Allele-Specific Prevention of Nonsense-Mediated Decay in Cystic Fibrosis Using Homology-Independent Genome Editing

Nonsense-mediated decay (NMD) is a major pathogenic mechanism underlying a diversity of genetic disorders. Nonsense variants tend to lead to more severe disease phenotypes and are often difficult targets for small molecule therapeutic development as a result of insufficient protein production. The treatment of cystic fibrosis (CF), an autosomal recessive disease caused by mutations in the CFTR gene, exemplifies the challenge of therapeutically addressing nonsense mutations in human disease. Therapeutic development in CF has led to multiple, highly successful protein modulatory interventions, yet no targeted therapies have been approved for nonsense mutations. Here, we have designed a CRISPR-Cas9-based strategy for the targeted prevention of NMD of CFTR transcripts containing the second most common nonsense variant listed in CFTR2, W1282X. By introducing a deletion of the downstream genic region following the premature stop codon, we demonstrate significantly increased protein expression of this mutant variant. Notably, in combination with protein modulators, genome editing significantly increases the potentiated channel activity of W1282X-CFTR in human bronchial epithelial cells. Furthermore, we show how the outlined approach can be modified to permit allele-specific editing. The described approach can be extended to other late-occurring nonsense mutations in the CFTR gene or applied as a generalized approach for gene-specific prevention of NMD in disorders where a truncated protein product retains full or partial functionality.

Modeling Niemann-Pick disease type C in a human haploid cell line allows for patient variant characterization and clinical interpretation

The accurate clinical interpretation of human sequence variation is foundational to personalized medicine. This remains a pressing challenge, however, as genome sequencing becomes routine and new functionally undefined variants rapidly accumulate. Here, we describe a platform for the rapid generation, characterization, and interpretation of genomic variants in haploid cells focusing on Niemann–Pick disease type C (NPC) as an example. NPC is a fatal neurodegenerative disorder characterized by a lysosomal accumulation of unesterified cholesterol and glycolipids. In 95% of cases, NPC is caused by mutations in the NPC1 gene, for which more than 200 unique disease-causing variants have been reported to date. Furthermore, the majority of patients with NPC are compound heterozygotes that often carry at least one private mutation, presenting a challenge for the characterization and classification of individual variants. Here, we have developed the first haploid cell model of NPC. This haploid cell model recapitulates the primary biochemical and molecular phenotypes typically found in patient-derived fibroblasts, illustrating its utility in modeling NPC. Additionally, we show the power of CRISPR/Cas9-mediated base editing in quickly and efficiently generating haploid cell models of individual patient variants in NPC. These models provide a platform for understanding the disease mechanisms underlying individual NPC1 variants while allowing for definitive clinical variant interpretation for NPC.

Quantitative analysis of light-phase restricted feeding reveals metabolic dyssynchrony in mice

Background

Considerable evidence suggests that the time of day at which calories are consumed markedly impacts body weight gain and adiposity. However, a precise quantification of energy balance parameters during controlled animal studies enforcing time-of-day-restricted feeding is currently lacking in the absence of direct human interaction.

Objective

The purpose of the present study was therefore to quantify the effects of restricted feeding during the light (sleep) phase in a fully-automated, computer-controlled comprehensive laboratory animal monitoring system (CLAMS) designed to modulate food access in a time-of-day-dependent manner. Energy balance, gene expression (within metabolically-relevant tissues), humoral factors, and body weight were assessed.

Results

We report that relative to mice fed only during the dark (active) phase, light (sleep) phase fed mice: 1) consume a large meal upon initiation of food availability; 2) consume greater total calories per day; 3) exhibit a higher RER (indicative of decreased reliance on lipid/fatty acid oxidation); 4) exhibit tissue-specific alterations in the phases and amplitudes of circadian clock and metabolic genes in metabolically active tissues (greatest phase differences observed in the liver, and diminution of amplitudes in epididymal fat, gastrocnemius muscle, and heart); 5) exhibit diminished amplitude in humoral factor diurnal variations (e.g., corticosterone); and 6) exhibit greater weight gain within 9 days of restricted feeding.

