous garlic (100 mg/kg) and ginger (500 mg/kg) for 3 weeks intraperitoneal. Then we anesthetized the mice, isolated the tumor, and determined its size. Glutathione reductase and peroxidase levels and HER2, PTEN, and Cullin3 genes expression were measured. We identified 20 hub genes for breast cancer. In animal phase we found that tumor size in all mice receiving garlic and ginger showed a significant decrease compared to the control. Glutathione reductase showed a significant increase in all groups, especially in ginger 500 and combined groups. Glutathione peroxidase increased almost in all groups, especially in ginger 500. Expression of HER2 decreased in all treated groups. Expression of PTEN increased just in the combined group. Taken together, we introduce a number of novel promising diagnostic biomarkers for breast cancer. The use of garlic and ginger in the treatment of cancer can be useful. This action is probably through the antioxidant mechanism, and regulation of the expression of cancer related genes such as PTEN.

Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours

IntroductionGut microbiome–derived nanoparticles, known as bacterial extracellular vesicles (bEVs), have garnered interest as promising tools for studying the link between the gut microbiome and human health. The diverse composition of bEVs, including their proteins, mRNAs, metabolites, and lipids, makes them useful for investigating diseases such as cancer. However, conventional approaches for studying gut microbiome composition alone may not be accurate in deciphering host–gut microbiome communication. In clinical microbiome research, there is a gap in the knowledge on the role of bEVs in solid tumor patients. ObjectivesAnalyzing the functionality of bEVs using (meta)genomics and proteomics could highlight the unique aspects of host–gut microbiome interactions in solid tumor patients. Therefore, we performed a comparative analysis of the proteome and microbiota composition of gut microbiome-derived bEVs isolated from patients with solid tumors and healthy controls. MethodsAfter isolating bEVs from the feces of solid tumor patients and healthy controls, we performed spectrometry analysis of their proteomes and next-generation sequencing (NGS) of the 16S gene. We also investigated the gut microbiomes of feces from patients and controls using 16S sequencing and machine learning to classify the samples into patients and controls based on their bEVs and fecal microbiomes. ResultsSolid tumor patients showed decreased microbiota richness and diversity in both the bEVs and feces. However, the bEV proteomes were more diverse in patients than in the controls and were enriched with proteins associated with the metabolism of amino acids and carbohydrates, nucleotide binding, and oxidoreductase activity. Metadata classification of samples was more accurate using fecal bEVs (100%) compared with fecal samples (93%). ConclusionOur findings suggest that bEVs are unique functional entities. There is a need to explore bEVs together with conventional gut microbiome analysis in functional cancer research to decipher the potential of bEVs as cancer diagnostic or therapeutic biomarkers.

Pan-cancer analysis reveals potential immunological and prognostic roles of COA6 in human cancers and preliminary exploration of COA6 in bladder cancer

BackgroundCytochrome C oxidase assembly factor 6 (COA6) is significantly involved in the progression of cancer and is aberrantly expressed in disease. Nevertheless, the comprehensive analysis of COA6 using many omics techniques, and its impact on the prognosis and immunological microenvironment of cancer patients, remains unexplored. MethodsWe gathered data from 33 cancer cases and conducted a thorough analysis of abnormalities in COA6 gene expression. This analysis included examining its relevance to disease, its diagnostic and prognostic value, pathway enrichment, the immune microenvironment, its association with immune checkpoints, and its ability to predict patient response to immunotherapy and natural small molecule drugs that target the COA6 protein. Ultimately, we examined the function of COA6 in bladder cancer by in vitro research. ResultsOur study revealed significant variations in gene expression and identified COA6 as a potential diagnostic biomarker for cancer. COA6 was also discovered to have a crucial function in pan-cancer involving the tumor microenvironment. COA6 has a strong correlation with well-known immunological checkpoints, including TMB and MSI. Molecular docking identified natural small chemical inhibitors that specifically target the COA6 protein. Ultimately, scientific evidence has verified that suppressing the expression of the COA6 gene hinders the growth and infiltration of bladder cancer cells. ConclusionsOur study emphasizes the significant potential of COA6 as a predictive and immunotherapeutic response biomarker. This finding may lead to future investigation into the mechanism of tumor infiltration and the therapeutic possibilities of COA6 in cancer.