TA Cloning Sequencing Research Articles

Diverse Head-to-Tail Sequences in the Circular Genome of Human Bocavirus Genotype 1 among Children with Acute Respiratory Infections Implied the Switch of Template Chain in the Rolling-Circle Replication Model.

Head-to-tail sequences have been reported in human bocavirus (HBoV) 1-4. To reveal their features and functions, HBoV DNA was screened among respiratory specimens from pediatric patients with an acute respiratory infection (ARI) between April 2020 and December 2022, followed by HBoV genotyping. Head-to-tail sequences were detected using nested PCR, TA cloning, and Sanger sequencing, and these findings were confirmed by mNGS and amplicon sequencing. The secondary structure was predicted using the Mfold web server. The results indicated that head-to-tail sequences were detected in 42 specimens through TA cloning from 351 specimens positive for HBoV1 DNA, yielding 92 sequences into 32 types and 2 categories. Additionally, head-to-tail sequences were detected in 16 specimens by amplicon sequencing, yielding 60 sequences categorized into 23 types. The 374nt type, detected in 13 specimens, contains variants 374a and 374b, which differ in the unpaired loop regions of the palindrome or complementary reverse sequences, implying a switch of template chains during the replication process. The mNGS results in three specimens confirmed the presence of circular genome in copies below 1%. In conclusion, head-to-tail sequences of HBoV1 were common in children with ARI and were highly diverse in length and sequences. The variants may be generated by the switch of the template chain in the rolling-circle replication model.

Genetic and mechanistic evaluation of an individual with para-Bombay phenotype associated with a compound heterozygote comprising two novel FUT1 variants.

As is well documented, the para-Bombay phenotype is typically characterized by the reduction or absence of ABH antigens on red blood cells but the presence of corresponding antigens in saliva. Herein, the underlying molecular mechanism of an individual with para-Bombay AB phenotype combined with two novel variants of the FUT1 gene was investigated. ABH antigens and antibodies were detected in the serum of the proband using conventional serological methods. The coding region nucleotides of the ABO, FUT1, and FUT2 genes were directly sequenced by polymerase chain reaction. Moreover, the FUT1 haploid type in the proband was analyzed by TA clone sequencing. The 3D structure of wild-type and mutant fucosyltransferases were simulated and analyzed using Phyre2 and Pymol software. Lastly, the effect of missense substitution on the function of fucosyltransferase was predicted by the Polymorphism Phenotyping algorithm (PolyPhen-2) and MutationTaster. ABH antigens were noted to be absent on the surface of red blood cells of the proband. The ABO genotype was ABO*A1.02/ABO*B.01, while the FUT2 genotype was FUT2*01/FUT2*c.357T. Interestingly, two novel missense variants (c.289G>A, p.Ala97Thr and c.575G>C, p.Arg192Pro) and one synonymous SNP (c.840G>A) were identified in the FUT1 gene. Furthermore, c.289G>A was detected in one haploid type, whereas c.575G>C and c.840G>A were discovered in another haploid type. Meanwhile, in silico analysis revealed that amino acid substitution caused by missense variants altered the partial spatial structure of the α-helices where residues 97 and 298 were located using 3D homology modeling software. Finally, both missense variants were defined as probably damaging based on PolyPhen-2 prediction. Two novel FUT1 variants were identified in a Chinese individual with para-Bombay AB phenotype, which can expand our understanding of the molecular mechanism underlying the para-Bombay phenotype and contribute to improving the safety of blood transfusion.

Clonality Analysis of Streptococcus pneumoniae in Clinical Specimens

Pneumococcal pneumonia is a significant cause of illness and death globally, particularly among young children and the elderly. The cpsB gene is involved in the biosynthesis of the capsule polysaccharide, and polymorphisms in the cpsB gene are the basis for sequetyping, a molecular biology-based approach to serotyping. In this study, we attempted the sequetyping of pneumococci directly from clinical sputum specimens collected from adult patients diagnosed with community-acquired pneumonia (CAP). We performed conventional PCR for the cpsB gene, followed by TA cloning and Sanger sequencing of the amplicon. The results showed the status of clonality of pneumococci in each specimen. We also performed real-time PCR targeting pneumococci for each specimen. It revealed a significant association between the Ct value of the real-time PCR and the clonality status of pneumococci among the specimens (p-value 0.0007 by Fisher’s exact test analysis). Specifically, when the Ct value was below 22, there was a high probability that pneumococcus existed as a single clone. Thus, this study demonstrates the possible correlation between pneumococcal clonality and bacterial load in clinical specimens, which might indicate the infection status.

