ISTQB-BCS Certified Tester Advanced Level - Test Manager Exam Dumps

TM12 Exam Format | Course Contents | Course Outline | Exam Syllabus | Exam Objectives

The ISTQB (International Software Testing Qualifications Board) advanced level certifications are part of the ISTQB internationally recognised software testing qualifications that include the following certifications:

Certified Tester Foundation Level (CTFL)
Certified Tester Advanced Level (CTAL)
&
Certified Tester Expert Level.

The Certified Tester Advanced Level comprises of three distinct core certifications namely Test Manager, Test Analyst and Technical Test Analyst and two specialist certifications, Security Tester and Test Automation Engineer.

Processworks BCS (British Computer Society) Accredited course provides an understanding of software testing that goes beyond the ISTQB Foundation level. It provides test managers, test analysts and technical test analysts with the essential common information.

The course will provide a good level of knowledge that enables analysis of various situations in order to present practical solutions.

The information gained on the course provides a portfolio of methods for designing tests for a variety software types within any type of software application. Emphasis will be made on domain testing. Templates and utilities will be provided to help students to devise tests that are both effective and efficient, giving best value for the testing being done in the time that is given.

An Advanced Test Manager can:

Implement the mission, goals, and testing processes established for the testing organisation. Organise and lead risk management activities and use risks to drive test planning and reporting. Create and implement test plans consistent with organisational policies and test strategies. Continuously monitor and control the test activities to achieve project activities. Access and report relevant and timely test status. Identify skills and resource gaps in their test team and participate in sourcing adequate resources. Identify and plan test team skills development. Propose a business case for test activities that outlines the costs and benefits expected. Ensure proper communication within the test team and with other project stakeholders. Actively lead test process improvement initiatives. Design and implement a defect classification scheme. Apply tools to support testing.

The Test Managers activities within the fundamental test process are covered with emphasis on the tasks of test planning, monitoring and control. Describes how to implement a project retrospective in order to validate processes and discover areas to improve.

Explains how to define test management tasks according to the context of a project and how to adjust the test activities to the software lifecycle in use. Risk-based testing for test prioritization and effort allocation is discussed with emphasis on product and project risk management. Participants learn how to take stakeholder views into account when assessing risk levels and defining the risk mitigation activities. Risk control activities and risk reporting are also covered.

Evaluates different types of test document and discusses how to tailor them to meet project and organization needs. Relevant standards are also considered.

Metric- and experienced-based methods for estimating testing effort are covered and participants learn how to communicate the value of testing. Distributed, outsourced and insourced forms of test organization are described.

Here the focus on defining an appropriate review plan and setting up the review to achieve the best results. Participants learn how to use metrics to optimize the review results and to show return on investment. This session also explains how to lead a review team through a formal review.

Describes how to set up a defect lifecycle tailored for the software lifecycle in use and explains how to analyse defect reports to evaluate the capability of the testing and software development processes.

Explains the generic steps for conducting a standard test process improvement initiative and how to create a test improvement plan. Includes the test process improvement models TMMi, TPI Next, CTP and STEP.

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Human neurons from Christianson syndrome iPSCs exhibit mutation-certain responses to rescue recommendations

INTRODUCTION

Christianson syndrome (CS) is an X-linked neurological disorder characterized via impaired cognitive construction and epilepsy, with a distinctive social conversation phenotype (1, 2). CS is caused with the aid of distinct mutations in SLC9A6, the gene encoding the endosomal Na+/H+ exchanger 6 (NHE6) (2, three). Given the social phenotype, which comprises a contented demeanor and autistic aspects, and the presentation of seizures and postnatal microcephaly, CS became at first termed X-linked Angelman syndrome (AS) (three). Postnatal microcephaly (as adversarial to basic microcephaly) is clinically determined when little ones are born with normal head circumference yet endure subsequent attenuation of the expected brain growth within the first years of life (four). The human mind increases in measurement by using about two- to threefold in the first years of existence, coincident with the emergence of adventure-based acquisition of brain function and habits. Thereby, study of human genetic problems with postnatal microcephaly, akin to CS or AS, might also allow for the identification of mechanisms concerned in early childhood mind development, together with those governing cognitive, motor, and social development (four). As neurogenesis is basically comprehensive in human mind earlier than beginning, postnatal microcephaly genes frequently alter later neurodevelopmental tactics worried in neuronal connectivity corresponding to neuronal axonogenesis, axonal and dendritic arborization, and synaptic development.

