Verification of protein biomarker specificity for the identification of biological stains by quadrupole time‐of‐flight mass spectrometry

Advances in proteomics technology over the past decade offer forensic serologists a greatly improved opportunity to accurately characterize the tissue source from which a DNA profile has been developed. Such information can provide critical context to evidence and can help to prioritize downstream DNA analyses. Previous proteome studies compiled panels of “candidate biomarkers” specific to each of five body fluids (i.e ., peripheral blood, vaginal/menstrual fluid, seminal fluid, urine, and saliva). Here, a multiplex quadrupole time‐of‐flight mass spectrometry assay has been developed in order to verify the tissue/body fluid specificity the 23 protein biomarkers that comprise these panels and the consistency with which they can be detected across a sample population of 50 humans. Single‐source samples of these human body fluids were accurately identified by the detection of one or more high‐specificity biomarkers. Recovery of body fluid samples from a variety of substrates did not impede accurate characterization and, of the potential inhibitors assayed, only chewing tobacco juice appeared to preclude the identification of a target body fluid. Using a series of 2‐component mixtures of human body fluids, the multiplex assay accurately identified both components in a single‐pass. Only in the case of saliva and peripheral blood did matrix effects appear to impede the detection of salivary proteins.     

Detection and identification of body fluid stains using antibody-nanoparticle conjugates

Body fluids are considered one of the most important evidence types in forensic casework. The presence and location of blood, semen and saliva can provide crucial information to investigators. Current practice relies on an accurate visual examination followed by the use of presumptive tests to determine the identity of the body fluid type. Further laboratory based tests are required to unequivocally confirm the identity of a stain. Body fluid stains can be difficult to detect with the naked eye, particularly on dark backgrounds and hence vital evidence may be overlooked. Current methods are fluid-type specific, with a separate, and different, test required for each body fluid. The laborious nature of such analysis and the impossibility of being carried out at the crime scene, leads to a delay in the investigation process that could prove detrimental to the solving of the case. Hence, there is a need for sensitive, specific and direct methods which can simultaneously detect, differentiate, and locate human fluids on items of forensic evidence. Here, we describe the preparation of functionalized iron oxide nanoparticles conjugated to antibodies specific to blood and saliva components and their use in detecting small traces against non-contrasting substrates including glass, ceramic tile, paper and black fabric. The advantage of our technique is that it can simultaneously detect blood and saliva and can spatially locate and differentiate these body fluid types. Most importantly, our technology, which exploits the superparamagnetic properties of iron oxide nanoparticles, works in situ with no need to remove the body fluid stains for testing and with no washing steps and does not interfere with downstream DNA profiling. Thus, our technology represents a novel and effective alternative to existing methods.     

Development of a body fluid identification multiplex via DNA methylation analysis

The goal of this study is to develop an epigenetic multiplex for body fluid identification based on tissue specific DNA methylation. A series of genetic loci capable of discerning the origin of DNA as coming from saliva, blood, vaginal epithelia, or semen were used for this application. The markers – BCAS4, CG06379435, VE_8, and ZC3H12D – were amplified together and then sequenced via pyrosequencing. Methylation values for cytosine guanine dinucleotide (CpG) sites at each locus were then measured across the four markers. In total, 124 samples were collected, and bisulfite modified to convert unmethylated DNA to uracil. This converted DNA was then amplified via multiplex PCR with reverse primers containing a biotin molecule. Biotinylated PCR products were then analyzed using pyrosequencing to generate a series of pyrograms containing 18 CpG sites. The percent methylation at each CpG site was determined, and then agglomerative hierarchical cluster analysis was used to create a model to indicate sample origin. Further analysis reduced the number of CpG sites required for optimal determination of body fluid type to five. This study demonstrates an efficient multiplexed body fluid identification process utilizing DNA methylation that can be easily implemented in forensic laboratories.     

