Biomarker discovery in ovarian cancer

Unlocking ovarian cancer heterogeneity: advancing immunotherapy through single-cell transcriptomics

Ovarian cancer, a highly fatal gynecological cancer, warrants the need for understanding its heterogeneity. The disease's prevalence and impact are underscored with statistics on mortality rates. Ovarian cancer is categorized into distinct morphological groups, each with its characteristics and prognosis. Despite standard treatments, survival rates remain low due to relapses and chemoresistance. Immune system involvement is evident in ovarian cancer's progression, although the tumor employs immune evasion mechanisms. Immunotherapy, particularly immune checkpoint blockade therapy, is promising, but ovarian cancer's heterogeneity limits its efficacy. Single-cell sequencing technology could be explored as a solution to dissect the heterogeneity within tumor-associated immune cell populations and tumor microenvironments. This cutting-edge technology has the potential to enhance diagnosis, prognosis, and personalized immunotherapy in ovarian cancer, reflecting its broader application in cancer research. The present review focuses on recent advancements and the challenges in applying single-cell transcriptomics to ovarian cancer.

Development of Aptamer-Based Molecular Tools for Rapid Intraoperative Diagnosis and In Vivo Imaging of Serous Ovarian Cancer

Diagnosis and treatment of ovarian cancer are based on intraoperative pathology and debulking surgery. The development of a novel molecular tool is significant for rapid intraoperative pathologic diagnosis, which instructs the decision-making on excision surgery and effective chemotherapy. In this work, we represent a DNA aptamer named mApoc46, which is generated from cell-SELEX by targeting patient-derived primary serous ovarian cancer (pSOC) cells. An average dissociation constant (K_d) was determined to be 0.15 ± 0.05 μM by flow cytometry. The mApoc46 aptamer displays a robust specificity to pSOC cells. Labeled with FAM, mApoc46 can selectively stain living pSOC cells in 30 min without staining commercial OC cell lines and cell lines associated with other cancers. Interestingly, FAM-mApoc46 displayed superb selectivity toward high-grade serous ovarian cancer (HG-SOC) tissues in frozen sections against low-grade SOC, ovarian borderline tumor, other nonepithelial ovarian tumors, and healthy ovarian tissue. These results lead to a potential application in the identification of OCs' histological subtypes during operation. In the patient-derived tumor xenograft NCG mice model, Cy5-labeled mApoc46 was found to accumulate at the tumor area and served as an in vivo imaging probe. The mApoc46 probe shows a robust and stable performance to visualize SOC tumors in the body. Therefore, aptamer mApoc46 holds great potential in rapid intraoperative detection, pathological diagnosis, fluorescence image-guided cancer surgery, and targeted drug delivery and therapy.

Expression of TBC1D16 Is Associated with Favorable Prognosis of Epithelial Ovarian Cancer

Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy with high recurrence and poor prognosis duo to the lack of effective biomarkers. TBC1 domain family member 16 (TBC1D16), a GTPase-activating protein, is involved in regulating intracellular trafficking in tumorigenesis and metastasis. However, the clinical significance of TBC1D16 in EOC remains unknown. In the present study, we investigated the expression and prognostic significance of TBC1D16 in EOC and its relationship with the expression of vascular endothelial growth factor (VEGF). The tissue specimens included 156 histologically confirmed EOC and 30 normal ovarian tissues. The expression of TBC1D16 and VEGF was detected by immunohistochemistry (IHC), and the immunoreactive score was calculated with signal intensity and percentage of positive cells. IHC results showed that TBC1D16 and VEGF were both mainly localized in cytoplasm of epithelial cells in normal ovarian tissues and were expressed in cancer cells. Based on the immunoreactive score, TBC1D16 expression in EOC was categorized as "high expression," compared with normal ovarian tissues (P < 0.05). The Chi-square test showed that high TBC1D16 expression was related to advanced pT stages (P = 0.029), but not correlated with other clinical features. Moreover, the TBC1D16 expression was significantly higher in EOC specimens with low VEGF expression (P < 0.001). Importantly, in both univariate and multivariate survival analyses, high expression of TBC1D16 was significantly correlated with good overall survival (OS). In conclusion, TBC1D16 is a predictive marker for favorable prognosis of EOC.

