Biomarker method validation in anticancer drug development

Anticancer Drug Discovery Based on Natural Products: From Computational Approaches to Clinical Studies

Globally, malignancies cause one out of six mortalities, which is a serious health problem. Cancer therapy has always been challenging, apart from major advances in immunotherapies, stem cell transplantation, targeted therapies, hormonal therapies, precision medicine, and palliative care, and traditional therapies such as surgery, radiation therapy, and chemotherapy. Natural products are integral to the development of innovative anticancer drugs in cancer research, offering the scientific community the possibility of exploring novel natural compounds against cancers. The role of natural products like Vincristine and Vinblastine has been thoroughly implicated in the management of leukemia and Hodgkin's disease. The computational method is the initial key approach in drug discovery, among various approaches. This review investigates the synergy between natural products and computational techniques, and highlights their significance in the drug discovery process. The transition from computational to experimental validation has been highlighted through in vitro and in vivo studies, with examples such as betulinic acid and withaferin A. The path toward therapeutic applications have been demonstrated through clinical studies of compounds such as silvestrol and artemisinin, from preclinical investigations to clinical trials. This article also addresses the challenges and limitations in the development of natural products as potential anti-cancer drugs. Moreover, the integration of deep learning and artificial intelligence with traditional computational drug discovery methods may be useful for enhancing the anticancer potential of natural products.

High Expression of Plasma Extracellular HSP90α is Associated With the Poor Efficacy of Chemotherapy and Prognosis in Small Cell Lung Cancer

Purpose: eHSP90α is closely related to tumor progression and prognosis. This study aimed to investigate the significance of eHSP90α in the response evaluation and prediction of small cell lung cancer.

Methods: We analyzed the relationship between eHSP90α expression and clinicopathological features in 105 patients with small cell lung cancer. Univariate and multivariate analyses were used to determine the association of parameters and ratios with response assessment, progression-free survival (PFS), and overall survival (OS).

Results: In SCLC patients, eHSP90α and NSE were positively correlated. The cutoff values of eHSP90α in OS, PFS, and response evaluation were 61.2 ng/ml, 48.7 ng/ml, and 48.7 ng/ml, respectively. eHSP90α could better predict OS, PFS, and response evaluation (AUC OS 0.791, PFS 0.662, 0.685). Radiotherapy and eHSP90α were independent variables for effective chemotherapy through univariate and multivariate analysis. In contrast, radiotherapy, eHSP90α, NSE, and M stage were independent variables for OS. eHSP90α, and M stage were independent variables for PFS. Kaplan-Meier analysis showed that higher eHSP90α expression predicted poorer OS and earlier progression in patients.

Conclusions: This study aims to provide new evidence for the efficacy response and prognostic assessment of SCLC. eHSP90α may be a better biomarker for SCLC.

Programmed cell death detection methods: a systematic review and a categorical comparison

Programmed cell death is considered a key player in a variety of cellular processes that helps to regulate tissue growth, embryogenesis, cell turnover, immune response, and other biological processes. Among different types of cell death, apoptosis has been studied widely, especially in the field of cancer research to understand and analyse cellular mechanisms, and signaling pathways that control cell cycle arrest. Hallmarks of different types of cell death have been identified by following the patterns and events through microscopy. Identified biomarkers have also supported drug development to induce cell death in cancerous cells. There are various serological and microscopic techniques with advantages and limitations, that are available and are being utilized to detect and study the mechanism of cell death. The complexity of the mechanism and difficulties in distinguishing among different types of programmed cell death make it challenging to carry out the interventions and delay its progression. In this review, mechanisms of different forms of programmed cell death along with their conventional and unconventional methods of detection of have been critically reviewed systematically and categorized on the basis of morphological hallmarks and biomarkers to understand the principle, mechanism, application, advantages and disadvantages of each method. Furthermore, a very comprehensive comparative analysis has been drawn to highlight the most efficient and effective methods of detection of programmed cell death, helping researchers to make a reliable and prudent selection among the available methods of cell death assay. Conclusively, how programmed cell death detection methods can be improved and can provide information about distinctive stages of cell death detection have been discussed.

Stable Zinc(II) Coordination Polymer as a Rapid and Highly Sensitive Fluorescence Sensor for the Discriminative Sensing of Biomarker 2-(2-Methoxyethoxy) Acetic Acid

A novel two-dimensional bilayer Zn-based luminescent coordination polymer (LCP) [Zn₂(μ₂-OH)(4-dptp)(3,4',5-bpt)] (LCP 1) [4-dptp = N³,N⁴-bis(pyridin-4-ylmethyl)thiophene-3,4-dicarboxamide and 3,4',5-H₃bpt = biphenyl-3,4',5-tricarboxylic acid] was successfully prepared under hydrothermal conditions and characterized by single-crystal X-ray diffraction, IR spectroscopy, powder X-ray diffraction, and luminescence spectroscopy. LCP 1 displayed excellent fluorescence-quenching efficiency toward a biomarker 2-(2-methoxyethoxy) acetic acid (MEAA) with a high K_sv (5.153 × 104 M^-1), a low limit of detection (0.244 μM), and a rapid response time (28 s). Additionally, LCP 1 can repeatedly detect MEAA at least eight times with excellent stability. The sensing mechanism was also carefully investigated through UV-vis absorption spectroscopy, density functional theory calculations, and fluorescence lifetime analysis.

Consensus guidelines for the validation of qRT-PCR assays in clinical research by the CardioRNA consortium

Despite promising findings, quantitative PCR (qPCR)-based tests for RNA quantification have experienced serious limitations in their clinical application. The noticeable lack of technical standardization remains a huge obstacle in the translation of qPCR-based tests. The incorporation of qPCR-based tests into the clinic will benefit from guidelines for clinical research assay validation. This will ultimately impact the clinical management of the patient, including diagnosis, prognosis, prediction, monitoring of the therapeutic response, and evaluation of toxicity. However, clear assay validation protocols for biomarker investigation in clinical trials using molecular assays are currently lacking. Here, we will focus on the necessary steps, including sample acquisition, processing and storage, RNA purification, target selection, assay design, and experimental design, that need to be taken toward the appropriate validation of qRT-PCR assays in clinical research. These recommendations can fill the gap between research use only (RUO) and in vitro diagnostics (IVD). Our contribution provides a tool for basic and clinical research for the development of validated assays in the intermediate steps of biomarker research. These guidelines are based on the current understanding and consensus within the EU-CardioRNA COST Action consortium (www.cardiorna.eu). Their applicability encompasses all clinical areas.