Extended specificity studies of mRNA assays used to infer human organ tissues and body fluids

Messenger RNA (mRNA) profiling is a technique increasingly applied for the forensic identification of body fluids and skin. More recently, an mRNA‐based organ typing assay was developed which allows for the inference of brain, lung, liver, skeletal muscle, heart, kidney, and skin tissue. When applying this organ typing system in forensic casework for the presence of animal, rather than human, tissue is an alternative scenario to be proposed, for instance that bullets carry cell material from a hunting event. Even though mRNA profiling systems are commonly in silico designed to be primate specific, physical testing against other animal species is generally limited. In this study, human specificity of the organ tissue inferring system was assessed against organ tissue RNAs of various animals. Results confirm human specificity of the system, especially when utilizing interpretation rules considering multiple markers per cell type. Besides, we cross‐tested our organ and body fluid mRNA assays against the target types covered by the other assay. Marker expression in the nontarget organ tissues and body fluids was observed to a limited extent, which emphasizes the importance of involving the case‐specific context of the forensic samples in deciding which mRNA profiling assay to use and when for interpreting results.     

Surface modified capillary electrophoresis combined with in solution isoelectric focusing and MALDI-TOF/TOF MS: A gel-free multidimensional electrophoresis approach for proteomic profiling—Exemplified on human follicular fluid

Development of miniaturized analytical tools continues to be of great interest to face the challenges in proteomic analysis of complex biological samples such as human body fluids. In the light of these challenges, special emphasis is put on the speed and simplicity of newly designed technological approaches as well as the need for cost efficiency and low sample consumption. In this study, we present an alternative multidimensional bottom-up approach for proteomic profiling for fast, efficient and sensitive protein analysis in complex biological matrices. The presented setup was based on sample pre-fractionation using microscale in solution isoelectric focusing (IEF) followed by tryptic digestion and subsequent capillary electrophoresis (CE) coupled off-line to matrix assisted laser desorption/ionization time of flight tandem mass spectrometry (MALDI TOF MS/MS). For high performance CE-separation, PolyE-323 modified capillaries were applied to minimize analyte–wall interactions. The potential of the analytical setup was demonstrated on human follicular fluid (hFF) representing a typical complex human body fluid with clinical implication. The obtained results show significant identification of 73 unique proteins (identified at 95% significance level), including mostly acute phase proteins but also protein identities that are well known to be extensively involved in follicular development.     

Analysis of DNA methylation markers for tissue identification in individuals with different clinical phenotypes

Deoxyribonucleic acid (DNA) methylation patterns can be used to identify the type of tissue or body fluid found at a crime scene. However, tissue-related methylation levels have not been analyzed in individuals with different illnesses and medical conditions in forensic-specific studies. The primary goal of this study was to investigate if certain clinical phenotypes can alter the methylation levels of CpG sites in genes involved in tissue typing. Four studies with focus on DNA methylation analysis on individuals with different clinical conditions were selected from the Gene Expression Omnibus database. Then, a list of 137 CpG sites was compiled for further investigation. Statistical tests were performed to compare the beta-values results obtained for the control groups and the individuals affected by medical conditions. For each study, CpG sites that presented significant statistical differences between patients and control group were identified and it was possible to notice that DNA methylation levels can be affected in sites with potential forensic use. Although the observed DNA methylation variation (less than 10% difference) in this study would likely not cause any issues in body fluid identification, the results are important to show that this type of analysis should be taken into consideration when investigating and further validating body fluid markers. The CpG sites identified in this study should be further investigated by future studies on body fluids identification, and due to the significant difference in methylation levels in samples from affected individuals, caution must be taken before including these sites in tissue identification investigations.     

Differential pre‐amplification of STR loci for fragmented forensic DNA profiling

DNA profiling of short tandem repeats (STR) has been successfully used for the identification of individuals in forensic samples, accidents and natural disasters. However, STR profiling of DNA isolated from old crime scenes and damaged biological samples is difficult due to DNA degradation and fragmentation. Here, we show that pre‐amplification of STR loci using biotinylated primers for the STR loci is an efficient strategy to obtain STR profiling results from fragmented forensic samples. Analysis of STR loci with longer amplicon sizes is generally hampered, since these relatively long loci are vulnerable to DNA fragmentation. This problem was overcome by using reduced or increased primer concentrations for loci with shorter or longer amplicon sizes, respectively, in our pre‐amplification strategy. In addition, pre‐amplification of STR loci into two groups of short or long amplicon size increases the efficiency of STR profiling from highly fragmented forensic DNA samples. Therefore, differential pre‐amplification of STR loci is an effective way to obtain DNA profiling results from fragmented forensic samples.     

