Recent advances in biomarkers for cancer diagnosis and treatment

An updated review on the development of a nanomaterial-based field-effect transistor-type biosensors to detect exosomes for cancer diagnosis

Cancer, a life-threatening genetic disease caused by abnormalities in normal cell growth regulatory functions, poses a significant challenge that current medical technologies cannot fully overcome. The current desired breakthrough is to diagnose cancer as early as possible and increase survival rates through treatments tailored to the prognosis and appropriate follow-up. From a perspective that reflects this contemporary paradigm of cancer diagnostics, exosomes are emerging as promising biomarkers. Exosomes, serving as mobile biological information repositories of cancer cells, have been known to create a microtumor environment in surrounding cells, and significant insight into the clinical significance of cancer diagnosis targeting them has been reported. Therefore, there are growing interests in constructing a system that enables continuous screening with a focus on patient-friendly and flexible diagnosis, aiming to improve cancer screening rates through exosome detection. This review focuses on a proposed exosome-embedded biological information-detecting platform employing a field-effect transistor (FET)-based biosensor that leverages portability, cost-effectiveness, and rapidity to minimize the stages of sacrifice attributable to cancer. The FET-applied biosensing technique, stemming from variations in an electric field, is considered an early detection system, offering high sensitivity and a prompt response frequency for the qualitative and quantitative analysis of biomolecules. Hence, an in-depth discussion was conducted on the understanding of various exosome-based cancer biomarkers and the clinical significance of recent studies on FET-based biosensors applying them.

Tumor Markers in Differential Diagnosis of Benign Ovarian Masses

Background

Although there are many benign tumors in the ovarian adnexal area, the four most common types are still luteal cyst, ovarian mature cystic teratoma (OMCT), ovarian endometriosis, and benign epithelial tumors of the ovary.

Purpose

This study aimed to examine the correlation between six tumor markers (CEA, AFP, CA125, CA19-9, SCC, HE4) in the differential diagnosis of female adnexal benign masses and assess their diagnostic value.

Patients and Methods

In this study, 135 patients with adnexal benign masses were treated in Zhengzhou first people's Hospital from January 2018 to January 2023. 135 patients were divided into four groups: luteal cyst (13.3%), OMCT (42.2%), ovarian endometriosis (23.7%) and benign epithelial tumors of the ovary (including mucinous cystadenoma and serous cystadenoma) in group D. The receiver-operating characteristic (ROC) curve was used to assess the diagnostic value of each marker and combined detection.

Results

The diameter of luteal cysts was significantly smaller than that of benign ovarian tumors (p < 0.001). ROC analysis showed that the combination of AFP, CA125, CA19-9, and SCC had a higher diagnostic rate for luteal cysts (AUC=0.871; sensitivity: 71.8%; specificity: 88.9). The SCC level in OMCT was significantly higher than in other benign ovarian tumors (p=0.007). ROC analysis indicated that the combination of AFP, HE4, and SCC had a higher diagnostic rate for OMCT (AUC=0.753; sensitivity: 65.4%; specificity: 75.4%). The CA125 level in ovarian endometriosis was significantly higher than in other accessory benign tumors (p < 0.001). ROC analysis demonstrated that the combination of AFP, CA125, and CA19-9 had a higher diagnostic rate for ovarian endometriosis (AUC=0.935; sensitivity: 76.7%; specificity: 96.9%). The tumor diameter of benign epithelial tumors of the ovary was significantly larger than that of other benign ovarian tumors (p < 0.001). ROC analysis revealed that the combination of CA125 and CA19-9 had a higher diagnostic rate for benign epithelial tumors of the ovary (AUC=0.792; sensitivity: 64.5%; specificity: 85.7%).

Conclusion

The findings of this study demonstrate that the combined use of tumor markers (CEA, AFP, CA125, CA19-9, SCC, and HE4) has value in diagnosing benign ovarian tumors, including luteal cysts, OMCT, ovarian endometriosis, and benign epithelial tumors of the ovary. However, it is important to acknowledge the limitations of this study, which include its single-center nature and the small sample size. Despite these limitations, the results highlight the potential utility of these markers in clinical practice.

Biosensors for Cancer Biomarkers Based on Mesoporous Silica Nanoparticles

Mesoporous silica nanoparticles (MSNs) exhibit highly beneficial characteristics for devising efficient biosensors for different analytes. Their unique properties, such as capabilities for stable covalent binding to recognition groups (e.g., antibodies or aptamers) and sensing surfaces, open a plethora of opportunities for biosensor construction. In addition, their structured porosity offers capabilities for entrapping signaling molecules (dyes or electroactive species), which could be released efficiently in response to a desired analyte for effective optical or electrochemical detection. This work offers an overview of recent research studies (in the last five years) that contain MSNs in their optical and electrochemical sensing platforms for the detection of cancer biomarkers, classified by cancer type. In addition, this study provides an overview of cancer biomarkers, as well as electrochemical and optical detection methods in general.

Human Triosephosphate Isomerase Is a Potential Target in Cancer Due to Commonly Occurring Post-Translational Modifications

Cancer involves a series of diseases where cellular growth is not controlled. Cancer is a leading cause of death worldwide, and the burden of cancer incidence and mortality is rapidly growing, mainly in developing countries. Many drugs are currently used, from chemotherapeutic agents to immunotherapy, among others, along with organ transplantation. Treatments can cause severe side effects, including remission and progression of the disease with serious consequences. Increased glycolytic activity is characteristic of cancer cells. Triosephosphate isomerase is essential for net ATP production in the glycolytic pathway. Notably, some post-translational events have been described that occur in human triosephosphate isomerase in which functional and structural alterations are provoked. This is considered a window of opportunity, given the differences that may exist between cancer cells and their counterpart in normal cells concerning the glycolytic enzymes. Here, we provide elements that bring out the potential of triosephosphate isomerase, under post-translational modifications, to be considered an efficacious target for treating cancer.