Evaluation of liver tissue extraction protocol for untargeted metabolomics analysis by ultra-high-performance liquid chromatography/tandem mass spectrometry

The aim of the untargeted metabolomics study is to obtain a global metabolome coverage from biological samples. Therefore, a comprehensive and systematic protocol for tissue metabolite extraction is highly desirable. In this study, we evaluated a comprehensive liver pretreatment strategy based on ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry to obtain more metabolites using four different protocols. These protocols included (A) methanol protein precipitation, (B) two-step extraction of dichloromethane-methanol followed by methanol-water, (C) two-step extraction of methyl tert-butyl ether-methanol followed by methanol-water, and (D) two-step extraction of isopropanol-methanol followed by methanol-water. Our results showed that protocol D was superior to the others due to more extracted features, annotated metabolites, and better reproducibility. And then, the stability and extraction sequence of protocol D were evaluated. The results showed that extraction with isopropanol-methanol followed by methanol-water was the optimum preparation sequence, which offered higher extraction efficiency, satisfactory repeatability, and acceptable stability. Furthermore, the optimal protocol was successfully applied by liver samples of rats after high-fat intervention. In summary, our protocol enabled a comprehensive and systematic evaluation of liver pretreatment to obtain more medium-polar and nonpolar metabolites and was suitable for high-throughput metabolomics analysis.

Necrosis Rather Than Apoptosis is the Dominant form of Alveolar Epithelial Cell Death in Lipopolysaccharide-Induced Experimental Acute Respiratory Distress Syndrome Model

Alveolar epithelial cell (AEC) death, which is classified as apoptosis or necrosis, plays a critical role in the pathogenesis of acute respiratory distress syndrome (ARDS). In addition to apoptosis, some types of necrosis are known to be molecularly regulated, and both apoptosis and necrosis can be therapeutic targets for diseases. However, the relative contribution of apoptosis and necrosis to AEC death during ARDS has not been elucidated. Here, we evaluated which type of AEC death is dominant and whether regulated necrosis is involved in lipopolysaccharide (LPS)-induced lung injury, an experimental ARDS model. In the bronchoalveolar lavage fluid from the LPS-induced lung injury mice, both the levels of cytokeratin 18-M65 antigen (a marker of total epithelial cell death) and cytokeratin 18-M30 antigen (an epithelial apoptosis marker) were increased. The M30/M65 ratio, which is an indicator of the proportion of apoptosis to total epithelial cell death, was significantly lower than that in healthy controls. In addition, the number of propidium iodide-positive, membrane-disrupted cells was significantly higher than the number of TUNEL-positive apoptotic cells in the lung sections of lung injury mice. Activated neutrophils seemed to mediate AEC death. Finally, we demonstrated that necroptosis, a regulated necrosis pathway, is involved in AEC death during LPS-induced lung injury. These results indicate that necrosis including necroptosis, rather than apoptosis, is the dominant type of AEC death in LPS-induced lung injury. Although further studies investigating human ARDS subjects are necessary, targeting necrosis including its regulated forms might represent a more efficient approach to protecting the alveolar epithelial barrier during ARDS.

Guidelines for Regulated Cell Death Assays: A Systematic Summary, A Categorical Comparison, A Prospective

Over the past few years, the field of regulated cell death continues to expand and novel mechanisms that orchestrate multiple regulated cell death pathways are being unveiled. Meanwhile, researchers are focused on targeting these regulated pathways which are closely associated with various diseases for diagnosis, treatment, and prognosis. However, the complexity of the mechanisms and the difficulties of distinguishing among various regulated types of cell death make it harder to carry out the work and delay its progression. Here, we provide a systematic guideline for the fundamental detection and distinction of the major regulated cell death pathways following morphological, biochemical, and functional perspectives. Moreover, a comprehensive evaluation of different assay methods is critically reviewed, helping researchers to make a reliable selection from among the cell death assays. Also, we highlight the recent events that have demonstrated some novel regulated cell death processes, including newly reported biomarkers (e.g., non-coding RNA, exosomes, and proteins) and detection techniques.

Fit-for-Purpose Validation and Establishment of Assay Acceptance and Reporting Criteria of Dendritic Cell Activation Assay Contributing to the Assessment of Immunogenicity Risk

Validation of key analytical and functional performance characteristics of in vitro immunogenicity risk assessment assays increases our confidence in utilizing them for screening biotherapeutics. Herein, we present a fit-for-purpose (FFP) validation of a dendritic cell (DC) activation assay designed to assess the immunogenicity liability of protein biotherapeutics. Characterization of key assay parameters was achieved using monocyte-derived DCs (MoDCs) treated with cell culture medium only (i.e., background control (BC)), keyhole limpet hemocyanin (KLH) as system positive control (SPC), and 2 therapeutic monoclonal antibodies (mAbs) with known clinical immunogenicity profiles (bococizumab and TAM163) as therapeutic controls (TCs). In the absence of established validation guidelines for primary cell-based assays, the present DC activation assay was validated using a novel FFP approach which allows more flexibility in selection of validation parameters and designing of experiments based on the intended use of the assay. The present FFP validation allowed us to understand the impact of experimental variables on assay precision, develop a clear concise readout for DC activation results, establish a reliable response threshold to define a result as a positive DC activation response, and define in-study donor acceptance criteria and cohort size. FFP validation of this DC activation assay indicated that the assay is sufficient to support its context of use, a preclinical immunogenicity risk management tool.

Acetaminophen Oxidation and Inflammatory Markers - A Review of Hepatic Molecular Mechanisms and Preclinical Studies

Acetaminophen is a widely used analgesic for pain management, especially useful in chronic diseases, such as rheumatoid arthritis. However, easy access to this medicine has increased the occurrence of episodes of poisoning. Patients often develop severe liver damage, which may quickly lead to death. Consequently, numerous studies have been conducted to identify new biomarkers that allow the prediction of the degree of acetaminophen intoxication and thus intervene in a timely manner to save patients' lives. This review highlights the main mechanisms of the induction and progression of liver damage arising from acetaminophen poisoning. In addition, we have discussed the possibility of using new clinical biomarkers for detecting acetaminophen poisoning.