CRISPR-mediated editing of β-lactoglobulin (BLG) gene in buffalo

Milk is a good source of nutrition but is also a source of allergenic proteins such as α-lactalbumin, β-lactoglobulin (BLG), casein, and immunoglobulins. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas technology has the potential to edit any gene, including milk allergens. Previously, CRISPR/Cas has been successfully employed in dairy cows and goats, but buffaloes remain unexplored for any milk trait. In this study, we utilized the CRISPR/Cas9 system to edit the major milk allergen BLG gene in buffaloes. First, the editing efficiency of designed sgRNAs was tested in fibroblast cells using the T7E assay and Sanger sequencing. The most effective sgRNA was selected to generate clonal lines of BLG-edited cells. Analysis of 15 single-cell clones, through TA cloning and Sanger sequencing, revealed that 7 clones exhibited bi-allelic (−/−) heterozygous, bi-allelic (−/−) homozygous, and mono-allelic (−/+) disruptions in BLG. Bioinformatics prediction analysis confirmed that non-multiple-of-3 edited nucleotide cell clones have frame shifts and early truncation of BLG protein, while multiple-of-3 edited nucleotides resulted in slightly disoriented protein structures. Somatic cell nuclear transfer (SCNT) method was used to produce blastocyst-stage embryos that have similar developmental rates and quality with wild-type embryos. This study demonstrated the successful bi-allelic editing (−/−) of BLG in buffalo cells through CRISPR/Cas, followed by the production of BLG-edited blastocyst stage embryos using SCNT. With CRISPR and SCNT methods described herein, our long-term goal is to generate gene-edited buffaloes with BLG-free milk.

Limb girdle muscular dystrophy 23 caused by compound heterozygous mutations of LAMA2 gene.

Mutations of LAMA2 gene are associated with congenital muscular dystrophy (CMD). The LAMA2-related CMD mainly consists of two diseases, merosin deficient congenital muscular dystrophies type 1A (MDC1A) and limb girdle muscular dystrophy 23 (LGMD23). LGMD23 is characterized by slowly progressive proximal muscle weakness, which primarily affects the lower limbs and results in gait difficulties. Additional clinical features include increased serum creatine kinase, abnormal electromyography with or without white matter abnormalities on brain imaging. Clinical data were collected from a Chinese Han family. Whole-exome sequencing, Sanger sequencing, RT-PCR and TA clone sequencing were performed on the family members. Compound heterozygous mutations of LAMA2: c.1693C > T (p. Q565*) (maternally inherited) and c.9212-6T > G (paternally inherited) were identified and confirmed in the proband. The mutation c.1693C > T (p. Q565*) was classified as pathogenic according to American College of Medical Genetics and Genomics (ACMG) guidelines. By performing RT-PCR and TA clone sequencing, an insertion of 40-bp intronic sequence (intron 64) was found in the transcripts of the proband and her father, which resulted in a frameshift and premature truncation codon of the LAMA2. In particular, the variant truncated the LamG domain of the LAMA2. Therefore, the c.9212-6T>G was classified as likely pathogenic according to American College of Medical Genetics and Genomics (ACMG) guidelines. Our findings described two novel mutations in a girl with LGMDR23, which contributes to the genetic counseling of the family and expands the clinical and molecular spectrums of the rare disease.

Production of MSTN Gene-Edited Embryos of Buffalo Using the CRISPR/Cas9 System and SCNT.