The Latest Developments in Using Proteomic Biomarkers from Urine and Serum for Non-Invasive Disease Diagnosis and Prognosis

Due to diagnostic improvements, medical diagnostics is demanding non-invasive or minimally invasive methods. Non-invasively obtained body fluids (eg., Urine, serum) can replace cerebral fluid, amniotic fluid, synovial fluid, bronchoalveolar lavage fluid, and others for diagnostic reasons. Many illnesses are induced by perturbations of cellular signaling pathways and associated pathway networks as a result of genetic abnormalities. These disturbances are represented by a shift in the protein composition of the fluids surrounding the tissues and organs that is, tissue interstitial fluid (TIF). These variant proteins may serve as diagnostic "signatures" for a variety of disorders. This review provides a concise summary of urine and serum biomarkers that may be used for the diagnosis and prognosis of a variety of disorders, including cancer, brain diseases, kidney diseases, and other system diseases. The studies reviewed in this article suggest that serum and urine biomarkers of various illnesses may be therapeutically useful for future diagnostics. Correct illness management is crucial for disease prognosis, hence non-invasive serum and urine biomarkers have been extensively studied for diagnosis, subclassification, monitoring disease activity, and predicting treatment results and consequences.

Carbon-based biosensors from graphene family to carbon dots: A viewpoint in cancer detection

According to the latest report by International Agency for Research on Cancer, 19.3 million new cancer cases and 10 million cancer deaths were globally reported in 2020. Early diagnosis can reduce these numbers significantly, and biosensors have appeared to be a solution to this problem as, unlike the traditional methods, they have low cost, rapid process, and do not need experts present on site for use. These devices have been incorporated to detect many cancer biomarkers and measure cancer drug delivery. To design these biosensors, a researcher must know about their different types, properties of nanomaterials, and cancer biomarkers. Among all types of biosensors, electrochemical and optical biosensors are the most sensitive and promising sensors for detecting complicated diseases like cancer. The carbon-based nanomaterial family has attracted lots of attention due to their low cost, easy preparation, biocompatibility, and significant electrochemical and optical properties. In this review, we have discussed the application of graphene and its derivatives, carbon nanotubes (CNTs), carbon dots (CDs), and fullerene (C60), for designing different electrochemical and optical cancer-detecting biosensors. Furthermore, the application of these carbon-based biosensors for detecting seven widely studied cancer biomarkers (HER2, CEA, CA125, VEGF, PSA, Alpha-fetoprotein, and miRNA21) is reviewed. Finally, various fabricated carbon-based biosensors for detecting cancer biomarkers and anticancer drugs are comprehensively summarized as well.

Biomarkers: Promising and valuable tools towards diagnosis, prognosis and treatment of Covid-19 and other diseases

The use of biomarkers as early warning systems in the evaluation of disease risk has increased markedly in the last decade. Biomarkers are indicators of typical biological processes, pathogenic processes, or pharmacological reactions to therapy. The application and identification of biomarkers in the medical and clinical fields have an enormous impact on society. In this review, we discuss the history, various definitions, classifications, characteristics, and discovery of biomarkers. Furthermore, the potential application of biomarkers in the diagnosis, prognosis, and treatment of various diseases over the last decade are reviewed. The present review aims to inspire readers to explore new avenues in biomarker research and development.

Pharmacogenetics of Anticancer Drugs: Clinical Response and Toxicity

Cancer is the most challenging disease for medical professionals to treat. The factors underlying the complicated situation include anticancer drug-associated toxicity, non-specific response, low therapeutic window, variable treatment outcomes, development of drug resistance, treatment complications, and cancer recurrence. The remarkable advancement in biomedical sciences and genetics, over the past few decades, however, is changing the dire situation. The discovery of gene polymorphism, gene expression, biomarkers, particular molecular targets and pathways, and drug-metabolizing enzymes have paved the way for the development and provision of targeted and individualized anticancer treatment. Pharmacogenetics is the study of genetic factors having the potential to affect clinical responses and pharmacokinetic and pharmacodynamic behaviors of drugs. This chapter emphasizes pharmacogenetics of anticancer drugs and its applications in improving treatment outcomes, selectivity, toxicity of the drugs, and discovering and developing personalized anticancer drugs and genetic methods for prediction of drug response and toxicity.

Sensing and imaging of exosomal CD26 secreted from cancer cells and 3D colorectal tumor model using a novel near-infrared fluorogenic probe

Cancer-derived exosomes or their specific components hold great promise for early diagnosis and precise staging of cancers. This work aimed to construct a novel enzyme-activatable fluorescent substrate for real-time detection and in situ imaging of a key exosomal surface protein CD26 in various biological systems, as well as to reveal the relevance of exosomal CD26 to the tumorigenesis. For these purposes, a group of Gly-Pro amides deriving from several near-infrared fluorophores were designed on the basis of the unique prolyl-cleaving dipeptidease activity of CD26, while molecular docking simulations were applied to assess the possibility of the designed amides as CD26 specific substrates. Following virtual screening and experimental validation, it was observed that GP-ACM displayed the best combination of high sensitivity and excellent specificity to CD26. The sensing and imaging ability of GP-ACM towards CD26 were examined in a range of biological systems, such as living cells, in situ tissues, and the exosomes secreted from cancer cells. Under physiological conditions, GP-ACM can be readily hydrolyzed by CD26 to release the fluorescent product ACM. The fluorescent product emits strong near-infrared fluorescence signals around 660 nm, which can be easily captured by the devices equipped with a fluorescence detector. GP-ACM prolyl-cleaving reaction shows excellent specificity and rapid response towards CD26, while its fluorescent product ACM displays good chemical stability and outstanding photostability. With the help of GP-ACM, CD26 in living cells, tissues and the tumor-secreted exosomes can be real-time monitored and in-situ imaged, while further investigations reveal that the exosomal CD26 activities are abnormally elevated with the progression of colon tumor. Collectively, the present study offers a practical optical assay for real-time monitoring CD26 activities in multiple complex biological systems including the exosomes secreted by tumor cells. The simplicity and effectiveness of this assay hold great potential for facilitating fundamental researches and clinical diagnosis of exosomal CD26 associated diseases.