Prognostic and Predictive Molecular Biomarkers for Colorectal Cancer: Updates and Challenges

Colorectal cancer (CRC) is a leading cause of death among cancer patients. This heterogeneous disease is characterized by alterations in multiple molecular pathways throughout its development. Mutations in RAS, along with the mismatch repair gene deficiency, are currently routinely tested in clinics. Such biomarkers provide information for patient risk stratification and for the choice of the best treatment options. Nevertheless, reliable and powerful prognostic markers that can identify “high-risk” CRC patients, who might benefit from adjuvant chemotherapy, in early stages, are currently missing. To bridge this gap, genomic information has increasingly gained interest as a potential method for determining the risk of recurrence. However, due to several limitations of gene-based signatures, these have not yet been clinically implemented. In this review, we describe the different molecular markers in clinical use for CRC, highlight new markers that might become indispensable over the next years, discuss recently developed gene expression-based tests and highlight the challenges in biomarker research.

Pharmacological Assessment of Sepiapterin Reductase Inhibition on Tactile Response in the Rat

There is an unmet medical need for nonopioid pain therapies in human populations; several pathways are under investigation for possible therapeutic intervention. Tetrahydrobiopterin (BH4) has received attention recently as a mediator of neuropathic pain. Recent reports have implicated sepiapterin reductase (SPR) in this pain pathway as a regulator of BH4 production. To evaluate the role of SPR inhibition on BH4 reduction, we developed analytical methods to monitor the relationship between the plasma concentration of test article and endogenous pterins and applied these in the rat spinal nerve ligation pain model. Sepiapterin is an endogenous substrate, which accumulates upon inhibition of SPR. In response to a potent inhibitor of SPR, plasma concentrations of sepiapterin increased proportionally with exposure. An indirect-effect pharmacokinetic/pharmacodynamic model was developed to describe the relationship between the plasma pharmacokinetics of test article and plasma sepiapterin levels in the rat, which was used to determine an in vivo SPR IC50 value. SPR inhibition and mechanical allodynia were assessed coordinately with pterin biomarkers in plasma and at the site of neuronal injury (i.e., dorsal root ganglion). Upon daily oral administration for 3 consecutive days, unbound plasma concentrations of test article exceeded the unbound in vivo rat SPR IC90 throughout the dose intervals, leading to a 60% reduction in BH4 in the dorsal root ganglion. Despite evidence for pharmacological modulation of the BH4 pathway, there was no significant effect on the tactile paw withdrawal threshold relative to vehicle-treated controls.

Evaluation of two-step liquid-liquid extraction protocol for untargeted metabolic profiling of serum samples to achieve broader metabolome coverage by UPLC-Q-TOF-MS

Untargeted metabolomics studies aim to extract a broad coverage of metabolites from biological samples, which largely depends on the sample preparation protocols used for metabolite extraction. The aim of this study was to evaluate a comprehensive sample pretreatment strategy using two-step liquid-liquid extraction to achieve broader metabolome coverage by ultra-high-performance liquid chromatography coupled with electrospray ionization time-of-flight mass spectrometry (UPLC-Q-TOF-MS). We compared four protocols: (A) methanol protein precipitation, (B) Ostro 96-well plates, (C) two-step extraction protocol of CHCL₃-MeOH followed by MeOH-H₂O, and (D) two-step extraction protocol of CH₂CL₂-MeOH followed by MeOH-H₂O. The number of extracted features, reproducibility and recovery were the major criteria for evaluation. Our results demonstrated that Protocols B, C and D, with approximately similar number of features, extracted more features than Protocol A. Protocols C and D appeared to have similar extraction reproducibility (low coefficient of variation < 30%) and Protocol D enabled an acceptable recovery of serum metabolites. The two-step extraction Protocol D (CH₂CL₂-MeOH followed by MeOH-H₂O) resulted in the greatest improvement in metabolite coverage, satisfactory extraction reproducibility, acceptable recovery and environmental safety. The selected protocol was applied to an obesity metabolomics study to obtain different metabolites between participants with obesity and the controls, and to investigate complex metabolic alterations in obesity during a 2-h oral glucose-tolerance test. Our results suggested that this protocol was useful for analyzing serum metabolome changes in obese individuals in the fasting and postprandial state.

Fully disposable microfluidic electrochemical device for detection of estrogen receptor alpha breast cancer biomarker

A novel fully disposable microfluidic electrochemical array device (µFED) was developed and successfully applied for detection of the biomarker estrogen receptor alpha (ERα). The µFED was constructed using low-cost materials and an inexpensive home cutter printer enabled the manufacture of dozens of µFEDs in less than 2h, at a cost of less than US$ 0.20 in material per device. The µFED incorporates counter and reference electrodes and eight carbon-based working electrodes, which were modified with DNA sequences known as estrogen response elements (DNA-ERE), where ERα binds specifically. Paramagnetic particles heavily decorated with anti-ERα antibody and horseradish peroxidase (MP-Ab-HRP) were used to efficiently capture ERα from the sample solution. The ERα-MP-Ab-HRP bioconjugate formed was injected into the µFED and incubated with the DNA-ERE-modified electrodes, followed by amperometric detection with application of -0.2V vs. Ag|AgCl while a mixture of H₂O₂ and hydroquinone was injected into the microfluidic device. An ultralow limit of detection of 10.0 fg mL^-1 was obtained with the proposed method. The performance of the assay, in terms of sensitivity and reproducibility, was studied using undiluted calf serum, and excellent recoveries in the range of 94.7-108% were achieved for the detection of ERα in MCF-7 cell lysate. The µFED system can be easily constructed and applied for multiplex biomarker detection, making the device an excellent cost-effective alternative for cancer diagnosis, especially in developing countries.