Gold nanoparticle-based homogeneous fluorescent aptasensor for multiplex detection

We developed a homogeneous fluorescence assay for multiplex detection based on the target induced conformational change of DNA aptamers. DNA aptamers were immobilized on quantum dots (QDs), and QDs conjugated ssDNA was adsorbed on the surface of gold nanoparticles (AuNPs) by electrostatic interaction between uncoiled ssDNA and the AuNPs. Subsequently the fluorescence of QDs was effectively quenched by the AuNPs due to fluorescence resonance energy transfer (FRET) of QDs to AuNPs. In the presence of targets, the QDs conjugated aptamers were detached from AuNPs by target induced conformational change of aptamers, consequently the fluorescence of the QDs was recovered proportional to the target concentration. In this study, three different QD/aptamer conjugates were used for multiplex detection of mercury ions, adenosine and potassium ions. In a control experiment, all of the three targets were simultaneously detected with high selectivity.     

Metabolic profiling of mouse cerebrospinal fluid by sheathless CE-MS

The need for sensitive analytical technologies applicable to metabolic profiling of volume-restricted biological samples is high. Here, we demonstrate feasibility of capillary electrophoresis (CE) coupled to electrospray ionization mass spectrometry (MS) with sheathless nano-electrospray interface for non-targeted profiling of ionogenic metabolites in body fluids of experimental animals. A representative mixture of the metabolites and body fluids of mice such as cerebrospinal fluid (CSF), urine and plasma were used as examples of low-volume biological samples for method evaluation. An injection volume of only 9?nL resulted in limits of detection between 0.7 and 12?nM for the metabolite mixture. The method allowed the detection of ～350 molecular features in mouse CSF (an injection volume of ca. 45?nL), while ～400 features were observed in mouse plasma and ～3,500 features in mouse urine (an injection volume of ca. 9?nL). The low-volume body fluid samples were analyzed directly after only 1:1 dilution with water, thereby fully retaining sample integrity, which is of crucial importance for non-targeted metabolic profiling. As little is known about the metabolic composition of mouse CSF, we identified a fraction of the molecular features in mouse CSF using accurate mass information, migration times, MS/MS data, and comparison with authentic standards. We conclude that sheathless CE-MS can be used for sensitive metabolic profiling of volume-restricted biological samples.     

Label-free aptamer biosensor for selective detection of thrombin

We fabricated a novel fluorescence biosensor for the selective detection of thrombin by using bovine serum albumin-capped CdS quantum dots (BSA-CdS QDs). Two kinds of designed DNA (DNA1 and DNA2) could bind to CdS QDs through the electrostatic interaction between DNA and Cd²⁺ on the surface of CdS QDs. The obtained DNA/BSA-CdS QDs kept stable in the solution with the fluorescence intensity obviously enhanced. Hairpin structure of DNA1contained two domains, one is the aptamer sequence of thrombin and the other is the complementary sequence of DNA2. When thrombin was added, it would bind to DNA1 and induce the hairpin structure of DNA1 changed into G-quadplex structure. Meanwhile, DNA2 would transfer from the surface of CdS QDs to DNA1 via hybridization, which resulted in the removal of DNA1 and DNA2 from the surface of CdS QDs, and led to the fluorescence intensity of CdS QDs reduced. Thus, the determination of thrombin could be achieved by monitoring the change of the fluorescence intensity of CdS QDs. The present method is simple and fast, and exhibits good selectivity for thrombin over other proteins. We have successfully detected thrombin in human serum samples with satisfactory results.     

