Junction Fragments Research Articles

Development of an event-specific PCR method to quantify genetically modified soybean DBN8002 on both real-time and digital PCR platforms

The genetically modified (GM) soybean DBN8002 has been approved for commercial planting in China. For enforcing GMO labeling policy, an event-specific real-time quantitative PCR (qPCR) method was developed to target the junction fragment between the T-DNA left border and the flanking genomic DNA, yielding a 104 base pair (bp) amplicon. This event-specific qPCR method can identify and quantify the DBN8002 event with high specificity, satisfactory linearity, and acceptable accuracy. Furthermore, the DBN8002-event specific primer/probe set was successfully transferred to a droplet digital PCR (ddPCR) platform for quantification. The quantitative results from qPCR were found to be comparable to those obtained from ddPCR, with a P-value exceeding 0.05, indicating no significant difference. The limit of detection (LOD) for both qPCR and ddPCR methods was determined to be 10 copies per reaction, while the limit of quantification (LOQ) was estimated to be 20 copies per reaction for qPCR and 40 copies per reaction for ddPCR. The collaborative validation demonstrated that the DBN8002 event-specific qPCR method had satisfactory repeatability and reproducibility. Both the event-specific qPCR and ddPCR methods are suitable for quantifying the DBN8002 content in samples. Additionally, ddPCR can be utilized for the characterization of DBN8002 reference materials.

A facile Agrobacterium-mediated transformation method for the model unicellular green algae Chlamydomonas reinhardtii

A reliable and simple Agrobacterium-mediated transformation system for the unicellular green algae model organism Chlamydomonas reinhardtii has been developed. The protocol has been successfully employed with both neomycin phosphotransferase II (nptII) and the phleomycin resistance (bleI) genes coupled with the selective agents paromomycin and zeocin, respectively. A set of binary vectors were assembled that carry the selectable marker cassettes under control either of the Rbcs2 alone or fused to the HSP270A leader sequence, PsaD, or ß-tubulin2 promoters. The corresponding T-DNA elements also harbored a cassette with a codon-optimized version of yellow fluorescence protein (YFP) under control of the Rbcs2 promoter in which the YFP open reading frame was interrupted with the first intron of Rbcs2 to prevent expression in Agrobacterium tumefaciens. The resultant binary vectors were introduced into A. tumefaciens strain C58C1/pMP90, and the derived transconjugants were used for transformation studies with the walled C. reinhardtii strain CC124. Estimated transformation frequencies ranged from 0.09 to 2.86 colonies per 106 cells inoculated. Molecular characterizations on a subset of the transgenic lineages revealed that most of the transgenic events harbored single locus insertions. Moreover, sequencing of captured junction fragments about the T-DNA insertion site showed that minimal disruption of the C. reinhardtii genome occurred. However, the transgenic lineages often harbored truncated T-DNA regions within the non-selectable marker gene cassettes.

Sustained oral spermidine supplementation rescues functional and structural defects in COL6-deficient myopathic mice

ABSTRACT COL6 (collagen type VI)-related myopathies (COL6-RM) are a distinct group of inherited muscle disorders caused by mutations of COL6 genes and characterized by early-onset muscle weakness, for which no cure is available yet. Key pathophysiological features of COL6-deficient muscles involve impaired macroautophagy/autophagy, mitochondrial dysfunction, neuromuscular junction fragmentation and myofiber apoptosis. Targeting autophagy by dietary means elicited beneficial effects in both col6a1 null (col6a1 –/– ) mice and COL6-RM patients. We previously demonstrated that one-month per os administration of the nutraceutical spermidine reactivates autophagy and ameliorates myofiber defects in col6a1 –/– mice but does not elicit functional improvement. Here we show that a 100-day-long spermidine regimen is able to rescue muscle strength in col6a1 –/– mice, with also a beneficial impact on mitochondria and neuromuscular junction integrity, without any noticeable side effects. Altogether, these data provide a rationale for the application of spermidine in prospective clinical trials for COL6-RM. Abbreviations: AChR: acetylcholine receptor; BTX: bungarotoxin; CNF: centrally nucleated fibers; Colch: colchicine; COL6: collagen type VI; COL6-RM: COL6-related myopathies; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; NMJ: neuromuscular junction; Spd: spermidine; SQSTM1/p62: sequestosome 1; TA: tibialis anterior; TOMM20: translocase of outer mitochondrial membrane 20; TUNEL: terminal deoxynucleotidyl transferase dUTP-mediated nick-end labeling.