Translational Prospects and Challenges in Human Induced Pluripotent Stem Cell Research in Drug Discovery

Despite continuous efforts to improve the process of drug discovery and development, achieving success at the clinical stage remains challenging because of a persistent translational gap between the preclinical and clinical settings. Under these circumstances, the discovery of human induced pluripotent stem (iPS) cells has brought new hope to the drug discovery field because they enable scientists to humanize a variety of pharmacological and toxicological models in vitro. The availability of human iPS cell-derived cells, particularly as an alternative for difficult-to-access tissues and organs, is increasing steadily; however, their use in the field of translational medicine remains challenging. Biomarkers are an essential part of the translational effort to shift new discoveries from bench to bedside as they provide a measurable indicator with which to evaluate pharmacological and toxicological effects in both the preclinical and clinical settings. In general, during the preclinical stage of the drug development process, in vitro models that are established to recapitulate human diseases are validated by using a set of biomarkers; however, their translatability to a clinical setting remains problematic. This review provides an overview of current strategies for human iPS cell-based drug discovery from the perspective of translational research, and discusses the importance of early consideration of clinically relevant biomarkers.

New potential biomarkers of acetaminophen-induced hepatotoxicity

Acetaminophen (APAP) is one of the most common antipyretic and analgesic drugs. Despite various precautions patients use APAP in amounts exceeding acceptable daily doses. APAP overdosing contributes to APAP intoxication, which leads to acute liver injury or necessity of exigent liver transplantation. Biomarkers that can be helpful in early diagnosis of liver injury during APAP overdosing are studied worldwide. This review presents recent reports on new potential biomarkers and their prospective application in clinical practice.

Circulating Levels of M30 and M65 Molecules in Transitional Cell Carcinoma of the Bladder and Their Relation to Tumor Progression

BACKGROUND

Various markers are suggested for diagnosis and monitoring of transitional cell carcinoma of the bladder (TCC), including cytokeratins (CKs).

OBJECTIVES

In the present study, the circulating CK18 (M65) and its caspase-cleaved form, ccCK18 (M30), have been investigated in a group of patients with TCC.

PATIENTS AND METHODS

Serum samples were obtained from 60 patients before surgical resection, among which the samples of 26 patients after resection were also included. We measured the levels of soluble M30 and M65 molecules by enzyme-linked immunosorbent assay. The relation between these markers and patients' clinical characteristics was evaluated.

RESULTS

M30 and M65 in total patient sera were 148 ± 16 U/L and 318 ± 34 U/L, respectively. A correlation existed between pre-operative M30 and M65 levels (P < 0.0001, Spearman r = 0.51). M65, but not M30, showed a significant relation to tumor stage and grade. The M65 quantity in patients with T3/T4 tumor stages (350 ± 42 U/L) was higher than that of patients with T1/T2 stages (293 ± 45U/L; P < 0.038). Patients with tumor grades III/IV also showed higher levels of M65 compared to patients with tumor grades I/II (P < 0.04). The M30:M65 ratio in all patients was 0.54 ± 0.04. There was a lower M30:M65 ratio in patients with T3/T4 stage tumors and those with tumor grades III/IV (P < 0.02). The M30 (133 ± 19 U/L) and M65 levels (240 ± 21 U/L) after surgery did not significantly differ compared to their pre-operative values. However, a correlation between the pre- and post-operative M30:M65 ratio in patients ≥ 70 years was seen (P = 0.009).

CONCLUSIONS

These data suggested a relationship of both M65 and the M30:M65 ratio to tumor progression which might imply their importance in TCC monitoring.

Development of liquid chromatography-tandem mass spectrometry methods for the quantitation of Anisakis simplex proteins in fish

The parasite Anisakis simplex is present in many marine fish species that are directly used as food or in processed products. The anisakid larvae infect mostly the gut and inner organs of fish but have also been shown to penetrate into the fillet. Thus, human health can be at risk, either by contracting anisakiasis through the consumption of raw or under-cooked fish, or by sensitisation to anisakid proteins in processed food. A number of different methods for the detection of A. simplex in fish and products thereof have been developed, including visual techniques and PCR for larvae tracing, and immunological assays for the determination of proteins. The recent identification of a number of anisakid proteins by mass spectrometry-based proteomics has laid the groundwork for the development of two quantitative liquid chromatography-tandem mass spectrometry methods for the detection of A. simplex in fish that are described in the present study. Both, the label-free semi-quantitative nLC-nESI-Orbitrap-MS/MS (MS1) and the heavy peptide-applying absolute-quantitative (AQUA) LC-TripleQ-MS/MS (MS2) use unique reporter peptides derived from anisakid hemoglobin and SXP/RAL-2 protein as analytes. Standard curves in buffer and in salmon matrix showed limits of detection at 1μg/mL and 10μg/mL for MS1 and 0.1μg/mL and 2μg/mL for MS2. Preliminary method validation included the assessment of sensitivity, repeatability, reproducibility, and applicability to incurred and naturally-contaminated samples for both assays. By further optimization and full validation in accordance with current recommendations the LC-MS/MS methods could be standardized and used generally as confirmative techniques for the detection of A. simplex protein in fish.

Urinary N1, N12-diacetylspermine is a non-invasive marker for the diagnosis and prognosis of non-small-cell lung cancer

BACKGROUND

Early detection of non-small-cell lung cancer (NSCLC) and accurate prognostic risk assessment could improve patient outcome. We examined the significance of urinary N(1), N(12)-diacetylspermine (DiAcSpm) in the detection and prognostic stratification of NSCLC patients.

METHODS

A DiAcSpm/cutoff ratio (DASr) was established for 260 NSCLC patients, 99 benign lung disease patients, and 140 healthy volunteers, using colloidal gold aggregation methods. The DASr was compared between patients and healthy controls, and the prognostic significance of DASr was examined.

RESULTS

The median urinary DASr of NSCLC patients was significantly higher than that of healthy controls (0.810 vs 0.534, P<0.001). The DASr was higher in squamous cell carcinoma (SqCC) patients than in adenocarcinoma patients (1.18 vs 0.756, respectively, P=0.039). An increased urinary DASr value was significantly associated with pathological stage, other histological invasive factors and unfavourable outcomes in patients with completely resected NSCLC. Multivariate Cox regression analysis showed that increased urinary DASr was an independent prognostic factor (hazard ratio=4.652, 95% confidence interval (CI), 2.092-10.35; P<0.001).