MicroRNA‑320 targets mitogen‑activated protein kinase 1 to inhibit cell proliferation and invasion in epithelial ovarian cancer

Ovarian cancer is the second most frequently occurring cancer and the most fatal gynecological malignancy of all gynecological cancers worldwide. MicroRNAs (miR) have been reported to be downregulated or upregulated in a variety of human malignancies, and involved in the formation and progression of the majority of human cancers, including epithelial ovarian cancer (EOC). miR‑320 has been identified as a tumor suppressor in multiple human cancers. However, the expression levels, biological role and underlying mechanisms of miR‑320 in EOC remain to be elucidated. In the present study, reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) was performed to detect miR‑320 expression in EOC tissues and cell lines. Following transfection with miR‑320 mimics, Cell Counting Kit 8 and cell invasion assays were utilized to investigate the effects of miR‑320 on EOC cell proliferation and invasion. Bioinformatic analysis, luciferase reporter assay, RT‑qPCR and western blotting were used to explore the underlying mechanism of how miR‑320 affects cell proliferation and invasion in EOC. Mitogen‑activated protein kinase (MAPK) 1 expression and its association with the miR‑320 expression level was examined in EOC tissues. The role of MAPK1 in EOC cells was additionally evaluated by using a loss‑of‑function assay. The results demonstrated that miR‑320 was markedly downregulated in EOC tissues and cell lines. A decreased miR‑320 expression was significantly correlated with the Federation of Gynecology and Obstetrics stage and lymph node metastasis of EOC patients. Additionally, reintroduction of miR‑320 expression suppressed cell proliferation and invasion in EOC. Furthermore, it was verified that MAPK1 is a direct target gene of miR‑320 in EOC. MAPK1 expression was markedly upregulated in EOC tissues and inversely correlated with miR‑320 expression. Furthermore, silencing of MAPK1 by RNA interference inhibited cell proliferation and invasion of EOC cells. Overall, the present study demonstrated that miR‑320 may act as a useful diagnostic and therapeutic target in the treatment of EOC.

Lipid profiling of the filarial nematodes Onchocerca volvulus, Onchocerca ochengi and Litomosoides sigmodontis reveals the accumulation of nematode-specific ether phospholipids in the host

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Onchocerciasis is an infectious disease caused by filarial nematodes.

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Three different filarial nematodes infecting cattle, humans and jirds were studied.

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Phospholipids in nematodes and hosts were determined by mass spectrometry.

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Filaria-specific ether phosphatidylethanolamine (PE) lipids accumulate in the host.

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These ether PE lipids could serve as potential biomarkers for onchocerciasis.

Onchocerciasis, a neglected tropical disease prevalent in western and central Africa, is a major health problem and has been targeted for elimination. The causative agent for this disease is the human parasite Onchocerca volvulus. Onchocerca ochengi and Litomosoides sigmodontis, infectious agents of cattle and rodents, respectively, serve as model organisms to study filarial nematode infections. Biomarkers to determine infection without the use of painful skin biopsies and microscopic identification of larval worms are needed and their discovery is facilitated by an improved knowledge of parasite-specific metabolites. In addition to proteins and nucleic acids, lipids may be suitable candidates for filarial biomarkers that are currently underexplored. To fill this gap, we present the phospholipid profile of the filarial nematodes O. ochengi, O. volvulus and L. sigmodontis. Direct infusion quadrupole time-of-flight (Q-TOF) mass spectrometry was employed to analyze the composition of phospholipids and their molecular species in the three nematode species. Analysis of the phospholipid profiles of plasma or serum of uninfected and infected hosts showed that nematode-specific phospholipids were below detection limits. However, several phospholipids, in particular ether lipids of phosphatidylethanolamine (PE), were abundant in O. ochengi worms and in bovine nodule fluid, suggesting that these phospholipids might be released from O. ochengi into the host, and could serve as potential biomarkers.

miR-494 inhibits ovarian cancer cell proliferation and promotes apoptosis by targeting FGFR2

MicroRNAs (miRs) have been reported to be key regulators in numerous types of cancer. The aim of the present study was to investigate the role of miR-494 in ovarian cancer. Expression of miR-494 was analyzed in ovarian cancer tissues and cell lines by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). miR-494 mimic or negative control was transiently transfected into A2780 and SKOV3 cell lines. A cell counting kit-8 assay was performed to assess the effects of miR-494 on cell proliferation, and flow cytometry was used to evaluate the apoptotic rate. The target gene of miR-494 was detected by luciferase assay. Expression of fibroblast growth factor receptor 2 (FGFR2) was identified using RT-qPCR and western blotting. In the present study, decreased expression of miR-494 was observed in ovarian cancer samples and cell lines. Overexpression of miR-494 inhibited ovarian cancer cell proliferation by inducing apoptosis. Additional investigation indicated that FGFR2 was a direct target of miR-494. Taken together, the results of the present study suggested that miR-494 suppressed ovarian cancer cell proliferation by inducing apoptosis via targeting FGFR2.