The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system and somatic cell nuclear transfer (SCNT) have been used to produce genome-edited farm animal species for improved production and health traits; however, these tools are rarely used in the buffalo and can play a pivotal role in milk and meat production in tropical and subtropical countries. In this study, we aimed to produce myostatin (MSTN) gene-edited embryos of the Murrah buffalo using the CRISPR/Cas9 system and SCNT. For this, fibroblast cells were electroporated with sgRNAs carrying all-in-one CRISPR/Cas9 plasmids targeting the first exon of the MSTN gene. Following puromycin selection, single-cell clonal populations were established and screened using the TA cloning and Sanger sequencing methods. Of eight single-cell clonal populations, one with a monoallelic and another with a biallelic heterozygous gene editing event were identified. These two gene-edited clonal cell populations were successfully used to produce blastocyst-stage embryos using the handmade cloning method. This work establishes the technical foundation for generation of genome-edited cloned embryos in the buffalo.

Diagnosis of patients with mucopolysaccharidosis type II via RNA sequencing

BackgroundMucopolysaccharidosis type II (MPS II) is an X-linked recessive lysosomal storage disorder caused by various variants in the IDS gene. It is known that genomic recombinants between IDS and its homologous pseudogene IDSP1 account for a small number of patients, for whom genetic diagnosis usually relies on restriction enzyme digestion at specific loci. Nevertheless, such approach cannot reveal the impact of rearrangements on IDS transcription, which is crucial for the interpretation of the pathogenicity of rearrangement variants. MethodsRNA sequencing (RNA-seq) was explored to analyze transcriptional alterations in four male MPS II patients who were negative for Sanger sequencing of the IDS gene. Reverse transcription-polymerase chain reaction and TA clone sequencing were used to validate RNA-seq analysis results. The IDS-IDSP1 recombinant was determined by sequencing the indicated loci in genome. ResultsDifferential expression analysis showed the expression levels of IDS gene in patients were largely reduced compared to the healthy individuals. Differential splicing analysis revealed skipping of exons 8 and 9 of IDS, without any splice-junction defects at the genomic level. In addition, two types of fusion transcripts, IDS_EOLA1 and IDS_EOLA1-DT_EOLA1 were identified by gene fusion analysis. Sequencing of the known rearrangement alleles showed these four patients have the same type of IDS-IDSP1 recombinant. ConclusionWe establish an RNA-seq workflow to analyze transcriptional characteristics of IDS gene from multiple perspectives. Our study validates the diagnostic value of RNA-seq in MPS II, including the discovery of transcriptional alterations and the potential to suggest genome-level rearrangements in IDS.

Characterization and clinical evaluation of microsatellite instability and loss of heterozygosity in tumor‑related genes in gastric cancer

Microsatellite instability (MSI) detection is widely used in the diagnosis and prognosis evaluation of colorectal cancer. However, for gastric cancer (GC), there is no standard panel of microsatellites (MSs) used in clinical guidance. The present study aimed to identify useful predictors of the clinical features and for the prognosis of GC, based on an investigation of MSI and loss of heterozygosity (LOH) in tumor-related genes. First, from 20 tumor-related genes which were proven to be important to the development of GC, 91 MSs were identified, and PCR amplification, short tandem repeat scanning analysis and TA clone sequencing were used to analyze MSI and LOH in the first set of 90 GC samples. Subsequently, the same method was used to detect the MSI/LOH of the optimized loci in the second set of 136 GC samples. MSI/LOH in the mismatch repair genes was highly consistent with that in oncogenes and tumor suppressor genes, respectively. The length of the core sequence was a main factor for the MSI/LOH rate. The MSI of 12 single loci was significantly associated with lymph node metastasis. The MSI in TP53-1 and the LOH in MGMT-10 were significantly associated with early stages of tumor infiltration depth. The LOH in MGMT-10, PTN-2 and MCC-17 was significantly associated with TNM stage. The LOH in TP53-1 and ERBB2-12 was associated with adenocarcinoma. The MSI/LOH in 6 single loci of 5 tumor-related genes was associated with poor prognosis of GC. The present study demonstrated that the MSI/LOH of loci in tumor-associated genes was associated with 4 clinicopathological characteristics and outcomes of GC. These results may provide potential specific biomarkers for the clinical prediction and treatment of GC.

