ItemDetailed statistical analysis plan for a randomised controlled trial of the effects of a modified muscle sparing posterior technique (SPAIRE) in hip hemiarthroplasty for displaced intracapsular fractures on post-operative function compared to a standard lateral approach: HemiSPAIRE(BioMed Central, 2022-11-05) Ball, S.; McAndrew, A.; Aylward, A.; Cockcroft, E.; Gordon, E.; Kerridge, A.; Morgan-Trimmer, S.; Powell, R.; Price, A.; Rhodes, S.; Timperley, A. J.; van Horik, J.; Wickins, R.; Charity, J.BACKGROUND: The HemiSPAIRE trial is being conducted to determine whether a modified muscle sparing technique (SPAIRE-Save Piriformis and Internus, Repairing Externus") in hip hemiarthroplasty brings clinical benefits compared to the standard lateral technique in adults aged 60 years or older, with a displaced intracapsular hip fracture. This article describes the detailed statistical analysis plan for the trial. METHODS AND DESIGN: HemiSPAIRE is a definitive, pragmatic, superiority, multicentre, randomised controlled trial (with internal pilot) with two parallel groups. Participants, ward staff and all research staff involved in post-operative assessments are blinded to allocation. This article describes in detail (1) the primary and secondary outcomes; (2) the statistical analysis principles, including a survivor average causal effect (SACE) method chosen specifically to address the issue of potential bias from differential survival between trial arms, which was seen from data review by the Trial Steering Committee, the participants that will be included in each analysis, the covariates that will be included in each analysis, and how the results will be presented; (3) planned main analysis of the primary outcome; (4) planned analyses of the secondary outcomes; and (5) planned additional analyses of the primary and secondary outcomes. TRIAL REGISTRATION: ClinicalTrials.gov NCT04095611. Registered on 19 September 2019." ItemDevelopment of a treatment selection algorithm for SGLT2 and DPP-4 inhibitor therapies in people with type 2 diabetes: a retrospective cohort study(Elsevier, 2022-12-01) Dennis, J. M.; Young, K. G.; McGovern, A. P.; Mateen, B. A.; Vollmer, S. J.; Simpson, M. D.; Henley, W. E.; Holman, R. R.; Sattar, N.; Pearson, E. R.; Hattersley, A. T.; Jones, A. G.; Shields, B. M.BACKGROUND: Current treatment guidelines do not provide recommendations to support the selection of treatment for most people with type 2 diabetes. We aimed to develop and validate an algorithm to allow selection of optimal treatment based on glycaemic response, weight change, and tolerability outcomes when choosing between SGLT2 inhibitor or DPP-4 inhibitor therapies. METHODS: In this retrospective cohort study, we identified patients initiating SGLT2 and DPP-4 inhibitor therapies after Jan 1, 2013, from the UK Clinical Practice Research Datalink (CPRD). We excluded those who received SGLT2 or DPP-4 inhibitors as first-line treatment or insulin at the same time, had estimated glomerular filtration rate (eGFR) of less than 45 mL/min per 1·73 m(2), or did not have a valid baseline glycated haemoglobin (HbA(1c)) measure (<53 or ≥120 mmol/mol). The primary efficacy outcome was the HbA(1c) value reached 6 months after drug initiation, adjusted for baseline HbA(1c). Clinical features associated with differential HbA(1c) outcome on the two therapies were identified in CPRD (n=26 877), and replicated in reanalysis of 14 clinical trials (n=10 414). An algorithm to predict individual-level differential HbA(1c) outcome on the two therapies was developed in CPRD (derivation; n=14 069) and validated in head-to-head trials (n=2499) and CPRD (independent validation; n=9376). In CPRD, we further explored heterogeneity in 6-month weight change and treatment discontinuation. FINDINGS: Among 10 253 patients initiating SGLT2 inhibitors and 16 624 patients initiating DPP-4 inhibitors in CPRD, baseline HbA(1c), age, BMI, eGFR, and alanine aminotransferase were associated with differential HbA(1c) outcome with SGLT2 inhibitor and DPP-4 inhibitor therapies. The median age of participants was 62·0 years (IQR 55·0-70·0). 10 016 (37·3%) were women and 16 861 (62·7%) were men. An algorithm based on these five features identified a subgroup, representing around four in ten CPRD patients, with a 5 mmol/mol or greater observed benefit with SGLT2 inhibitors in all validation cohorts (CPRD 8·8 mmol/mol [95% CI 7·8-9·8]; CANTATA-D and CANTATA-D2 trials 5·8 mmol/mol [3·9-7·7]; BI1245.20 trial 6·6 mmol/mol [2·2-11·0]). In CPRD, predicted differential HbA(1c) response with SGLT2 inhibitor and DPP-4 inhibitor therapies was not associated with weight change. Overall treatment discontinuation within 6 months was similar in patients predicted to have an HbA(1c) benefit with SGLT2 inhibitors over DPP-4 inhibitors (median 15·2% [13·2-20·3] vs 14·4% [12·9-16·7]). A smaller subgroup predicted to have greater HbA(1c) reduction with DPP-4 inhibitors were