Omics-Based Biomarkers: Application of Metabolomics in Neuropsychiatric Disorders

One of the major concerns of modern society is to identify putative biomarkers that serve as a valuable early diagnostic tool to identify a subset of patients with increased risk to develop neuropsychiatric disorders. Biomarker identification in neuropsychiatric disorders is proposed to offer a number of important benefits to patient well-being, including prediction of forthcoming disease, diagnostic precision, and a level of disease description that would guide treatment choice. Nowadays, the metabolomics approach has unlocked new possibilities in diagnostics of devastating disorders like neuropsychiatric disorders. Metabolomics-based technologies have the potential to map early biochemical changes in disease and hence provide an opportunity to develop predictive biomarkers that can be used as indicators of pathological abnormalities prior to development of clinical symptoms of neuropsychiatric disorders. This review highlights different -omics strategies for biomarker discovery in neuropsychiatric disorders. We also highlight initial outcomes from metabolomics studies in psychiatric disorders such as schizophrenia, bipolar disorder, and addictive disorders. This review will also present issues and challenges regarding the implementation of the metabolomics approach as a routine diagnostic tool in the clinical laboratory in context with neuropsychiatric disorders.

Overexpression of FOXM1 predicts poor prognosis and promotes cancer cell proliferation, migration and invasion in epithelial ovarian cancer

BACKGROUND

The Forkhead box M1 (FOXM1), an important regulator of cell differentiation and proliferation, is overexpressed in a number of aggressive human carcinomas. The purpose of this study was to examine the expression levels of FOXM1 in epithelial ovarian cancer (EOC), to identify the relationship between FOXM1 expression and patient survival, and to investigate the role of FOXM1 in human ovarian cancer development.

METHODS

Immunohistochemical analysis for FOXM1 was performed in a total of 158 ovarian tissue specimens, all with linked clinical outcome data. Kaplan-Meier method and Cox proportional hazards analysis were used to relate FOXM1 expression to clinicopathological variables and to progression-free survival (PFS) and overall survival (OS). In vitro studies were performed to determine the function of FOXM1 in cell proliferation, migration and invasion in EOC cells using pcDNA3.1-FOXM1 and FOXM1 shRNA.

RESULTS

Elevated FOXM1 levels were associated with lymph node metastasis (P = 0.009), but not with age, FIGO stage, histological grade and histological type. Patients with high expression of FOXM1 had poorer PFS (P = 0.0001) and OS (P < 0.0001) than patients with low expression of FOXM1. Furthermore, multivariate analyses indicated that FOXM1 positivity was an independent prognostic factor for PFS (P = 0.046) and OS (P = 0.022), respectively. Overexpression of FOXM1 increased expression and activity of matrix metalloproteinase-2 (MMP-2), MMP-9 and vascular endothelial growth factor-A (VEGF-A), and cancer cell proliferation, migration and invasion of HO-8910 cells, whereas knockdown of FOXM1 reduced expression and activity of MMP-2, MMP-9 and VEGF-A, and cancer cell proliferation, migration and invasion of HO-8910 PM cells.

CONCLUSIONS

Our results suggest that FOXM1 expression is likely to play important roles in EOC development and progression. FOXM1 expression is a potential prognostic factor for PFS and OS, and it could be a novel treatment target in EOC patients.

Basigin-2 is the predominant basigin isoform that promotes tumor cell migration and invasion and correlates with poor prognosis in epithelial ovarian cancer

Background

Basigin, which has four isoforms, has been demonstrated to be involved in progression of various human cancers. The aim of this study was to examine the prognostic value of basigin-2 protein expression in epithelial ovarian cancer. Furthermore, the function of basigin-2 in ovarian cancer was further investigated in cell culture models.

Methods

Immunohistochemistry staining was performed to investigate basigin-2 expression in a total of 146 ovarian tissue specimens. Kaplan Meier analysis and Cox proportional hazards model were applied to assess the relationship between basigin-2 and progression-free survival (PFS) and overall survival (OS). Real-time PCR, RT-PCR and western blot were used to explore basigin-2, basigin-3 and basigin-4 expression in ovarian cancer cell lines and tissues. To evaluate possible contributions of basigin-2 to MMP secretion and cell migration and invasion, the overexpression vectors pcDNA3.1-basigin-2 and basigin-2 siRNA were transfected into HO-8910 and HO-8910 PM cells respectively.

Results

High basigin-2 expression was associated with lymph-vascular space involvement, lymph node metastasis and poor prognosis of epithelial ovarian cancer. Multivariate analyses indicated that basigin-2 positivity was an independent prognostic factor for PFS (P = 0.006) and OS (P = 0.019), respectively. Overexpression of basigin-2 increased the secretion of MMP-2/9 and cancer cell migration and invasion of HO-8910 cells, whereas knockdown of basigin-2 reduced active MMP-2/9 production, migration and invasion of HO-8910 PM cells.

Conclusions

The expression of basigin-2 might be an independent prognostic marker and basigin-2 inhibition would be a potential strategy for epithelial ovarian cancer patients, especially in inhibiting and preventing cancer cell invasion and metastasis.