Endosomes play a crucial role in the construction of neuronal connectivity by way of more than a few mechanisms, together with through their involvement within the trafficking, recycling, and degradation of cargo, as well as through serving in endosomal signaling (5, 6). In selected, neurotrophin signaling, comparable to through the brain-derived neurotrophic factor (BDNF)/tropomyosin receptor kinase B (TrkB) pathway, represents the classically studied endosomal signaling mechanism standard for neurite outgrowth and arborization (5). Tight regulation of intraendosomal proton concentration serves an important function in endosome maturation and performance (7). The vacuolar H+-ATPase (V-ATPase) is a pump that mediates acidification of endosomes and lysosomes. The endosomal NHEs (peculiarly NHE6 and NHE9) allow proton efflux and counter the V-ATPase by using regulating relative alkalization of the lumen (eight). lack of NHE6 in simple mouse neurons revealed a different endosomal phenotype, particularly, overacidification of the endosome lumen (9). reduced endosomal pH in setting up NHE6-null neurons become linked to attenuation of BDNF signaling by means of TrkB and diminished neuronal arborization in vitro and in vivo. Exogenous addition of BDNF to NHE6-null murine cultures rescued the arborization defect, consistent with the previously proven pH-based lessen in ligand-receptor binding (10).

Given the disorder burden experienced by means of americans with CS, we sought to enhance an prompted pluripotent stem cell (iPSC) system that can be used to examine the mobile mechanisms of CS in human neurons, as well as serve for therapeutic construction. In CS, lots of the mutations are nonsense mutations or strong splice mutations; besides the fact that children, further mutations representing missense or in-frame amino acid deletions have also been pronounced (2, three). patient-derived iPSCs offer the opportunity to dissect mechanisms mediated via particular human mutations from the endogenous genomic locus. As has been smartly established currently for therapeutic building for cystic fibrosis, selected patient mutations demonstrate proof of mutation-selected responses to cures (11). Given our prior statistics on BDNF, one rescue method examined here is the exogenous, or mobilephone-nonautonomous, addition of trophic elements. Such factors could encompass not handiest BDNF however also insulin-like boom component-1 (IGF-1). BDNF and IGF-1 have verified exercise on neurite growth and arborization (12), and further nonetheless, IGF-1 is in scientific trials for different neurodevelopmental issues with postnatal microcephaly and/or autistic elements (as an example, NCT01970345 and NCT01525901; clinicaltrials.gov). We also examined a rescue strategy involving reexpression of NHE6 via transfection of human NHE6 complementary DNA (cDNA) into mutant neurons. This therapeutic strategy may be pursued via gene therapy or perhaps through up-rules of the linked endosomal NHE9 in patients with CS.

in this look at, we present a considerable iPSC aid that we've developed to examine CS ailment mechanisms and therapeutic responses. This useful resource contains a collection of pathogenic mutations, in addition to genetically related controls and isogenic controls. We used this resource to determine selected action of mutations in patient-derived neurons, in addition to distinct mutation-specific responses to rescue strategies. Whereas exogenous addition of BDNF or IGF-1 to affected person neurons rescued neuronal phenotypes inspite of affected person mutation, gene transfer options showed successful rescue in a fashion that's stylish on the nature of the mutation.

results Most CS mutations cause loss of protein via nonsense-mediated decay mechanisms