Conclusions

Collectively, these data suggest that weight gain following light (sleep) phase restricted feeding is associated with significant alterations in energy balance, as well as dyssynchrony between metabolically active organs.

Experimental Haemophilus somnus infection in pregnant cattle

Of five pregnant cows inoculated intravenously with 5 X 10(8) viable 'Haemophilus somnus', one aborted within 5 days and excreted 'H. somnus' from the vagina for a further 7 weeks. A second cow proceeded to full term parturition but both it and its apparently healthy calf persistently excreted 'H. somnus'. The other animals underwent normal full term calvings and 'H. somnus' was not isolated from them or their calves. Lesions attributable to 'H. somnus' were detected only in the aborted fetus which showed an acute generalized inflammatory cell response consistent with a systemic Gram-negative bacterial infection. 'H. somnus' was isolated from all fetal tissues, including the placenta. The fetus and placenta also showed evidence of damage prior to inoculation. The placental damage may have predisposed the fetus and placenta to infection with 'H. somnus'. The placental epithelial cells contained intracytoplasmic organisms with the morphological and antigenic properties of 'H. somnus'.

Reporting elder abuse: limitations of statutes

When it comes to protecting abused elders and determining physicians' legal responsibilities, each state has its own legislation - there is no federal policy. In the extreme, this can mean 50 variations on a theme. Few laws clearly delineate differences between neglect and abuse, nor do they provide graduated remedies to address differing degrees of severity. Even though many states have passed mandatory reporting laws, most provide little or no funding for meaningful intervention. All physicians should become familiar with applicable elder abuse laws and the procedure for referring a suspected case. This presentation of our findings is necessarily brief and should not take the place of familiarity with the legislation in the reader's own state. A copy of relevant state legislation generally can be obtained from the local state legislator's office or law library.

Arthropathy associated with Brucella abortus strain 19 vaccination in cattle. I. Examination of field cases

Thirty cows presenting with lameness and persistent serological reactions to Brucella abortus had chronic granulomatous arthropathy of the femorotibial and occasionally other joints. Attempts to culture Brucella or other pathogens gave negative results but organisms of Brucella morphology were seen in fluorescent antibody-stained cryostat sections of synovial tissue. The synovial fluids contained high titres of antibodies to B. abortus and Yersinia enterocolitica O:9 and had elevated total protein and immunoglobulin concentrations showing an oligoclonal electrophoretic profile. Immune complexes and rheumatoid factor were detected in some of the fluids.

Arthropathy associated with Brucella abortus strain 19 vaccination in cattle. II. Experimental studies

Attempts to reproduce in calves the arthropathy associated with Brucella abortus strain 19 (S19) vaccination by direct intra-articular injection of S19 or virulent Brucella cells were unsuccessful. Intra-articular injection of rabbits and a calf with immune complexes isolated from the synovial fluid of a field case produced clinical and histological signs of arthropathy accompanied by the development of rheumatoid factor.

Experimental Brucella abortus infection in pigs

Sixteen pigs inoculated by the intra-conjunctival, intravenous or subcutaneous routes with Brucella abortus Strain 544 developed a short-lived infection usually accompanied by conjunctival and vaginal excretion of the organism for up to 99 days post-inoculation. Serological tests performed by the agglutination, complement fixation, Rose Bengal plate, antiglobulin, immunodiffusion or ELISA procedures with B. abortus antigens disclosed wide variations in the antibody responses of individual animals. In some cases the serological tests were negative even though the animal was shown to be excreting B. abortus. The intradermal test for delayed hypersensitivity to Brucella antigens gave more consistent results, especially when supported by histological evaluation of the skin reactions.

