Protocol for editing fibroblasts with in vitro transcribed Cas9 mRNA and profile off-target editing by optimized GUIDE-seq.

CRISPR-Cas9 gene editing is an efficient technique to modify specific sites/regions of DNA. Delivery of the Cas9 by mRNA is particularly promising in pre-clinical genome editing applications for its transient, nonintegrating feature. However, the off-target of Cas9-gRNA still remains a concern and needs a specific monitor. Here, we present a revised protocol to edit fibroblasts by in vitro transcribed Cas9 mRNA and profile its off-target effect by the optimized GUIDE-seq method. This protocol can also be applied to other cell lines. For complete details on the use and execution of this protocol, please refer to Ganna Reint et al. (2021).1.

Rapid genome editing by CRISPR-Cas9-POLD3 fusion.

Precision CRISPR gene editing relies on the cellular homology-directed DNA repair (HDR) to introduce custom DNA sequences to target sites. The HDR editing efficiency varies between cell types and genomic sites, and the sources of this variation are incompletely understood. Here, we have studied the effect of 450 DNA repair protein-Cas9 fusions on CRISPR genome editing outcomes. We find the majority of fusions to improve precision genome editing only modestly in a locus- and cell-type specific manner. We identify Cas9-POLD3 fusion that enhances editing by speeding up the initiation of DNA repair. We conclude that while DNA repair protein fusions to Cas9 can improve HDR CRISPR editing, most need to be optimized to the cell type and genomic site, highlighting the diversity of factors contributing to locus-specific genome editing outcomes.

DNB-based on-chip motif finding: A high-throughput method to profile different types of protein-DNA interactions.

Here, we report a sensitive DocMF system that uses next-generation sequencing chips to profile protein-DNA interactions. Using DocMF, we successfully identified a variety of endonuclease recognition sites and the protospacer adjacent motif (PAM) sequences of different CRISPR systems. DocMF can simultaneously screen both 5' and 3' PAMs with high coverage. For SpCas9, we found noncanonical 5'-NAG-3' (~5%) and 5'-NGA-3' (~1.6%), in addition to its common PAMs, 5'-NGG-3' (~89.9%). More relaxed PAM sequences of two uncharacterized Cas endonucleases, VeCas9 and BvCas12a, were extensively characterized using DocMF. Moreover, we observed that dCas9, a DNA binding protein lacking endonuclease activity, preferably bound to the previously reported 5'-NGG-3' sequence. In summary, our studies demonstrate that DocMF is the first tool with the capacity to exhaustively assay both the binding and the cutting properties of different DNA binding proteins.

KIT/PDGFRA/KDR amplification defines a novel molecular subtype of adenoid cystic carcinoma patients who may benefit from treatment with tyrosine kinase inhibitors.

BACKGROUND: Adenoid cystic carcinoma (ACC) is a rare cancer with an aggressive phenotype and the high incidence of recurrence and distant metastasis severely affects the overall survival of ACC patients. Understanding the molecular mechanisms that drives ACC could improve the treatment and outcomes of patients with this disease. METHODS: Actionable genetic alterations in 52 surgically resected ACC tissue samples were identified using targeted next generation sequencing (NGS). Expression of c-KIT/PDGFRα/VEGFR2 was assessed by immunohistochemistry (IHC). Sunitinib, a multi-targeted small molecule inhibitor of receptor tyrosine kinases (RTKs), was used off-label in one ACC patient harboring the KIT/PDGFRA/KDR amplification. RESULTS: Potentially actionable genetic alterations were detected in 61.5% (32/52) of patients. In addition to the common actionable targets identified in NOTCH signaling and FGF/PI3K pathway, multiple novel gene fusions were detected in 7.7% (4/52) of ACC patients. Specifically, the KIT/PDGFRA/KDR amplification was identified in 2 of 52 (3.8%) cases and triple positive c-KIT/PDGFRα/VEGFR2 by IHC was associated with a significantly higher likelihood of distant metastasis. Furthermore, an advanced ACC patient with the KIT/PDGFRA/KDR amplification and who was positive for three encoded proteins showed a partial response to sunitinib. CONCLUSIONS: A total of 61.5% of ACC patients were found to harbor at least one actionable genetic alteration via a targeted NGS in this study. The KIT/PDGFRA/KDR amplification as well as triple positive c-KIT/PDGFRα/VEGFR2 defined a distinctive molecular phenotype that was characterized by distant metastasis. Clinical trials investigating the application of RTKs in ACC patients with the KIT/PDGFRA/KDR amplification or triple positive c-KIT/PDGFRα/VEGFR2 are warranted.

