Biomarkers For Cancer Screening Research Articles

Expression and hypermethylation of JAM and EPB41L3 in cervical squamous cell carcinoma: Clinical significance and applications.

This study aimed to explore the expression and hypermethylation of EPB41L3 and JAM3 in cervical squamous cell carcinoma (CSCC) and to investigate their clinical significance. JAM3 and EPB41L3 mRNA expression was analyzed using a public database, and protein expression was detected using immunohistochemistry. The methylation status of JAM3 and EPB41L3 was detected in CSCC tissues and cervical cytological specimens using a quantitative methylation-specific PCR (qMSP). JAM3 and EPB41L3 mRNA were downregulated in CSCC. The JAM3 protein was positively detected in 39.4% of CSCC tissues and frequently expressed in those with lower FIGO stage and no lymph node metastasis. EPB41L3 was expressed in 18.9% of CSCC tissues. The hypermethylation of JAM3 was detected in 52.3% of CSCC tissues and related to higher FIGO stage and lymph node metastasis. EPB41L3 hypermethylation was detected in 72.7% of CSCC tissues and related to older ages and lymph node metastasis. In cervical cytological specimens, no methylation of JAM3 and EPB41L3 was found in normal or inflamed cervical epithelial cells. The methylation of JAM3 was detected in 0%, 8.3%, and 6.3% of ASCUS, LSIL, and HSIL samples, while EPB41L3 was detected in 12.5%, 42.9%, and 71.4%, respectively. The sensitivity of the combination of JAM3 and EPB41L3 methylation detection in ASCUS, LSIL, and HSIL was 8.3%, 15.6%, and 85.7%, respectively. The specificity of the combination of JAM3 and EPB41L3 methylation detection was 100%. Downregulation of JAM3 and EPB41L3 by hypermethylation was detected in CSCC. JAM3 and EPB41L3 hypermethylation are potential biomarkers for cervical cancer screening.

Exosomal Thomsen-Friedenreich Glycoantigen: A New Liquid Biopsy Biomarker for Lung and Breast Cancer Diagnoses.

Exosomes or small extracellular vesicles have emerged as potent biomarkers of cancer liquid biopsy. We discovered a new exosomal carbohydrate marker, TF-Ag-α (Galβ1-3GalNAc-α), and showed that exosomal TF-Ag-α detected both lung and breast cancers with >95% accuracy. Our findings demonstrated that exosomal TF-Ag-α is a promising liquid biopsy biomarker for cancer screening and early detection.

Evaluation of mtDNA common deletion in esophageal squamous cell carcinoma.

Mitochondrial defects are thought to play a role in cancer initiation and progression for a long time. Because of the absence of protective histones and an inefficiency in the DNA repair process, mitochondrial DNA is known to be prone to mutations. The deletion of 4977bp is one of the most common mutations in human cancers. This study aimed to investigate the relationship between 4977bp common deletion and Esophageal Squamous Cell Carcinoma Disease (SCC) to provide prognostic information. By using a PCR protocol, this study identified the 4977bp deletion of mtDNA. A PCR method was used on tumor samples from 41 squamous cell carcinoma patients and blood samples from 50 healthy individuals to detect DNA. Among the 41 tumor samples (80.5%), 33 were found to have the 4977bp deletion, while none of the blood samples from healthy individuals contained it. It is shown that the deletion of 4977bp of mtDNA correlates significantly with SCC in this study. A 4977bp deletion could be used as an effective cancer screening indicator and biomarker for early diagnosis and prevention of cancer.

Identification and validation of screening models for breast cancer with 3 serum miRNAs in an 11,349 samples mixed cohort.