Whole Genome Sequencing Applied in Familial Hamartomatous Polyposis Identifies Novel Structural Variations.

Hamartomatous polyposis syndromes (HPS) are rare cancer-predisposing disorders including Juvenile polyposis (JPS), Peutz–Jeghers (PJS) and PTEN hamartomatous syndromes (PHS). Penetrant mutations in corresponding genes (SMAD4, BMPR1A, STK11, PTEN and AKT1), are usually diagnosed via a next-generation-sequencing gene panel (NGS-GP) for tailored surveillance and preimplantation testing for monogenic disorders (PGT-M). Five probands with HPS phenotype, with no genetic diagnosis per genetic workup, underwent whole-genome sequencing (WGS) that identified structural genetic alterations: two novel inversions in BMPRA1 and STK11, two BMPR1A-deletions, known as founders among Bukharan Jews, and BMPR1A microdeletion. BMPR1A inversion was validated by “junction fragment” amplification and direct testing. PGT-M was performed via multiplex-PCR and enabled successful birth of a non-carrier baby. WGS may be considered for HPS patients with no NGS-GP findings to exclude structural alterations.

Circulating Virus-Host Chimera DNAs in the Clinical Monitoring of Virus-Related Cancers.

Simple SummaryCell-free tumor DNA (ctDNA), the DNA released into circulation from tumors, is a promising tumor marker with versatile applications. The associations of the amount, somatic mutation frequency, and epigenetic modifications of ctDNA with the tumor burden, tumor behavior, and prognosis have been widely investigated in different types of tumors. However, there are still some challenging issues to be resolved before ctDNA can complement or even replace current serum tumor markers. We propose employing exogenous viral DNA integration that produces unique virus–host chimera DNA (vh-DNA) at junction sites. Cell-free vh-DNA may become a new biomarker because it overcomes background interference detection problems, takes advantage of virus tropism to localize the tumor, and acts as a universal marker for monitoring clonal expansion or tumor loads in tumors related to oncogenic viruses.The idea of using tumor-specific cell-free DNA (ctDNA) as a tumor biomarker has been widely tested and validated in various types of human cancers and different clinical settings. ctDNA can reflect the presence or size of tumors in a real-time manner and can enable longitudinal monitoring with minimal invasiveness, allowing it to be applied in treatment response assessment and recurrence monitoring for cancer therapies. However, tumor detection by ctDNA remains a great challenge due to the difficulty in enriching ctDNA from a large amount of homologous non-tumor cell-free DNA (cfDNA). Only ctDNA with nonhuman sequences (or rearrangements) can be selected from the background of cfDNA from nontumor DNAs. This is possible for several virus-related cancers, such as hepatitis B virus (HBV)-related HCC or human papillomavirus (HPV)-related cervical or head and neck cancers, which frequently harbor randomly integrated viral DNA. The junction fragments of the integrations, namely virus–host chimera DNA (vh-DNA), can represent the signatures of individual tumors and are released into the blood. Such ctDNA can be enriched by capture with virus-specific probes and therefore exploited as a circulating biomarker to track virus-related cancers in clinical settings. Here, we review virus integrations in virus-related cancers to evaluate the feasibility of vh-DNA as a cell-free tumor marker and update studies on the development of detection and applications. vh-DNA may be a solution to the development of specific markers to manage virus-related cancers in the future.

Loss of mouse Stmn2 function causes motor neuropathy

Amyotrophic lateral sclerosis (ALS) is characterized by motor neuron degeneration accompanied by aberrant accumulation and loss of function of the RNA-binding protein TDP43. Thus far, it remains unresolved to what extent TDP43 loss of function directly contributes to motor system dysfunction. Here, we employed gene editing to find whether the mouse ortholog of the TDP43-regulated gene STMN2 has an important function in maintaining the motor system. Both mosaic founders and homozygous loss-of-function Stmn2 mice exhibited neuromuscular junction denervation and fragmentation, resulting in muscle atrophy and impaired motor behavior, accompanied by an imbalance in neuronal microtubule dynamics in the spinal cord. The introduction of human STMN2 through BAC transgenesis was sufficient to rescue the motor phenotypes observed in Stmn2 mutant mice. Collectively, our results demonstrate that disrupting the ortholog of a single TDP43-regulated RNA is sufficient to cause substantial motor dysfunction, indicating that disruption of TDP43 function is likely a contributor to ALS.

