Targeted S5 RNA sequencing assay for the identification and direct association of common body fluids with DNA donors in mixtures.

The evidentiary value of DNA profiles varies depending upon the context in which the DNA was found. Linking a DNA profile to a particular cellular phenotype in mixtures may aid in assessing its evidentiary relevance and value. We report the development of two dual-function high-resolution messenger RNA (mRNA) sequencing assays that can each identify the presence of 6 body fluids/tissues (blood, semen, saliva, vaginal secretions, menstrual blood, skin) and, via coding region SNPs (cSNPs) present in the body fluid-specific mRNA transcripts, directly associate particular body fluids with their specific DNA donors in mixtures. The original blood, semen, and saliva (BSS) assay contains 23 cSNPs for blood, semen, and saliva, while the expanded 6F (all 6 fluids/tissues) assay encompasses the BSS assay and also contains 23 additional cSNPs for vaginal secretions, menstrual blood, and skin. Software tools were developed to infer the identity of the body fluids present as well as providing the corresponding cSNP genotypes. Concomitant genomic DNA assays (BSS-d and 6F-d), required to genotype the same cSNPs from persons of interest/inferred contributors to the body fluid mixture, were also developed. Body fluid specificity was demonstrated by the ability to identify the body fluid origin of single-source and two-fluid admixtures. The discriminatory power (European Caucasians) for all body fluids is 0.957-0.997, with linkage disequilibrium considered. Reciprocal body fluid admixtures (mixture pairs with the same two donors but reversed body fluid types) were used to demonstrate the ability to identify the body fluid source of origin as well as associate the donor of each of the two fluids.

Application of SNaPshot Technology in Semen-Specific cSNP Genetic Marker.

OBJECTIVES: To explore the feasibility of genetic marker detection of semen-specific coding region single nucleotide polymorphism (cSNP) based on SNaPshot technology in semen stains and mixed body fluid identification. METHODS: Genomic DNA (gDNA) and total RNA were extracted from 16 semen stains and 11 mixtures composed of semen and venous blood, and the total RNA was reverse transcribed into complementary DNA (cDNA). The cSNP genetic markers were screened on the validated semen-specific mRNA coding genes. The cSNP multiplex detection system based on SNaPshot technology was established, and samples were genotyped by capillary electrophoresis (CE). RESULTS: A multiplex detection system containing 5 semen-specific cSNPs was successfully established. In 16 semen samples, except the cSNP located in the TGM4 gene showed allele loss in cDNA detection results, the gDNA and cDNA typing results of other cSNPs were highly consistent. When detecting semen-venous blood mixtures, the results of cSNP typing detected were consistent with the genotype of semen donor and were not interfered by the genotype of venous blood donor. CONCLUSIONS: The method of semen-specific cSNPs detection by SNaPshot technology method can be applied to the genotyping of semen (stains) and provide information for determining the origin of semen in mixed body fluids (stains).

Application and Prospect of RNA Profiling Analysis in Forensic Body Fluid Identification.

In forensic physical evidence identification, the accurate identification of the individual origin and their body fluid composition of the biological samples obtained from the crime scene play a critical role in determining the nature of a crime. In recent years, RNA profiling has become one of the fastest developing methods for body fluids identification. Due to the characteristics of tissue or body fluid specific expression, various types of RNA markers have been proven to be promising candidate markers for body fluids identification in previous studies. This review summarizes the research progress of RNA markers in body fluids identification, including the RNA markers that have been effectively verified in current research and their advantages and disadvantages. Meanwhile, this review prospects the application of RNA markers in forensic medicine.

An mRNA profiling assay incorporating coding region InDels for body fluid identification and the inference of the donor in mixed samples.

Biological traces discovered at crime scenes hold significant significance in forensic investigations. In cases involving mixed body fluid stains, the evidentiary value of DNA profiles depends on the type of body fluid from which the DNA was obtained. Recently, coding region polymorphism analysis has proved to be a promising method for directly linking specific body fluids to their respective DNA contributors in mixtures, which may help to avoid "association fallacy" between separate DNA and RNA evidence. In this study, we present an update on previously reported coding region Single Nucleotide Polymorphisms (cSNPs) by exploring the potential application of coding region Insertion/Deletion polymorphisms (cInDels). Nine promising cInDels, selected from 70 mRNA markers based on stringent screening criteria, were integrated into an existing mRNA profiling assay. Subsequently, the body fluid specificity of our cInDel assay and the genotyping consistency between complementary DNA (cDNA) and genomic DNA (gDNA) were examined. Our study demonstrates that cInDels can function as important multifunctional genetic markers, as they provide not only the ability to confirm the presence of forensically relevant body fluids, but also the ability to associate/dissociate specific body fluids with particular donors.