The study focuses on enhancing breast cancer (BC) prognosis through early detection, aiming to establish a non-invasive, clinically viable BC screening method using specific serum miRNA levels. Involving 11,349 participants across BC, 11 other cancer types, and control groups, the study identified serum biomarkers through feature selection and developed two BC screening models using six machine learning algorithms. These models underwent evaluation across test, internal, and external validation sets, assessing performance metrics like accuracy, sensitivity, specificity, and the area under the curve (AUC). Subgroup analysis was conducted to test model stability. Based on the three serum miRNA biomarkers (miR-1307-3p, miR-5100, and miR-4745-5p), a BC screening model, SM4BC3miR model, was developed. This model achieved AUC performances of 0.986, 0.986, and 0.939 on the test, internal, and external sets, respectively. Furthermore, the SSM4BC model, utilizing ratio scores of miR-1307-3p/miR-5100 and miR-4745-5p/miR-5100, showed AUCs of 0.973, 0.980, and 0.953, respectively. Subgroup analyses underscored both models' robustness and stability. This research introduced the SM4BC3miR and SSM4BC models, leveraging three specific serum miRNA biomarkers for breast cancer screening. Demonstrating high accuracy and stability, these models present a promising approach for early detection of breast cancer. However, their practical application and effectiveness in clinical settings remain to be further validated.

The associations between dysregulation of human blood metabolites and lung cancer risk: evidence from genetic data

BackgroundMetabolic dysregulation is recognized as a significant hallmark of cancer progression. Although numerous studies have linked specific metabolic pathways to cancer incidence, the causal relationship between blood metabolites and lung cancer risk remains unclear.MethodsGenomic data from 29,266 lung cancer patients and 56,450 control individuals from the Transdisciplinary Research in Cancer of the Lung and the International Lung Cancer Consortium (TRICL-ILCCO) were utilized, and findings were replicated using additional data from the FinnGen consortium. The analysis focused on the associations between 486 blood metabolites and the susceptibility to overall lung cancer and its three major clinical subtypes. Various Mendelian randomization methods, including inverse-variance weighting, weighted median estimation, and MR-Egger regression, were employed to ensure the robustness of our findings.ResultsA total of 19 blood metabolites were identified with significant associations with lung cancer risk. Specifically, oleate (OR per SD = 2.56, 95% CI: 1.51 to 4.36), 1-arachidonoylglyceropholine (OR = 1.79, 95% CI: 1.22 to 2.65), and arachidonate (OR = 1.67, 95% CI: 1.16 to 2.40) were associated with a higher risk of lung cancer. Conversely, 1-linoleoylglycerophosphoethanolamine (OR = 0.57, 95% CI: 0.40 to 0.82), ADpSGEGDFXAEGGGVR, a fibrinogen cleavage peptide (OR = 0.60, 95% CI: 0.47 to 0.77), and isovalerylcarnitine (OR = 0.62, 95% CI: 0.49 to 0.78) were associated with a lower risk of lung cancer. Notably, isoleucine (OR = 9.64, 95% CI: 2.55 to 36.38) was associated with a significantly higher risk of lung squamous cell cancer, while acetyl phosphate (OR = 0.11, 95% CI: 0.01 to 0.89) was associated with a significantly lower risk of small cell lung cancer.ConclusionThis study reveals the complex relationships between specific blood metabolites and lung cancer risk, highlighting their potential as biomarkers for lung cancer prevention, screening, and treatment. The findings not only deepen our understanding of the metabolic mechanisms of lung cancer but also provide new insights for future treatment strategies.

A Four-Gene Panel in Rectal Swab Samples as a Biomarker for Colorectal Cancer Screening.

