Application Of Molecular Diagnosis Research Articles

Self-Powered FEN1 Biosensor Based on Accelerated CRISPR/Cas Trans-Cleavage around Porous Fe3O4 Nanoparticles.

Flap endonuclease 1 (FEN1) is a structure-specific endonuclease that plays a critical role in the maintenance of genome integrity. In this work, we demonstrate a novel self-powered electrochemical FEN1 biosensor for potential applications in molecular diagnosis. Porous Fe3O4 nanoparticles are first prepared, and single-strand DNA probes are absorbed on the surface of the nanoparticles. Thus, electrochemical species of [Fe(CN)6]3- can be encapsulated inside the porous nanoparticles with the molecular gate of negatively charged DNA. On the other hand, a dumbbell structured DNA probe with 5' flap is designed. FEN1 is able to cleave the flap and activate the CRISPR/Cas system for the digestion of single-stranded DNA around Fe3O4 nanoparticles. As a result, the leakage of [Fe(CN)6]3- contributes to an enhanced electrochemical response, which can be used to reveal the level of FEN1. The high sensitivity of this biosensor is due to the application of porous nanomaterials and Mn2+ accelerated CRISPR/Cas cleavage. It succeeds in detection of biological samples and screening of FEN1 inhibitors. Therefore, this proposed method has potential applications in the early diagnosis of diseases and drug discovery.

High-throughput Approaches to Detect Cytokines and Chemokines Secretion by Both Autophagy and Endosome Vesicle Fusion of HBMEC by Knocking Down the NLRP2 Gene

Background: Given the rapid increase in serious infectious and inflammatory diseases in the general population worldwide, it is vital to advance our understanding of the process of infection and inflammation. Objective: These illnesses can be treated by diverse cytokines, chemokines, and chemical compounds, but how to find and identify effective protein drugs is unknown. In this study, large–scale analytical approaches, such as high–throughput chips with RNA-Seq that construct the protein regulatory networks, were established. Methods: NLRP2:shRNA (1–3) and GFP: Control lentivirus were fabricated to infect Human Brain Microvascular Endothelial Cells (HBMEC) to knock down NLRP2 gene that not only possesses biochemical activity but also bio-mechanical properties. Once HBMEC was loaded on the 18mmX18mm circular soft cover slip, by knocking down NLRP2 gene processing and adding puromycin, a large number of cytokines were secreted to activate both autophagy and endosome vesicle signaling by KEGG pathway analysis, which was successfully detected by both ELISA approach and QAH-Neu-1 chip. However, no secretion from GFP: Control was reported. Results: It was demonstrated that the NLRP2 gene was highly responsive to cytokines. The protein regulatory network from RNA–Seq platform demonstrated that the secretion by knocking down the NLRP2 gene was highly correlated with autophagy, endosome, multivesicular body, phosphatidylinositol, and necrosis signalling pathway. Furthermore, most of the cytokines expressed were found to be specific for intracellular vesicle–dependent secretion, leading to obvious cell swelling and shedding, membrane protein dotting to nucleation, and actin dynamics. Interestingly, it was also found that autophagy, together with endosome signalling, was collectively activated to boost the secretion to cause a “cytokine storm”, which led to lipid phase separation. Conclusion: This study proposed high throughput approaches centered on the NLRP2 gene network for many severe diseases, providing novel insight into biological pathways influencing infection and inflammation (e.g., COVID-19/E.coli). They can be modulated as potential therapeutic targets and used as biomarkers in the diagnosis and treatment of many diseases to promote human health. This increases our interest in developing new leadless-peptides at the genomics and proteomics levels to obtain cytokines and chemokines for micro-array constructions (VirD‒cytokines, VirD‒enzymes), antibody and vaccine development for infections, diabetes, cardiovascular disease, atherosclerosis, non–alcoholic fatty liver, auto-immune, neurodegenerative disorder, and even cancer-related disease therapy. They have the most valuable applications in molecular diagnosis, protein marker discovery, and bio-therapy.