CONCLUSIONS

Urinary DASr was significantly increased in NSCLC, especially in SqCC. Urinary DASr was an independent poor prognostic indicator in patients with completely resected NSCLC. The DASr could be a useful biomarker for detecting malignancies and predicting prognosis.

Biomarker- versus drug-driven tumor growth inhibition models: an equivalence analysis

The mathematical modeling of tumor xenograft experiments following the dosing of antitumor drugs has received much attention in the last decade. Biomarker data can further provide useful insights on the pathological processes and be used for translational purposes in the early clinical development. Therefore, it is of particular interest the development of integrated pharmacokinetic-pharmacodynamic (PK-PD) models encompassing drug, biomarker and tumor-size data. This paper investigates the reciprocal consistency of three types of models: drug-to-tumor, such as established drug-driven tumor growth inhibition (TGI) models, drug-to-biomarker, e.g. indirect response models, and biomarker-to-tumor, e.g. the more recent biomarker-driven TGI models. In particular, this paper derives a mathematical relationship that guarantees the steady-state equivalence of the cascade of drug-to-biomarker and biomarker-to-tumor models with a drug-to-tumor TGI model. Using the Simeoni TGI model as a reference, conditions for steady-state equivalence are worked out and used to derive a new biomarker-driven model. Simulated and real data are used to show that in realistic cases the steady-state equivalence extends also to transient responses. The possibility of predicting the drug-to-tumor potency of a new candidate drug based only on biomarker response is discussed.

Total protein is an effective loading control for cerebrospinal fluid western blots

BACKGROUND

Cerebrospinal fluid (CSF) has been used to identify biomarkers of neurological disease. CSF protein biomarkers identified by high-throughput methods, however, require further validation. While Western blotting (WB) is well-suited to this task, the lack of a validated loading control for CSF WB limits the method's accuracy.

NEW METHOD

We investigated the use of total protein (TP) as a CSF WB loading control. Using iodine-based reversible membrane staining, we determined the linear range and consistency of the CSF TP signal. We then spiked green fluorescent protein (GFP) into CSF to create defined sample-to-sample differences in GFP levels that were measured by WB before and after TP loading correction. Levels of CSF complement C3 and cystatin C measured by WB with TP loading correction and ELISA in amyotrophic lateral sclerosis and healthy control CSF samples were then compared.

RESULTS

CSF WB with the TP loading control accurately detected defined differences in GFP levels and corrected for simulated loading errors. Individual CSF sample Western blot and ELISA measurements of complement C3 and cystatin C were significantly correlated and the methods showed a comparable ability to detect between-groups differences.

COMPARISON WITH EXISTING METHOD

CSF TP staining has a greater linear dynamic range and sample-to-sample consistency than albumin, a commonly used CSF loading control. The method accurately corrects for simulated errors in loading and improves the sensitivity of CSF WB compared to using no loading control.

CONCLUSIONS

The TP staining loading control improves the sensitivity and accuracy of CSF WB results.

Optimisation of immunofluorescence methods to determine MCT1 and MCT4 expression in circulating tumour cells

BACKGROUND

The monocarboxylate transporter-1 (MCT1) represents a novel target in rational anticancer drug design while AZD3965 was developed as an inhibitor of this transporter and is undergoing Phase I clinical trials ( http://www.clinicaltrials.gov/show/NCT01791595 ). We describe the optimisation of an immunofluorescence (IF) method for determination of MCT1 and MCT4 in circulating tumour cells (CTC) as potential prognostic and predictive biomarkers of AZD3965 in cancer patients.

METHODS

Antibody selectivity was investigated by western blotting (WB) in K562 and MDAMB231 cell lines acting as positive controls for MCT1 and MCT4 respectively and by flow cytometry also employing the control cell lines. Ability to detect MCT1 and MCT4 in CTC as a 4(th) channel marker utilising the Veridex™ CellSearch system was conducted in both human volunteer blood spiked with control cells and in samples collected from small cell lung cancer (SCLC) patients.

RESULTS

Experimental conditions were established which yielded a 10-fold dynamic range (DR) for detection of MCT1 over MCT4 (antibody concentration 6.25 μg/mL; integration time 0.4 seconds) and a 5-fold DR of MCT4 over MCT 1 (8 μg/100 μL and 0.8 seconds). The IF method was sufficiently sensitive to detect both MCT1 and MCT4 in CTCs harvested from cancer patients.

CONCLUSIONS

The first IF method has been developed and optimised for detection of MCT 1 and MCT4 in cancer patient CTC.

Development and validation of an enzyme-linked immunosorbent assay to measure adalimumab concentration

Background: Adalimumab is a therapeutic antibody used for treating inflammatory diseases. To understand interindividual PK variability, there is a need to develop and validate an assay to measure serum adalimumab concentrations. Methods: An ELISA was developed on microtiter plates coated with TNF-α. Seven nonzero adalimumab standards ranging from 0.05 to 50 mg/l and three quality controls (0.2, 2.5 and 7 mg/l) were tested for their intra and interday precision on six occasions. Results: The LOD, LLOQ and ULOQ of the assay were 0.022, 0.073 and 9 mg/l, respectively. Conclusion: This method is accurate, reproducible and may be useful for PK studies and for therapeutic drug monitoring of adalimumab.

Recommendations for adaptation and validation of commercial kits for biomarker quantification in drug development

Increasingly, commercial immunoassay kits are used to support drug discovery and development. Longitudinally consistent kit performance is crucial, but the degree to which kits and reagents are characterized by manufacturers is not standardized, nor are the approaches by users to adapt them and evaluate their performance through validation prior to use. These factors can negatively impact data quality. This paper offers a systematic approach to assessment, method adaptation and validation of commercial immunoassay kits for quantification of biomarkers in drug development, expanding upon previous publications and guidance. These recommendations aim to standardize and harmonize user practices, contributing to reliable biomarker data from commercial immunoassays, thus, enabling properly informed decisions during drug development.