To establish a patient-derived cellular model for translational research in CS, we reprogrammed peripheral blood mononuclear cells from 5 families into iPSCs. The cells from the affected newborn each and every contained a distinct mutation in NHE6 (13) (table 1). Most NHE6 mutations in CS seem like lack of feature, reminiscent of putatively protein truncating because of early frameshift, nonsense, or splicing mutations, whereas a few missense or in-body deletions have also been said, seemingly with residual protein (2, 3). Our iPSC collection protected a mutational collection of 4 different frameshift/nonsense mutations and one recurrent missense mutation in NHE6, the latter of which we hypothesized could additionally affect mRNA splicing. These mutations are as follows: family 1, a single–base pair duplication in exon 11 leading to a frameshift and untimely cease codon between estimated transmembrane domains (TM) 10 and eleven (c.1414dupA, p.R472fsX4); family 2, a nonsense mutation in exon 12 in expected TM12 (c.1568G>A, p.W523X); family three, a missense mutation on the first base pair of exon 9 in envisioned TM8 (c.1148G>A, p.G383D); family unit 4, an eight–base pair duplication in exon 3 resulting in a frameshift and untimely cease codon in predicted TM4 (c.540_547dupAGAAGTAT, p.F183fsX1); and family 5, a nonsense mutation in exon 14 found within the cytoplasmic tail (c.1710G>A, p.W570X) (2) (Fig. 1A, desk 1, and figs. S1 and S2). iPSCs were additionally derived from each proband’s genetically related, noncarrier male sibling for use as a paired manage. control and CS iPSCs had equivalent morphologies to human embryonic stem cells (hESCs), expressed endogenous pluripotency markers, had usual karyotypes, formed embryoid our bodies in vitro, and formed teratomas in vivo, thereby demonstrating successful reprogramming (desk S1 and figs. S3 to S10).

table 1 iPSC substances for examine of CS.

materials include the following: (i) iPSCs derived from 5 families with distinctive mutations in NHE6, including paired affected person and biologically related, noncarrier, unaffected male siblings (family 1 to five); (ii) isogenic CS and genome-corrected iPSC strains (isogenic pair 1); and (iii) isogenic manage and NHE6 brought about-mutation iPSC lines (isogenic pair 2). Mutations in NHE6 are listed on the groundwork of Ensembl transcript ENST00000370695. TM became expected using TMHMM based on ENSP00000359729.

Fig. 1 evaluation of NHE6 gene expression in iPSCs from patients with NHE6 mutations and from linked controls.

(A) iPSCs had been derived from 5 patients with CS and from their genetically linked, unaffected brothers without NHE6 mutation as controls. proven is a schematic of the NHE6 protein with the anticipated locations of the proband mutations, in keeping with NHE6 transcript NM_001042537. NHE6 TM was predicted by way of the transmembrane hidden Markov model (TMHMM) (30) for Ensembl transcript ENST00000370695 and protein ENSP00000359729 (31). (B) NHE6 mRNA expression in control and CS iPSCs turned into quantified on the foundation of Northern blots. Northern blotting become carried out the use of samples from CS and control iPSCs handled (+) or untreated (−) with CHX. Expression of NHE6 mRNA became normalized to GAPDH and plotted as a percentage of untreated handle cells. n = three experiments (see fig. S11 for Northern blots of households four and 5, and records file S7 for mRNA expression quantification records). (C) NHE6 mRNA expression in handle and CS iPSCs became quantified on the basis of NanoString records. RNA samples collected from CS and coupled handle iPSCs handled (+) or untreated (−) with CHX have been analyzed the usage of a customized NanoString platform. Expression of NHE6 mRNA became normalized to hybridization controls and to a set of housekeeping genes: B2M, GAPDH, GUSB, HPRT1, RPL13a, RPL27, and POLR2A (left). Fold exchange in NHE6 mRNA expression, within the presence or absence of CHX medicine, turned into quantified for every CS and paired manage iPSC (correct). n = 15 samples per community (three replicate wells from each and every of five manage lines with or with out CHX remedy and three replicate wells from each of five CS strains with or with out CHX medication). DMSO, dimethyl sulfoxide. (D) UPF1 and UPF3 mRNA expression in CS iPSCs from household 1 handled with a manage set of scrambled siRNA oligonucleotides or siRNA oligonucleotides focused on UPF genes became quantified. After siRNA remedy, expression of UPF1 and UPF3 mRNA changed into determined the usage of a customised NanoString platform (left). Western blotting become carried out the usage of antibodies against UPF1 (excellent) to verify for knockdown of UPF1 and against tubulin (bottom) as a loading manage (appropriate). shown is a consultant blot using manage and CS samples from family 2. (E) NHE6 mRNA expression in CS iPSCs from family unit 1 treated with a control set of scrambled siRNA oligonucleotides or siRNA oligonucleotides targeting UPF genes became quantified. After siRNA medication, expression of NHE6 mRNA changed into decided using a customised NanoString platform (left). NHE6 mRNA become normalized to hybridization controls and to a collection of housekeeping genes: B2M, GAPDH, HPRT1, RPL13a, and POLR2A. Fold alternate in NHE6 mRNA expression after knockdown of UPF1, UPF3, or UPF1 + UPF3 turned into quantified. shown are results for samples from family 1 CS iPSCs (appropriate). n = four replicates. statistics signify capability ± SEM. Unpaired student’s t tests have been used. *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001.