Visualizing DNA/RNA, Proteins, and Small Molecule Metabolites within Live Cells.

Live cell imaging is essential for obtaining spatial and temporal insights into dynamic molecular events within heterogeneous individual cells, in situ intracellular networks, and in vivo organisms. Molecular tracking in live cells is also a critical and general requirement for studying dynamic physiological processes in cell biology, cancer, developmental biology, and neuroscience. Alongside this context, this review provides a comprehensive overview of recent research progress in live-cell imaging of RNAs, DNAs, proteins, and small-molecule metabolites, as well as their applications in molecular diagnosis, immunodiagnosis, and biochemical diagnosis. A series of advanced live-cell imaging techniques have been introduced and summarized, including high-precision live-cell imaging, high-resolution imaging, low-abundance imaging, multidimensional imaging, multipath imaging, rapid imaging, and computationally driven live-cell imaging methods, all of which offer valuable insights for disease prevention, diagnosis, and treatment. This review article also addresses the current challenges, potential solutions, and future development prospects in this field.

Photocleavable DNA Nanotube-Based Dual-Amplified Resonance Rayleigh Scattering System for MicroRNA Detection Incorporating Molecular Computing-Cascaded Keypad Lock Functionality.

Cascade molecular events in complex systems are of vital importance for enhancing molecular diagnosis and information processing. However, the conversion of a cascaded biosensing system into a multilayer encrypted molecular keypad lock remains a significant challenge in the development of molecular logic devices. In this study, we present a photocleavable DNA nanotube-based dual-amplified resonance Rayleigh scattering (RRS) system for detecting microRNA-126 (miR-126). The cascading dual-amplification biosensing system provides a multilayer-encrypted prototype with the functionality of a molecular computing cascade keypad lock. RRS signals were greatly amplified by using photocleavable DNA nanotubes and enzyme-assisted strand displacement amplification (SDA). In the presence of miR-126, enzyme-assisted SDA produced numerous identical nucleotide fragments as the target, which were then specifically attached to magnetic beads through the DNA nanotube by using a Y-shaped DNA scaffold. Upon ultraviolet irradiation, the DNA nanotube was released into the solution, resulting in an increase in the intensity of the RRS signal. This strategy demonstrated a low limit of detection (0.16 fM) and a wide dynamic range (1 fM to 1 nM) for miR-126. Impressively, the enzyme-assisted SDA offers a molecular computing model for generating the target pool, which serves as the input element for unlocking the system. By cascading the molecular computing process, we successfully constructed a molecular keypad lock with a multilevel authentication technique. The proposed system holds great potential for applications in molecular diagnosis and information security, indicating significant value in integrating molecular circuits for intelligent sensing.

A flash signal amplification approach for ultrasensitive and rapid detection of single nucleotide polymorphisms in tuberculosis

In recent years, the demand for rapid, sensitive, and simple methods for diagnosing deoxyribonucleic acid (DNA) has grown due to the increase in the variation of infectious diseases. This work aimed to develop a flash signal amplification method coupled with electrochemical detection for polymerase chain reaction (PCR)-free tuberculosis (TB) molecular diagnosis. We exploited the slightly miscible properties of butanol and water to instantly concentrate a capture probe DNA, a single-stranded mismatch DNA, and gold nanoparticles (AuNPs) to a small volume to reduce the diffusion and reaction time in the solution. In addition, the electrochemical signal was enhanced once two strands of DNA were hybridized and bound to the surface of the gold nanoparticle at an ultra-high density. To eliminate non-specific adsorption and identify mismatched DNA, the self-assembled monolayers (SAMs) and Muts proteins were sequentially modified on the working electrode. This sensitive and specific approach can detect as low as attomolar levels of DNA targets (18 aM) and is successfully applied to detecting tuberculosis-associated single nucleotide polymorphisms (SNPs) in synovial fluid. More importantly, as this biosensing strategy can amplify the signal in only a few seconds, it possesses a great potential for point-of-care and molecular diagnosis applications.