Comprehensive Molecular Characterization of Young Chinese Patients with Lung Adenocarcinoma Identified a Distinctive Genetic Profile.

BACKGROUND: Occurrence at a younger age has been demonstrated to be associated with a distinct biology in non-small cell lung cancer. However, genomics and clinical characteristics among younger patients with lung adenocarcinoma remain to be determined. Here we studied the potentially targetable genetic alterations by next-generation sequencing (NGS) assay in young Chinese patients with lung adenocarcinoma. MATERIALS AND METHODS: Seventy-one surgically resected lung adenocarcinoma tissue samples from patients aged less than 45 years were collected with informed consent from all patients. Targeted NGS assays were used to identify actionable genetic alterations in the cancer tissues. Additionally, the genomic and clinicopathologic characteristics of 106 patients with lung adenocarcinoma who received NGS testing over the same period were analyzed retrospectively. RESULTS: The frequencies of targetable genetic alterations in 177 patients with lung adenocarcinoma were analyzed by defined age categories, which unveiled a distinctive molecular profile in the younger group, aged less than 45 years. Notably, higher frequency of ALK and HER2 genetic alterations were associated with young age. However, a reverse trend was observed for KRAS, STK11 and EGFR exon 20 mutations, which were more frequently identified in the older group, aged more than 46 years. Furthermore, concurrent EGFR/TP53 mutations were much more prevalent in the younger patients (81.6% vs. 46.8%), which might have a poor response to treatment with epidermal growth factor receptor tyrosine kinase inhibitor. CONCLUSION: In this study, NGS assay revealed a distinctive genetic profile in younger patients with adenocarcinoma. High frequency of concurrent EGFR/TP53 mutations was found in the younger patients, which especially warranted personalized treatment in this population. IMPLICATIONS FOR PRACTICE: Further investigation is needed to understand the genomics and clinical characteristics of young patients with lung adenocarcinoma. In the present study, hybrid capture-based next-generation sequencing assays were used to identify targeted genetic alterations in young lung adenocarcinoma patients. Young patients with lung adenocarcinoma, aged less than 45 years, harbored a higher frequency of ALK and HER2 genetic alterations compared with patients aged more than 46 years. Dramatically, concurrent EGFR/TP53 mutations were much more prevalent in younger patients, which had a poor response to treatment with epidermal growth factor receptor kinase inhibitor. These results reveal a distinctive genetic profile in younger patients with adenocarcinoma, which might improve the treatment of this subpopulation.

Publisher Correction: Discovery of targetable genetic alterations in advanced non-small cell lung cancer using a next-generation sequencing-based circulating tumor DNA assay.

A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.

Targeted next generation sequencing in Chinese colorectal cancer patients guided anti-EGFR treatment and facilitated precision cancer medicine.

OBJECTIVE: Colorectal cancer (CRC) patients with both RAS and BRAF wild-type tumors determined by non-next generation sequencing (NGS) testing may still not respond due to the presence of additional mutated genes such as PIK3CA or PTEN. In this study, a broad, hybrid capture-based NGS assay was used to identify RAS, BRAF and additional targetable genetic alterations from Chinese CRC tissues. METHODS: Fifty-seven cases of CRC were enrolled, and all the patients signed the informed consent. In total, 7708 exons of 508 tumor-related genes and 78 introns of 19 frequently rearranged genes were assessed for base substitutions, INDELs, copy number alterations, and gene fusions. RESULTS: The study found that 50.9% (29/57) of the tumors harbored KRAS mutations, 3.5% (2/57) harbored NRAS mutations and 3.5% (2/57) harbored BRAF mutations. More specifically, 89.7% (26/29) of RAS mutations were located in codon 12. Except for RAS and RAF, anti-EGFR therapy response genetic mutations in PTEN (n=2) and PIK3CA (n=1) were found in 4.7% (3/64) of the samples. Actionable alterations were found in HER2 (n = 7), CCND2 (n = 2), NF1 (n = 1), and BRCA1 (n = 1). CONCLUSIONS: Our results illustrated that 82.5% (47/57) of the samples harbored at least one actionable genetic alteration identified by NGS. HER2 amplifications or mutations, which were identified in 12.3% of the tissues, defined a unique molecular subtype of CRC. The study suggests that high-throughput NGS testing in CRC tissues is a comprehensive and efficient genomic profiling assay to guide personalized therapy.