To assess the results of the pathogenic mutations on NHE6 gene and protein expression, we performed mRNA and Western blot analyses of consultant mutations and subclonal strains. In all four of the putative protein-truncating nonsense mutations, we found NHE6 mRNA to be absent. These mRNA results have been corroborated the usage of two diverse strategies: Northern blot (Fig. 1B and fig. S11) and NanoString nCounter (Fig. 1C). These consequences are most in keeping with a loss of mRNA by means of nonsense-mediated decay (NMD).

To check no matter if NHE6 mRNA is degraded via NMD, we treated iPSCs with cycloheximide (CHX), which prevents NMD through inhibiting translation and thereby interfering with recognition of a untimely cease codon. Upon CHX remedy, the NHE6 transcript was recovered in CS lines with these nonsense mutations (Fig. 1, B and C). The NHE6 missense mutation G383D behaved in another way than the nonsense mutations. The NHE6 mRNA transcript in cells with the missense mutation became not absent but instead became reduced to fifty eight ± 18.4% of handle amounts with the aid of Northern blot analysis and to fifty six.four ± four.7% via NanoString nCounter analysis. youngsters, the volume of transcript become recoverable with CHX remedy to seventy seven.9 ± 6.four% of handle quantities, suggesting some component of NMD (Fig. 1, B and C). as a result of CHX may have huge results past blockading NMD, we performed extra controls. To further implicate NMD because the trigger for loss of NHE6 mRNA in mutant strains, we centered NMD the use of specific small interfering RNA (siRNA) targeting of NMD components UP-frameshift 1 (UPF1) and UPF3 (14, 15) (Fig. 1D). once more, we followed a strong healing of NHE6 mRNA after siRNA-mediated reduction in NMD components. alone, reduction in UPF1 showed the strongest outcomes, whereas aggregate siRNA against UPF1 and UPF3 confirmed additive outcomes on restoration of NHE6 mRNA (Fig. 1E).

loss of mRNA within the nonsense/frameshift mutations became associated with an obvious finished loss of protein. using Western blot on NHE6 immunoprecipitates, NHE6 protein appeared to be absent in all CS strains carrying nonsense/frameshift mutations (Fig. 2, A and B). therefore, these results set up that the majority CS mutations, specifically, these leading to nonsense mutations, are likely to cause disorder via a loss-of-function mechanism involving NMD. The outcomes additional point out that truncated NHE6 proteins are unlikely to be translated in large quantities.

Fig. 2 evaluation of protein expression of pathogenic NHE6 mutations and extra analyze of the complicated alternative splicing and missense mutation G383D.