Active older dancers have lower C-terminal Agrin fragment concentration, better balance and gait performance than sedentary peers.

Motor neuron degeneration, denervation, neuromuscular junction (NMJ) fragmentation and loss of motor units (MUs), play a key-role in the development of sarcopenia. The aim of the present study was to investigate the beneficial effects of regular practice of dancing in physically active elders on concentration of C-terminal Agrin fragment (CAF), a marker of NMJ instability, muscle mass, strength, and physical performance in a group of 16 recreationally active older dancers (AOD; 70.1±3.4yr) compared to 15 age-matched sedentary peers (OS; 70.9±6.2yr). Circulating concentration of CAF was measured in serum, while morphology of the vastus lateralis and multifidus muscles was assessed by ultrasound imaging. In addition, the participants underwent two functional performance tests, the Timed Up and Go (TUG) and the 10-meter walk test (10-MWT), a lower and upper limb isometric strength test, a static and a dynamic balance test. Although no statistically significant differences were detected for both muscle morphology and isometric strength, higher CAF concentration (20%, p<0.01) was found in OS. AOD showed a better performance in TUG (22%, p<0.001), 10-MWT (17%, p<0.001) and dynamic balance (25%, p<0.01) than OS. Notably, CAF concentration correlated with dynamic balance performance (r=0.3711, p<0.05). Our results provide evidence that the regular practice of dancing in older age, together with non-structured light aerobic physical activities, is associated to lower CAF concentration and improved walking and balance performance. Our findings also suggest that NMJ instability, as indicated by elevated CAF serum concentration, seems to precede the loss of muscle size and alterations in muscle architecture normally associated with sarcopenia.

A rare transgenic event of rice with Agrobacterium binary vector backbone integration at the right T-DNA border junction

Agrobacterium tumefaciens precisely transfers the transferred DNA (T-DNA) between the right border (RB) and the left border (LB) and integrates it in the plant genome. However, transfer of the binary vector backbone (BVB) at the LB junction has been frequently reported. Here, we describe a complex T-DNA integration in the rice transgenic event CG27 with BVB at the RB junction. Amplification of an RB-plant DNA junction fragment by genome walking and its sequencing revealed that the T-DNA portion ended at the 1st bp of RB, but is followed by a binary vector backbone (BVB) along with an RB-flanking T-DNA portion, both in an inverse orientation. This is followed by a 5-bp filler sequence and the rice chromosome 1 sequence. The configuration of the BVB integration at the RB junction was independently confirmed by PCR. Disruption of native chromosome 1 sequence was confirmed by PCR with chromosome 1-specific primers designed from either side of the T-DNA integration site. BVB sequence close to the RB is transferred and integrated into the CG27 plant genome by a mechanism that does not involve LB-skipping and RB read-through. Therefore, a check for BVB sequences at both LB and RB junctions in a transgenic crop is important in biosafety evaluation.

A new computed tomography scoring system to assess osteochondral allograft transplantation for the knee: inter-observer and intra-observer agreement.

To describe a new semiquantitative computed tomography (CT) scoring system for multi-feature analysis of cartilage defect repair by osteochondral allografts for the knee and to assess its intra-observer and inter-observer variability. A semiquantitative assessment CT osteochondral allograft (ACTOCA) scoring system was designed based on fresh osteochondral allograft transplantations for the knee. The system includes five CT features: density relative to host bone, integration at the host-graft junction, surface percentage with a discernible cleft at the host-graft junction, cystic changes, and intra-articular fragments. Inter-observer variability was calculated by three observers blinded to the patient's medical history and treatment. Intra-observer variability was also determined. Inter-observer agreement was moderate to substantial for all CT score components and intra-observer agreement was moderate to almost perfect for all CT score components (κ > 0.5, p < 0.05). The ACTOCA score is a reliable tool to evaluate integration of osteochondral allograft transplantations. It provides an accurate evaluation of bone changes and may help to standardize CT scan reports following osteochondral allograft transplantation for the knee.

Cancer cachexia in a mouse model of oxidative stress.