Discovery of targetable genetic alterations in advanced non-small cell lung cancer using a next-generation sequencing-based circulating tumor DNA assay.

Next-generation sequencing (NGS)-based circulating tumor DNA (ctDNA) assays have provided a new method of identifying tumor-driving genes in patients with advanced non-small cell lung carcinoma (NSCLC), especially in those whose cancer tissues are unavailable or in those that have acquired treatment resistance. Here, we describe a total of 119 patients with advanced EGFR-TKI-naive NSCLC and 15 EGFR-TKI-resistant patients to identify somatic SNVs, small indels, CNVs and gene fusions in 508 tumor-related genes. Somatic ctDNA mutations were detected in 82.8% (111/134) of patients in the total cohort. Of the 119 patients with advanced NSCLC, 27.7% (33/119) were suitable for treatment with National Comprehensive Cancer Network (NCCN) guideline-approved targeted drugs. Actionable genetic alterations included 25 EGFR mutations, 5 BRAF mutations, and 1 MET mutation, as well as 1 EML4-ALK gene fusion and 1 KIF5B-RET gene fusion. In 19.3% (23/119) of the patients, we also identified genomic alterations with that could be targeted by agents that are in clinical trials, such as mTOR inhibitors, PARP inhibitors, and CDK4/6 inhibitors. Additionally, the EGFR T790M mutation was found in 46.7% (7/15) of the patients with EGFR-TKI-resistant NSCLC, suggesting that the NGS-based ctDNA assay might be an optional method to monitor EGFR-TKI resistance and to discover mechanisms of drug resistance.

Effective treatment of aggressive fibromatosis with celecoxib guided by genetic testing.

Aggressive fibromatosis (AF) or desmoid tumors is an aggressive fibroblastic proliferation which is locally invasive but can not metastasize. The treatment of AF is challenging. Surgery was the main treatment modality for AF in the past, other strategies including radiotherapy, systemic therapies and wait-and-see policy. The use of non-steroidal anti-inflammatory drugs (NSAIDs) and targeted therapies has demonstrated good results. In the case report, a 39-year-old man presented with progressive chest wall pain. Computed tomography (CT) showed an approximately 46× 13 mm soft-tissue mass between the inside of the fifth and sixth rib on the right side. The entire mass was excised and an AF was confirmed based on histopathology. Four months after surgery, magnetic resonance imaging (MRI) showed a soft-tissue mass in surgical areas and biopsy confirmed local recurrence. Therefore, Tomotherapy was administered. However, two months later, an (18)F-fluorodeoxyglucose (FDG) Positron Emission Tomography combined with CT (PET-CT) revealed the presence of an FDG-avid mass in the area of local recurrence. Genetic testing reported the presence of a p.T41A mutations on the CTNNB1 gene, which predicted that he is sensitive to the COX-2 inhibitor celecoxib. The tumor regressed rapidly after the application of celecoxib. Within the 20-month follow-up period, the patient showed remarkable regression without any signs and symptoms. Our case report provides further evidence for the efficacy of celecoxib in AF with CTNNB1 gene mutations. To our knowledge, this is the first report of AF treated with celecoxib under the guidance of the genetic testing. However, further studies are required.

Human umbilical cord mesenchymal stem cells and derived hepatocyte-like cells exhibit similar therapeutic effects on an acute liver failure mouse model.

Mesenchymal stem cells (MSCs) have exhibited therapeutic effects in multiple animal models so that are promising liver substitute for transplantation treatment of end-stage liver diseases. However, it has been shown that over-manipulation of these cells increased their tumorigenic potential, and that reducing the in vitro culture time could minimize the risk. In this study, we used a D-galactosamine plus lipopolysaccharide (Gal/LPS)-induced acute liver failure mouse model, which caused death of about 50% of the mice with necrosis of more than 50% hepatocytes, to compare the therapeutic effects of human umbilical cord MSCs (hUCMSCs) before and after induction of differentiation into hepatocyte (i-Heps). Induction of hUCMSCs to become i-Heps was achieved by treatment of the cells with a group of growth factors within 4 weeks. The resulted i-Heps exhibited a panel of human hepatocyte biomarkers including cytokeratin (hCK-18), α-fetoprotein (hAFP), albumin (hALB), and hepatocyte-specific functions glycogen storage and urea metabolism. We demonstrated that transplantation of both cell types through tail vein injection rescued almost all of the Gal/LPS-intoxicated mice. Although both cell types exhibited similar ability in homing at the mouse livers, the populations of the hUCMSCs-derived cells, as judged by expressing hAFP, hCK-18 and human hepatocyte growth factor (hHGF), were small. These observations let us to conclude that the hUCMSCs was as effective as the i-Heps in treatment of the mouse acute liver failure, and that the therapeutic effects of hUCMSCs were mediated largely via stimulation of host hepatocyte regeneration, and that delivery of the cells through intravenous injection was effective.