(A) Western blotting was performed to examine NHE6 protein expression in manage and CS iPSCs. Lysates of CS and coupled handle iPSCs from households 1, 2, four, and 5 had been immunoprecipitated (IP) the usage of a custom-made anti-NHE6 antibody and subsequently analyzed via Western blot using the equal antibody. Blotting in opposition t tubulin became used as a loading handle. IB, immunoblot. (B) NHE6 protein expression, in response to Western blots comparable to these presented in (A), changed into quantified. The signal from immunoprecipitated NHE6 become normalized to the respective sign from tubulin, and the normal signal depth for the manage of family 1 became set to a worth of 1. n ≥ three experiments. a.u., arbitrary contraptions. (C) Western blotting became performed to verify NHE6 protein expression peculiarly in manage and CS iPSCs from household 3 (left). Samples have been organized and analyzed as described for (A). quantities of NHE6 protein monomer and dimer in CS and matched handle samples from family three had been quantified, and the monomer:dimer ratios have been decided (middle and appropriate). The sign from immunoprecipitated NHE6 turned into normalized to the respective signal from tubulin; the records are plotted as a percent of handle. n = 7 experiments. (D) The G383D mutation generates an choice transcript by exon skipping. Reverse transcription polymerase chain reaction (RT-PCR) changed into carried out on cDNA amassed from iPSCs handled or untreated with CHX. The resulting bands had been sequenced and revealed the presence of an option splicing adventure in which exon 9 turned into skipped. The purple asterisk in the diagram suggests the approximate place of the c.1148G>A/p.G383D mutation. (E) Conservation of NHE6 protein became analyzed using ConSurf. shown are variable and conserved regions (turquoise via maroon) mapped onto the NHE6 structural model. (F) Hydrophobicity evaluation of the NHE6 structural mannequin was performed. Hydrophobic (orange) residues can be found in TM, whereas hydrophilic (blue) residues can be found in loop areas. (G) The protein structure of wild-type (WT) and G383D-mutant NHE6 become modeled. The model of NHE6 predicts that the G383D mutation disrupts helix packing between TM8 and TM2, maybe due to hydrogen bonding of D383 with N166 and loss of an interaction between N166 and E377 (insets, dotted lines). alternatively, the G383D variant might kind a salt-bridge with R500 on TM11 (reduce inset, dotted line). information characterize potential ± SEM. Unpaired scholar’s t assessments were used (B and C). ** P < 0.01 and **** P < 0.0001.

The missense G383D mutation demonstrates complex results on mRNA splicing and on protein coding

we now have previously suggested a affected person with a de novo c.1148G>A (p.G383D) mutation (2). via foreign ascertainment of patients, we have recognized a 2d unrelated pedigree with this identical mutation presented here (see the Supplementary materials for details on sufferers); therefore, we've now determined this mutation to be recurrent in sufferers with CS. The NHE6 gene and protein in cells with the missense mutation G383D behaved otherwise than the nonsense mutations. against this to nonsense mutations, the volume of NHE6 protein in the G383D cells became decreased, but NHE6 protein turned into now not totally absent. Relative to manage, NHE6 G383D protein in cells changed into 20.7 ± four.7% (NHE6 monomer) and three.1 ± 1.1% (NHE6 dimer) (Fig. 2C). The reduction in volume of detectable NHE6 protein changed into more famous for the dimer as compared with the monomer, such that the proportion of attainable monomer (mirrored by using monomer-to-dimer ratio) become extensively accelerated within the G383D cells compared with handle cells (Fig. 2C).

moreover creating a missense coding exchange, the G383D mutation occurs at the first base pair of exon 9 and therefore directly adjoining to the three′ splice acceptor site (fig. S1). We expected that this mutation can also disrupt splicing, namely, skipping of exon 9 and splicing of exon 8 to exon 10, thereby leading to a frameshift and untimely stop codon two codons downstream of the exon eight/10 junction. Reverse transcription polymerase chain reaction and sequencing of cDNA from iPSCs with the G383D mutation revealed the presence of an option splicing experience generated via skipping of exon 9 (Fig. 2nd). for this reason, two mRNAs are produced: one with exon skipping leading to a nonsense mutation (discipline to NMD, as supported by using transcript recovery in the presence of CHX, which reduces the volume of mRNA in these cells) and a second mRNA encoding for a protein product with the G383D missense mutation.