Bioanalytical methods for metabolomic profiling: Detection of head and neck cancer,including oral cancer

Metabolomics is an emerging field dealing with the measurement and interpretation of small molecular byproducts of biochemical processes, or metabolites, which can be used to generate profiles from biological samples. Promising for use in pathophysiology, metabolomic profiles give the immediate biological state of a sample. These profiles are altered in diseases and are detectable in biological samples, such as tissue, blood, urine, saliva, and others. Most remarkably, metabolic profiles usually are altered before symptoms appear in a patient. For this reason, metabolomics has potential as a reliable method for an early diagnosis of diseases through disease biomarker identification. This application is most prevalent in cancer, such as head and neck cancer (HNC). Metabolomic studies offer avenues to improve on current medical techniques through the application of mass spectrometry (MS), nuclear magnetic resonance spectroscopy (NMR), and statistical analysis to determine better biomarkers than those currently known. In this review, we discuss the use of MS and NMR tools for detecting biomarkers in tissue and fluid samples, and the appropriateness of metabolomics in analyzing cancer. Advantages, disadvantages, and recent studies on metabolomic profiling techniques in HNC analysis are also discussed herein.     

FINDER: A Fluidly Confined CRISPR-Based DNA Reporter on Living Cell Membranes for Rapid and Sensitive Cancer Cell Identification

The accurate, rapid, and sensitive identification of cancer cells in complex physiological environments is significant in biological studies, personalized medicine, and biomedical engineering. Inspired by the naturally confined enzymes on fluid cell membranes, a f luidly confin ed CRISPR-based D NA reporter (FINDER) was developed on living cell membranes, which was successfully applied for rapid and sensitive cancer cell identification in clinical blood samples. Benefiting from the spatial confinement effect for improved local concentration, and membrane fluidity for higher collision efficiency, the activity of CRISPR-Cas12a was, for the first time, found to be significantly enhanced on living cell membranes. This new phenomenon was then combined with multiple aptamer-based DNA logic gate for cell recognition, thus a FINDER system capable of accurate, rapid and sensitive cancer cell identification was constructed. The FINDER rapidly identified target cells in only 20 min, and achieved over 80 % recognition efficiency with only 0.1 % of target cells presented in clinical blood samples, indicating its potential application in biological studies, personalized medicine, and biomedical engineering.     

Synthesis of NAC capped near infrared-emitting CdTeS alloyed quantum dots and application for in vivo early tumor imaging

The synthesis of water-soluble near-infrared (NIR)-emitting quantum dots (QDs) has recently received extensive attention for non-invasive detection of biological information in living subjects. Highly fluorescent CdTeS alloyed QDs for biological application are introduced in this paper. QDs were synthesized by a hydrothermal method and coated with N-acetyl-l-cysteine (NAC) as both bioactive ligand and sulfur source for biocompatibility and biological stability. The optical properties, morphology and structure of CdTeS alloyed QDs were characterized. The in vitro and in vivo toxicity was intensively investigated. Furthermore, the dynamics and bio-distribution of CdTeS alloyed QDs on living mice were studied. To explore biomedical application, folate-polyethylene glycol (FA-PEG) was used to decorate the CdTeS alloyed QDs (FP-CdTeS QDs) for targeted imaging of tumors over-expressing the folate receptor (FR). The tumor targeting capability of FP-CdTeS QDs on tumor bearing nude mice was demonstrated. The results showed that the prepared CdTeS QDs have excellent optical properties and low toxicity, which makes them an ideal inorganic material for biomedical imaging. In addition, the folate-PEG conjugated NIR-QDs displayed good biocompatibility as well as excellent sensitivity and specificity for optical imaging of tumors which can extend the application of CdTeS QDs.     