Biosensors Designed for Clinical Applications

Emerging and validated biomarkers promise to revolutionize clinical practice, shifting the emphasis away from the management of chronic disease towards prevention, early diagnosis and early intervention. The challenge of detecting these low abundance protein and nucleic acid biomarkers within the clinical context demands the development of highly sensitive, even single molecule, assays that are also capable of selectively measuring a small number of defined analytes in complex samples such as whole blood, interstitial fluid, saliva or urine. Success relies on significant innovations in nanomaterials, bioreceptor engineering, transduction strategies and microfluidics. Primarily using examples from our work, this article discusses some recent advance in the selective and sensitive detection of disease biomarkers, highlights key innovations in sensor materials and identifies issues and challenges that need to be carefully considered especially for researchers entering the field.

ICG/5-Fu coencapsulated temperature stimulus response nanogel drug delivery platform for chemo-photothermal/photodynamic synergetic therapy

The multiple diagnosis and treatment mechanisms of chemotherapy combined with photothermal/photodynamic therapy have very large application prospects in the field of cancer treatment. Therefore, in order to achieve effective and safe antitumour treatment, it is necessary to design an intelligent responsive polymer nanoplatform as a drug delivery system. Herein, the thermosensitive poly-N-isopropylacrylamide (PNIPAM) nanogel particles were prepared by soap-free emulsion polymerization and loaded with a large amount of photosensitizer indocyanine green (ICG) and anticarcinogen 5-fluorouracil (5-Fu), which effectively to realize the cooperative chemotherapy and photothermal/photodynamic therapy for tumours. The 5-Fu@ICG-PNIPAM nanogels significantly improved the bioavailability of the drug and achieved controlled release. In addition, under near-infrared laser (NIR) irradiation at 808 nm, 5-Fu@ICG-PNIPAM nanogels generated lots of heat and reactive oxygen, which significantly enhanced cellular uptake and in vitro antitumour treatment effects. The results showed that 5-Fu@ICG-PNIPAM nanogels were effectively endocytosed by HeLa cells, which also enhanced the drug's entrance into the nucleus. Moreover, compared with alone chemotherapy or photothermal/photodynamic therapy, 5-Fu@ICG-PNIPAM nanogels significantly increased cytotoxicity under NIR irradiation, suggesting that chemotherapy and photothermal/photodynamic synergistic therapy had excellent antitumour properties. Therefore, this temperature-responsive nanogel platform probably has great application prospects in clinical antitumour treatment.

Urinary Biomarkers and Their Potential for the Non-Invasive Detection of Endometrial Cancer

Endometrial cancer is the most common malignancy of the female genital tract and its incidence is rising in parallel with the mounting prevalence of obesity. Early diagnosis has great potential to improve outcomes as treatment can be curative, especially for early stage disease. Current tests and procedures for diagnosis are limited by insufficient accuracy in some and unacceptable levels of invasiveness and discomfort in others. There has, therefore, been a growing interest in the search for sensitive and specific biomarkers for endometrial cancer detection based on non-invasive sampling methodologies. Urine, the prototype non-invasive sample, is attractive for biomarker discovery as it is easily accessible and can be collected repeatedly and in quantity. Identification of urinary biomarkers for endometrial cancer detection relies on the excretion of systemic biomarkers by the kidneys or urinary contamination by biomarkers shed from the uterus. In this review, we present the current standing of the search for endometrial cancer urinary biomarkers based on cytology, genomic, transcriptomic, proteomic, and metabolomic platforms. We summarize the biomarker candidates and highlight the challenges inherent in urinary biomarker discovery. We review the various technologies with promise for biomarker detection and assess these novel approaches for endometrial cancer biomarker research.

A bifunctional DNA probe for sensing pH and microRNA using a nanopore

We have developed a bifunctional probe based on triplex molecular beacons for the measurement of environmental pH and quantification of microRNA-10b using a nanopore. The probe responds sharply to solution pH changes in the range of 6.0-7.5. The limit of detection for microRNA-10b is as low as 5.0 pM.

An accurate and sensitive analytical method for the simultaneous determination of glycine, methionine and homocysteine in biological matrices by matrix matching strategy and LC-quadrupole-time-of-flight-MS/MS

Nowadays, it is well known that early diagnosis directly affects the success of treatment. Biomarkers play a crucial role in early diagnosis of diseases or explanation of pathological condition. The investigation of new biomarkers depends on the reliable quantification of analytes in biological matrices. Regarding to the critical roles of amino acids in metabolism, functions and nutrition of human body, the careful monitoring of their levels in biological samples is required to evaluate their potential in biomarker studies for clinical research. In this study, a reliable and accurate analytical strategy was developed for the simultaneous determination of glycine, methionine and homocysteine using LC-quadrupole-time of flight-tandem MS system. The method detection limit was found to be 0.73 μg/mL, 0.017 μg/mL and 0.019 μg/mL for glycine, methionine and homocysteine, respectively. The calibration curves were obtained with great linearity (R² ≥ 0.9993) and low relative standard deviation values showed the repeatability of proposed method. The method applicability was determined using human plasma and urine samples, and high percent recoveries demonstrated the accuracy of method developed. Each measurement was taken less than 4.0 min indicating a promising strategy for the fast and reliable quantification of target amino acids in clinical laboratories.

Prion Protein Targeted by a Prostate Cancer Cell Binding Aptamer, a Potential Tumor Marker?