with regard to the G383D mutation, through use of structural modeling of the protein, we investigated whether this missense mutation turned into estimated to have an effect on protein structure. We built a homology mannequin of NHE6 in accordance with the crystal structure of the Escherichia coli NHE Na+/H+ antiporter A (NhaA) (sixteen), which was in the past used to mannequin different participants of the SLC9 household (17). ConSurf analysis, which calculates the rate of evolution at each and every amino acid according to phylogenetic family members between homologous sequences, confirmed the optimum conservation ranking for the G383 residue (Fig. 2E) (see additionally fig. S12 for sequence comparisons demonstrating conservation of the G383 residue throughout NHE homologs). The NHE6 structural mannequin confirmed that, akin to different membrane proteins, hydrophobic residues are located in the TM (transmembrane domains), whereas polar residues can be found in loops (Fig. 2F); these consequences improved our self assurance within the mannequin. The mannequin predicted that the G383 residue is located toward the endosomal end of NHE6 facing the core of the transporter on TM8. This domain has been proposed to feature in the law of ion transport mediated by way of NHE members of the family (18). Mutation of this nonpolar glycine residue to an acidic aspartate residue is therefore prone to affect the transporter’s structure through disrupting helix packing between TM7 and TM8. Modeling of the G383D variant recommended that this layer may additionally also disrupt the transporter structure by using forming a hydrogen bond with N166 on TM2 (Fig. 2G). alternatively, the G383D variant might kind a salt bridge with R500 on TM11, thereby stabilizing the inward open NHE6 conformation (Fig. 2G). for that reason, structural modeling means that the G383D mutation hampers the constitution and dynamics of the TM of NHE6, negatively affecting ion transport. In summary, the G383D mutation is expected to be lack of feature through complicated mechanisms, together with defects in splicing and a protein missense mutation. The residual mutant protein product is anticipated to have impaired transport in response to structural analyses.

Postnatal microcephaly is associated with defects in neuronal arborization in patient-derived neurons and is not caused by alterations in proliferation or cellphone demise

Postnatal microcephaly, akin to followed in sufferers with CS, can result from deficiencies of neuronal arborization in the neocortex, as hostile to differences in progenitor mobilephone proliferation; in contrast, simple microcephaly commonly occurs because of defects in cortical progenitor neurogenesis, cell destiny resolution, or cell demise pathways (four). To examine the capabilities mechanisms of postnatal microcephaly in CS, we differentiated CS and control iPSCs to an excitatory cortical neuronal destiny the usage of a monolayer differentiation protocol involving dual SMAD inhibition (19) (fig. S13). Our differentiation protocol validated effective down-rules of stem phone genes and up-legislation of neuronal genes in iPSC-derived neurons (figs. S14 and S15).

To determine the possibility that variations in neuronal progenitor proliferation, phone destiny determination, or cell dying may make contributions to CS-linked microcephaly, CS and control neuronal cultures had been examined the use of immunocytochemistry and RNA expression profiling. by using immunocytochemistry, CS and handle neuronal cultures had related percentages of cells expressing markers for neuronal progenitors [paired box protein 6 (PAX6)], neurons [microtubule associated protein 2 (MAP2)], and deep-layer cortical projection neurons [T-box brain transcription factor 1 (TBR1) and Chicken ovalbumin upstream promoter transcription factor (COUP-TF)-interacting protein 2 (CTIP2)] (fig. S14). We further examined the mobile destiny of CS and handle neuronal cultures using our NanoString-based mostly panel of mRNAs regarding neuronal cell fate determination (records file S1 and fig. S15). Upon neuronal differentiation, iPSC-derived neurons up-regulated neuronal genes and down-regulated stem phone destiny genes (facts info S2 to S4). extra, in differential gene expression studies, which were carried out using iPSCs or iPSC-derived neurons, we found neurons from both genotypes to express similar and high quantities of neuronal progenitor, neuronal, and cortical markers and extremely low amounts of mesodermal, endodermal, glial, and midbrain markers (figs. S15 to S21, desk S2, and records files S2 to S5). for this reason, these analyses demonstrate that cortical cell destiny determination in these cultures doesn't look like plagued by NHE6 mutations in patient-derived cells. We additionally ruled out adjustments in neuronal cellphone proliferation or mobilephone dying between CS and handle iPSC-derived neurons. The number of mitotically biking cells effective for Ki67 became now not diverse between CS and manage cultures at day 35 after neuronal induction (fig. S22). similarly, there was no change within the variety of apoptotic cells between CS and manage neuronal cultures (fig. S22). We conclude that mechanisms generally concerned in simple microcephaly akin to differences in mobile destiny decision, progenitor telephone proliferation, or cell loss of life are unlikely to make a contribution to CS-associated secondary or postnatal microcephaly.