Droplet digital recombinase polymerase amplification for multiplexed detection of human coronavirus.

Since the outbreak of coronavirus 2019 (COVID-19), detection technologies have been attracting a great deal of attention in molecular diagnosis applications. In particular, the droplet digital PCR (ddPCR) has become a promising tool as it offers absolute quantification of target nucleic acids with high specificity and sensitivity. In recent years, the combination of the isothermal amplification strategies has made ddPCR a popular method for on-site testing by enabling amplification at a constant temperature. However, the current isothermal ddPCR assays are still challenging due to inherent non-specific amplification. In this paper, we present a multiplexed droplet digital recombinase polymerase amplification (MddRPA) with precise initiation of the reaction. First, the reaction temperature and dynamic range of reverse transcription (RT) and RPA were characterized by real-time monitoring of fluorescence intensities. Using a droplet-based microfluidic chip, the master mix and the initiator were fractionated and rapidly mixed within well-confined droplets. Due to the high heat transfer and mass transfer of the droplets, the precise initiation of the amplification was enabled and the entire assay could be conducted within 30 min. The concentrations of target RNA in the range from 5 copies per μL to 2500 copies per μL could be detected with high linearity (R2 > 0.999). Furthermore, the multiplexed detection of three types of human coronaviruses was successfully demonstrated with high specificity (>96%). Finally, we compared the performance of the assay with a commercial RT-qPCR system using COVID-19 clinical samples. The MddRPA assay showed a 100% concordance with the RT-qPCR results, indicating its reliability and accuracy in detecting SARS-CoV-2 nucleic acids in clinical samples. Therefore, our MddRPA assay with rapid detection, precise quantification, and multiplexing capability would be an interesting method for molecular diagnosis of viral infections.

Tuning Plasmonic Properties of Gold Nanoparticles by Employing Nanoscale DNA Hydrogel Scaffolds

Noble metals have always fascinated researchers due to their feasible and facile approach to plasmonics. Especially the extensive utilization of gold (Au) has been found in biomedical engineering, microelectronics, and catalysis. Surface plasmonic resonance (SPR) sensors are achievable by employing plasmonic nanoparticles. The past decades have seen colossal advancement in noble metal nanoparticle research. Surface plasmonic biosensors are advanced in terms of sensing accuracy and detection limit. Likewise, gold nanoparticles (AuNPs) have been widely used to develop distinct biosensors for molecular diagnosis. DNA nanotechnology facilitates advanced nanostructure having unique properties that contribute vastly to clinical therapeutics. The critical element for absolute control of materials at the nanoscale is the engineering of optical and plasmonic characteristics of the polymeric and metallic nanostructure. Correspondingly, AuNP's vivid intense color expressions are dependent on their size, shape, and compositions, which implies their strong influence on tuning the plasmonic properties. These plasmonic properties of AuNPs have vastly exerted the biosensing and molecular diagnosis applications without any hazardous effects. Here, we have designed nanoscale X-DNA-based Dgel scaffolds utilized for tuning the plasmonic properties of AuNPs. The DNA nanohydrogel (Dgel) scaffolds engineered with three different X-DNAs of distinct numbers of base pairs were applied. We have designed X-DNA base pair-controlled size-varied Dgel scaffolds and molar ratio-based nano assemblies to tune the plasmonic properties of AuNPs. The nanoscale DNA hydrogel's negatively charged scaffold facilitates quaternary ammonium ligand-modified positively charged AuNPs to flocculate around due to electrostatic charge attractions. Overall, our study demonstrates that by altering the DNA hydrogel scaffolds and the physical properties of the nanoscale hydrogel matrix, the SPR properties can be modulated. This approach could potentially benefit in monitoring diverse therapeutic biomolecules.