Identification a novel de novo RUNX2 frameshift mutation associated with cleidocranial dysplasia.

BACKGROUND: Cleidocranial dysplasia (CCD) is a rare genetic disorder affecting bone and cartilage development. Clinical features of CCD comprise short stature, delayed ossification of craniofacial structures with numerous Wormian bones, underdeveloped or aplastic clavicles and multiple dental anomalies. Several studies have revealed that CCD development is strongly linked with different mutations in runt-related transcription factor 2 (RUNX2) gene. OBJECTIVE: Identification and functional characterization of RUNX2 mutation associated with CCD. METHODS: We performed genetic testing of a patient with CCD using whole exome sequencing and found a novel RUNX2 frameshift mutation: c.1550delT in a sporadic case. We also compared the functional activity of the mutant and wild-type RUNX2 through immunofluorescence microscopy and osteocalcin promoter luciferase assay. RESULTS: We found a novel RUNX2 frameshift mutation, c.1550delT (p.Trp518Glyfs*60). Both mutant RUNX2 and wild-type RUNX2 protein were similarly confined in the nuclei. The novel mutation caused abrogative transactivation activity of RUNX2 on osteocalcin promoter. CONCLUSIONS: We explored a novel RUNX2 deletion/frameshift mutation in a sporadic CCD patient. This finding suggests that the VWRPY domain may play a key role in RUNX2 transactivation ability.

Dynamically probing ATP-dependent RNA helicase A-assisted RNA structure conversion using single molecule fluorescence resonance energy transfer.

RNA helicase A (RHA) as a member of DExH-box subgroup of helicase superfamily II, participates in diverse biological processes involved in RNA metabolism in organisms, and these RNA-mediated biological processes rely on RNA structure conversion. However, how RHA regulate the RNA structure conversion was still unknown. In order to unveil the mechanism of RNA structure conversion mediated by RHA, single molecule fluorescence resonance energy transfer was adopted to in our assay, and substrates RNA were from internal ribosome entry site of foot-and-mouth disease virus genome. We first found that the RNA structure conversion by RHA against thermodynamic equilibrium in vitro, and the process of dsRNA YZ converted to dsRNA XY through a tripartite intermediate state. In addition, the rate of the RNA structure conversion and the distribution of dsRNA YZ and XY were affected by ATP concentrations. Our study provides real-time insight into ATP-dependent RHA-assisted RNA structure conversion at the single molecule level, the mechanism displayed by RHA may help in understand how RHA contributes to many biological functions, and the basic mechanistic features illustrated in our work also underlay more complex protein-assisted RNA structure conversions.

Evaluating the performance of five up-to-date DNA/RNA co-extraction methods for forensic application.

The importance of RNA evidence is growing with new developments in RNA profiling methods and purposes. As forensic samples often can be of small quantity, extraction methods with high yields of both DNA and RNA are desirable. In order to identify the optimal DNA/RNA co-extraction workflow for forensic samples, we evaluated the performance of three frequently-used methods, two new approaches for DNA/RNA co-extraction and a manual phenol/chloroform RNA-only extraction method on blood and saliva samples. Based on a comprehensive analysis of the RNA and DNA quantities, as well as the STR genotyping and mRNA profiling results, we conclude that the two frequently-used co-extraction methods, combining commercially available DNA and RNA extraction kits, achieved the best performance. However, not any combination of commercially available DNA and RNA extraction kits works well and extensive optimization is necessary, as seen in the poor results of the two new approaches.

The potential use of Piwi-interacting RNA biomarkers in forensic body fluid identification: A proof-of-principle study.