reduced neuronal arborization can also contribute to postnatal microcephaly in CS, certainly in easy of our facts above showing no variations in telephone proliferation or death. In prior stories in NHE6-null mice, we recognized abnormalities in neuronal arborization each in vitro and in vivo (9). therefore, to extend on our prior findings in mouse, however now in neurons from patients, we examined neurite outgrowth and arborization in neurons differentiated from iPSCs from sufferers with CS. throughout all CS mutations examined, using numerous different techniques, we noticed in demand defects reflecting irregular neurite increase and arborization in CS. We carried out time-lapse are living-imaging analysis of CS neurons plated on laminin stripes (Fig. 3A). The neurons adhered alongside the laminin stripes and extended and retracted their neurites. We discovered decreases within the elongation charges and retraction rates, in assessment to their respective controls, for specific CS strains (Fig. 3B). in addition, the use of Sholl analysis on green fluorescent protein (GFP)–transfected neurons to verify arborization, we followed powerful defects in arborization in CS neurons despite the CS mutation studied (Fig. three, C and D, and fig. S23). together, these information from are living-imaging and Sholl analysis suggest that defects in arborization might underlie phenotypes of sufferers with CS comparable to postnatal microcephaly.

Fig. three Rescue of deficits in neuronal arborization by using reexpression of NHE6 in CS strains with frameshift or nonsense mutations, however now not within the CS missense mutation line.

(A) Neurite outgrowth dynamics were monitored in iPSC-derived neurons. Time-lapse images of iPSC-derived neurons plated on laminin-striped coverslips had been acquired using Volocity application at 4 XY positions every 5 min for 12 hours. representative photos are shown from the CS and paired manage lines for family unit 3, G383D. Tracings of neurites are shown in pink and cyan for the control line to exhibit tracking of diverse neurites. Scale bars, 20 μm. (B) The quotes of neurite elongation and retraction had been measured the use of ImageJ application for the primary 2 hours. manage family 1: n = 17 cells/32 neurites/841 measurements; household 1, R472fsX4: n = 13 cells/25 neurites/875 measurements; handle household 2: n = 12 cells/15 neurites/635 measurements; family 2, W523X: n = eight cells/9 neurites/724 measurements; handle family 3: n = 28 cells/55 neurites/827 measurements; family three, G383D: n = 52 cells/126 neurites/2163 measurements; control household four: n = 8 cells/17 neurites/622 measurements; family four, F183fsX1: n = 9 cells/13 neurites/708 measurements. (C) consultant images reflective of each and every circumstance of gene transfection experiments are proven from family 1, R472fsX4. iPSC-derived neurons had been transfected with a assemble encoding for GFP on my own or with two constructs collectively encoding for GFP + full-size human NHE6-HA and analyzed after 5 days. Scale bars, 20 μm. (D) Sholl evaluation of manage iPSC-derived neurons (black lines), CS iPSC–derived neurons (magenta traces), and CS iPSC–derived neurons transfected with a construct encoding for NHE6-HA (cyan strains) was performed. The standard number of neurite intersections with Sholl radii turned into plotted as a feature of distance from the soma for each condition. n = 20 to 25 cells per situation. statistics represent means ± SEM. Welch’s t assessments (B) and two-method ANOVA adopted by using Bonferroni correction for varied comparisons (D) have been used. *P < 0.045, **P < 0.008, and ***P < 0.00008 (B). *P < 0.05, **P < 0.01, ***P < 0.0001, and ****P < 0.00001 (D). Magenta asterisks denote importance when evaluating CS to handle cells. Cyan asterisks denote significance when evaluating CS to CS cells transfected with a assemble encoding for NHE6-HA.

