Functional annotation of variants of the BRCA2 gene via locally haploid human pluripotent stem cells

Mutations in the BRCA2 gene are associated with sporadic and familial cancer, cause genomic instability and sensitize cancer cells to inhibition by the poly(ADP-ribose) polymerase (PARP). Here we show that human pluripotent stem cells (hPSCs) with one copy of BRCA2 deleted can be used to annotate variants of this gene and to test their sensitivities to PARP inhibition. By using Cas9 to edit the functional BRCA2 allele in the locally haploid hPSCs and in fibroblasts differentiated from them, we characterized essential regions in the gene to identify permissive and loss-of-function mutations. We also used Cas9 to directly test the function of individual amino acids, including amino acids encoded by clinical BRCA2 variants of uncertain significance, and identified alleles that are sensitive to PARP inhibitors used as a standard of care in BRCA2-deficient cancers. Locally haploid human pluripotent stem cells can facilitate detailed structure-function analyses of genes and the rapid functional evaluation of clinically observed mutations.

Peptide-mediated delivery of CRISPR enzymes for the efficient editing of primary human lymphocytes

CRISPR-mediated genome editing of primary human lymphocytes is typically carried out via electroporation, which can be cytotoxic, cumbersome and costly. Here we show that the yields of edited primary human lymphocytes can be increased substantially by delivering a CRISPR ribonucleoprotein mixed with an amphiphilic peptide identified through screening. We evaluated the performance of this simple delivery method by knocking out genes in T cells, B cells and natural killer cells via the delivery of Cas9 or Cas12a ribonucleoproteins or an adenine base editor. We also show that peptide-mediated ribonucleoprotein delivery paired with an adeno-associated-virus-mediated homology-directed repair template can introduce a chimaeric antigen receptor gene at the T-cell receptor α constant locus, and that the engineered cells display antitumour potency in mice. The method is minimally perturbative, does not require dedicated hardware, and is compatible with multiplexed editing via sequential delivery, which minimizes the risk of genotoxicity. The peptide-mediated intracellular delivery of ribonucleoproteins may facilitate the manufacturing of engineered T cells.

Species- and site-specific genome editing in complex bacterial communities

Understanding microbial gene functions relies on the application of experimental genetics in cultured microorganisms. However, the vast majority of bacteria and archaea remain uncultured, precluding the application of traditional genetic methods to these organisms and their interactions. Here, we characterize and validate a generalizable strategy for editing the genomes of specific organisms in microbial communities. We apply environmental transformation sequencing (ET-seq), in which nontargeted transposon insertions are mapped and quantified following delivery to a microbial community, to identify genetically tractable constituents. Next, DNA-editing all-in-one RNA-guided CRISPR-Cas transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-seq are used to enable organism- and locus-specific genetic manipulation in a community context. Using a combination of ET-seq and DART in soil and infant gut microbiota, we conduct species- and site-specific edits in several bacteria, measure gene fitness in a nonmodel bacterium and enrich targeted species. These tools enable editing of microbial communities for understanding and control.

Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia

The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Ca_v2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca²⁺ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Ca_v2.2 in normal human neurodevelopment.

Case Report - Pyknodysostosis

Pyknodysostosis is an extremely rare lysosomal storage disease of the bone. Osteosclerosis of the skeleton is due to a decrease of the bone turnover. A plethora of clinical and radiological findings are observed. Patients are short statured with acroosteolysis and dense bones and develop multiple spontaneous bone fractures. A female patient presented with frontal bossing, small and thick fingers and toes. The classical clinical and radiological findings confirmed it as pyknodysostosis.

Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data

BACKGROUND

Human genome sequencing has transformed our understanding of genomic variation and its relevance to health and disease, and is now starting to enter clinical practice for the diagnosis of rare diseases. The question of whether and how some categories of genomic findings should be shared with individual research participants is currently a topic of international debate, and development of robust analytical workflows to identify and communicate clinically relevant variants is paramount.

METHODS

The Deciphering Developmental Disorders (DDD) study has developed a UK-wide patient recruitment network involving over 180 clinicians across all 24 regional genetics services, and has performed genome-wide microarray and whole exome sequencing on children with undiagnosed developmental disorders and their parents. After data analysis, pertinent genomic variants were returned to individual research participants via their local clinical genetics team.

FINDINGS

Around 80,000 genomic variants were identified from exome sequencing and microarray analysis in each individual, of which on average 400 were rare and predicted to be protein altering. By focusing only on de novo and segregating variants in known developmental disorder genes, we achieved a diagnostic yield of 27% among 1133 previously investigated yet undiagnosed children with developmental disorders, whilst minimising incidental findings. In families with developmentally normal parents, whole exome sequencing of the child and both parents resulted in a 10-fold reduction in the number of potential causal variants that needed clinical evaluation compared to sequencing only the child. Most diagnostic variants identified in known genes were novel and not present in current databases of known disease variation.