In the forensic community, RNA profiling has been investigated as a potential method to identify body fluids. Several RNA molecules, including messenger RNA (mRNA), microRNA (miRNA) and circular RNA (circRNA), have been explored as biomarkers to distinguish different body fluids and have led to considerable interest in the development of RNA biomarkers for forensic purposes. Piwi-interacting RNA (piRNA), a class of noncoding RNAs, is a potential biomarker for body fluid identification because of its short length (˜24-32 nt) and specific expression pattern in human tissues. In this proof-of-principle study, we examined the expression levels of four carefully selected piRNAs in forensically relevant biological fluids (venous blood, saliva, semen, menstrual blood and vaginal secretions) using TaqMan quantitative real-time polymerase chain reaction (TaqMan qPCR). piR-55521, which was not detectable in saliva, can differentiate semen from other body fluids because it was strongly expressed in semen compared to the remaining three fluids (> 4000-fold change). Furthermore, piR-55521 could be detected in semen samples made from as little as 200 pg of total RNA, and addition of female component had no effect on the detection limit. Furthermore, the expression differences of other piRNAs, piR-61648, piR-43994 and piR-33151, were statistically significant between at least two types of body fluids. Stability tests also indicated that these piRNAs could be effectively detected in dried samples under laboratory and outdoor conditions for at least six months. Although limited to four piRNAs, this study suggests that the expression pattern of piRNAs could be used to identify body fluids, and that piRNA (piR-55521) is specifically expressed in semen. Such findings suggest that additional work could identify other piRNAs that could serve as biomarkers to identify body fluids.

Expression profile analysis of piwi-interacting RNA in forensically relevant biological fluids.

During the last decade, RNA profiling has emerged as one of the fastest developed methods for discriminating forensically relevant biological samples. As a category of small non-coding RNA, piwi-interacting RNA (piRNA) has recently been proposed to be differentially expressed in different types of body fluids, which indicates that its potential in forensic science is worth exploring. In this study, small RNA from 6 types of biological samples (venous blood, menstrual blood, saliva, semen, vaginal secretions and skin) was prepared and sequenced in order to characterize the expression pattern of piRNA using Ion S5 XL platform. Multiple bioinformatic methods were applied to make interpretation of the massively parallel sequencing data and identify representative biomarkers. A total of 376 piRNAs were initially identified after normalization and filtering. Hierarchical clustering and partial least squares-discriminant analysis (PLS-DA) revealed that their expression profiles exhibited an acceptable discriminating ability for most biological samples. Besides, a panel consists of 37 piRNA candidates was subsequently established for further analysis. The results suggested that with the optimal number of PLS components, the marker-reduced panel was sufficient to construct a PLS-DA model with the same performance as that can be achieved by the entire 376 piRNAs (classification error rate = 0.04). In addition, 5 targeted candidates were further selected for validation. TaqMan RT-qPCR assay results verified the potential of 3 piRNAs (piR-hsa-27622, piR-hsa-1207 and piR-hsa-27493) in distinguishing venous blood and menstrual blood, as well as 2 piRNA (piR-hsa-27493 and piR-hsa-26591) for the discrimination of saliva and vaginal secretions, which emphasized the feasibility of our biomarker selection approach. In brief, our study expanded the amount of potential piRNA biomarkers and demonstrated that the expression features of piRNA could provide valuable information for discriminating forensically relevant biological samples.

Effects of Incorporating Carboxymethyl Chitosan into PMMA Bone Cement Containing Methotrexate.

Treatment of bone metastases usually includes surgical resection with local filling of methotrexate (MTX) in polymethyl methacrylate (PMMA) cement. We investigated whether incorporating carboxymethyl chitosan (CMCS) in MTX-PMMA cement might overcome disadvantages associated with MTX. To determine the optimal CMCS+MTX concentration to suppress the viability of cancer cells, an integrated microfluidic chip culturing highly metastatic lung cancer cells (H460) was employed. The mechanical properties, microstructure, and MTX release of (CMCS+MTX)-PMMA cement were evaluated respectively by universal mechanical testing machine, scanning electron microscopy (SEM), and incubation in simulated body fluid with subsequent HPLC-MS. Implants of MTX-PMMA and (CMCS+MTX)-PMMA cement were evaluated in vivo in guinea pig femurs over time using spiral computed tomography with three-dimensional image reconstruction, and SEM at 6 months. Viability of H460 cells was significantly lowest after treatment with 57 µg/mL CMCS + 21 µg/mL MTX, which was thus used in subsequent experiments. Incorporation of 1.6% (w/w) CMCS to MTX-PMMA significantly increased the bending modulus, bending strength, and compressive strength by 5, 2.8, and 5.2%, respectively, confirmed by improved microstructural homogeneity. Incorporation of CMCS delayed the time-to-plateau of MTX release by 2 days, but increased the fraction released at the plateau from 3.24% (MTX-PMMA) to 5.34%. Relative to the controls, the (CMCS+MTX)-PMMA implants integrated better with the host bone. SEM revealed pores in the cement of the (CMCS+MTX)-PMMA implants that were not obvious in the controls. In conclusion, incorporation of CMCS in MTX-PMMA appears a feasible and effective modification for improving the anti-tumor properties of MTX-PMMA cement.