Dual-readout test strips platform for portable and highly sensitive detection of alkaline phosphatase in human serum samples

In this work, a very simple dual-readout lateral flow test strip (LFTS) platform was developed for sensitive detection of alkaline phosphatase (ALP) based on a portable device. In this assay, quantum dots (QDs) conjugated with bovine serum albumin (QDs-BSA) were chosen as fluorescence signal labels. In the absence of ALP, MnO₂ nanosheets aggregate on the test line and exhibit an obvious brown color, which can be observed by naked eyes to realize semi-qualitative analysis. Meanwhile, fluorescence intensity of QDs-BSA can also be effectively quenched by MnO₂ nanosheets due to inner-filter effect. Correspondingly, in the presence of ALP, ALP can catalyze the hydrolysis of ascorbic acid 2-phosphate (AAP) to generate L-ascorbic acid (AA), which can reduce MnO₂ into Mn²⁺, accompanying with the obvious fluorescence recovery of the QDs. By simply monitoring the change of colorimetric and fluorescent signal on the test line, trace amount of ALP can be quantitatively detected. Under the optimal conditions, measurable evaluation of ALP was reached in a linear range from 1 U/L to 20 U/L with a detection limit of 0.7 U/L based on fluorescence signal. Furthermore, this colorimetric/fluorescent dual-readout assay was successfully applied to monitor ALP in human serum samples, showing its great potential as a point of care biosensor for clinical diagnosis.     

双靶向CdTe量子点的制备及其在细胞标记中的应用

以巯基乙酸和巯基乙酰肼为稳定剂,制备了酸度敏感型CdTe量子点。经与抗体链接,该量子点具备酸度敏感、免疫识别双重靶向功能。经荧光光谱分析、透射电镜图像及细胞免疫成像证明,抗体已成功链接于量子点表面,且该量子点具有酸度敏感及抗体识别的双重靶向功能,可以实现对肿瘤细胞的特异性标记。     

Long-term exposure to CdTe quantum dots causes functional impairments in live cells

Several studies suggested that the cytotoxic effects of quantum dots (QDs) may be mediated by cadmium ions (Cd2+) released from the QDs cores. The objective of this work was to assess the intracellular Cd2+ concentration in human breast cancer MCF-7 cells treated with cadmium telluride (CdTe) and core/shell cadmium selenide/zinc sulfide (CdSe/ZnS) nanoparticles capped with mercaptopropionic acid (MPA), cysteamine (Cys), or N-acetylcysteine (NAC) conjugated to cysteamine. The Cd2+ concentration determined by a Cd2+-specific cellular assay was below the assay detection limit (<5 nM) in cells treated with CdSe/ZnS QDs, while in cells incubated with CdTe QDs, it ranged from approximately 30 to 150 nM, depending on the capping molecule. A cell viability assay revealed that CdSe/ZnS QDs were nontoxic, whereas the CdTe QDs were cytotoxic. However, for the various CdTe QD samples, there was no dose-dependent correlation between cell viability and intracellular [Cd2+], implying that their cytotoxicity cannot be attributed solely to the toxic effect of free Cd2+. Confocal laser scanning microscopy of CdTe QDs-treated cells imaged with organelle-specific dyes revealed significant lysosomal damage attributable to the presence of Cd2+ and of reactive oxygen species (ROS), which can be formed via Cd2+-specific cellular pathways and/or via CdTe-triggered photoxidative processes involving singlet oxygen or electron transfer from excited QDs to oxygen. In summary, CdTe QDs induce cell death via mechanisms involving both Cd2+ and ROS accompanied by lysosomal enlargement and intracellular redistribution.     

Use of quantum dots in the development of assays for cancer biomarkers

Biomarker assays may be useful for screening and diagnosis of cancer if a set of molecular markers can be quantified and statistically differentiated between cancerous cells and healthy cells. Markers of disease are often present at very low concentrations, so methods capable of low detection limits are required. Quantum dots (QDs) are nanoparticles that are emerging as promising probes for ultrasensitive detection of cancer biomarkers. QDs attached to antibodies, aptamers, oligonucleotides, or peptides can be used to target cancer markers. Their fluorescent properties have enabled QDs to be used as labels for in-vitro assays to quantify biomarkers, and they have been investigated as in-vivo imaging agents. QDs can be used as donors in assays involving fluorescence resonance energy transfer (FRET), or as acceptors in bioluminescence resonance energy transfer (BRET). The nanoparticles are also capable of electrochemical detection and are potentially useful for “lab-on-a-chip” applications. Recent developments in silicon QDs, non-blinking QDs, and QDs with reduced-size and controlled-valence further make these QDs bioanalytically attractive because of their low toxicity, biocompatibility, high quantum yields, and diverse surface modification flexibility. The potential of multiplexed sensing using QDs with different wavelengths of emission is promising for simultaneous detection of multiple biomarkers of disease.