Cas9 Mediated Correction of β-catenin Mutation and Restoring the Expression of Protein Phosphorylation in Colon Cancer HCT-116 Cells Decrease Cell Proliferation in vitro and Hamper Tumor Growth in Mice in vivo.

PurposeColorectal cancer (CRC) is one of the major contributors to cancer mortality and morbidity. Finding strategies to fight against CRC is urgently required. Mutations in driver genes of APC or β-catenin play an important role in the occurrence and progression of CRC. In the present study, we jointly apply CRISPR/Cas9-sgRNA system and Single-stranded oligodeoxynucleotide (ssODN) as templates to correct a heterozygous ΔTCT deletion mutation of β-catenin present in a colon cancer cell line HCT-116. This method provides a potential strategy in gene therapy for cancer.MethodsA Cas9/β-catenin-sgRNA-eGFP co-expression vector was constructed and co-transfected with ssODN into HCT-116 cells. Mutation-corrected single-cell clones were sorted by FACS and judged by TA cloning and DNA sequencing. Effects of CRISPR/Cas9-mediated correction were tested by real-time quantitative PCR, Western blotting, CCK8, EDU dyeing and cell-plated clones. Moreover, the growth of cell clones derived tumors was analyzed at nude mice xenografts.ResultsCRISPR/Cas9-mediated β-catenin mutation correction resulted in the presence of TCT sequence and the re-expression of phosphorylation β-catenin at Ser45, which restored the normal function of phosphorylation β-catenin including reduction of the transportation of nuclear β-catenin and the expression of downstream c-myc, survivin. Significantly reduced cell growth was observed in β-catenin mutation-corrected cells. Mice xenografted with mutation-corrected HCT-116 cells showed significantly smaller tumor size than uncorrected xenografts.ConclusionThe data of this study documented that correction of the driven mutation by the combination of CRISPR/Cas9 and ssODN could greatly remedy the biological behavior of the cancer cell line, suggesting a potential application of this strategy in gene therapy of cancer.

Apple polysaccharide could promote the growth of Bifidobacterium longum

It is widely accepted that regulating microbiome could improve human health. We previously observed apple polysaccharide (AP) reversed high-fat-induced microbial dysbiosis, but the mechanism remains to be elucidated.In this study, the function of AP in vitro was evaluated in Bifidobacterium longum (B. longum) and Lactobacillus rhamnosus (L. rhamnosus). The effects of AP on the composition of fecal bacteria of normal SD rats were investigated by qPCR, TA cloning and 16S sequencing. 0.125–2% AP showed no significant effect on the growth of B. longum and L. rhamnosus. DNA concentration of fecal bacteria cultured with 1% AP was significantly higher than that of control group. qPCR revealed that the number of Bifidobacterium and Lactobacillus in fecal flora incubated by 1% AP was significantly higher than that of control group. Three strains of escherichia coli (E. coli) in fecal bacteria were screened out and analyzed. AP can be utilized by one E. coli and the metabolic products of AP could enhance the proliferation of B. longum.These data suggest that AP could promote the growth of B. longum indirectly, and provide another basis to understand the health care function of apple.

Targeted knockout of <italic>Kcna3</italic> and its function in Jurkat T cells using the CRISPR/Cas9 system

To explore the use of the CRISPR/Cas9 system to target Kv1.3 channel-encoding genes Kcna3 and elucidate the pathophysiological function mediated by Kv1.3 channels in Jurkat T cells. The first exon sgRNA of human Kcna3 in pX458-sgRNA recombinant vector was transferred into human Jurkat T cells via electroporation. T7EN1 digestion, Genomic PCR products and TA cloning sequencing, Western blot, and functional assays, such as electrophysiology, live-cell calcium imaging and ELISA were used to validate Kcna3 knockout effect in Jurkat T cells. The results of the sequencing analysis showed that the CRISPR/Cas9 recombinant plasmids pX458-sgRNA targeting Kcna3 were successfully constructed. The designed sgRNA2 can efficiently cleave genomic DNA. Kv1.3 protein expression could not be detected using Western blot analysis. Genomic PCR products and TA cloning sequencing showed the presence of Indel mutation. Whole-cell patch clamp experiments showed that Kv1.3 channel currents could not be recorded in Kcna3 knockout Jurkat T cells. Live-cell calcium imaging showed that the increase in free Ca2+ concentration in Kcna3 knockout Jurkat T cells was significantly lower than that in wild type Jurkat T cells. ELISA results showed that the IL-2 level of Kcna3 knockout Jurkat T cells was significantly decreased compared with that in wild-type Jurkat T cells ( P Kcna3 in Jurkat T cells using the CRISPR/Cas9 system strongly proved that Kv1.3 mediated the immune inflammatory response of Jurkat T cells, which provides a novel cell model for further study of the pathophysiological function of the Kv1.3 channel.