Development of an ultrasensitive immunoassay for detecting tartrazine.

We have developed an ultrasensitive indirect competitive enzyme-linked immunosorbent assay for the determination of tartrazine. Two carboxylated analogues of tartrazine with different spacer lengths, and one derivative from commercial tartrazine after a little chemical modification, were synthesized as haptens in order to produce antibodies specific to tartrazine. The effect of sulfonic acid groups on the hapten structure of tartrazine was also studied carefully for the first time. A most specific monoclonal antibody against tartrazine was created and exhibited an IC50 value of 0.105 ng/mL and a limit of detection of 0.014 ng/mL, with no cross-reactivity to other structurally-related pigments. The established immunoassay was applied to the determination of tartrazine in fortified samples of orange juice and in real positive samples of carbonated beverages.

The specific binding of peptide ligands to cardiomyocytes derived from mouse embryonic stem cells.

Purification of pluripotent stem cell (PSC)-derived cardiomyocytes is critical for the application of cardiomyocytes both in clinical and basic research. Finding a specific cell marker is a promising method for purifying induced cells. The present study employed phage display technology to search for particular cell markers that could bind specifically to PSC-derived cardiomyocytes. After three rounds of biopanning, several peptides were obtained. The ELISA results show the no. 3 sequence peptide (QPFTTSLTPPAR), and other four sequences having a consensus motif [SS(Q)PPQ(S)], no. 9, 11, 14, and 10, have relatively high affinity and specificity to cardiomyocytes. Immunofluorescence confirmed that the selected peptides could bind specifically to the PSC-derived cardiomyocytes. Competition tests with chemically synthesized peptides revealed the binding ability was caused by the peptide itself. Western blot analysis proved the phages were both bound to two 17 kDa cardiomyocyte membrane proteins and the no. 9 sequence showed a 55 kDa protein that was not observed in the no. 3 sequence. These results suggest that the selected peptides specifically target receptors on PSC-derived cardiomyocyte membranes. The results will pave the way for further studies of cell surface markers and their applications, such as labeling, purification, and as vehicles for drug delivery.

Simultaneous determination of nine types of phthalate residues in commercial milk products using HPLC-ESI-MS-MS.

A multi-residue method was developed for the confirmation and quantitation of nine types of phthalates in milk using high-performance liquid chromatography electrospray ionization tandem mass spectrometry. The samples were extracted with acetonitrile. The analytes were separated using a 0.1% formic acid-methanol system as the mobile phase, and a linear gradient elution program. Mass spectral acquisition was achieved by selectively monitoring the ions in electro-spray ionization mode. Qualitative analysis was based on the retention time and the mass spectrum results, and the quantity was carried out by comparison with the external standard. The mean recoveries for each analyte ranged from 65.2% to 98.3%, with relative standard deviations below 11.2%. The limits of detection were 5∼25 µg/kg, and the limits of quantitation were 17∼83 µg/kg, depending on the compounds. This method has the merits of convenient operation, high sensitivity, and good repeatability, making it an effective method for analysis of phthalates in milk. And the proposed analytical method has been applied to the analysis of phthalates presented in four commercial milk products. The main phthalate residues were DBP and DMP. And the amount of DBP was found to be more than 100 µg/kg in all this milk products.

Mapping of QTL for tiller number at different stages of growth in wheat using double haploid and immortalized F2 populations.

Effective tiller number is one of the most important traits for wheat (Triticum aestivum L.) yield, but the inheritance of tillering is poorly understood. A set of 168 doubled haploid (DH) lines derivatives of a cross between two winter wheat cultivars (Huapei 3 and Yumai 57), and an immortalized F(2) (IF(2)) population generated by randomly permutated intermating of these DHs were investigated, and QTLs of tillering related to the maximum tillering of pre-winter (MTW), maximum tillering in spring (MTS), and effective tillering in harvest (ETH) were mapped. Phenotypic data were collected for the two populations from two different environments. Using inclusive composite interval mapping (ICIM), a total of 9 and 18 significant QTL were detected across environments for tillering in the DH and IF(2) populations, respectively. Four QTLs were common between two populations. A major QTL located on the 5D chromosome with the allele originating from Yumai 57 was detected and increased 1.92 and 3.55 tillers in MTW and MTS, respectively. QTLs (QMts6D, QEth6D) having a neighbouring marker interval at Xswes679.1 and Xcfa2129 on chromosome 6D was detected in MTS and ETH. These results provide a better understanding of the genetic factors for selectively expressing the control of tiller number in different growth stages and facilitate marker-assisted selection strategy in breeding.