The dysregulation of gene expression is one of the key molecular features of colorectal cancer (CRC) development. This study aimed to investigate whether such dysregulation is reflected in rectal swab specimens of CRC patients and to evaluate its potential as a non-invasive approach for screening. We compared the expression level of 14 CRC-associated genes in tumor and adjacent non-tumor tissue of CRC patients and examined the correlation of their levels in tissue with paired rectal swab specimens. The level of these 14 genes in rectal swab specimens was compared among patients with CRC or polyp and control subjects, and the diagnostic potential of each dysregulated gene and the gene panel were evaluated. The expression of CXCR2, SAA, COX1, PPARδ, PPARγ, Groγ, IL8, p21, c-myc, CD44 and CSF1 was significantly higher in CRC, and there was a significant correlation in the levels of most of them between the CRC and rectal swab specimens. In the training study, we showed that CD44, IL8, CXCR2 and c-myc levels were significantly higher in the rectal swab specimens of the CRC patients. Such result was confirmed in the validation study. A panel of these four genes was developed, and ROC analysis showed that this four-gene panel could identify CRC patients with an AUC value of 0.83 and identify overall polyp and precancerous adenoma patients with AUC values of 0.6522 and 0.7322, respectively. Finally, the predictive study showed that the four-gene panel demonstrated sensitivities of 63.6%, 76.9% and 88.9% in identifying overall polyp, precancerous adenoma and CRC patients, respectively, whereas the specificity for normal subjects was 72.2%. The expression of CRC-associated genes in rectal swab specimens reflects the dysregulation status in colorectal tissue, and the four-gene panel is a potential non-invasive biomarker for early precancerous adenoma and CRC screening.

The Role of Biomarkers in Lung Cancer Screening.

Lung Cancer Screening (LCS) is an evolving field with variations in its implementation in various countries. There are only scarce data from National LCS programs. We aim to provide an up-to-date overview of the current evidence regarding the use of biomarkers in LCS. A multidisciplinary Task Force experts' panel collaborated and conducted a systematic literature search, followed by screening, review and synthesis of available evidence. Biomarkers in LCS could be used to improve risk stratification in high-risk participants, improve clarification regarding indeterminate lung nodules and avoid overdiagnosis in suspicious lung findings. Currently, there seem to be promising biomarkers (blood/serum/breath) that have been studied in various trials; however, there is still a lack of solid evidence in clinical validation that would pave the way for their integration into LCS programs. Biomarkers are the next logical step in improving the LCS pathway and its efficiency by playing an adjuvant role in a minimally invasive way. National LCS programs and pilot studies should integrate biomarkers to validate their accuracy in real-life LCS participants.

Circulating MiR-1185¸ MiR-3183, and MiR-584 Levels in Plasma as Diagnostic Non-invasive Biomarkers for Early Detection of Breast Cancer

Introduction: MicroRNAs (miRNAs) are non-coding RNA molecules with short sequences that function as main post-transcriptional gene regulators of different biological pathways via negative regulation of gene expression, thereby leading to either mRNA degradation or translational blockade. Dysregulated expression of these miRNAs has been related etiologically to many human diseases, including breast cancer. Various cellular processes of breast cancer progression, including cell proliferation, apoptosis, metastasis, recurrence and chemodrug resistance, are modulated by oncogenic miRNA (oncomiR). Objective: The objective of this investigation was to study the expression level and potential diagnostic/ prognostic roles of circulating microRNAs (miR-3183, miR-1185, and miR-584) as novel breast cancer biomarkers. Method: The current study was conducted on 99 breast cancer (BC) female patients, aged between 20-63 years old, as the case group and 50 age-matched healthy females as control (HC). After microRNA extraction from the serum samples, real-time PCR was carried out for relative expression quantification of miR-1185, miR-3183a, and miR-584. The ROC curve analysis was performed to investigate the diagnostic value of miRNAs. Result: It was demonstrated that miRNA-1185, miRNA-584, and miRNA-3183 were significantly up-regulated (p-values <0.0001) in female BC cases compared to the control group. Besides, based on the ROC analysis for BC versus HC, it was revealed that the AUC for miRNA-584 was 0.844 (95% confidence interval (CI) and could be proposed as a diagnostic biomarker for breast cancer screening and follow-up. Conclusion: MiRNAs expression profiling using blood-based samples demonstrated their upregulation in the serum and plasma and revealed the concept that circulating miRNAs have high potential as novel noninvasive biomarkers for cancer diagnosis and screening.

Unveiling the potential of SLURP1 protein as a biomarker for prostate cancer screening.