Cell-SELEX is an effective strategy to discover aptamers that can distinguish the molecular signatures of target cells from control cells. The molecular targets of such aptamers have the potential to be biomarkers. Here, we report target identification of aptamer wy-5a generated by cell-SELEX against a prostate cancer cell line, PC-3. This aptamer specifically binds PC-3 cells and a doxorubicin-resistant breast cell line, MCF-7R, as well as tissue sections of prostate cancer with high risk of metastasis. Prion protein was identified to be the molecular target of wy-5a by stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative proteomic method. The octapeptide repeat region of prion protein was demonstrated to be the binding site of aptamer wy-5a. The expression levels of prion protein in cancer tissues were further tested by immunohistochemical staining of tissue sections from 48 prostate cancer patients and 98 breast cancer patients. The results suggest that prion protein has the potential to be one of the referenced markers of prostate and breast cancers.

Autoluminescence-Free Prostate-Specific Antigen Detection by Persistent Luminous Nanorods and Au@Ag@SiO2 Nanoparticles

The sensitive detection of biomarker with high selectivity and accuracy is of remarkable significance for the early screening and clinical diagnosis of malignant cancer. Persistent phosphors play a role in illumination-free biosensing owing to their unparalleled optical properties, which produces long-lasting luminescence without the illumination to eliminate the interference of autofluorescence and scattering light from biological matrix. In this study, ZnGeO:Mo persistent luminescence nanorods (PLNRs) were prepared and showed tunable luminescence intensity and decay patterns. An excitation-free luminescent aptasensor was proposed for the detection of prostate specific antigen (PSA) by using ZnGeO:Mo PLNRs as probes and Au@Ag@SiO₂ nanoparticles as quenchers. Under optimal conditions, the limit of detection for PSA was 9.2 pg mL^-1. This work creates a possibility for the preparation of multiplex colored persistent luminescence nanomaterials with desired decay patterns for multiple bioassay and time-resolved fluoroimmunoassay.

Adult Gastric Bronchogenic Cyst With Elevated Tumor Marker in Containing Fluid: A Case Report and Literature Review

Introduction:

Duplication cysts are rare malformations that exist in the alimentary tract, and the mucosa of gastric bronchogenic cyst lined by pseudostratified columnar ciliated epithelium (PCCE) is even more rare. We reviewed related literatures to depict this unique abnormality.

Case presentation:

Herein we report an abdominal mass that was found incidentally in a 52-year-old female. The biochemical test of contents revealed a high concentration of tumor markers unusually. A laparoscopic surgery was undertaken to remove the lesion. The cyst was found to originate from the stomach but did not show any anatomic communication with the stomach lumen. Pathologic examination confirmed the mucosa was lined by PCCE.

Conclusion:

The symptoms and radiologic presentations of GDC are nonspecific. It should be distinguished with other abdominal cystic masses. Surgery is advised in respective of malignancy.

Clinical biomarkers for cancer recognition and prevention: A novel approach with optical measurements

Cancer is the most important cause of death worldwide, and early cancer detection is the most fundamental factor for efficacy of treatment, prognosis, and increasing survival rate. Over the years great effort has been devoted to discovering and testing new biomarkers that can improve its diagnosis, especially at an early stage. Here we report the potential usefulness of new, easily applicable, non-invasive and relatively low-cost clinical biomarkers, based on abnormalities of oral mucosa spectral reflectance and fractal geometry of the vascular networks in several different tissues, for identification of hereditary non-polyposis colorectal cancer carriers as well for detection of other tumors, even at an early stage. In the near future the methodology/technology of these procedures should be improved, thus making possible their applicability worldwide as screening tools for early recognition and prevention of cancer.

A dual-label time-resolved fluorescence immunoassay for the simultaneous determination of carcinoembryonic antigen and squamous cell carcinoma antigen

Among women worldwide, cervical cancer is the second-most common cancer, and cervical smears and DNA detection have low sensitivity or are too expensive. The concentrations of carcinoembryonic antigen (CEA) and squamous cell carcinoma (SCC) in the serum were detected using a sandwich immunoassay. The CEA and SCC in the serum were captured by anti-CEA and anti-SCC antibodies. After combining other anti-CEA- and anti-SCC-labeled antibodies with europium (III) (Eu³⁺ ) and samarium (III) (Sm³⁺ ) chelates, CEA and SCC were detected with time-resolved fluorometry (TRF). The linear correlation coefficients (R² ) of the CEA and SCC standard curves were 0.9997 and 0.9997, respectively. The minimum detection level for CEA was 1.15 ng/mL (the linear dynamic range was 3.24-543.67 ng/mL), and the average recovery was 100.83%. The sensitivity for SCC detection was 0.54 ng/mL (the linear dynamic range was 2.47-96.58 ng/mL), and the average recovery was 101.02%. High R² between the results of commercial assays and this method were obtained (R²  = 0.9983 for CEA, R²   = 0.9878 for SCC). These findings indicated that the dual-label TRFIA invented in this study has high sensitivity, accuracy, and specificity in clinical analysis, which indicates that this method could be used for the early diagnosis and follow-up surveillance of cervical cancer.

Squamous Cellular Carcinoma Antigen Serum Determination as a Biomarker of Barrett Esophagus and Esophageal Cancer: A Phase III Study

GOAL

To evaluate the potential role of the determination of the immunocomplexed form of squamous cell carcinoma antigen [SCCA-immunoglobulin (Ig)M] for the screening of Barrett esophagus (BE) and esophageal adenocarcinoma (EAC).

BACKGROUND

The cost-effectiveness of surveillance in BE is still debated and the use of biomarkers in screening and surveillance still not recommended. No information is available regarding SCCA-IgM determination in BE.