INTERPRETATION

Implementation of a robust translational genomics workflow is achievable within a large-scale rare disease research study to allow feedback of potentially diagnostic findings to clinicians and research participants. Systematic recording of relevant clinical data, curation of a gene-phenotype knowledge base, and development of clinical decision support software are needed in addition to automated exclusion of almost all variants, which is crucial for scalable prioritisation and review of possible diagnostic variants. However, the resource requirements of development and maintenance of a clinical reporting system within a research setting are substantial.

FUNDING

Health Innovation Challenge Fund, a parallel funding partnership between the Wellcome Trust and the UK Department of Health.

Role of ultraosonography in grading of penile fractures

INTRODUCTION

Penile fracture is an uncommon and less reported condition. Early diagnosis with corrective measures is the order of the day.

AIM

To perform ultrasonography of penis and to understand its role in making correct diagnosis of fractures. To know how it will help surgeon in its management and in adopting a grading system.

MATERIALS AND METHODS

Emergency evaluation of 15 cases of penile fractures by ultrasonography before surgery. Entire penis was scanned all along its length and circumference. Tunica albugenia was seen as white covering of both corpora cavernosa and break in its continuity is seen as wedge shape defect. Hematoma on either sides of tunica was well appreciated.

RESULTS

After ultrasonography all patients underwent emergency surgery, the defect in corpora was well appreciated. Repair of tunica albugenia was done which confirmed our findings.

CONCLUSION

Ultrasonography is the modality of choice for quick diagnosis, and no other radiological workup is required before surgery.

Large-scale discovery of novel genetic causes of developmental disorders

Despite three decades of successful, predominantly phenotype-driven discovery of the genetic causes of monogenic disorders, up to half of children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis. Particularly challenging are those disorders rare enough to have eluded recognition as a discrete clinical entity, those with highly variable clinical manifestations, and those that are difficult to distinguish from other, very similar, disorders. Here we demonstrate the power of using an unbiased genotype-driven approach to identify subsets of patients with similar disorders. By studying 1,133 children with severe, undiagnosed developmental disorders, and their parents, using a combination of exome sequencing and array-based detection of chromosomal rearrangements, we discovered 12 novel genes associated with developmental disorders. These newly implicated genes increase by 10% (from 28% to 31%) the proportion of children that could be diagnosed. Clustering of missense mutations in six of these newly implicated genes suggests that normal development is being perturbed by an activating or dominant-negative mechanism. Our findings demonstrate the value of adopting a comprehensive strategy, both genome-wide and nationwide, to elucidate the underlying causes of rare genetic disorders.

Tetra-phocomelia: a rarest of rare case

We present a rarest of rare case of Tetra-Phocomelia evaluated by antenatal Ultrasonography. It is a condition seen in 0.62 per 100,000 live births. An ultrasonogram was done at 18 wk of pregnancy to assess the fetus and after termination gross specimen was evaluated and X-ray infantograms were done to confirm the findings. The case showed classic Tetra-Phocomelia with limbs like flippers of a seal. Our findings make it rarest of rare as only few cases have been so far reported.

Outcomes of Ilizarov ring fixation in recalcitrant infected tibial non-unions - a prospective study

Background

Infected non-union of long bones is a problem in the developing countries. Persistent infection, deformity, shortening, bone loss, joint stiffness and disability complicate the non-union. Secondary procedures are often required for correction of bone defects and deformity. Ilizarov method addresses all the above problems simultaneously and offers a panacea for infected non-unions. The stability of the fixation and provision for bone transport allows bridging of bone defects, limb lengthening, early weight bearing ambulation and joint mobilisation.

Aim of the study

To know the suitability of this procedure in recalcitrant infected tibial non-unions in the Indian population and the influence of socio-economic factors in the functional outcome.

Method of study

This was a 3-year prospective study in 22 consecutive patients with an average follow up of 13 months following fracture union. The results were analysed using the ASAMI scoring system.

Results

Of 22 patients in the study, 13 patients who underwent external bone transport, had an average bone gap of 4 cms [2–11 cms] with an average duration of fixation of 9.3 months [6.5–13 months]. There were 4 excellent, 3 good, 4 fair and 2 poor bony results and 1 excellent, 3 good, 6 fair and 2 poor results. 1 patient was lost for follow up at final functional analysis. 9 patients who underwent internal bone transport had an average bone gap of 5.4 cms [1.5–9 cms] with an average duration of fixation of 8.5 months [4–11 months]. There were 3 good 4 fair and 2 poor bony results and 1 good, 3 fair, and 2 poor functional results. Good to excellent results were witnessed in well-motivated patients with adequate social and financial support. Patients with fair to poor results preferred amputation to limb salvage despite the fact that they retained their limbs.

Conclusion

Treatment of infected non-unions of Tibia with Ilizarov ring fixation is effective but for optimal results the treatment needs to be individualised by the treating surgeon with due consideration of the socio-economic factors.