Molecularly Imprinted Polymer Coated Quantum Dots for Multiplexed Cell Targeting and Imaging

Advanced tools for cell imaging are of great interest for the detection, localization, and quantification of molecular biomarkers of cancer or infection. We describe a novel photopolymerization method to coat quantum dots (QDs) with polymer shells, in particular, molecularly imprinted polymers (MIPs), by using the visible light emitted from QDs excited by UV light. Fluorescent core–shell particles specifically recognizing glucuronic acid (GlcA) or N‐acetylneuraminic acid (NANA) were prepared. Simultaneous multiplexed labeling of human keratinocytes with green QDs conjugated with MIP‐GlcA and red QDs conjugated with MIP‐NANA was demonstrated by fluorescence imaging. The specificity of binding was verified with a non‐imprinted control polymer and by enzymatic cleavage of the terminal GlcA and NANA moieties. The coating strategy is potentially a generic method for the functionalization of QDs to address a much wider range of biocompatibility and biorecognition issues.     

Highly sensitive polymerase chain reaction-free quantum dot-based quantification of forensic genomic DNA

Forensic DNA samples can degrade easily due to exposure to light and moisture at the crime scene. In addition, the amount of DNA acquired at a criminal site is inherently limited. This limited amount of human DNA has to be quantified accurately after the process of DNA extraction. The accurately quantified extracted genomic DNA is then used as a DNA template in polymerase chain reaction (PCR) amplification for short tandem repeat (STR) human identification. Accordingly, highly sensitive and human-specific quantification of forensic DNA samples is an essential issue in forensic study. In this work, a quantum dot (Qdot)-labeled Alu sequence was developed as a probe to simultaneously satisfy both the high sensitivity and human genome selectivity for quantification of forensic DNA samples. This probe provided PCR-free determination of human genomic DNA and had a 2.5-femtogram detection limit due to the strong emission and photostability of the Qdot. The Qdot-labeled Alu sequence has been used successfully to assess 18 different forensic DNA samples for STR human identification.     

One-pot synthesis of strongly fluorescent DNA-CuInS2 quantum dots for label-free and ultrasensitive detection of anthrax lethal factor DNA

Herein, high quality DNA-CuInS₂ QDs are facilely synthesized through a one-pot hydrothermal method with fluorescence quantum yield as high as 23.4%, and the strongly fluorescent DNA-CuInS₂ QDs have been utilized as a novel fluorescent biosensor for label-free and ultrasensitive detection of anthrax lethal factor DNA. L-Cysteine (L-Cys) and a specific-sequence DNA are used as co-ligands to stabilize the CuInS₂ QDs. The specific-sequence DNA consists of two domains: phosphorothiolates domain (sulfur-containing variants of the usual phosphodiester backbone) controls the nanocrystal passivation and serves as a ligand, and the functional domain (non-phosphorothioates) controls the biorecognition. The as-prepared DNA-CuInS₂ QDs have high stability, good water-solubility and low toxicity. Under the optimized conditions, a linear correlation was established between the fluorescence intensity ratio I/I₀ (I₀ is the original fluorescence intensity of DNA-CuInS₂ QDs, and I is the fluorescence intensity of DNA-CuInS₂ QDs/GO with the addition of various concentrations of anthrax lethal factor DNA) and the concentration of anthrax lethal factor DNA in the range of 0.029–0.733 nmol L⁻¹ with a detection limit of 0.013 nmol L⁻¹. The proposed method has been successfully applied to the determination of anthrax lethal factor DNA sequence in human serum samples with satisfactory results. Because of low toxicity and fine biocompatibility, DNA-CuInS₂ QDs also hold potential applications in bioimaging.