Rapid generation and selection of Cas9-engineering TRP53 R172P mice that do not have off-target effects

BackgroundGenetic mutations cause severe human diseases, and suitable animal models to study the regulatory mechanisms involved are required. The CRISPR/Cas9 system is a powerful, highly efficient and easily manipulated tool for genetic modifications. However, utilization of CRISPR/Cas9 to introduce point mutations and the exclusion of off-target effects in mice remain challenging. TP53-R175 is one of the most frequently mutated sites in human cancers, and it plays crucial roles in human diseases, including cancers and diabetes.ResultsHere, we generated TRP53-R172P mutant mice (C57BL/6 J, corresponding to TP53-R175P in humans) using a single microinjection of the CRISPR/Cas9 system. The optimal parameters comprised gRNA selection, donor designation (silent mutations within gRNA region), the concentration of CRISPR components and the cellular sites of injection. TRP53-R172P conversion was genetically and functionally confirmed. Combination of TA cloning and Sanger sequencing helped identify the correctly targeted mice as well as the off-target effects in the engineered mice, which provide us a strategy to select the on-target mice without off-target effects quickly and efficiently.ConclusionsA single injection of the this optimized CRISPR/Cas9 system can be applied to introduce particular mutations in the genome of mice without off-target effects to model various human diseases.

ADRB2 Gene Knockout in Human Primary T Cells by Multiple sgRNAs Construced using CRISPR/Cas9 Technology

To knockout ADRB2 gene rapidly and efficiently in human primary T cells by using CRISPR/Cas9 technology and multiple sgRNAs strategy. Six paired-sgRNAs, which were designed to target the 5' constitutive coding exons of ADRB2 gene, were cloned into pGL3-U6-sgRNA-PGK-Puro vector separately. The expre-ssion vectors containing the single sgRNAs were constructed and transiently co-transfected into HEK-293T cell line with Cas9 expression vector. The sgRNA-mediated cleavage efficiency was tested by T7EN I digestion assay. Concatenating four highly efficient paired sgRNAs were cloned into pGL3-U6-sgRNA-ccdB-EF1α-Puro expression vector. The reco-mbinant plasmid allows the cells to express 4 sgRNAs, which target different sites on the ADRB2 genomic locus. The cleavage efficiency and mutation model were tested by T7EN I digest assay and T-A cloning technique. Multiple sgRNAs plasmid and Cas9 plasmid was transiently transferred into human primary T cells by electroporation. Flow cytometry (FCM) was used to detect the knockout efficiency of β2 adrenergic receptor (β2-AR). The results of T7EN I digestion and TA cloning sequencing showed that the multiple sgRNAs strategy could obtain more abundant mutation types and higher gene editing efficiency than single sgRNA. In addition to the deletion and insertion of bases, large fragment DNA deletions and inversions could be observed. All of the random 10 TA clones for detection were genetically modified, thus the mutation efficiency was as high as 100%. FCM assay showed that 43.09% of the cells in the control T cells were β2-AR positive, but the proportion of β2-AR positive cells in the multiple sgRNAs electrotransformed T cells decreased to 25.61%. A method, which is simple and operable, for knocking out β2-AR in human primary T cells has been established preliminarily. The results are helpful for the further study of the role of β2-AR in human T cells.

CRISPR/Cas9 Ribonucleoprotein-mediated Precise Gene Editing by Tube Electroporation.