Biomarkers of tobacco smoke exposure

Diseases and death caused by exposure to tobacco smoke have become the single most serious preventable public health concern. Thus, biomarkers that can monitor tobacco exposure and health effects can play a critical role in tobacco product regulation and public health policy. Biomarkers of exposure to tobacco toxicants are well established and have been used in population studies to establish public policy regarding exposure to second-hand smoke, an example being the nicotine metabolite cotinine, which can be measured in urine. Biomarkers of biological response to tobacco smoking range from those indicative of inflammation to mRNA and microRNA patterns related to tobacco use and/or disease state. Biomarkers identifying individuals with an increased risk for a pathological response to tobacco have also been described. The challenge for any novel technology or biomarker is its translation to clinical and/or regulatory application, a process that requires first technical validation of the assay and then careful consideration of the context the biomarker assay may be used in the regulatory setting. Nonetheless, the current efforts to investigate new biomarker of tobacco smoke exposure promise to offer powerful new tools in addressing the health hazards of tobacco product use. This review will examine such biomarkers, albeit with a focus on those related to cigarette smoking.

Circulating biomarkers in hepatocellular carcinoma

PURPOSE

Our aims are to determine levels of circulating cellular and protein biomarkers in hepatocellular carcinoma (HCC) patients and to analyse any relationships with clinical parameters.

METHODS

Fifty-four consenting patients were recruited. Circulating tumour cells (CTCs) were enumerated (by CellSearch) and characterised via filtration [by isolation by size of epithelial tumour cells (ISET)] with downstream immunohistochemistry (IHC). Glypican-3 (GPC3) expression in tumour biopsies and CTCs (by IHC) was compared, and levels of circulating caspase-cleaved and full-length cytokeratin 18 (CK18, measured using M30 and M65 ELISAs) were examined as a putative prognostic factor and marker of tumour burden.

RESULTS

CTCs were identified in 14 out of 50 (28%) patients by CellSearch and in 19 out of 19 (100%) patients by ISET. The presence of GPC3-positive CTCs by ISET was 100% concordant with the presence of GPC3-positive cells in the original tumour (n = 5). No statistically significant correlations were observed between CTC number and clinical characteristics, although trends were noted between CTC subtypes, Child-Pugh score and tumour node metastasis stage. Serum M30 and M65 levels (as continuous variables) significantly correlated with overall survival (OS) in a univariate analysis (p = 0.003 and p < 0.001, respectively); M65 levels remained statistically significant in a multivariate analysis (p = 0.029).

CONCLUSIONS

This is the first study to detect GPC3-positive CTCs in HCC, important for drug development with this target. The significant association of circulating CK18 with OS in HCC further exemplifies the utility of circulating biomarkers in cancer.

Optimisation of an immunohistochemistry method for the determination of androgen receptor expression levels in circulating tumour cells

BACKGROUND

AZD3514 inhibits and down regulates the androgen receptor (AR) and has undergone clinical trials in prostate cancer. To provide proof-of-mechanism (POM) in patients, an immunohistochemistry (IHC) method for determination of AR in circulating tumour cells (CTC) was developed and validated.

METHODS

After an assessment of specificity validation focused on intra- and inter-operator reproducibility utilising a novel modification of incurred sample reanalysis (ISR). β-Content γ-confidence tolerance intervals (BCTI) and Cohen's Kappa (κ) were employed in statistical analysis of results.

RESULTS

In a first set of IHC reproducibility experiments, almost perfect agreement was recorded (κ=0.94) when two different operators scored CTC as overall positive or negative for AR. However, BCTI analysis identified a specific bias in scoring staining intensity, where one operator favoured moderate over strong assignments, whereas the reverse was the case with the second operator. After a period of additional training involving deployment of a panel of standardised images, a second set of validation experiments were conducted. These showed correction of the inter-operator bias by BCTI with κ for scoring intensity increasing from 0.59 to 0.81, indicative of almost perfect agreement.

CONCLUSIONS

By application of BCTI to the validation of IHC, operator bias and therefore poor reproducibility can be identified, characterised and corrected to achieve a level of error normally associated with a quantitative biomarker assay, such as an ELISA. The methodological approach described herein can be applied to any generic IHC technique.

A matrix approach to guide IHC-based tissue biomarker development in oncology drug discovery

Immunohistochemistry (IHC) is a core platform for the analysis of tissue samples, and there is an increasing demand for reliable and quantitative IHC-based tissue biomarkers in oncology clinical research and development (R&D) environments. Biomarker assay and drug development proceed in parallel. Furthermore, biomarker assay requirements change with each phase of drug development. We have therefore developed a matrix tool to enable researchers to evaluate whether a particular IHC biomarker assay is fit for purpose. Experience gained from the development of 130 IHC biomarkers, supporting a large number of oncology drug projects, was used to formulate a practical approach to IHC assay development. The resultant matrix grid and accompanying work flow incorporates 16 core decision points that link antibody and assay specificity and sensitivity, and assay performance in preclinical and clinical samples, with stages of drug development. The matrix provides a means to ensure that relevant information on an IHC assay in development is recorded and communicated consistently and that minimum assay validation requirements are met.

Stratification of paracetamol overdose patients using new toxicity biomarkers: current candidates and future challenges

One of the most common causes of acute liver failure in the Western world is paracetamol (acetaminophen) overdose. Specific and sensitive detection of liver injury is important for the prompt and safe treatment of patients with the antidote N-acetylcysteine (NAC) and for the determination of NAC efficacy. Despite many years of intense research, the precise mechanisms of paracetamol-induced liver injury in humans are still not defined, and few studies have examined the optimal dosing regimen for clinical NAC use. It has been widely acknowledged that circulating biomarkers such as microRNA-122, keratin-18 and high mobility group box-1 hold potential to inform on the mechanistic-basis of human drug-induced liver injury. Here, we provide a perspective on the application of these mechanistic biomarkers to the deeper understanding of paracetamol hepatotoxicity in clinical and preclinical studies. Also, we discuss current barriers to using these experimental biomarkers to stratify patients presenting to hospital with this common medical emergency.

Systematic reference sample generation for multiplexed serological assays

Quality controls of serological assays have to contain defined amounts of human antibodies specific for the targeted antigen. A prevailing issue for array-based antigen assays is that dozens of antigens are targeted within the same assay. Commonly different patient sera are combined and optimal pools are empirically identified. Here, we report a mathematical approach how an optimal sample pool composition can be systematically calculated and accurately compiled. The approach was used to compose suitable quality controls for a 71 plex Tuberculosis antigen bead array using a limited number of positive human sera.