Increased diagnostic yield in a cohort of hearing loss families using a comprehensive stepwise strategy of molecular testing.

Hearing loss is one of the most common sensory disorders in humans. This study proposes a stepwise strategy of deafness gene detection using multiplex PCR combined with high-throughput sequencing, Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), and whole-exome sequencing (WES) to explore its application in molecular diagnosis of hearing loss families. A total of 152 families with hearing loss were included in this study, the highest overall diagnosis rate was 73% (111/152). The diagnosis rate of multiplex PCR combined with high-throughput sequencing was 52.6% (80/152). One families was diagnosed by Sanger sequencing of GJB2 exon 1. Two families were diagnosed by MLPA analysis of the STRC gene. The diagnosis rate with additional contribution from WES was 18.4% (28/152). We identified 21 novel variants from 15 deafness genes by WES. Combining WES and deep clinical phenotyping, we diagnosed 11 patients with syndromic hearing loss (SHL). This study demonstrated improved diagnostic yield in a cohort of hearing loss families and confirmed the advantages of a stepwise strategy in the molecular diagnosis of hearing loss.

Clinical Exome Sequencing Identifies NDP Gene Variants in Two Chinese Families with X-Linked Norrie Disease

Purpose: To explore the genetic defects in two Chinese families with X-linked Norrie disease (ND). Methods: We analyzed two Chinese families with ND at molecular level through clinical exome sequencing and the variations were identified by Sanger sequencing. Results: Two genetic variations were found in the NDP gene by clinical exome sequencing, a partial deletion of 801 bp contained the whole exon 2 and a missense variant (164G>A) within codon 55 that resulted in the interchange of cysteine by phenylalanine. Clinical findings were more severe in the patients who presented the missense variant. Conclusion: We report two genetic variations in the NDP gene in Chinese that extend the mutational and phenotypic spectra of NDP gene, and also demonstrate the feasibility of clinical exome sequencing in application of molecular diagnosis.

A Portable Digital Loop-Mediated Isothermal Amplification Platform Based on Microgel Array and Hand-Held Reader.

Digital polymerase chain reaction (dPCR) has found widespread applications in molecular diagnosis of various diseases owing to its sensitive single-molecule detection capability. However, the existing dPCR platforms rely on the auxiliary procedure to disperse DNA samples, which needs complicated operation, expensive apparatus, and consumables. Besides, the complex and costly dPCR readers also impede the applications of dPCR for point-of-care testing (POCT). Herein, we developed a portable digital loop-mediated isothermal amplification (dLAMP) platform, integrating a microscale hydrogel (microgel) array chip for sample partition, a miniaturized heater for DNA amplification, and a hand-held reader for digital readout. In the platform, the chip with thousands of isolated microgels holds the capability of self-absorption and partition of DNA samples, thus avoiding auxiliary equipment and professional personnel operations. Using the integrated dLAMP platform, λDNA templates have been quantified with a good linear detection range of 2-1000 copies/μL and a detection limit of 1 copy/μL. As a demonstration, the epidermal growth factor receptor L858R gene mutation, a crucial factor for the susceptibility of the tyrosine kinase inhibitor in non-small-cell lung cancer treatment, has been accurately identified by the dLAMP platform with a spiked plasma sample. This work shows that the developed dLAMP platform provides a low-cost, facile, and user-friendly solution for the absolute quantification of DNA, showing great potential for the POCT of nucleic acids.