Gene editing nucleases, represented by CRISPR-associated protein 9 (Cas9), are becoming mainstream tools in biomedical research. Successful delivery of CRISPR/Cas9 elements into the target cells by transfection is a prerequisite for efficient gene editing. This protocol demonstrates that tube electroporation (TE) machine-mediated delivery of CRISPR/Cas9 ribonucleoprotein (RNP), along with single-stranded oligodeoxynucleotide (ssODN) donor templates to different types of mammalian cells, leads to robust precise gene editing events. First, TE was applied to deliver CRISPR/Cas9 RNP and ssODNs to induce disease-causing mutations in the interleukin 2 receptor subunit gamma (IL2RG) gene and sepiapterin reductase (SPR) gene in rabbit fibroblast cells. Precise mutation rates of 3.57%-20% were achieved as determined by bacterial TA cloning sequencing. The same strategy was then used in human iPSCs on several clinically relevant genes including epidermal growth factor receptor (EGFR), myosin binding protein C, cardiac (Mybpc3), and hemoglobin subunit beta (HBB). Consistently, highly precise mutation rates were achieved (11.65%-37.92%) as determined by deep sequencing (DeepSeq). The present work demonstrates that tube electroporation of CRISPR/Cas9 RNP represents an efficient transfection protocol for gene editing in mammalian cells.

Novel mutations in Chinese Han patients with tuberous sclerosis complex: Case series and review of the published work.

Tuberous sclerosis complex (TSC) is an autosomal dominant genetic disease characterized by hamartomas in multiple organ systems. This study was performed in one familial and two sporadic cases with TSC. Two novel mutations (c.1884_1887delAAAG and c.5266A>G) and two previously reported mutations (c.4258_4261delTCAG and c.1960G>C) were identified by direct DNA sequencing. Of the four mutations, c.1884_1887delAAAG and c.1960G>C were found in a family and identified in the same allele by TA cloning sequencing. However, c.1960G>C was reported to be non-pathogenic. Furthermore, correlations between genotypes and phenotypes of Chinese Han patients since 2014 were performed by paired χ2 -tests in our published work review, which has not been reported. The results showed that patients with TSC2 mutations had a higher frequency of mental retardation and there were no significant differences of seizures and skin lesions with TSC1 mutations. Genetically, they had a higher frequency of familial inheritance.

Establishment of a technological system via zygote injection of CRISPR/Cas9 system for the generation of gene modified ziwuling black goats

Zygote injection of CRISPR/Cas9 system is an efficient method for generation of gene modified animals. Efficiency of zygote collection, embryo survival rate after micro-injection and pregnancy rate of surrogate are the key influence factors for the generation of gene modified animals using this strategy. Here, we investigated the influence of CIDR treatment at different time during the estrus cycle to the superovulation, and analyzed the influence of the estrus terminal time between embryo donor and embryo receptor to the pregnancy rate in Ziwuling black goats. We designed three sgRNAs targeting myostatin ( MSTN ) and also optimized the micro-injected parameter of the CRISPR/Cas9 system. The results showed that embryo donor goats effectively increase the corpus luteum amount (15.25±3.69) and zygote amount (13.875±4.015) when they were treated with CIDR at the fourth day of estrus cycle. The mixture including Cas9 mRNA (60 ng/μL) and sgRNAs (60 ng/μL) targeting MSTN was injected into zygote cytoplasm using a micromanipulator at the optimized injection parameters (Pi, Ti and Pc was 300, 0.5 and 60, respectively). Embryo cleavage rate was 76.79 % after 24 h of embryo injection. Pregnancy rate of embryo receptors whose terminal estrus time was delayed 12–16 h compared with that of embryo donor was the highest (38.46%). A total of 19 living lambs were obtained, and indels were detected in all the lambs using TA cloning sequencing. Overall, we established the technological system based on the zygote injection of CRISPR/Cas9 in Ziwuling black goats. The established technological system is the basic for generation of gene modified goats.