BackgroundCancer is associated with muscle atrophy (cancer cachexia) that is linked to up to 40% of cancer‐related deaths. Oxidative stress is a critical player in the induction and progression of age‐related loss of muscle mass and weakness (sarcopenia); however, the role of oxidative stress in cancer cachexia has not been defined. The purpose of this study was to examine if elevated oxidative stress exacerbates cancer cachexia.MethodsCu/Zn superoxide dismutase knockout (Sod1KO) mice were used as an established mouse model of elevated oxidative stress. Cancer cachexia was induced by injection of one million Lewis lung carcinoma (LLC) cells or phosphate‐buffered saline (saline) into the hind flank of female wild‐type mice or Sod1KO mice at approximately 4 months of age. The tumour developed for 3 weeks. Muscle mass, contractile function, neuromuscular junction (NMJ) fragmentation, metabolic proteins, mitochondrial function, and motor neuron function were measured in wild‐type and Sod1KO saline and tumour‐bearing mice. Data were analysed by two‐way ANOVA with Tukey–Kramer post hoc test when significant F ratios were determined and α was set at 0.05. Unless otherwise noted, results in abstract are mean ±SEM.ResultsMuscle mass and cross‐sectional area were significantly reduced, in tumour‐bearing mice. Metabolic enzymes were dysregulated in Sod1KO mice and cancer exacerbated this phenotype. NMJ fragmentation was exacerbated in tumour‐bearing Sod1KO mice. Myofibrillar protein degradation increased in tumour‐bearing wild‐type mice (wild‐type saline, 0.00847 ± 0.00205; wildtype LLC, 0.0211 ± 0.00184) and tumour‐bearing Sod1KO mice (Sod1KO saline, 0.0180 ± 0.00118; Sod1KO LLC, 0.0490 ± 0.00132). Muscle mitochondrial oxygen consumption was reduced in tumour‐bearing mice compared with saline‐injected wild‐type mice. Mitochondrial protein degradation increased in tumour‐bearing wild‐type mice (wild‐type saline, 0.0204 ± 0.00159; wild‐type LLC, 0.167 ± 0.00157) and tumour‐bearing Sod1KO mice (Sod1KO saline, 0.0231 ± 0.00108; Sod1 KO LLC, 0.0645 ± 0.000631). Sciatic nerve conduction velocity was decreased in tumour‐bearing wild‐type mice (wild‐type saline, 38.2 ± 0.861; wild‐type LLC, 28.8 ± 0.772). Three out of eleven of the tumour‐bearing Sod1KO mice did not survive the 3‐week period following tumour implantation.ConclusionsOxidative stress does not exacerbate cancer‐induced muscle loss; however, cancer cachexia may accelerate NMJ disruption.

Whole Genome Low-Coverage Sequencing Concurrently Detecting Copy Number Variations and Their Underlying Complex Chromosomal Rearrangements by Systematic Breakpoint Mapping in Intellectual Deficiency/Developmental Delay Patients.

Simple copy number variations (CNVs) detected by chromosomal microarray (CMA) can result from complex structural changes. Therefore, it is necessary to characterize potential structural changes that cause pathogenic CNVs. We applied whole-genome low-coverage sequencing (WGLCS) to concurrently detect pathogenic CNVs and their associated chromosomal rearrangements in 15 patients. All the patients had an average of 2–3 pathogenic CNVs involving 1–2 chromosomes. WGLCS identified all the 34 pathogenic CNVs found by microarray. By identifying chimeric read pairs, WGLCS mapped 70 breakpoints in these patients, of which 47 were finely mapped at the nucleotide level and confirmed by subsequent PCR amplification and Sanger sequencing of the junction fragments. In 15 patients, structural rearrangements were defined at molecular level in 13 patients. In 13 patients, WGLCS reveal no additional results in two patients. In another 11 patients, WGLCS revealed new breakpoints or finely mapped the genes disrupted by breakpoints or 1–6 bp microhomology and/or short insertion (4–70 bp) in the breakpoints junctions. However, structural changes in the other two patients still remained unclear after WGLCS was performed. The structural alteration identified in the 13 patients could be divided into the following categories: (1) interstitial inverted duplication with concomitant terminal deletion (inv dup del) (P1,P4,P9,P11); (2) the product of pericentric inversion (P5); (3) ring chromosome (P8); (4) interstitial duplication and/or triplication (P6, P7); and (5) +der(22)t(11;22) (P2,P15); (6) complex structural rearrangements (P3,P12,P14). WGLCS displayed the ability to discover CNVs and define breakpoints and its disrupted genes and its surrounding sequences in one experiment at base-pair-resolution, which help us to learn more about the mechanisms of formation of observed genomic rearrangements, and in which DNA replicative/repair mechanism might contribute to the formation of complex rearrangements in 11 patients. Clear karyotype at molecular level could help provide an accurate evaluation of recurrent risk and guide prenatal diagnosis or reproductive planning.