A fast and ultrasensitive detection of zinc ions based on “signal on” mode of electrochemiluminescence from single oxygen generated by porphyrin grafted onto palladium nanocubes

Zinc ions (Zn2+) act as a transcription factor in eukaryotic cells for mediating protein-protein interactions in human healthy. The simple and sensitive detection of Zn2+ is the crucial mission in analytical field. This work demonstrated a novel and fast Zn2+ detection strategy based on “signal on” mode with electrochemiluminescence (ECL) luminophore, in which singlet oxygen was generated via electrocatalytic reduction of zinc proto-porphyrin IX grafted onto Pd nanocubes (ZnPPIX-Pd NCs). In protocol, Pd NCs were synthetized under hydrothermal conditions and aminated through thermal oxidative polymerization of 3-aminopropyltriethoxysilane (APTES), followed by further linking with PPIX via amide reaction. The resulting PPIX-Pd NCs effectively captured Zn2+ in chelation and monitored by Fourier transform infrared (FTIR) spectroscopy and ultraviolet-visible (UV-vis) absorption spectroscopy. By virtue of the metal resonance responses of Pd NCs, an intense monochromic, potential shuffling and enhanced ECL irradiation shows up for the hybrid nanocomposite with H2O2 as the coreactant. To this end, an ultrasensitive method based on the nanocomposite with a “signal-on” model was developed for Zn2+ detection with a low detection limit down to 0.38 nM (based on a S/N= 3), excellent precision and high stability. The ECL strategy reveals the potential application in molecular diagnosis and offers a new avenue for bioassay of structural Zn(II) proteins and zinc finger-binding nucleotides.

Nongenetically Encoded and Erasable Imaging Strategy for Receptor-Specific Glycans on Live Cells.

Glycans on specific receptors play a crucial role in regulating receptor functions and indicating cell pathological states. For a detailed glycosylation regulatory mechanism, live cell imaging of receptor-specific glycans becomes significantly important. In this work, we present a nongenetically encoded labeling strategy to specifically install a fluorescence resonance energy transfer (FRET) pair onto the receptor of interest by ligand-receptor binding and metabolic glycan engineering. This method breaks the limitation that the receptors have to possess an extracellular terminus which can be used to attach a fluorescent tag, avoiding the undesired effects introduced by inserting amino acids into proteins. Furthermore, the donor-equipped ligand can be flexibly competed with an unlabeled compound, leading to an efficient erasure of donor fluorescence signal. We envision that this strategy will have the potential to sequentially identify and characterize multiple receptor-specific glycans on the live cell surface through multiple cycles including labeled ligand binding, FRET-induced fluorescence imaging, and the unlabeled compound competing for fluorescence erasure. Besides, this in situ glycan profiling strategy will have wide applications in molecular diagnosis and cellular targeted therapies.

Microfluidic biosensor and its application in molecular diagnosis

In recent years, with advances in development of materials science and micro-electro-mechanical-systems, the frontiers of devices for laboratory medicine are pushed toward miniaturization, integration, and automation. The microfluidic biosensors, which combine advantages of microfluidics and biosensor technologies, are particularly eye-catching and show enormous potential for future applications in laboratory medicine. Here, the characteristics and technical principles of microfluidic biosensors and their application in molecular diagnosis are briefly reviewed.(Chin J Lab Med, 2018, 41: 634-637) Key words: Microfluidics; Biosensing techniques; Molecular diagnostic techniques

Application of Molecular Diagnosis in Ovarian Cancer Diagnosis

Application of Molecular Diagnosis in Ovarian Cancer Diagnosis

A CD44-specific peptide, RP-1, exhibits capacities of assisting diagnosis and predicting prognosis of gastric cancer.

Early diagnosis and evaluation of prognosis are both crucial for preventing poor prognosis of patients with gastric cancer (GC), a leading cause of cancer-related deaths worldwide. Cluster of differentiation 44 (CD44), an indicator of cancer stem cells, can be specifically targeted by molecular probes and detected in tissues of GC in a large quantity. In current study we found that RP-1, a specific peptide binding to CD44 protein, exhibited the potentials of specific binding to CD44 high-expressing cancer cells both in vitro and in vivo, and the capacity of predicting prognosis of human GC in a microarray assay. Results showed that RP-1 was characterized by high affinity, sensitivity and specificity, and low toxicity, suggesting RP-1 could be an ideal bio-probe for accessory diagnosis of GC. Further immunohistochemical studies and statistical analysis of tissue microarray of human GC demonstrated similar sensitivity and specificity of RP-1 with the monoclonal anti-CD44 antibody in the diagnosis of GC, and even proved that positive RP-1 could be an independent risk factor. Therefore, this study suggests RP-1 has the potentials of binding to CD44 protein expressed on the membrane of GC cells, and demonstrates the feasibility and reliability of its further application in molecular diagnosis and prognostic prediction of GC.