STUDY

SCCA-IgM levels were determined (enzyme-linked immunosorbent assay) in 231 patients prospectively recruited, 71 with BE, 53 with EAC, and 107 controls, including 42 blood donors and 65 patients with gastroesophageal reflux. SCCA-IgM cutoffs between BE/EAC and controls and for BE "at risk" versus short nondysplastic BE were calculated by receiver operating characteristic curves. Immunostaining for SCCA-IgM was obtained in a subgroup of patients.

RESULTS

Median SCCA-IgM values were significantly higher in BE and EAC than in controls (P=0.0001). Patients with SCCA-IgM levels above the cutoff had a 33 times higher relative risk of harboring BE or EAC (P=0.0001). Patients "at risk," with long or dysplastic BE had SCCA-IgM levels significantly higher than those with short nondysplastic BE (P=0.035) and patients with SCCA-IgM above the cutoff had a 8 times higher relative risk of having BE "at risk." SCCA was expressed in Barrett mucosa but not in cardiac metaplasia.

CONCLUSIONS

Serum SCCA-IgM determination allows the identification of patients at risk for BE/EAC and the stratification of BE patients in subgroups with different cancer risk. Because of the still limited number of controls, large, prospective studies are required to confirm this evidence.

Advances in point-of-care diagnostic devices in cancers

The early diagnosis and monitoring of the progress of cancers are limited due to the lack of adequate screening tools.

Cerebrospinal fluid biomarkers of malignancies located in the central nervous system

CNS malignancies include primary tumors that originate within the CNS as well as secondary tumors that develop as a result of metastatic cancer. The delicate nature of the nervous systems makes tumors located in the CNS notoriously difficult to reach, which poses several problems during diagnosis and treatment. CSF can be acquired relatively easy through lumbar puncture and offers an important compartment for analysis of cells and molecules that carry information about the malignant process. Such techniques have opened up a new field of research focused on the identification of specific biomarkers for several types of CNS malignancies, which may help in diagnosis and monitoring of tumor progression or treatment response. Biomarkers are sought in DNA, (micro)RNA, proteins, exosomes and circulating tumor cells in the CSF. Techniques are rapidly progressing to assess these markers with increasing sensitivity and specificity, and correlations with clinical parameters are being investigated. It is expected that these efforts will, in the near future, yield clinically relevant markers that aid in diagnosis, monitoring and (tailored) treatment of patients bearing CNS tumors. This chapter provides a summary of the current state of affairs of the field of biomarkers of different types of CNS tumors.

Measures of biomarker dependence using a copula-based multivariate epsilon-skew-normal family of distributions

In this note we develop a new multivariate copula model based on epsilon-skew-normal marginal densities for the purpose of examining biomarker dependency structures. We illustrate the flexibility and utility of this model via a variety of graphical tools and a data analysis example pertaining to salivary biomarker. The multivariate normal model is a sub-model of the multivariate epsilon-skew-normal distribution.

Sp1 transcription factor: A long-standing target in cancer chemotherapy

Sp1 (specificity protein 1) is a well-known member of a family of transcription factors that also includes Sp2, Sp3 and Sp4, which are implicated in an ample variety of essential biological processes and have been proven important in cell growth, differentiation, apoptosis and carcinogenesis. Sp1 activates the transcription of many cellular genes that contain putative CG-rich Sp-binding sites in their promoters. Sp1 and Sp3 proteins bind to similar, if not the same, DNA tracts and compete for binding, thus they can enhance or repress gene expression. Evidences exist that the Sp-family of proteins regulates the expression of genes that play pivotal roles in cell proliferation and metastasis of various tumors. In patients with a variety of cancers, high levels of Sp1 protein are considered a negative prognostic factor. A plethora of compounds can interfere with the trans-activating activities of Sp1 and other Sp proteins on gene expression. Several pathways are involved in the down-regulation of Sp proteins by compounds with different mechanisms of action, which include not only the direct interference with the binding of Sp proteins to their putative DNA binding sites, but also promoting the degradation of Sp protein factors. Down-regulation of Sp transcription factors and Sp1-regulated genes is drug-dependent and it is determined by the cell context. The acknowledgment that several of those compounds are safe enough might accelerate their introduction into clinical usage in patients with tumors that over-express Sp1.

Cervical cancer: Biomarkers for diagnosis and treatment

Cervical cancer is a major gynecological cancer which involves uncontrolled cell division and tissue invasiveness of the female uterine cervix. With the availability of new technologies researchers have increased their efforts to develop novel biomarkers for early diagnosis, and evaluation and monitoring of therapeutic treatments. This approach will help in the development of early diagnosis and in increasing treatment efficacy with decreased recurrence. The present review explains the currently available biomarkers for cervical cancer diagnosis and prognosis. Apart from the currently available biomarkers the review also explains strategies for the development of biomarkers based on cellular and molecular approaches such as DNA, protein and other metabolic markers with suitable clinical examples. The investigations of specific proteins, enzymes and metabolites will establish more useful biomarkers for accurate detection and management of gynecological cancers especially cervical cancer.

Ordinal Logic Regression: A classifier for discovering combinations of binary markers for ordinal outcomes

In medicine, it is often useful to stratify patients according to disease risk, severity, or response to therapy. Since many diseases arise from complex gene-gene and gene-environment interactions, patient strata may be defined by combinations of genetic and environmental factors. Traditional statistical methods require specifying interactions a priori making it difficult to identify high order interactions. Alternatively, machine learning methods can model complex interactions, however these models are often difficult to interpret in a clinical setting. Logic regression (LR) enables modeling a binary outcome using logical combinations of binary predictors yielding easily interpretable models. However LR, as currently available, cannot model ordinal responses. This paper extends LR to model an ordinal response and the resulting method is called Ordinal Logic Regression (OLR). Several simulations comparing OLR and Classification and Regression Trees (CART) demonstrate that OLR is superior to CART for identifying variable interactions associated with an ordinal response. OLR is applied to data from a study to determine associations between genetic and health factors with severity of adult periodontitis.