Method validation of circulating tumour cell enumeration at low cell counts

Background

Circulating tumour cells (CTC) are receiving increasing attention as prognostic, predictive and pharmacodynamic biomarkers in cancer patients. However, their clinical significance can be dependent on an accurate determination of CTC around cut-off values at low cell counts (<10 cells/7.5 ml). Consequently, we have conducted method validation of the CellSearch™ system focusing on clinical samples containing CTC in the cut-off region.

Methods

Analytical accuracy was first assessed employing quality controls (QC) and spiked healthy volunteer blood specimens. Results were analysed by β-expectation tolerance intervals (BETI). Inter-operator error (6 different readers) was then characterised in 38 different patient samples, 68% of which had ≤5 CTC and data were analysed by β-content γ-confidence tolerance intervals (BCTI).

Results

Results from QCs and spiked blood confirmed a 3-4-fold higher degree of imprecision at the low (48 cells, BETI = + 0.288/-0.345, β = 95%) compared to the high QC (987 cells, BETI = +0.065/-0.140, β = 95%). However, when data for individual analysts were interrogated characteristic systematic errors were detected. In the analysis of patient samples again individual analysts introduced a highly specific error into the interpretation of CTC images, which correlated to the level of training and experience. When readers were selected based on BETI and BCTI results, the high level of between-operator error (up to 170%) observed at CTC of ≤ 5 was reduced to < 30%.

Conclusions

Inter-operator variability in enumeration of CTC at low cell counts can be considerable, but is also potentially avoidable by following simple guidance steps.

Serum markers in small cell lung cancer: opportunities for improvement

Lung cancer is one of the leading causes of death from malignancy worldwide. In particular small cell lung cancers, which comprise about 15-20% of all lung cancers, are extremely aggressive and cure rates are extremely low. Therefore, new treatment modalities are needed and detection at an early stage of disease, as well as adequate monitoring of treatment response is essential in order to improve outcome. In this respect, the use of non-invasive tools for screening and monitoring has gained increasing interest and the clinical applicability of reliable, tumor-related substances that can be detected as tumor markers in easily accessible body fluids is subject of intense investigation. Some of these indicators, such as high LDH levels in serum as a reflection of the disease, have been in use for a long time as a general tumor marker. To allow for improved monitoring of the efficacy of new therapeutic modalities and for accurate subtyping, there is a strong need for specific and sensitive markers that are more directly related to the biology and behavior of small cell lung cancer. In this review the current status of these potential markers, like CEA, NSE, ProGRP, CK-BB, SCC, CgA, NCAM and several cytokeratins will be critically analyzed with respect to their performance in blood based assays. Based on known cleavage sites for cytoplasmic and extracellular proteases, a prediction of stable fragments can be obtained and used for optimal test design. Furthermore, insight into the synthesis of specific splice variants and neo-epitopes resulting from protein modification and cleavage, offers further opportunities for improvement of tumor assays. Finally, we discuss the possibility that detection of SCLC related autoantibodies in paraneoplastic disease can be used as a very early indicator of SCLC.

Orally administered S-1 suppresses circulating endothelial cell counts in metastatic breast cancer patients

BACKGROUND

S-1 is an oral cytotoxic preparation that contains tegafur. Gamma-butyrolactone (GBL) is a metabolite of tegafur that is known to suppress vascular endothelial growth factor (VEGF)-mediated angiogenic activity. The aim of this study was to determine the change in circulating endothelial cell (CEC) counts, GBL levels, and angiogenesis-related factors during S-1 administration in metastatic breast cancer (MBC) patients.

METHODS

Patients with HER2-negative MBC were eligible. S-1 was administered orally twice daily in a 4 week on/2 week off cycle until disease progression or unacceptable toxicity occurred. Blood was collected on the following: days 1, 43, 85 (before each cycle of S-1 administration), days 15, 57 (1 h after S-1 administration), and day 29. The CellSearch(®) system was used to count the CECs. The gas chromatographic-mass spectrometric method was used to measure plasma GBL and 5-FU levels. Levels of VEGF were assayed by enzyme-linked immunosorbent assay.

RESULTS

A total of 18 patients were enrolled. The plasma GBL levels on days 15 and 57 were 41.3 ± 15.8 and 41.0 ± 11.2 ng/mL, respectively. The CEC levels decreased on day 15, and significantly low levels were maintained until day 85 (P = 0.002 vs day 1). The plasma VEGF levels significantly decreased on day 15 (P = 0.012 vs day 1) and had a tendency to decrease until day 57.

CONCLUSIONS

This exploratory study showed that GBL levels increased, VEGF levels decreased, and CEC levels were suppressed during S-1 administration. S-1 appears to have anti-angiogenic activity.

Repeating tests: different roles in research studies and clinical medicine

Researchers often decide whether to average multiple results in order to produce more precise data, and clinicians often decide whether to repeat a laboratory test in order to confirm its validity or to follow a trend. Some of the major sources of variation in laboratory tests (analytical imprecision, within-subject biological variation and between-subject variation) and the effects of averaging multiple results from the same sample or from the same person over time are discussed quantitatively in this article. This analysis leads to the surprising conclusion that the strategy of averaging multiple results is only necessary and effective in a limited range of research studies. In clinical practice, it may be important to repeat a test in order to eliminate the possibility of a rare type of error that has nothing to do analytical imprecision or within-subject variation, and for this reason, paradoxically, it may be most important to repeat tests with the highest sensitivity and/or specificity (i.e., ones that are critical for clinical decision-making).

Determination of apoptotic and necrotic cell death in vitro and in vivo

Cell death research during the last decades has revealed many molecular signaling cascades, often leading to distinct cell death modalities followed by immune responses. For historical reasons, the prototypic and best characterized cell death modes are apoptosis and necrosis (dubbed necroptosis, to indicate that it is regulated). There is mounting evidence for the interplay between cell death modalities and their redundant action when one of them is interfered with. This increase in cell death research points to the need for characterizing cell death pathways by different approaches at the biochemical, cellular and if possible, physiological level. In this review we present a selection of techniques to detect cell death and to distinguish necrosis from apoptosis. The distinction should be based on pharmacologic and transgenic approaches in combination with several biochemical and morphological criteria. A particular problem in defining necrosis is that in the absence of phagocytosis, apoptotic cells become secondary necrotic and develop morphologic and biochemical features of primary necrosis.