Evaluation of five commercial methods for the extraction and purification of DNA from human faecal samples for downstream molecular detection of the enteric protozoan parasites Cryptosporidium spp., Giardia duodenalis, and Entamoeba spp

High quality, pure DNA is required for ensuring reliable and reproducible results in molecular diagnosis applications. A number of in-house and commercial methods are available for the extraction and purification of genomic DNA from faecal material, each one offering a specific combination of performance, cost-effectiveness, and easiness of use that should be conveniently evaluated in function of the pathogen of interest. In this comparative study the marketed kits QIAamp DNA stool mini (Qiagen), SpeedTools DNA extraction (Biotools), DNAExtract-VK (Vacunek), PowerFecal DNA isolation (MoBio), and Wizard magnetic DNA purification system (Promega Corporation) were assessed for their efficacy in obtaining DNA of the most relevant enteric protozoan parasites associated to gastrointestinal disease globally. A panel of 113 stool specimens of clinically confirmed patients with cryptosporidiosis (n=29), giardiasis (n=47) and amoebiasis by Entamoeba histolytica (n=3) or E. dispar (n=10) and apparently healthy subjects (n=24) were used for this purpose. Stool samples were aliquoted in five sub-samples and individually processed by each extraction method evaluated. Purified DNA samples were subsequently tested in PCR-based assays routinely used in our laboratory. The five compared methods yielded amplifiable amounts of DNA of the pathogens tested, although performance differences were observed among them depending on the parasite and the infection burden. Methods combining chemical, enzymatic and/or mechanical lysis procedures at temperatures of at least 56°C were proven more efficient for the release of DNA from Cryptosporidium oocysts.

Potential of Cell-free Circulating DNA in Diagnosis of Cancer

Circulating cell-free DNA (cf-DNA) is characterized as extracellular DNA that may be present in the blood of healthy individuals in low concentrations. Cf-DNA is released by apoptosis or necrosis into the bloodstream. Increased levels are found in pathological conditions, such as inflammation, autoimmune diseases, or stress. Significant increase of cf-DNA is particularly evident in patients with malignancies, especially in the advanced stages of the disease. In this case, the tumor specific cf-DNA is released by necrosis from the cells of primary tumor and metastases. Recently, many studies concentrate on the so-called 'liquid biopsies' that allow detection of circulating tumor cells and circulating nucleic acids from peripheral blood for tumor diagnostics. Quantitative methods and detection of genetic and epigenetic alternations of cf-DNA in patients with different malignancies have potential applications in molecular diagnosis, prognosis, monitoring of disease progression and response to treatment. This review focuses on potential utility of cf-DNA as a blood biomarker in selected solid tumors and hematologic malignancies.

Towards High-throughput Immunomics for Infectious Diseases: Use of Next-generation Peptide Microarrays for Rapid Discovery and Mapping of Antigenic Determinants