Structure characterization of a heavily fucosylated chondroitin sulfate from sea cucumber (H. leucospilota) with bottom-up strategies

Two bottom-up strategies, disaccharide and oligosaccharide analyses, were applied to elucidate the structure of a fucosylated chondroitin sulfate (FCS). The FCS was hydrolyzed with mild acid. The remained part was digested with CS lyase for disaccharide analysis. The products from each step were analyzed and the results revealed that mild sulfuric acid mainly released sulfated fucose branches, but also affected some residues and sulfo-groups on the backbone. Over 140 oligosaccharide fragments were generated by catalytic oxidation and identified by HPSEC-MS, including sulfated fucose oligosaccharides exclusively from branches, sulfated backbone fragments, and junctional fragments. Based on the results provided by these two methods, the proposed backbone of the FCS is mainly composed of GlcA→GalNAc4S6S and GlcA→GalNAc6S, and the branch is mainly located at GalNAc. The longest branch observed is nonasaccharide, and most of the fucose on the branches are mono and/or di-sulfated. NMR results supported the conclusion.

Recurrent De Novo NAHR Reciprocal Duplications in the ATAD3 Gene Cluster Cause a Neurogenetic Trait with Perturbed Cholesterol and Mitochondrial Metabolism

Recent studies have identified both recessive and dominant forms of mitochondrial disease that result from ATAD3A variants. The recessive form includes subjects with biallelic deletions mediated by non-allelic homologous recombination. We report five unrelated neonates with a lethal metabolic disorder characterized by cardiomyopathy, corneal opacities, encephalopathy, hypotonia, and seizures in whom a monoallelic reciprocal duplication at the ATAD3 locus was identified. Analysis of the breakpoint junction fragment indicated that these 67 kb heterozygous duplications were likely mediated by non-allelic homologous recombination at regions of high sequence identity in ATAD3A exon 11 and ATAD3C exon 7. At the recombinant junction, the duplication allele produces a fusion gene derived from ATAD3A and ATAD3C, the protein product of which lacks key functional residues. Analysis of fibroblasts derived from two affected individuals shows that the fusion gene product is expressed and stable. These cells display perturbed cholesterol and mitochondrial DNA organization similar to that observed for individuals with severe ATAD3A deficiency. We hypothesize that the fusion protein acts through a dominant-negative mechanism to cause this fatal mitochondrial disorder. Our data delineate a molecular diagnosis for this disorder, extend the clinical spectrum associated with structural variation at the ATAD3 locus, and identify a third mutational mechanism for ATAD3 gene cluster variants. These results further affirm structural variant mutagenesis mechanisms in sporadic disease traits, emphasize the importance of copy number analysis in molecular genomic diagnosis, and highlight some of the challenges of detecting and interpreting clinically relevant rare gene rearrangements from next-generation sequencing data.

Long-Term AAV-Mediated Factor VIII Expression in Nine Hemophilia A Dogs: A 10 Year Follow-up Analysis on Durability, Safety and Vector Integration