Optimizing dendritic cell preparation for fusion with melanoma cells.

BACKGROUND: Fusion of dendritic cells (DCs) with melanoma cells could reinforce the antigenicity of tumors as a strategy for the treatment of malignant melanoma. However, the insufficient quantity of DCs and the low fusion efficiency limits the development of such approach. OBJECTIVE: To define the dosage of the stimulating factors as well as the induction condition for the optimal DCs preparation and cell fusion. METHODS: DCs were generated from murine bone marrow cells, and cultured with four different concentrations of the granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-4 (IL-4). DCs were confirmed to be mature by detecting the expression of MHC-II, CD11c, CD80, and CD83 by flow cytometry. DCs-melanoma fusion cells were generated using polyethylene glycols (PEG) with different molecular weights and the fusion efficiency was detected by fluorescence-activated cell sorter (FACS). RESULTS: The largest quantity of DCs was found when cells were cultured with 1000 U/ ml of GM-CSF and 500 U/ml of IL-4 (1.69 ± 0.04 ×106 ml⁻¹, p<0.001 when compared with the other three groups). The expression levels of MHC-II and CD83 on day 7 after incubation were significantly lower than those on day 3 (MHC-II: p<0.001; CD83: p<0.001). The efficiency of cell fusion under induction of PEG-3000 was significantly higher than that of PEG-4000 (15.4 ± 0.56% vs. 11.1 ± 0.45%, p<0.001). CONCLUSIONS: The largest quantity for mature DCs was stimulated with 1000 U/ml of GM-CSF and 500 U/ml of IL-4 and the highest fusion efficiency was under induction of PEG-3000.

YAP-mediated regulation of the chondrogenic phenotype in response to matrix elasticity.

Matrix elasticity exerts considerable influence on the phenotype of terminally differentiated chondrocytes via physical cues. The Yes-associated protein (YAP) transcription co-activator is recognized as a key mediator that may be involved in the nuclear transduction of physical cues controlling cellular behavior and function. However, whether substrate elasticity in the regulation of the chondrocyte phenotype is associated with YAP remains unclear. In this work, we developed micropatterned substrates with varying stiffnesses to investigate the function of YAP and its related Hippo pathway kinases in the regulation of chondrocyte phenotype on soft and stiff substrates. We found that the phenotypic variation of chondrocytes in response to substrate stiffness is concomitant with the changes in YAP localization. The downregulation of YAP expression helps to maintain the chondrogenic phenotype while inhibiting chondrocyte proliferation. Furthermore, the change in the chondrocyte phenotype response to LATS1 kinase inactivation in the Hippo pathway varies significantly between soft and stiff substrates. We also found that LATS1 kinase inactivation promotes chondrocyte dedifferentiation only on stiff substrate. Collectively, these findings reveal that YAP may be involved in the changes that occur in chondrocytes cultured on substrates with different stiffnesses and that these changes do not entirely depend on the Hippo pathway kinase LATS1. Importantly, our findings indicate that YAP inactivation is conducive to the maintenance of the chondrogenic phenotype, thereby providing new insight into articular cartilage repair and regeneration mechanisms.

A new effective scaffold to facilitate peripheral nerve regeneration: chitosan tube coated with maggot homogenate product.

Recent efforts in scientific research in the field of peripheral nerve regeneration have been directed towards the development of artificial nerve guides. Chitosan tubes applied as a biocompatible and biodegradable bilateral guide for nerve repair is a hot spot in research to date. In previous study, we have found the homogenate product from disinfected maggot larvae can promote wound nerve regeneration and neuropeptides release. Wound nerves belong to the peripheral nerve system. We thus hypothesize that maggot homogenate product use as an external layer outside the chitosan tube will be an effective therapy to facilitate peripheral nerve regeneration.