Analysis of a multiple osteochondroma case caused by novel splice mutation (c.1164+1G to A) of EXT1 gene

To detect potential mutation of EXT1 gene in a pedigree affected with multiple osteochondroma and explore its pathogenic mechanism. The coding regions and their flanking sequences of the EXT1/EXT2 genes were subjected to PCR amplification and Sanger sequencing. Suspected mutations were verified by excluding possible single nucleotide polymorphisms and bioinformatics analysis. Transcripts of the EXT1 gene in the proband were analyzed by TA clone-sequencing, with its abundance compared with that of healthy controls. DNA sequencing has identified in the proband a novel heterozygous point mutation (c.1164+1G to A) at the 5'splice sites of intron 3 of the EXT1 gene. The same mutation was not found in the healthy controls. Bioinformatics analysis indicated that the mutation is highly conserved and can lead to skipping of exon 3 or aberrant splicing. TA clone-sequencing indicated that the numbers of transcripts with skipping of exon 3 has significantly increased in the proband (< 0.05) compared with the controls. The c.1164+1G to A mutation has resulted in skipping of exon 3 in a proportion of EXT1 gene transcripts. As the result, the number of transcripts with tumor suppressing function is relatively reduced and has ultimately led to the tumors.

CRISPR/Cas9 mediated chicken Stra8 gene knockout and inhibition of male germ cell differentiation.

An efficient genome editing approach had been established to construct the stable transgenic cell lines in the domestic chicken (Gallus gallus domesticus) at present. Our objectives were to investigate gene function in the differentiation process of chicken embryonic stem cells (ESCs) into spermatogonial stem cells(SSCs). Three guides RNA (gRNAs) were designed to knockout the Stra8 gene, and knockout efficiency was evaluated in domestic chicken cells using cleavage activity of in vitro transcription of gRNA, Luciferase-SSA assay, T7 endonuclease I assay(T7E1) and TA clone sequence. In addition, the Cas9/gRNA plasmid was transfected into ESCs to confirm the function of Stra8. SSA assay results showed that luciferase activity of the vector expressing gRNA-1 and gRNA- 2 was higher than that of gRNA-3. TA clone sequencing showed that the knockdown efficiency was 25% (10/40) in DF-1 cells, the knockdown efficiency was 23% (9/40) in chicken ESCs. T7E1 assay indicated that there were cleavage activity for three individuals, and the knockdown efficiency was 12% (3/25). Cell morphology, qRT-PCR, immunostaining and FCS indicated that Cas9/gRNA not only resulted in the knockout of Stra8 gene, but also suggested that the generation of SSCs was blocked by the Stra8 gene knockdown in vitro. Taken together, our results indicate that the CRISPR/Cas9 system could mediate stable Stra8 gene knockdown in domestic chicken’s cells and inhibit ECSs differentiation into SSCs.

Enabling Reverse Genetics in Medicago truncatula Using High-Throughput Sequencing for Tnt1 Flanking Sequence Recovery.

The genome sequence of Medicago truncatula was published and released in 2011. A Tnt1 insertional mutant population with 21,700 independently regenerated lines was completed in 2012 at The Samuel Roberts Noble Foundation. With an estimated 25 insertions per line, the Tnt1 mutant population harbors more than 500,000 insertions in the M. truncatula genome. Based on the genome size, average gene length, and random insertion of Tnt1into the genome, the mutant population affects about 90% of genes in the M. truncatula genome. Therefore, the mutant population enables functional characterization of most genes in the M. truncatula genome. From 2006 to 2011, we sequenced about 33,000 flanking sequence tags (FSTs) from 2600 Tnt1 lines using TAIL-PCR followed by TA cloning, plasmid isolation, and traditional Sanger sequencing. To accelerate FST sequencing, we developed a two-dimensional DNA pooling strategy coupled with next-generation sequencing and produced about 380,000 FSTs from all 21,700 lines in a relatively short time. All FSTs are BLAST searchable in a web-based database. One can quickly search the database to find M. truncatula mutant lines with Tnt1 insertions in most genes of interest.