Hemophilia is an X-linked bleeding disorder caused by a deficiency in clotting factor VIII (FVIII)(hemophilia A, HA) or factor IX (FIX)(hemophilia B, HB). While early clinical trials of AAV delivery of FIX for HB have demonstrated stable FIX expression for &amp;gt;8 years, an ongoing clinical trial of AAV-FVIII delivery for HA achieved high levels of transgene expression that unexpectedly declined after 1 year. Here we describe preclinical studies of AAV-canine FVIII (cFVIII) delivery in nine HA dogs with sustained FVIII expression for the duration of the study, as long as 10 years. FVIII was delivered using two delivery approaches: (1) co-administration of two AAV vectors encoding separate cFVIII heavy and light chains driven by the thyroxine binding globulin (TBG) promoter (Two chain approach)(TC) (n=5) at two AAV doses (2.5 x 1013vg/kg; F24, Woodstock, J60) and (1.2 x 1013vg/kg; Linus, H19) or (2) delivery of cFVIII as a single chain driven by the human alpha-1 anti-trypsin (hAAT) promoter (Single chain approach)(SC)(n=4) at two AAV doses (4 x 1013 vg/kg; M50, M06) and (2 x 1013vg/kg; M66, L51) (Sabatino 2011). We demonstrated that both strategies were efficacious; preventing &amp;gt;95% of spontaneous bleeding episodes without toxicity. We now report the long-term follow-up of between 2.2 and 10.1 years for these treated dogs. Dose-dependent cFVIII:C (Coatest SP4 FVIII) was observed. At the final time point, the cFVIII:C was 2.7% (F24), 7.1% (Woodstock), 4.5% (J60), 11.3% (Linus) and 2.5% (H19) for TC dogs. For the SC dogs, the cFVIII:C was 9.4% (M06), 10.3% (M50), 1.9% (L51) and 3.7% (M66). Stable FVIII expression was maintained for seven of the dogs over the course of the study. Two dogs (Linus, M50) had a gradual increase in FVIII:C that began about three years after vector administration and continued for an additional seven years (Linus) and four years (M50), until the termination of the study. Liver function tests, serum alpha-fetoprotein concentrations, fibrinogen levels as well as liver pathology did not suggest altered liver function or tumor development in Linus and M50 compared to the other dogs. Clinically, there was no evidence of malignancy and no tumors were detected at the time of necropsy in any dog. One of the safety concerns for AAV-mediated gene therapy approaches is the potential for AAV integration events to be genotoxic and lead to tumorigenesis. While recombinant AAV primarily remains as an episome, integration events have been observed in mouse models and hepatocellular carcinoma has been observed after neonatal delivery of AAV vectors. In addition, the increase in FVIII expression in Linus and M50 prompted us to investigate integration and clonal expansion as a potential mechanism for these observations. Vector copy number (VCN) analysis was performed on liver samples (5-29 per dog, n=8 dogs) by Q-PCR and detected DNA copy numbers between 0.0 and 7.8 per diploid genome (Fig 1A). We performed integration target site analysis on liver samples (n=3/dog) from six of the AAV-treated HA dogs and naïve HA dogs (n=2) by ligation-mediated PCR, Ilumina paired-end sequencing and analysis using the custom software pipeline, AAVenger. Analysis of the 20 samples identified &amp;gt;2,000 unique AAV integration events (IE). There was a correlation between the DNA copy number and the number of integration events detected. Clonal abundances were estimated by counting the unique genome breaks associated with integration positions, which showed that the maximum clonal abundance ranged from 1 to 138. The integration events were distributed across the canine genome. Clonal expansions were observed with integration near genes previously associated with growth control and transformation in humans (Fig 1B) with the most abundant clones located in DLEU2L (Linus), PEBP4 (J60) and EGR3 (M50). Integration events in EGR3, EGR2, CCND1, LTO1 and ZNF365 were detected in multiple dogs. Validation of integration sites in the most abundant clones was performed using targeted PCR to isolate junction fragments followed by Sanger sequencing. While AAV integration and clonal expansion was observed, the dogs had no evidence for tumorigenesis and it is not clear if the increase in FVIII expression is associated with the clonal expansions detected. Overall, these studies demonstrate long-term sustained FVIII expression for up to 10 years with clonal expansion, but without clinical adverse events after AAV-mediated gene therapy for hemophilia. Disclosures Sabatino: Spark Therapeutics: Patents &amp; Royalties.

Skeletal muscle mTORC1 regulates neuromuscular junction stability.