Development of improved methods for the transport and isolation of Haemophilus somnus

The survival of several strains of Haemophilus somnus under various simulated transport conditions was investigated. Recovery of H somnus from alginate swabs kept at room temperature was possible for up to 27 hours after sampling, but this period could be extended to 72 hours if the swabs were refrigerated. Storage of swabs in transport media did not prolong survival time significantly but did increase the number of bacterial contaminants, thus making recovery of H somnus less likely. The sensitivity of several strains of H somnus to a number of dyes, antibiotics and other antimicrobial agents was determined and a selective isolation medium then formulated. This medium which consisted of brain heart infusion agar supplemented with 5 per cent ovine blood, 5 per cent equine serum, 0.5 per cent yeast extract, cycloheximide (100 micrograms ml-1) and lincomycin (3 micrograms ml-1), facilitated the isolation of H somnus from contaminated material. However, while this medium was effective against many contaminants, it did not prevent swarming by Proteus species.

Characterization of Yersinia enterocolitica strains isolated from cattle, sheep and pigs in the United Kingdom

The properties of 48 cultures identified as Yersinia enterocolitica or Y. enterocolitica-like organisms, including Y. frederiksenii, Y. intermedia and Y. kristensenii, were examined. Of these, 39 were isolated from faeces of apparently healthy pigs, five from healthy cattle, one from an aborted bovine fetus, one from an aborted lamb and one from a lamb suffering from acute enteritis. Most isolates from healthy animals were of Y. enterocolitica biotype 1 or Y. intermedia and belonged to O serogroups not usually associated with disease in man or animals. The isolates from abortion or enteritis cases were of Y. enterocolitica biotypes 3, 4 and 5 and belonged to the pathogenic serogroups 0:5b and 0:2a, 2b, 3. No organisms of serogroup 0:9 were found.

Characterization of the major antigens of Haemophilus equigenitalis (contagious equine metritis organism)

Immunoelectrophoresis of ultrasonically disrupted Haemophilus equigenitalis (contagious equine metritis organism) cells against rabbit and equine antisera disclosed at least 11 precipitating antigens. Two of these, a polysaccharide and a lipopolysaccharide-protein complex, were of high molecular weight and located on the cell surface. The remaining antigens were intracellular and were small- to medium-sized proteins. The surface antigens were the most significant in relation to the serological response in infected horses. They also reacted with sera from apparently healthy cattle, but the reason for this was not determined. No serological cross-reaction between H. equigenitalis and species of Achromobacter and Moraxella was detected.

Disc electrophoresis of phenol:acetic acid:water-soluble proteins for the identification of Yersinia species

Disc electrophoresis of phenol:acetic acid:water extracts of Yersinia pestis, Y produced pseudotuberculosis, Y enterocolitica, Y philomiragia and Y ruckeri protein separation patterns characteristic of each species. The patterns produced by Y pestis, Y pseudotuberculosis, Y enterocolitica and Y ruckeri showed features in common. Those given by Y philomiragia strains were quite distinctive and showed little similarity to the other Yersinia species. All Y enterocolitica strains produced similar patterns irrespective of biochemical properties. Strains classified as Y intermedia or Y enterocolitica-like produced patterns indistinguishable from those given by Y enterocolitica.

Isolation and properties of an RNA fraction present in Brucella culture supernatants

The supernatant fluids of batch and continuous cultures of Brucella strains contained up to 100 mg/l of soluble RNA which could be recovered by precipitation with lysozyme, This RNA fraction had many of the properties of ribosomal RNA and was single-stranded, sensitive to ribonuclease, with an approximate sedimentation constant of 5S, a molecular weight of about 35000 daltons and an adenine; guanine; cytosine; uracil content of 17.5; 26.5; 33; 23 mol% respectively. RNA fractions from lysozyme precipitates evoked high titres of Brucella agglutinins on injection into rabbits and induced acute inflammatory responses in guinea-pig skin. Highly purified RNA fractions prepared by phenol extraction of lysozyme precipitates did not evoke antibodies to Brucella abortus.