Crispr/Cas9-Induced DNMT3A Mutations in the K562 Human Leukemic Cell Line As a Model of DNMT3A-Mutated Leukemogenesis

Background:DNA methyltransferase 3A(DNMT3A) is a member of the DNA methyltransferase family primarily involved in de novo gene methylation. Mutations in DNMT3A are associated with a wide range of hematological malignancies, most frequently acute myeloid leukemia (AML). DNMT3A mutations are thought to produce a pre-leukemic state, rendering cells vulnerable to secondary oncogenic mutations and malignant transformation. Mutations in DNMT3A often coexist with secondary lesions in leukemia-related genes such as NPM1 and FLT3 (Ley T et al., N Engl J Med, 2010). Furthermore, healthy individuals harboring DNMT3A-driven clonal hematopoiesis are at increased risk of future hematologic malignancies and all-cause mortality (Jaiswal S et al., N Engl J Med, 2014). Despite these important clinical associations, the mechanisms by which DNMT3A mutations contribute to malignant transformation have not been well-defined. Dnmt3a-knockout (KO)mouse hematopoietic stem cells (HSCs) preferentially self-renew rather than undergo differentiation, leading to their accumulation in the bone marrow (Challen GA et al., Nat Genet, 2011). DNMT3A loss has also been shown to drive hypomethylation and subsequent activation of leukemia-related genes (Lu R et al., Cancer Cell, 2016; Yang L et al., Cancer Cell, 2016). However, these findings have not been recapitulated using human tissue. The goals of this study were thus to determine the transcriptional and biological effects of DNMT3A mutations which contribute towards malignant transformation in human cells.Methods:To elucidate the effects of DNMT3A mutation, we introduced DNMT3A frameshift mutations into K562 cells using the CRISPR/Cas9 gene-editing system. We then performed various functional and genomic assays to better elucidate effects of DNMT3A loss.Results and Discussion:We successfully created 4 DNMT3A-KO K562 clones and 1 clone containing a mutation that produces an altered DNMT3A protein with an intact catalytic domain (DNMT3A-alt). We first assessed effects of DNMT3A loss on cell growth and apoptosis. DNMT3A-KO clones exhibited impaired growth compared to wild-type (WT) cells. DNMT3A-KO clones also displayed significantly increased apoptotic activity after exposure to 5-fluorouracil (5-FU). The DNMT3A-alt clone had similar growth and apoptotic activity to WT cells. We examined how DNMT3A loss impacted differentiation using phorbal 12-myristate 13-acetate (PMA), known to induce megakaryocytic differentiation of K562 cells. After overnight exposure to PMA, DNMT3A-KO clones exhibited less CD61 expression, a marker of megakaryocytic differentiation, than did WT cells. Again, the differentiation of the DNMT3A-alt clonewas comparable to WT. Finally, we performed karyotype analysis to elucidate a potential role of DNMT3A in maintaining genomic integrity. Surprisingly, DNMT3A-KO clones exhibited profound cytogenetic variability and genomic instability compared to WT, with most DNMT3A-KO clones containing dicentric chromosomes and ring forms in multiple spreads (Figure 1). The DNMT3A-alt clone had a karyotype identical to WT. CRISPR/Cas9-edited K562 clones without DNMT3A mutation (transfected WT or tWT) also had identical karyotypes to WT K562. TA cloning and mRNA sequencing were employed to elucidate whether loss of DNMT3A would lead to transcriptome instability. DNMT3A-KOand DNMT3A-altclones exhibited distorted splicing patterns, while tWT cell lines were comparable to WT. To further assess the effect of DNMT3A ablation on genomic integrity, we examined DNA-damage responses by measuring DNA double-stranded breaks (DSBs) after treatment with 5-FU. DNMT3A-KO clones were significantly more susceptible to DNA damage than were WT cells, while the DNMT3A-alt clone exhibited more DNA DSBs compared to WT only at high concentrations of 5-FU.Conclusion:CRISPR/Cas9-mediated DNMT3A-KO K562 cells may be used to model effects of DNMT3A mutations in human cells. Consistent with previous reports, our data suggest that DNMT3A is involved in the differentiation of multipotent progenitors. Novel to this approach, our findings implicate induction of genomic instability as a mechanism by which DNMT3A mutations might predispose to malignancy. [Display omitted] DisclosuresHosokawa:Aplastic Anemia and MDS International Foundation: Research Funding. Townsley:Novartis: Research Funding. Young:GSK/Novartis: Research Funding.