BackgroundSkeletal muscle is a plastic tissue that can adapt to different stimuli. It is well established that Mammalian Target of Rapamycin Complex 1 (mTORC1) signalling is a key modulator in mediating increases in skeletal muscle mass and function. However, the role of mTORC1 signalling in adult skeletal muscle homeostasis is still not well defined.MethodsInducible, muscle‐specific Raptor and mTOR k.o. mice were generated. Muscles at 1 and 7 months after deletion were analysed to assess muscle histology and muscle force.ResultsWe found no change in muscle size or contractile properties 1 month after deletion. Prolonging deletion of Raptor to 7 months, however, leads to a very marked phenotype characterized by weakness, muscle regeneration, mitochondrial dysfunction, and autophagy impairment. Unexpectedly, reduced mTOR signalling in muscle fibres is accompanied by the appearance of markers of fibre denervation, like the increased expression of the neural cell adhesion molecule (NCAM). Both muscle‐specific deletion of mTOR or Raptor, or the use of rapamycin, was sufficient to induce 3–8% of NCAM‐positive fibres (P < 0.01), muscle fibrillation, and neuromuscular junction (NMJ) fragmentation in 24% of examined fibres (P < 0.001). Mechanistically, reactivation of autophagy with the small peptide Tat‐beclin1 is sufficient to prevent mitochondrial dysfunction and the appearance of NCAM‐positive fibres in Raptor k.o. muscles.ConclusionsOur study shows that mTOR signalling in skeletal muscle fibres is critical for maintaining proper fibre innervation, preserving the NMJ structure in both the muscle fibre and the motor neuron. In addition, considering the beneficial effects of exercise in most pathologies affecting the NMJ, our findings suggest that part of these beneficial effects of exercise are through the well‐established activation of mTORC1 in skeletal muscle during and after exercise.

Genotyping Genetically Modified (GM) Mice.

Prior to generating a new mouse model, it is important to plan the method that will be used to detect which of the mice generated have the mutation(s) desired. Nearly, all types of mutations may be detected using PCR. However, the choice of primers will differ depending upon the method used to generate the model. Transgenic mice should be genotyped across a unique junction fragment. Targeted ES cells used to generate knock-out or knock-in mice should be genotyped using primers from a unique marker in the construct and a region outside of the construct. Targeting in ES cells can also be detected using a genomic Southern blot. Mice targeted using CRISPR/Cas9 should have the region of interest amplified using PCR, and then be assessed for size changes (for large changes in sequence) by Surveyor Assay (for gene knock-out and point mutations) and/or sequenced to verify the mutation. Each of these models has a unique requirement for genotyping, and failure to understand the requirements can easily lead to loss of the gene in subsequent generations.

Severe hemophilia A caused by an unbalanced chromosomal rearrangement identified using nanopore sequencing

Unlabelled Box BackgroundNo F8 genetic abnormality is detected in about 2% of severe hemophilia A patients using conventional genetic approaches. In these patients, deep intronic variation or F8 disrupting genomic rearrangement could be causal. ObjectiveTo characterize, in a genetically unresolved severe hemophilia A patient, a new Xq28 rearrangement disrupting F8 using comprehensive molecular techniques including nanopore sequencing. ResultsLong‐range polymerase chain reaction (PCR) performed throughout F8 identified a nonamplifiable region in intron 25 indicating the presence of a genomic rearrangement. F8messanger ribonucleic acid (mRNA) analysis including 3′rapid amplification of complementary deoxyribonucleic acid (cDNA) ends and nanopore sequencing found the presence of a F8 fusion transcript in which F8 exon 26 was replaced by a 742‐bp pseudoexon corresponding to a noncoding region located at the beginning of the long arm of chromosome X (Xq12; chrX: 66 310 352‐66 311 093, GRCh37/hg19). Cytogenetic microarray analysis found the presence of a Xq11.1q12 gain of 3.8 Mb. The PCR amplification of junction fragments and fluorescent in situ hybridization (FISH) analysis found that the Xq11q12 duplicated region was inserted in the F8 intron 25 genomic region. ConclusionWe characterized a novel genomic rearrangement in which a 3.8‐Mb Xq11.1q12 gain inserted in the F8 intron 25 led to an aberrant fusion transcript in a patient with severe hemophilia A (HA), using comprehensive molecular techniques. This study highlights the value of single‐molecule long‐read sequencing technologies for molecular diagnosis of HA especially when conventional genetic approaches have failed.

Cell-free junctional DNA fragment from hepatitis B virus integration in HCC for monitoring postresection recurrence and clonality.