Prostate cancer (PCa) develops slowly and lacks obvious symptoms in the early stage, which makes early screening and diagnosis difficult. Urine collection is simple and is an ideal source of biomarkers. In this study, we performed urinary proteomic studies in PCa patients to screen proteins and apply them to the non-invasive early diagnosis of PCa. Urine samples from PCa patients, benign prostatic hyperplasia (BPH) patients and normal control group were collected. Mass spectrometry was used for proteomic analysis and screening target proteins. Western blot and enzyme-linked immunosorbent assay (ELISA) were used to verify the results. Correlations with clinical indicators were explored, and receiver operating characteristic (ROC) curves were drawn to evaluate the value of target proteins in PCa. A total of 1065 proteins were identified. Urinary SLURP1 protein was significantly elevated in patients with PCa compared with normal controls and patients with BPH patients. Western blot and ELISA further verified the expression changes of SLURP1. The immunohistochemical staining results revealed a substantial increase in positive SLURP1 expression within PCa tumor tissue. Correlation analysis showed a positive correlation between the expression level of urine SLURP1 protein and serum PSA. ROC curve analysis of the SLURP1 protein in the urine of both normal individuals and PCa patients is determined to be 0.853 (95% CI=0.754 to 0.954). The concentration of SLURP1 protein in urine of PCa patients is increased, which can serve as a biomarker for screening PCa.

Exploring research progress in studying serum exosomal miRNA-21 as a molecular diagnostic marker for breast cancer.

Breast cancer is one of the most prevalent malignancies affecting women globally and poses a significant public health challenge. Early clinical detection plays a pivotal role in providing optimal treatment opportunities and favorable prognoses, crucial for reducing breast cancer mortality and enhancing patients' quality of life. Therefore, the timely identification and diagnosis of breast cancer are imperative. Conventional tumor markers, such as carcinoembryonic antigen (CEA) and carbohydrate antigen 15-3 (CA15-3), serve as reliable methods for actively monitoring disease progression and have become a routine auxiliary diagnostic approach in clinical settings. However, these biomarkers exhibit limitations in sensitivity and specificity, particularly in the early screening and diagnosis of tumors, often yielding results inconsistent with clinical manifestations. In recent years, research has increasingly focused on exosomes released by tumor cells as potential new biomarkers for early stage breast cancer screening. Exosomes carry various components, including tumor-derived proteins, nucleic acids, and lipids. This paper delves into the specific utilization of serum exosomal microRNA-21 (miR-21) as a biomarker for early detection and diagnosis of breast cancer, evaluating its efficacy within this framework.

A compact microfluidic laser-induced fluorescence immunoassay system using avalanche photodiode for rapid detection of alpha-fetoprotein.

Alpha-fetoprotein (AFP), commonly employed for early diagnosis of liver cancer, serves as a biomarker for cancer screening and diagnosis. Combining the high sensitivity and specificity of fluorescence immunoassay (FIA), developing a low-cost and efficient immunoassay system for AFP detection holds significant importance in disease diagnosis. In this work, we developed a miniaturized oblique laser-induced fluorescence (LIF) immunoassay system, coupled with a microfluidic PMMA/paper hybrid chip, for rapid detection of AFP. The system employed an avalanche photodiode (APD) as the detector, and implemented multi-level filtering in the excitation light channel using the dichroic mirror and optical trap. At first, we employed the Savitzky-Golay filter and baseline off-set elimination methods to denoise and normalize the original data. Then the cutoff frequency of the low-pass filter and the reverse voltage of the APD were optimized to enhance the detection sensitivity of the system. Furthermore, the effect of laser power on the fluorescence excitation efficiency was investigated, and the sampling time during the scanning process was optimized. Finally, a four-parameter logistic (4PL) model was utilized to establish the concentration-response equation for AFP. The system was capable of detecting concentrations of AFP standard solution within the range of 1-500 ng/mL, with a detection limit of 0.8 ng/mL. The entire immunoassay process could be completed within 15 min. It has an excellent potential for applications in low-cost portable diagnostic instruments for the rapid detection of biomarkers.