Projecting Benefits and Harms of Novel Cancer Screening Biomarkers: A Study of PCA3 and Prostate Cancer

BACKGROUND

New biomarkers for early detection of cancer must pass through several phases of development. Early phases provide information on diagnostic properties but not on population benefits and harms. Prostate cancer antigen 3 (PCA3) is a promising prostate cancer biomarker still in early development. We use simulation modeling to project the impact of adding PCA3 to prostate-specific antigen (PSA) screening on prostate cancer detection and mortality in the United States.

METHODS

We used data from a recent study of PCA3 in men referred for prostate biopsy to extend an existing simulation model of PSA growth, disease progression, and survival. We specified several PSA-PCA3 strategies designed to improve specificity and reduce overdiagnosis. Using these strategies to screen a cohort of men biennially between ages 50 and 74, we projected true- and false-positive tests, overdiagnoses, and lives saved relative to a PSA-based strategy with a cutoff of 4.0 ng/mL for biopsy referral.

RESULTS

We identified several PSA-PCA3 strategies that substantially reduced false-positive tests and overdiagnoses while preserving the majority of lives saved. PCA3>35 for biopsy referral in men with PSA between 4.0 and 10.0 ng/mL retained 85% of lives saved while approximately halving false positives and reducing overdiagnoses by 25%.

CONCLUSIONS

Adding PCA3 to PSA screening can significantly reduce adverse screening outcomes. Strategies can be identified that preserve most of the lives saved relative to PSA-based screening.

IMPACT

Simulation modeling provides advance projections of population outcomes of new screening biomarkers and may help guide early detection research.

Biomarkers from biosimulations: Transcriptome-To-Reactome™ Technology for individualized medicine

We validated a model of the TGF-β signaling pathway using reactions from Reactome. Using a patentpending technique, gene expression profiles from individual patients are used to determine model parameters. Gene expression profiles from 45 women, normal, or benign tumor and malignant breast cancer were used as training and validating sets for assessing clinical sensitivity and specificity. Biomarkers were identified from the biosimulation results using sensitivity analyses and derivative properties from the model. A membrane signaling marker had sensitivity of 80% and specificity of 60%; while a nuclear transcription factor marker had sensitivity of 80% and specificity of 90% to predict malignancy. Use of Fagan's nomogram increased probability from 7.5% for positive mammogram to 39% with positive results of the biosimulation for the nuclear marker. Our technology will allow researchers to identify and develop biomarkers and assist clinicians in diagnostic and treatment decision making.

Circulating microRNA biomarkers for glioma and predicting response to therapy

The need for glioma biomarkers with improved sensitivity and specificity has sparked research into short non-coding RNA known as microRNA (miRNA). Altered miRNA biogenesis and expression in glioma plays a vital role in important signaling pathways associated with a range of tumor characteristics including gliomagenesis, invasion, and malignancy. This review will discuss current research into the role of miRNA in glioma and altered miRNA expression in biofluids as candidate biomarkers with a particular focus on glioblastoma, the most malignant form of glioma. The isolation and characterization of miRNA using cellular and molecular biology techniques from the circulation of glioma patients could potentially be used for improved diagnosis, prognosis, and treatment decisions. We aim to highlight the links between research into miRNA function, their use as biomarkers, and how these biomarkers can be used to predict response to therapy. Furthermore, increased understanding of miRNA in glioma biology through biomarker research has led to the development of miRNA therapeutics which could restore normal miRNA expression and function and improve the prognosis of glioma patients. A panel of important miRNA biomarkers for glioma in various biofluids discovered to date has been summarized here. There is still a need, however, to standardize techniques for biomarker characterization to bring us closer to clinically relevant miRNA-based diagnostic and therapeutic signatures. A clinically validated biomarker panel has potential to improve time to diagnosis, predicting response to treatment and ultimately the prognosis of glioma patients.

Multiplexed electrochemical protein detection and translation to personalized cancer diagnostics

Measuring diagnostic panels of multiple proteins promises a new, personalized approach to early detection and therapy of diseases like cancer. Levels of biomarker proteins in patient serum can provide a continually updated record of disease status. Research in electrochemical detection of proteins has produced exquisitely sensitive approaches. Most utilize ELISA-like sandwich immunoassays incorporating various aspects of nanotechnology. Several of these ultrasensitive methodologies have been extended to microfluidic multiplexed protein detection, but engineered solutions are needed to measure more proteins in a single device from a small patient sample such as a drop of blood or tissue lysate. To achieve clinical or point-of-care (POC) use, simplicity and low cost are essential. In multiplexed microfluidic immunoassays, required reagent additions and washing steps pose a significant problem calling for creative engineering. A grand challenge is to develop a general cancer screening device to accurately measure 50-100 proteins in a simple, cost-effective fashion. This will require creative solutions to simplified reagent addition and multiplexing.

Clinical implications of microRNAs in cancer

MicroRNAs (miRNAs) are endogenously produced non-coding RNAs that serve as micromanagers by negatively regulating gene expression. MiRNAs are implicated in several biological pathways including development of neoplasia. Because altered miRNA expression is implicated in the pathobiology of various cancers, these molecules serve as potential therapeutic targets. Using miRNA mimics to restore levels of aberrantly down-regulated miRNAs or miRNA inhibitors to inactivate over-expressed miRNAs shows promise as the next generation of therapeutic strategies. Manipulation of miRNAs offers an alternative therapeutic approach for chemo- and radiation-resistant tumors. Similarly, miRNA expression patterns can be used for diagnosis and to predict prognosis and efficacy of therapy. We present here an overview of how miRNAs affect cancers, how they may be used as biomarkers, and the clinical implications of miRNAs in cancer.