Development of an indirect enzyme-linked immunosorbent assay for the organophosphorus pesticide paraoxon-methyl.

In the present study, the synthesis of hapten for the organophosphorus (OP) pesticide paraoxon-methyl was developed, with a spacer arm (aminocarboxylic acid) attached at the aromatic ring. It was conjugated to bovine serum albumin (BSA) for use as an immunogen and to ovalbumin (OVA) for coating antigen for ELISA testing. Rabbits were immunized with the immunogen and two polyclonal antisera were produced and screened against the coating antigen using competitive indirect enzyme-linked immunosorbent assay (ELISA). For application to textile samples, the influence of several factors such as organic solvent, ionic strength, and pH on the ELISA results were studied. Under optimized conditions, the quantitative working range was 0.012-1.158 microg/mL with a limit of detection (LOD) of 0.005 microg/mL and the IC(50) was 0.115 microg/mL.There was negligible cross reactivity (CR) with other OP pesticides. The recoveries obtained by standard paraoxon-methyl addition to the different textile samples such as cotton, wool and muslin delaine were all from 86.0% to 108.0%. Therefore, the optimized ELISA may become a new convenient and economical analytical tool for monitoring paraoxon-methyl residues in textile samples.

Rapid and sensitive detection of microcystin by immunosensor based on nuclear magnetic resonance.

A stable and sensitive toxin residues immunosensor based on the relaxation of magnetic nanoparticles was developed. The method was performed in one reaction and offered sensitive, fast detection of target toxin residues in water. The target analyte, microcystin-LR (MC-LR) in Tai lake water, competed with the antigens on the surface of the magnetic nanoparticles and then influenced the formation of aggregates of the magnetic nanoparticles. Accordingly, the magnetic relaxation time of the magnetic nanoparticles was changed under the effect of the target analyte. The calibration curve was deduced at different concentrations of the target analyte. The limit of detection (LOD) of MC-LR was 0.6 ng g(-1) and the detection range was 1-18 ng g(-1). Another important feature of the developed method was the easy operation: only two steps were needed (1) to mix the magnetic nanoparticle solution with the sample solution and (2) read the results through the instrument. Therefore, the developed method may be a useful tool for toxin residues sensing and may find widespread applications.

Simultaneous and sensitive determination of multiplex chemical residues based on multicolor quantum dot probes.

Biotinylated denatured bovine serum albumin (Bt-dBSA)-coated cadmium telluride (CdTe) quantum dot (QD) conjugates were prepared and used to develop the multiplexed fluoroimmunoassay for the simultaneous determination of five chemical residues. An immune complex was formed using avidin as the bridge to link the Bt-dBSA-QDs with the antibodies. Primarily, individual quantitative determinations of five representative chemical residues were carried out based on the different emission properties of the QDs. Five antibodies were then conjugated with the corresponding QDs to establish the indirect competition fluorescent-linked immunosorbent assay (ic-FLISA) for the simultaneous detection of five chemicals in one well of a microplate. The linear range for dexamethason (DEX) was from 0.33 microg/kg to 10 microg/kg, 0.28 microg/kg to 10 microg/kg for gentamicin (GM), 0.16 microg/kg to 25 microg/kg for clonazepam (CZP), 0.17 microg/kg to 10 microg/kg for medroxyprogesterone acetate (MPA) and 0.32 microg/kg to 25 microg/kg for ceftiofur (CEF), respectively. The limit of detection (LOD) for the simultaneous determination of DEX, GM, CZP, MPA and CEF were as low as 0.13 microg/kg, 0.16 microg/kg, 0.07 microg/kg, 0.06 microg/kg and 0.14 microg/kg, respectively. This detection method was used to analyze samples of pork muscle and the recoveries ranged from 61.3% to 80.3% for DEX and from 74.0% to 87.2% for MPA. Further more, good correlation between the novel ic-FLISA and traditional ELISA was demonstrated during the determination of DEX and MPA residues in real samples. The QD-based protocol described here is less time consuming than the classical method and it may be sufficiently flexible to be used in other systems for the simultaneous multicolor detection of the drugs.