Dynamic mutation late acceptance hill climbing aided red fox optimization for metabolomic biomarkers selection from lung cancer patient sera

The accurate selection of serum metabolomic biomarkers for early lung cancer screening remains a significant challenge in the clinical context. Consequently, this study introduces the Red Fox Optimization (RFO) that integrates Dynamic Mutation Late Acceptance Hill Climbing (DM-LAHC), with the aim of selecting a panel of serum metabolomic biomarkers suitable for distinguishing between benign and malignant pulmonary nodules. The key innovation is the dynamic adjustment of the mutation probability in the Late Acceptance Hill Climbing algorithm, which greatly enhances the local search capabilities. And the RFO's reproduction mechanism has been improved through the utilization of a more efficient interpolation form. The biomarker selection model employs a multi-objective fitness function that takes into account both accuracy and quantity. After this, the optimal model yielded a biomarker panel, including Inosine, Hippuric acid, Alanine, and other metabolites. This model demonstrates outstanding performance on an independent test dataset, achieving a fitness value of 0.9136, an AUC (Area Under the Curve) of 0.9926, a sensitivity of 0.9643, and a specificity of 0.9412. Furthermore, the clinical net benefit is highlighted across various risk thresholds by decision curve analysis. These results underscore the significance of DM-LAHC aided RFO in the selection of serum metabolomic biomarkers for lung cancer. The supporting source codes of this work can be found at: https://github.com/zzl2022/DM-LAHC-aided-RFO.

Wide-Targeted Semi-Quantitative Analysis of Acidic Glycosphingolipids in Cell Lines and Urine to Develop Potential Screening Biomarkers for Renal Cell Carcinoma.

Glycosphingolipids (GSLs), mainly located in the cell membrane, play various roles in cancer cell function. GSLs have potential as renal cell carcinoma (RCC) biomarkers; however, their analysis in body fluids is challenging because of the complexity of numerous glycans and ceramides. Therefore, we applied wide-targeted lipidomics using liquid chromatography-tandem mass spectrometry (LC-MS/MS) with selected reaction monitoring (SRM) based on theoretical mass to perform a comprehensive measurement of GSLs and evaluate their potency as urinary biomarkers. In semi-quantitative lipidomics, 240 SRM transitions were set based on the reported/speculated structures. We verified the feasibility of measuring GSLs in cells and medium and found that disialosyl globopentaosylceramide (DSGb5 (d18:1/16:0)) increased GSL in the ACHN medium. LC-MS/MS analysis of urine samples from clear cell RCC (ccRCC) patients and healthy controls showed a significant increase in the peak intensity of urinary DSGb5 (d18:1/16:0) in the ccRCC group compared with that in the control group. Receiver operating characteristic analysis indicated that urinary DSGb5 could serve as a sensitive and specific marker for RCC screening, with an AUC of 0.89. This study demonstrated the possibility of urinary screening using DSGb5 (d18:1/16:0). In conclusion, urinary DSGb5 (d18:1/16:0) was a potential biomarker for cancer screening, which could contribute to the treatment of RCC patients.

The high FKBP1A expression in WBCs as a potential screening biomarker for pancreatic cancer