4090 Background: About one-third of patients suffer tumor recurrence within the first year after surgical resection of HCC. Early recurrence compromised their overall survival. Timing detection of HCC recurrence and its clonality is required to implement therapeutic trials appropriately. This study examined the virus-host chimera DNA (vh-chimera DNA), generated from junctions of HBV integration in HCC chromosome and released into blood, as a potential circulating biomarker for this clinical setting. Methods: We established a capture-next generation sequencing (NGS) platform to identify the HBV integrations in 50 resected HBV-related HCC. For individual HCC, the major clonal HBV integration sites were chosen to design specific primers for droplet digital PCR (ddPCR) to detect and quantify the vh-chimera DNA in plasma samples, collected either just before surgery or two months after surgery. Levels of vh-chimera DNA were then correlated with baseline HCC size or recurrence in one-year follow up. Results: We succeeded in detecting HBV integrations in the HCC from 44 out of 50 HBV-related HCC patients (88%). The copy number of vh-chimera DNA in plasma at surgery from 42 patients correlated with tumor sizes, with the detection limit at 1.5-2 cm. Among the plasma collected 2 months after surgery, 26.2% of samples contained the same HCC signature vh-chimera DNA as baseline plasma, indicating a possible residual tumor. Consistently, 81.8% of them suffered HCC recurrence within one year. The signature vh-DNA in the plasma suggested the majority of recurrences coming from the original HCC clones, whereas 2 from de novo ones. Conclusions: This study supported vh-chimera DNA as a new circulation marker for detecting the existence of most HBV-related HCC. This new biomarker may complement AFP to help detect residual or recurrent HCC and their clonality after curative therapies.

Nonlesional Atopic Dermatitis Skin Shows Alterations in Langerhans Cells in Close Proximity to Tight Junction Fragmentation

Nonlesional Atopic Dermatitis Skin Shows Alterations in Langerhans Cells in Close Proximity to Tight Junction Fragmentation

Abstract LB-334: Elucidation of integrated HPV DNA structure in a cervical carcinoma cell line by combined high resolution and long range sequencing analyses

Abstract Purpose/Objectives: Integration of human papillomavirus (HPV) DNA into the human genome occurs in a fraction of viral infections and is a near ubiquitous factor in cervical tumorigenesis. While use of next-generation sequencing (NGS) methods has significantly advanced our understanding of HPV DNA integration and its consequences, short read approaches may yield false positives or misinterpretation of associated genomic structural variants. With the goal of resolving genomic rearrangements, we applied both HPV16 hybridization capture-NGS and long read Nanopore technology to the well-studied CaSki cervical carcinoma cell line that has many sites of HPV16 DNA integration. Methods: CaSki genomic DNA was sheared, ligated to Illumina adaptors, hybridized to HPV16 capture probes (Roche Nimblegen SeqCap EZ System), and sequenced by Illumina HiSeq 2500, paired end, 300 bp mode. Reads were aligned to a custom human (GRCh37/hg19) plus HPV16 reference genome using BWA mem, and junction fragments were computationally identified using Delly and SplazerS. For long read analysis, isolated CaSki DNA was sheared to 20 kb. Genomic libraries were prepared and sequenced on an Oxford Nanopore MinION Mk1b device (ONT) using standard 48 hour scripts. Base calling and fastq file extraction were performed with Albacore v2.0. Reads were aligned using Ngmlr, and structural variants called using Sniffles. Results: For Illumina analysis, 34 million demultiplexed read pairs were obtained with average, HPV genome coverage depth of 2.8*106. 47 previously identified, HPV-human junctions were verified along with 193 novel junctions. Use of PCR has validated 4 of 6 novel junctions tested to date. Multiple junctions were noted to be clustered at some chromosomal locations, with 30 (13.5%) called less than 1kb apart on the human genomic side. For long read analysis, ~150K reads were obtained. Mean read length was 16K with genome and HPV16 coverage of 0.60X and 220X, respectively. Integrations were detected on chromosomes 2, 5, 7, 10, 19, 20, and X, and all consisted of &amp;gt;2 tandem viral genomes. Discussion: Our molecular approaches generated unprecedented long-range analyses of HPV DNA integration sites in the CaSki cervical carcinoma cell line. HPV DNA was often present in tandem arrays. We interpret the clusters of nearby HPV-human junctions as potential evidence of frequent, ongoing, subclonal, genomic rearrangements at these sites. Combining deep-sequencing and long-range methodologies allowed important insights, and we are currently analyzing clinical cancer samples using them. Citation Format: Anne Van Arsdale, Jack Lenz, Nicole Patterson, Elaine Maggi, Dennis Y. Kuo, Cristina Montagna. Elucidation of integrated HPV DNA structure in a cervical carcinoma cell line by combined high resolution and long range sequencing analyses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-334.