twice as likely to discontinue SGLT2 inhibitors than DPP-4 inhibitors (median 26·8% [23·4-31·0] vs 14·8% [12·9-16·8]). INTERPRETATION: A validated treatment selection algorithm for SGLT2 inhibitor and DPP-4 inhibitor therapies can support decisions on optimal treatment for people with type 2 diabetes. FUNDING: BHF-Turing Cardiovascular Data Science Award and the UK Medical Research Council. ItemHERC2 deficiency activates C-RAF/MKK3/p38 signalling pathway altering the cellular response to oxidative stress(Springer, 2022-10-14) Sala-Gaston, J.; Pedrazza, L.; Ramirez, J.; Martinez-Martinez, A.; Rawlins, L. E.; Baple, E. L.; Crosby, A. H.; Mayor, U.; Ventura, F.; Rosa, J. L.HERC2 gene encodes an E3 ubiquitin ligase involved in several cellular processes by regulating the ubiquitylation of different protein substrates. Biallelic pathogenic sequence variants in the HERC2 gene are associated with HERC2 Angelman-like syndrome. In pathogenic HERC2 variants, complete absence or marked reduction in HERC2 protein levels are observed. The most common pathological variant, c.1781C > T (p.Pro594Leu), encodes an unstable HERC2 protein. A better understanding of how pathologic HERC2 variants affect intracellular signalling may aid definition of potential new therapies for these disorders. For this purpose, we studied patient-derived cells with the HERC2 Pro594Leu variant. We observed alteration of mitogen-activated protein kinase signalling pathways, reflected by increased levels of C-RAF protein and p38 phosphorylation. HERC2 knockdown experiments reproduced the same effects in other human and mouse cells. Moreover, we demonstrated that HERC2 and RAF proteins form molecular complexes, pull-down and proteomic experiments showed that HERC2 regulates C-RAF ubiquitylation and we found out that the p38 activation due to HERC2 depletion occurs in a RAF/MKK3-dependent manner. The displayed cellular response was that patient-derived and other human cells with HERC2 deficiency showed higher resistance to oxidative stress with an increase in the master regulator of the antioxidant response NRF2 and its target genes. This resistance was independent of p53 and abolished by RAF or p38 inhibitors. Altogether, these findings identify the activation of C-RAF/MKK3/p38 signalling pathway in HERC2 Angelman-like syndrome and highlight the inhibition of RAF activity as a potential therapeutic option for individuals affected with these rare diseases. ItemBi-allelic CAMSAP1 variants cause a clinically recognizable neuronal migration disorder(Cell Press, 2022-11-03) Khalaf-Nazzal, R.; Fasham, J.; Inskeep, K. A.; Blizzard, L. E.; Leslie, J. S.; Wakeling, M. N.; Ubeyratna, N.; Mitani, T.; Griffith, J. L.; Baker, W.; Al-Hijawi, F.; Keough, K. C.; Gezdirici, A.; Pena, L.; Spaeth, C. G.; Turnpenny, P. D.; Walsh, J. R.; Ray, R.; Neilson, A.; Kouranova, E.; Cui, X.; Curiel, D. T.; Pehlivan, D.; Akdemir, Z. C.; Posey, J. E.; Lupski, J. R.; Dobyns, W. B.; Stottmann, R. W.; Crosby, A. H.; Baple, E. L.Non-centrosomal microtubules are essential cytoskeletal filaments that are important for neurite formation, axonal transport, and neuronal migration. They require stabilization by microtubule minus-end-targeting proteins including the CAMSAP family of molecules. Using exome sequencing on samples from five unrelated families, we show that bi-allelic CAMSAP1 loss-of-function variants cause a clinically recognizable, syndromic neuronal migration disorder. The cardinal clinical features of the syndrome include a characteristic craniofacial appearance, primary microcephaly, severe neurodevelopmental delay, cortical visual impairment, and seizures. The neuroradiological phenotype comprises a highly recognizable combination of classic lissencephaly with a posterior more severe than anterior gradient similar to PAFAH1B1(LIS1)-related lissencephaly and severe hypoplasia or absence of the corpus callosum; dysplasia of the basal ganglia, hippocampus, and midbrain; and cerebellar hypodysplasia, similar to the tubulinopathies, a group of monogenic tubulin-associated disorders of cortical dysgenesis. Neural cell rosette lineages derived from affected individuals displayed findings consistent with these phenotypes, including abnormal morphology, decreased cell proliferation, and neuronal differentiation. Camsap1-null mice displayed increased perinatal mortality, and RNAScope studies identified high expression levels in the brain throughout neurogenesis and in facial structures, consistent with the mouse and human neurodevelopmental and craniofacial phenotypes. Together our findings confirm a fundamental role of CAMSAP1 in neuronal migration and brain development and define bi-allelic variants as a cause of a clinically distinct neurodevelopmental disorder in humans and mice. ItemIncomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts(Frontiers Media, 2022-08-20) Kingdom, R.; Wright, C. F.The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.