Given the limitation of current routine approaches for pancreatic cancer screening and detection, the mortality rate of pancreatic cancer cases is still critical. The development of blood-based molecular biomarkers for pancreatic cancer screening and early detection which provide less-invasive, high-sensitivity, and cost-effective, is urgently needed. The goal of this study is to identify and validate the potential molecular biomarkers in white blood cells (WBCs) of pancreatic cancer patients. Gene expression profiles of pancreatic cancer patients from NCBI GEO database were analyzed by CU-DREAM. Then, mRNA expression levels of three candidate genes were determined by quantitative RT-PCR in WBCs of pancreatic cancer patients (N = 27) and healthy controls (N = 51). ROC analysis was performed to assess the performance of each candidate gene. A total of 29 upregulated genes were identified and three selected genes were performed gene expression analysis. Our results revealed high mRNA expression levels in WBCs of pancreatic cancer patients in all selected genes, including FKBP1A (p < 0.0001), PLD1 (p < 0.0001), and PSMA4 (p = 0.0002). Among candidate genes, FKBP1A mRNA expression level was remarkably increased in the pancreatic cancer samples and also in the early stage (p < 0.0001). Moreover, FKBP1A showed the greatest performance to discriminate patients with pancreatic cancer from healthy individuals than other genes with the 88.9% sensitivity, 84.3% specificity, and 90.1% accuracy. Our findings demonstrated that the alteration of FKBP1A gene in WBCs serves as a novel valuable biomarker for patients with pancreatic cancer. Detection of FKBP1A mRNA expression level in circulating WBCs, providing high-sensitive, less-invasive, and cost-effective, is simple and feasible for routine clinical setting that can be applied for pancreatic cancer screening and early detection.

Prospects for liquid biopsy using microRNA and extracellular vesicles in breast cancer.

Among the analytes circulating in body fluids, microRNAs, a type of non-coding RNA and known to exist 2655 in primates, have attracted attention as a novel biomarker for cancer screening. MicroRNAs are signaling molecules with important gene expression regulatory functions that can simultaneously control many gene functions and multiple different pathways in living organisms. These microRNAs are transported in extracellular vesicles (EVs), which are lipid bilayers with 50-150 nm in diameter, and are used as communication tools between cells. Furthermore, the EVs that carry these microRNAs circulate in the bloodstream and have other important implications for understanding the pathogenesis and diagnosis of breast cancer. The greatest benefit from cancer screening is the reduction in breast cancer mortality rate through early detection. Other benefits include reduced incidence of breast cancer, improved quality of life, prognosis prediction, contribution to personalized medicine, and relative healthcare cost containment. This paper outlines the latest developments in liquid biopsy for breast cancer, especially focusing on microRNA and EV diagnostics.

Current role of viral biomarkers in cervical carcinogenesis

Viral biomarkers for cervical cancer screening are valuable in improving timely diagnosis and detection at early stage. The various biomarkers currently there is evidence include high-risk human papillomavirus (hrHPV) deoxyribonucleic acid (DNA) testing, there is place for further research for biomarkers such as hrHPV genotyping hrHPV transcriptional status, and host DNA methylation. Though the evidence is conclusive for hrHPV DNA testing, there is place for further research for biomarkers such as hrHPV genotyping hrHPV transcriptional status, and host DNA methylation. This application of these biomarkers in context of low resource settings has its limitations despite high prevalence of the disease. Improved women participation can be achieved by use of self-samples thereby improving diagnoses rate of the disease and higher cost effectiveness of the screening programme. In due course, biomarkers will be made available in the screening programmes together with self-sampling that will detect hrHPV infections and low-grade squamous intraepithelial lesions (LSIL) before they progress to high-grade squamous intraepithelial lesions (HSIL), and from there to malignancy. This would facilitate prudent timely clinical decisions, reduced patient anxiety, reduction in over referral and unnecessary treatments in women, especially in developing countries.

Abstract 7030: Reference materials for analysis of DNA methylation in cell-free circulating tumor DNA