Complete characterization of antibody specificities associated to natural infections is expected to provide a rich source of serologic biomarkers with potential applications in molecular diagnosis, follow-up of chemotherapeutic treatments, and prioritization of targets for vaccine development. Here, we developed a highly-multiplexed platform based on next-generation high-density peptide microarrays to map these specificities in Chagas Disease, an exemplar of a human infectious disease caused by the protozoan Trypanosoma cruzi. We designed a high-density peptide microarray containing more than 175,000 overlapping 15mer peptides derived from T. cruzi proteins. Peptides were synthesized in situ on microarray slides, spanning the complete length of 457 parasite proteins with fully overlapped 15mers (1 residue shift). Screening of these slides with antibodies purified from infected patients and healthy donors demonstrated both a high technical reproducibility as well as epitope mapping consistency when compared with earlier low-throughput technologies. Using a conservative signal threshold to classify positive (reactive) peptides we identified 2,031 disease-specific peptides and 97 novel parasite antigens, effectively doubling the number of known antigens and providing a 10-fold increase in the number of fine mapped antigenic determinants for this disease. Finally, further analysis of the chip data showed that optimizing the amount of sequence overlap of displayed peptides can increase the protein space covered in a single chip by at least ∼threefold without sacrificing sensitivity. In conclusion, we show the power of high-density peptide chips for the discovery of pathogen-specific linear B-cell epitopes from clinical samples, thus setting the stage for high-throughput biomarker discovery screenings and proteome-wide studies of immune responses against pathogens.

Assembly of multiple DNA components through target binding toward homogeneous, isothermally amplified, and specific detection of proteins.

We describe a strategy of utilizing specific target binding to trigger assembly of three DNA components that are otherwise unable to spontaneously assemble with one another. This binding-induced DNA assembly forms a three-arm DNA junction, subsequently initiating nicking endonuclease-assisted isothermal fluorescence signal amplification. Real-time monitoring of fluorescence enables amplified detection of specific protein targets. The implementation of the strategy necessitates the simultaneous binding of a single target molecule with two affinity ligands each conjugated to a DNA motif. Simple alternation of affinity ligands enables different protein targets to induce the formation of the DNA junction and subsequent isothermal amplification. The use of the strategy allowed us to develop a sensitive assay for proteins with three appealing features: homogeneous analysis without the need for separation, isothermal amplification, and high specificity. Streptavidin was chosen as an initial target to establish and optimize the assay. Sensitivity of protein detection was improved by 1000-fold upon the application of isothermal amplification. A limit of detection of 10 pM was achieved for detection of prostate-specific antigen in buffer and diluted serum. The combination of its three appealing features makes the assay attractive for potential applications in molecular diagnosis, point-of-care testing, and on-site analysis.

Plasma DNA methylation of shp1 in patients with diffuse large B cell lymphoma

To explore the methylation status of shp1 gene in plasma DNA from patients with diffuse large B cell lymphoma (DLBCL) and discuss its possible application in molecular diagnosis and targeted therapy of the disease. Methylation-specific polymerase chain reaction (MSP) was used to detect the methylation status of shp1 gene in plasma and peripheral blood leukocytes (PBLs) of 35 DLBCL patients. The formaldehyde-fixed, paraffin-embedded (FFPE) tumor tissue samples were collected from 28 DLBCL patients, 6 patients of benign lymphoid hyperplasia and 13 healthy volunteers were selected as nonmalignant controls from January 2012 to December 2013. Methylation frequencies of shp1 gene in different groups were compared and the associations of shp1 methylation status with clinicopathological characteristics were analyzed. No methylation of shp1 was detected in any of the 19 nonmalignant controls. The methylation rate of shp1 in plasma, PBLs and FFPE tumor tissues from patients with DLBCL was 51.4% (18/35), 28.6% (10/35) and 64.3% (18/28) respectively; there was a high methylation consistency of shp1 between plasma and FFPE tumor tissues (κ = 0.78, P = 0.00).However, methylation consistency was lower between PBLs and FFPE tumor tissues (κ = 0.36, P = 0.01). Methylation of shp1 was frequently detected in plasma and FFPE tumor tissues samples from patients with a high serum level of lactate dehydrogenase (13/16 vs 5/19, 11/12 vs 7/16, P = 0.02, 0.04) .However, no such association was detected in PBLs (P = 0.14). Methylation of shp1 in plasma DNA can represent shp1 methylation status in tumor tissue. And it may serve as a promising biomarker in aiding DLBCL diagnosis and guiding targeted therapy.