Advances in gas chromatographic methods for the identification of biomarkers in cancer

Screening complex biological specimens such as exhaled air, tissue, blood and urine to identify biomarkers in different forms of cancer has become increasingly popular over the last decade, mainly due to new instruments and improved bioinformatics. However, despite some progress, the identification of biomarkers has shown to be a difficult task with few new biomarkers (excluding recent genetic markers) being considered for introduction to clinical analysis. This review describes recent advances in gas chromatographic methods for the identification of biomarkers in the detection, diagnosis and treatment of cancer. It presents a general overview of cancer metabolism, the current biomarkers used for cancer diagnosis and treatment, a background to metabolic changes in tumors, an overview of current GC methods, and collectively presents the scope and outlook of GC methods in oncology.

Predictive value of Sp1/Sp3/FLIP signature for prostate cancer recurrence

Prediction of prostate cancer prognosis is challenging and predictive biomarkers of recurrence remain elusive. Although prostate specific antigen (PSA) has high sensitivity (90%) at a PSA level of 4.0 ng/mL, its low specificity leads to many false positive results and considerable overtreatment of patients and its performance at lower ranges is poor. Given the histopathological and molecular heterogeneity of prostate cancer, we propose that a panel of markers will be a better tool than a single marker. We tested a panel of markers composed of the anti-apoptotic protein FLIP and its transcriptional regulators Sp1 and Sp3 using prostate tissues from 64 patients with recurrent and non-recurrent cancer who underwent radical prostatectomy as primary treatment for prostate cancer and were followed with PSA measurements for at least 5 years. Immunohistochemical staining for Sp1, Sp3, and FLIP was performed on these tissues and scored based on the proportion and intensity of staining. The predictive value of the FLIP/Sp1/Sp3 signature for clinical outcome (recurrence vs. non-recurrence) was explored with logistic regression, and combinations of FLIP/Sp1/Sp3 and Gleason score were analyzed with a stepwise (backward and forward) logistic model. The discrimination of the markers was identified by sensitivity-specificity analysis and the diagnostic value of FLIP/Sp1/Sp3 was determined using area under the curve (AUC) for receiver operator characteristic curves. The AUCs for FLIP, Sp1, Sp3, and Gleason score for predicting PSA failure and non-failure were 0.71, 0.66, 0.68, and 0.76, respectively. However, this increased to 0.93 when combined. Thus, the “biomarker signature” of FLIP/Sp1/Sp3 combined with Gleason score predicted disease recurrence and stratified patients who are likely to benefit from more aggressive treatment.

DNA methylation biomarkers offer improved diagnostic efficiency in lung cancer

The exceptional high mortality of lung cancer can be instigated to a high degree by late diagnosis. Despite the plethora of studies on potential molecular biomarkers for lung cancer diagnosis, very few have reached clinical implementation. In this study, we developed a panel of DNA methylation biomarkers and validated their diagnostic efficiency in bronchial washings from a large retrospective cohort. Candidate targets from previous high-throughput approaches were examined by pyrosequencing in an independent set of 48 lung tumor/normal paired. Ten promoters were selected and quantitative methylation-specific PCR (qMSP) assays were developed and used to screen 655 bronchial washings from the Liverpool Lung Project (LLP) subjects divided into training (194 cases and 214 controls) and validation (139 cases and 109 controls) sets. Three statistical models were used to select the optimal panel of markers and to evaluate the performance of the discriminatory algorithms. The final logit regression model incorporated hypermethylation at p16, TERT, WT1, and RASSF1. The performance of this 4-gene methylation signature in the validation set showed 82% sensitivity and 91% specificity. In comparison, cytology alone in this set provided 43% sensitivity at 100% specificity. The diagnostic efficiency of the panel did not show any biases with age, gender, smoking, and the presence of a nonlung neoplasm. However, sensitivity was predictably higher in central (squamous and small cell) than peripheral (adenocarcinomas) tumors, as well as in stage 2 or greater tumors. These findings clearly show the impact of DNA methylation-based assays in the diagnosis of cytologically occult lung neoplasms. A prospective trial is currently imminent in the LLP study to provide data on the enhancement of diagnostic accuracy in a clinical setting, including by additional markers.

Mining the proteome: the application of tandem mass spectrometry to endocrine cancer research

Tandem mass spectrometry (MS/MS) permits the detection of femtomolar quantities of protein from a wide variety of tissue sources. As endocrine cancers are frequently aetiologically complex, they are particularly amenable to mass spectrometry. The most widely studied aspect is the search for novel reliable biomarkers that would allow cancers to be diagnosed earlier and distinguished from benign tumours. MS/MS allows for the rapid analysis of blood and urine in addition to tumour tissue, and in this regard it has been applied on research involving thyroid, pancreatic, adrenal and ovarian cancers with varying degrees of success, as well as additional organ sites including breast and lung. The description of an individual cancer proteome potentially allows for personalized management of each patient, avoiding unnecessary therapies and targeting treatments to those which will have the most effect. The application of MS/MS to interaction proteomics is a field that has generated recent novel targets for chemotherapy. However, the technology involved in MS/MS has a number of drawbacks that at present prevent its widespread use in translational cancer research, including a poor reproducibility of results, in part due to the large amount of data generated and the inability to accurately differentiate true from false-positive results. Further, the current cost of running MS/MS restricts the number of times the experiments can be repeated, contributing to the lack of significance and concordance between studies. Despite these problems, however, MS/MS is emerging as a front line tool in endocrine cancer research and it is likely that this will continue over the next decade.

Use of electroporation and reverse iontophoresis for extraction of transdermal multibiomarkers

Background

Monitoring of biomarkers, like urea, prostate-specific antigen (PSA), and osteopontin, is very important because they are related to kidney disease, prostate cancer, and ovarian cancer, respectively. It is well known that reverse iontophoresis can enhance transdermal extraction of small molecules, and even large molecules if reverse iontophoresis is used together with electroporation. Electroporation is the use of a high-voltage electrical pulse to create nanochannels within the stratum corneum, temporarily and reversibly. Reverse iontophoresis is the use of a small current to facilitate both charged and uncharged molecule transportation across the skin. The objectives of this in vitro study were to determine whether PSA and osteopontin are extractable transdermally and noninvasively and whether urea, PSA, and osteopontin can be extracted simultaneously by electroporation and reverse iontophoresis.