Abstract Aberrant DNA methylation is associated with many cancers including breast, liver, bone, and colon and has been identified as a biomarker for early cancer screening. Liquid biopsies are beginning to screen for DNA methylation in cancer-derived DNA, but accurate assessment of methylation is not trivial, and methods like bisulfite sequencing can result in biased data. Reference materials for establishing the analytical validity of measurements of CpG methylation are not widely available. In order to prepare such reference materials, genomic DNA (gDNA) was extracted from the well characterized human reference cell line GM24385 and fragmented to a circulating tumor DNA (ctDNA)-like size distribution. This DNA was processed further to prepare CpG-methylated and unmethylated versions. The size distribution was determined by using the Bioanalyzer High Sensitivity DNA Kit (Agilent, Santa Clara, CA). Methylation status in the reference materials was confirmed by both digital PCR (dPCR) and NGS based methods. A digital PCR method was developed to analyze heterozygous single nucleotide polymorphisms (SNPs) using the Bio-Rad QX200™ Droplet Digital PCR (ddPCR) System. To determine methylation levels by NGS, the NEBNext™ Enzymatic Methyl-seq Kit was used (EM-seq). Paired-end sequencing of the libraries was performed on a NextSeq™ 2000 (Illumina, San Diego, CA). Data alignment to hg19 was done with the bwa-meth (Pedersen, BS., et al.) aligner, and assessment of methylation in the aligned data was done with MethylDackel (Ryan, D.). Each reference material had an average peak size of ~160 bp in length, similar to patient cfDNA. By dPCR, the unmethylated reference material had an average of 0.73% DNA methylation, while the methylated reference material had an average of 100.10% DNA methylation. Values can be above 100% by dPCR due to unequal representation of both alleles. By NGS, the unmethylated reference material had an average of 0.93 % CpG methylation, which was similar to the background of 1.13 % and 1.31 % for CHG and CHH methylation, respectively. The methylated reference material had an average of 93.95 % CpG methylation, with a background of 0.69 % and 0.74 % for CHG and CHH methylation, respectively. Because EM-seq relies on enzymatic protection and conversion steps, it may be that these reactions did not allow for full protection and full conversion, which led to values above 0 % for unmethylated and below 100 % for methylated materials. We have developed reference materials for the assessment of DNA methylation in ctDNA. One unmethylated and one methylated reference material was created. These reference materials can be mixed together to the level of methylation required to help aid in assay design, optimization, and validation. Citation Format: Alysha Higgs, Angelique Ryan, Jayanthi Ramprakash, Dana Ruminski Lowe, Yves Konigshofer, Catherine Huang, Andrew Anfora, Russell Garlick, Bharathi Anekella. Reference materials for analysis of DNA methylation in cell-free circulating tumor DNA [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 7030.

Abstract B051: Genome-wide association studies of 26,187 women without ovarian cancer identifies 12 genetic loci of blood CA125

Abstract Background: CA125 is elevated in women with ovarian cancer and is the single best ovarian cancer screening biomarker candidate to date, although two randomized screening trials showed no clinically significant difference in ovarian cancer mortality. Consideration of genetic variants that influence blood CA125 levels in healthy women could improve its performance as an ovarian cancer screening biomarker. Furthermore, while studies have suggested CA125 is associated with ovarian carcinogenesis and progression, its biological role remains unclear. Thus, we aimed to identify genetic variants of CA125 in women without ovarian cancer. Methods: We conducted a genome-wide association analysis to identify common genetic variants associated with CA125 using data on 26,187 women without ovarian cancer, leveraging existing blood CA125 data and genetic data from Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO), European Prospective Investigation into Cancer and Nutrition (EPIC), Nurses’ Health Studies (NHS/NHSII), and New England Case Control Study (NEC). All genotype data were inputted using TOPMed. For blood CA125 measurement, PLCO, NHS/NHSII, and NEC used the CA125II assay and EPIC used the MSD assay. We used multivariable linear regression models adjusting for age, study, and population ancestry (top 4 principal components). Analyses were conducted separately by CA125 assay, genotyping platforms, and menopausal status at blood draw. Because epidemiological predictors of CA125 differ by menopausal status, we conducted analyses stratified by menopausal status. When we meta-analyzed these results, there were no significant heterogeneity by menopausal status in majority of the genome-wide significant SNPs. Therefore, we performed a fixed-effects meta-analysis to combine summary statistics across all the results. Results: We identified 12 independent loci associated with CA125 at a genome-wide significance level (p&amp;lt;5 × 10−8), of which one SNP (rs73005869) had been previously linked with CA125 and is located in the MUC16 gene. In our meta-analysis, 7 SNPs were associated with lower and 5 were associated with higher levels of CA125. We discovered SNPs on chromosome 16 in the TET2 gene that were significantly associated with increased CA125 levels. We also discovered SNPs in MSLN, a gene reported to be overexpressed in ovarian tumors that contributes to metastasis in the peritoneal microenvironment, were associated with lower CA125 levels. SNPs in the HIC1 gene on chromosome 17, a tumor suppressor gene whose aberrant methylation has been observed in ovarian tumors, was associated with lower CA125 levels. Conclusion: We identified 12 independent loci associated with blood CA125 levels in women without ovarian cancer, providing novel biological insights on the role of CA125. Accounting for these genetic factors that influence blood CA125 levels could improve the performance of CA125 as ovarian cancer screening biomarker in average risk women, substantially improving survival through earlier detection of this deadly disease. Citation Format: Naoko Sasamoto, Jihye Kim, Constance Turman, Shelley S. Tworoger, Rudolf Kaaks, Renée T. Fortner, Daniel W. Cramer, Kathryn L. Terry, Nicolas Wentzensen, Peter Kraft. Genome-wide association studies of 26,187 women without ovarian cancer identifies 12 genetic loci of blood CA125 [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr B051.

Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues

Colorectal cancer poses a significant threat to global health, necessitating the development of effective early detection techniques. However, the potential of the fungal microbiome as a putative biomarker for the detection of colorectal adenocarcinoma has not been extensively explored. We analyzed the viability of implementing the fungal mycobiome for this purpose. Biopsies were collected from cancer and polyp patients. The total genomic DNA was extracted from the biopsy samples by utilizing a comprehensive kit to ensure optimal microbial DNA recovery. To characterize the composition and diversity of the fungal mycobiome, high-throughput amplicon sequencing targeting the internal transcribed spacer 1 (ITS1) region was proposed. A comparative analysis revealed discrete fungal profiles among the diseased groups. Here, we also proposed pipelines based on a predictive model using statistical and machine learning algorithms to accurately differentiate colorectal adenocarcinoma and polyp patients from normal individuals. These findings suggest the utility of gut mycobiome as biomarkers for the detection of colorectal adenocarcinoma. Expanding our understanding of the role of the gut mycobiome in disease detection creates novel opportunities for early intervention and personalized therapeutic strategies for colorectal cancer.•Detailed method to identify the gut mycobiome in colorectal cancer patients using ITS-specific amplicon sequencing.•Application of machine learning algorithms to the identification of potential mycobiome biomarkers for non-invasive colorectal cancer screening.•Contribution to the advancement of innovative colorectal cancer diagnostic methods and targeted therapies by applying gut mycobiome knowledge.

Exploration of potential biomarkers for early bladder cancer based on urine proteomics.

Bladder cancer is a common malignant tumor of the urinary system. The progression of the condition is associated with a poor prognosis, so it is necessary to identify new biomarkers to improve the diagnostic rate of bladder cancer. In this study, 338 urine samples (144 bladder cancer, 123 healthy control, 32 cystitis, and 39 upper urinary tract cancer samples) were collected, among which 238 samples (discovery group) were analyzed by LC-MS. The urinary proteome characteristics of each group were compared with those of bladder cancer, and the differential proteins were defined by bioinformatics analysis. The pathways and functional enrichments were annotated. The selected proteins with the highest AUC score were used to construct a diagnostic panel. One hundred samples (validation group) were used to test the effect of the panel by ELISA. Compared with the healthy control, cystitis and upper urinary tract cancer samples, the number of differential proteins in the bladder cancer samples was 325, 158 and 473, respectively. The differentially expressed proteins were mainly related to lipid metabolism and iron metabolism and were involved in the proliferation, metabolism and necrosis of bladder cancer cells. The AUC of the panel of APOL1 and ITIH3 was 0.96 in the discovery group. ELISA detection showed an AUC of 0.92 in the validation group. This study showed that urinary proteins can reflect the pathophysiological changes in bladder cancer and that important molecules can be used as biomarkers for bladder cancer screening. These findings will benefit the application of the urine proteome in clinical research.