Protein biomarkers of ovarian cancer: the forest and the trees

The goal of effective population-based screening for ovarian cancer remains elusive despite intense efforts aimed at improving upon biomarker and imaging modalities. While dozens of potential serum biomarkers for ovarian cancer have been identified in recent years, none have yet overcome the limitations that have hindered the clinical use of CA-125. Avenues of opportunity in biomarker development are emerging as investigators are beginning to appreciate the significance of remote, as well as local or regional, sources of biomarkers in the construction of diagnostic panels, as well as the importance of evaluating biomarkers in prediagnostic settings. As the list of candidate biomarkers of ovarian cancer continues to grow, refinements in the methods through which specific proteins are selected for further development as components of diagnostic panels are desperately sought. Such refinements must take into account both the bioinformatic and biological significance of each candidate. Approaches incorporating these considerations may potentially overcome the challenges to early detection posed by the histological heterogeneity of ovarian cancer. Here, we review the recent progress achieved in efforts to develop diagnostic biomarker panels for ovarian cancer and discuss the challenges that remain.

Pilot study: alteration of deleted in liver cancer1 and phosphorylated focal adhesion kinase Y397 cytoplasmic expression and the prognostic value in advanced epithelial ovarian carcinoma

Background

Deletion in liver cancer gene (DLC1) and phosphorylated focal adhesion kinase (p-FAK) have recently been reported as metastasis-related genes. However, the roles and prognostic values of their expression in epithelial ovarian carcinomas (EOCs) remain unclear.

Methods

The expression and prognostic value of DLC1 and p-FAK Y397 in EOC were evaluated by immunohistochemistry and multivariate analysis.

Results

Low expression of DLC1 and high expression of p-FAK Y397 were found in the 76 cases of EOC. The expression of DLC1 and p-FAK Y397 were negatively correlated. Multivariate analysis showed that the combination of them was an independent prognostic marker of EOC (P = 0.0319).

Conclusions

DLC1 and pFAK Y397 had an association with the clinicopathologic characteristics of EOC. Expression of neither of these genes was a prognostic factor alone, but the combination revealed a significant prognostic value in the 60 cases of advanced stage EOC.

Proteogenomic studies in epithelial ovarian cancer: established knowledge and future needs

There has been a concerted effort over the last decade to improve our understanding of the complex biology of ovarian cancer. A linear growth in published proteogenomic studies has addressed a variety of questions regarding its molecular pathogenesis. A number of genes have been identified by transcriptomic approaches, some of which are being investigated as putative tumor markers (HE4, OPN, Ep-CAM and Mesothelin), whilst others are potential targets for molecular therapeutic approaches (VEGF, IO4, EGFR, MUC1, CLDN4 and SLPI). Proteogenomics has the potential to further change our current characterization and treatment of ovarian cancer. Additional advances will depend on integrated study designs, interdisciplinary collaborations, use of robust high-throughput platforms, as well as uniform guidelines for bioinformatic analyses.

Screening for the early detection of ovarian cancer

Evaluation of: Menon U, Gentry-Maharaj A, Hallett R et al.: Sensitivity and specificity of multimodal and ultrasound screening for ovarian cancer, and stage distribution of detected cancers: results of the prevalence screen of the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS). Lancet Oncol. 10, 327–340 (2009). A randomized, controlled trial was undertaken to assess the use of serum CA125 and ovarian ultrasound as diagnostic markers in the early detection of ovarian cancer. The trial consisted of 202,638 postmenopausal women who were assessed annually between 2001 and 2005. A nonscreen group and two screening groups were investigated. The screening groups included serum CA125, which was based on a rate-of-change algorithm, plus transvaginal ultrasound (in at-risk women); and an ovarian ultrasound group only, prior to clinical review and surgery. The sensitivity, specificity and positive predictive values for all primary ovarian and tubal cancers for the combined test group was 89.4, 99.8 and 43.3%, respectively, and for the ultrasound group 84.9, 98.2 and 5.3%, respectively, with a significant difference in specificity between groups. The combined test provides the requisite specificity for a screening test for ovarian cancer in postmenopausal women.

Analytical strategies in lipidomics and applications in disease biomarker discovery

Lipidomics is a lipid-targeted metabolomics approach aiming at comprehensive analysis of lipids in biological systems. Recently, lipid profiling, or so-called lipidomics research, has captured increased attention due to the well-recognized roles of lipids in numerous human diseases to which lipid-associated disorders contribute, such as diabetes, obesity, atherosclerosis and Alzheimer's disease. Investigating lipid biochemistry using a lipidomics approach will not only provide insights into the specific roles of lipid molecular species in health and disease, but will also assist in identifying potential biomarkers for establishing preventive or therapeutic approaches for human health. Recent technological advancements in mass spectrometry and rapid improvements in chromatographic techniques have led to the rapid expansion of the lipidomics research field. In this review, emphasis is given to the recent advances in lipidomics technologies and their applications in disease biomarker discovery.