Methods

All in vitro experiments were conducted using a diffusion cell assembled with the stratum corneum of porcine skin. Three different symmetrical biphasic direct currents (SBdc), five various electroporations, and a combination of the two techniques were applied to the diffusion cell via Ag/AgCl electrodes. The three different SBdc had the same current density of 0.3 mA/cm², but different phase durations of 0 (ie, no current, control group), 30, and 180 seconds. The five different electroporations had the same pulse width of 1 msec and number of pulses per second of 10, but different electric field strengths of 0 (ie, no voltage, control group), 74, 148, 296, and 592 V/cm. Before and after each extraction experiment, skin impedance was measured at 20 Hz.

Results

It was found that urea could be extracted transdermally using reverse iontophoresis alone, and further enhancement of extraction could be achieved by combined use of electroporation and reverse iontophoresis. Conversely, PSA and osteopontin were found to be extracted transdermally only by use of reverse iontophoresis and electroporation with a high electrical field strength (>296 V/cm). After application of reverse iontophoresis, electroporation, or a combination of the two techniques, a reduction in skin impedance was observed.

Conclusion

Simultaneous transdermal extraction of urea, PSA, and osteopontin is possible only for the condition of applying reverse iontophoresis in conjunction with high electroporation.

Histologic, molecular, and cytogenetic features of ovarian cancers: implications for diagnosis and treatment

Ovarian epithelial carcinoma (OEC), the most common ovarian malignancy, is a heterogeneous disease with several histologic subtypes that show characteristic cytogenetic features, molecular signatures, oncologic signaling pathways, and clinical-biologic behavior. Recent advances in histopathology and cytogenetics have provided insights into pathophysiologic features and natural history of OECs. Several studies have shown that high- or low-grade serous, endometrioid, and clear cell carcinomas are characterized by mutations involving the TP53, K-ras/BRAF, CTNNB1, and PIK3CA genes, respectively. High-grade serous carcinomas, the most common subtype, often manifest with early transcoelomic spread of disease beyond the ovaries, whereas low-grade serous and mucinous carcinomas commonly manifest with early-stage disease, with a resultant excellent prognosis. On the basis of pathogenetic mechanisms, recent findings suggest a dualistic model of ovarian carcinogenesis consisting of types I and II. Type I (low-grade serous, mucinous, and endometrioid) cancers commonly arise from well-described, genetically stable precursor lesions (usually borderline tumors); manifest as large adnexal masses with early-stage disease; and have a relatively indolent clinical course, with an overall good prognosis. In contrast, type II carcinomas (high-grade serous, endometrioid, mixed, and undifferentiated variants) originate de novo from the adnexal epithelia, often demonstrate chromosomal instability, and have aggressive biologic behavior. Better knowledge of hereditary ovarian cancer syndromes and associated cytogenetic abnormalities has led to increased interest in novel biomarkers and molecular therapeutics. Genetic changes, pathologic features, imaging findings, and natural histories of a variety of histologic subtypes of OEC are discussed in this article.

Magnetic particles in ultrasensitive biomarker protein measurements for cancer detection and monitoring

IMPORTANCE OF THE FIELD: Devices for the reliable detection of panels of biomarker proteins facilitated by magnetic bead-based technologies have the potential to greatly improve future cancer diagnostics. The reason for this review is to highlight promising research on emerging procedures for protein capture, transport and detection featuring magnetic particles. AREAS COVERED IN THIS REVIEW: The review covers applications of magnetic particles in protein immunoassays in emerging research and commercial methods, and stresses multiplexed protein assays for reliable future cancer diagnostics. Research literature over the past dozen years has been surveyed and specific examples are presented in detail. EXPERT OPINION: Magnetic particles are important components of emerging protein detection systems. They need to be integrated into simple inexpensive systems for accurate, sensitive detection of fully validated panels of biomarker proteins to be widely useful in clinical cancer diagnostics.

Biomarkers in Barrett’s esophagus and esophageal adenocarcinoma: Predictors of progression and prognosis

Barrett’s esophagus is a well-known premalignant lesion of the lower esophagus that is characterized by intestinal metaplasia of the squamous epithelium. It is clinically important due to the increased risk (0.5% per annum) of progression to esophageal adenocarcinoma (EA), which has a poor outcome unless diagnosed early. The current clinical management of Barrett’s esophagus is hampered by the lack of accurate predictors of progression. In addition, when patients develop EA, the current staging modalities are limited in stratifying patients into different prognostic groups in order to guide the optimal therapy for an individual patient. Biomarkers have the potential to improve radically the clinical management of patients with Barrett’s esophagus and EA but have not yet entered mainstream clinical practice. This is in contrast to other cancers like breast and prostate for which biomarkers are utilized routinely to inform clinical decisions. This review aims to highlight the most promising predictive and prognostic biomarkers in Barrett’s esophagus and EA and to discuss what is required to move the field forward towards clinical application.

Carbon nanotubes in cancer theragnosis

Carbon nanotubes as a unique and novel class of nanomaterials have shown considerable promise in cancer therapy and diagnosis amidst the myriad of nanocarriers. The presence of a large surface area enables the engineering of the surface of nanotubes, thus making them biocompatible, and large benefits can be harnessed from them. Together with their ability to encapsulate small molecules, stacking interactions and conjugation, nanotubes have improved the profile of anticancer agents. The propensity to absorb the body transparent NIR radiation also envisages photothermal and photoacoustic therapy using nanotubes. This article sheds light on the role of carbon nanotubes in cancer therapy and diagnosis based on recent findings.