Mass Spectrometry-Based Multiplexing for the Analysis of Biomarkers in Drug Development and Clinical Diagnostics- How Much is too Much?

Biomarkers, or more specifically molecular markers, can detect biochemical changes associated with disease processes and drug effects before histopathological and pathophysiological changes occur. Multiplexing technologies such as high-performance liquid chromatography/mass spectrometry (LC-MS) allow for the measurement of molecular marker patterns that confer significantly more information than the measurement of a single parameter alone. The use of multiplexing assays for drug development, and as diagnostic tools, is attractive but will require regulatory review and approval and thus requires validation following regulatory guidances. Multiplexing assays always constitute a compromise. The number of analytes that can reasonably be included in a mass spectrometry-based multiplexing assay depend on the physico-chemical properties of the analytes and their integration into a single assay in terms of extraction, HPLC separation, ionization conditions and mass spectrometry detection. Another aspect includes biomedical considerations such as the differences in physiological concentrations of analytes, the required concentration range, and how much variability is acceptable before the clinical utility of a marker is negatively affected. Regulatory considerations include validation and quality control during sample analysis. Current bioanalytical regulatory guidelines have mostly been developed for single drug compounds and are not always adequate for multiplexing molecular marker assays that often quantify endogenous compounds. Specific guidances for multiplexing assays should be developed. Even if it is possible to integrate a wide variety and large number of analytes into a multiplexing assay, it should always be taken into consideration that a set of shorter, more specialized assays, may offer a more manageable and efficient alternative.

Determination of soluble vascular endothelial growth factor receptor 3 (sVEGFR-3) in plasma as pharmacodynamic biomarker

Soluble VEGFR-3 (sVEGFR-3) is a potential biomarker for the anti-angiogenic activity of tyrosine kinase inhibitors. The aim of this investigation was the validation of an enzyme-linked immunosorbent assay (ELISA) to measure sVEGFR-3 in human plasma and the investigation of its applicability in clinical trials as first step of the biomarker validation process. General validation criteria were assessed based on current guidelines and recommendations for immunoassays. The ELISA was applied in two clinical trials including healthy volunteers and metastatic colorectal cancer (mCRC) patients receiving 50 or 37.5mg sunitinib per day, respectively. SVEGFR-3 was measured at predefined time points. Undiluted, inactivated fetal calf serum was identified as surrogate matrix to substitute for human plasma. Dilutional linearity and parallelism could be successfully confirmed. The analyte was measured in the study matrix with intra- and inter-run precision and accuracy ≤20%. Stability was proven over a period of at least 15 months as well as upon three freeze-thaw cycles. SVEGFR-3 concentrations decreased in response to sunitinib to 57% (IQR 50-88%) and 58% (IQR 47-80%) of the respective baseline concentrations in healthy volunteers and mCRC patients, respectively, with subsequent increase after stop of treatment. The ELISA for the quantification of sVEGFR-3 in human plasma was successfully validated. The applicability of the assay was demonstrated in two clinical trials.

Biomarkers of cell death applicable to early clinical trials

The development of biomarkers of cell death to reflect tumor biology and drug-induced response has garnered interest with the development of several classes of drugs aimed at decreasing the cellular threshold for apoptosis and exploiting pre-existing oncogenic stresses. These novel anticancer drugs, directly targeted to the apoptosis regulatory machinery and aimed at abrogating survival signaling pathways, are entering early clinical trials provoking the question of how to monitor their impact on cancer patients. The parallel development of drugs with predictive biomarkers and their incorporation into early clinical trials are anticipated to support the pharmacological audit trail, to speed the development and reduce the attrition rate of novel drugs whose objective is to provoke tumor cell death. Tumor biopsies are an ideal matrix to measure apoptosis, but surrogate less invasive biomarkers such as blood samples and functional imaging are less challenging to acquire clinically. Archetypal and exploratory examples illustrating the importance of biomarkers to drug development are given. This review explores the substantive challenges associated with the validation, deployment, interpretation and utility of biomarkers of cell death and reviews recent advances in their incorporation in preclinical and early clinical trial contexts.

S-glutathionylated serine proteinase inhibitors as plasma biomarkers in assessing response to redox-modulating drugs

Many cancer drugs impact cancer cell redox regulatory mechanisms and disrupt redox homeostasis. Pharmacodynamic biomarkers that measure therapeutic efficacy or toxicity could improve patient management. Using immunoblot analyses and mass spectrometry, we identified that serpins A1 and A3 were S-glutathionylated in a dose- and time-dependent manner following treatment of mice with drugs that alter reactive oxygen or nitrogen species. Tandem mass spectrometry analyses identified Cys(256) of serpin A1 and Cys(263) of serpin A3 as the S-glutathionylated residues. In human plasma from cancer patients, there were higher levels of unmodified serpin A1 and A3, but following treatments with redox active drugs, relative S-glutathionylation of these serpins was higher in plasma from normal individuals. There is potential for S-glutathionylated serpins A1 and A3 to act as pharmacodynamic biomarkers for evaluation of patient response to drugs that target redox pathways.

The Use of Immunohistochemistry for Biomarker Assessment—Can It Compete with Other Technologies?

A morphology-based assay such as immunohistochemistry (IHC) should be a highly effective means to define the expression of a target molecule of interest, especially if the target is a protein. However, over the past decade, IHC as a platform for biomarkers has been challenged by more quantitative molecular assays with reference standards but that lack morphologic context. For IHC to be considered a “top-tier” biomarker assay, it must provide truly quantitative data on par with non-morphologic assays, which means it needs to be run with reference standards. However, creating such standards for IHC will require optimizing all aspects of tissue collection, fixation, section thickness, morphologic criteria for assessment, staining processes, digitization of images, and image analysis. This will also require anatomic pathology to evolve from a discipline that is descriptive to one that is quantitative. A major step in this transformation will be replacing traditional ocular microscopes with computer monitors and whole slide images, for without digitization, there can be no accurate quantitation; without quantitation, there can be no standardization; and without standardization, the value of morphology-based IHC assays will not be realized.