Gene switch ends up in phone-independent rescue of neuronal arborization in affected person neurons with nonsense mutations however not in neurons with the missense mutation

using Sholl analysis to assess arborization, we observed strong discounts in neuronal arborization inspite of the CS mutation studied (Fig. 3D). youngsters, with reference to rescue of these defects the use of cDNA transfection in patient-derived neurons, cells with nonsense mutations behaved akin to each other however in a different way from the cells with the G383D missense/splice mutation. For these experiences, we transfected CS and handle neurons with a single assemble encoding for GFP or with a construct encoding for GFP in conjunction with a assemble encoding for full-size NHE6 tagged with hemagglutinin (HA) (Fig. 3C). Expression of NHE6-HA via gene transfer resulted in sought after, telephone-autonomous rescue of arbor complexity (through Sholl analysis) in neurons with nonsense mutations; besides the fact that children, rescue absolutely failed in neurons from the patient with the complicated missense/splice mutation, G383D (Fig. 3D and fig. S23).

G383D missense-mutant protein has both loss-of-function and dominant-negative residences

The means to rescue affected person-derived neurons with nonsense mutations by the use of expression of wild-category NHE6, but the failure to rescue arborization in G383D-mutant neurons with the identical strategy suggests that the residual endogenously expressed NHE6 G383D protein may additionally exert a dominant-bad function. We hypothesized that the mechanism can be probably through formation of nonfunctional heterodimers with exogenously expressed NHE6. here is a crucial question in regards to therapy as a result of if residual, nonfunctioning protein is lively as a dominant-poor during this class of CS mutations, then gene remedy concepts will doubtless now not be a feasible method in these sufferers.

To determine the purposeful residences of G383D protein, we subsequent confirmed the means of G383D-mutant protein to alkalinize endosomes, an established characteristic of endosomal NHEs. For these stories, we generated a CRISPR-Cas9 genome-edited human embryonic kidney (HEK) 293T cellphone line wherein deleterious mutations were prompted in NHE6 and during which we accompanied a lessen in endosomal pH relative to control (fig. S24). Exogenous expression of wild-class NHE6 in NHE6-null HEK293T cells resulted in an alkalization of endosomes, as in comparison with untransfected NHE6-null HEK293T cells. youngsters, exogenous expression of NHE6 G383D in NHE6-null HEK293T cells didn't alkalinize endosomes (Fig. 4A). These outcomes indicate that the G383D missense protein fails to characteristic accurately in cation trade, in keeping with loss-of-function predictions via the structural modeling (Fig. 2G). Coexpression of NHE6 G383D together with wild-classification NHE6 inhibited the capacity of exogenously expressed wild-category NHE6 to alkalinize endosomes (Fig. 4A).

Fig. four Loss-of-function and dominant-bad endeavor of NHE6 G383D mutation in legislation of intraendosomal pH and mislocalization in cells.

(A) The capacity of NHE6 G383D-mutant protein to rescue endosomal pH defects in NHE6-null HEK293T cells become decided. Endosomal pH become assayed the usage of a transferrin-based mostly components through which cells have been incubated with pH-delicate and pH-insensitive fluorescent conjugates of transferrin and then analyzed through circulate cytometry. Endosomal pH became measured in wild-class HEK293T cells (WT) (black font), HEK293T cells lacking NHE6 by the use of gene editing (NHE6-null) (black font), and HEK293T cells missing NHE6 however expressing mCherry-tagged WT (pink font) and/or G383D-mutant NHE6 (red font). information are offered as a bar graph (right) and as individual records features in which each dot represents the ordinary of three replicates from one independent scan (bottom). n = 3 experiments. (B) Lysates from HEK293T cells expressing HA- or GFP-tagged types of NHE6, as indicated, have been immunoprecipitated the usage of an anti-HA antibody and due to this fact analyzed by using Western blot using antibodies in opposition t GFP (accurate) and HA (middle). Protein input became decided through Western blot of lysates that had no longer undergone immunoprecipitation for HA-tagged protein the usage of an antibody in opposition t GFP (backside). (C) The relative amount of immunoprecipitated NHE6 dimer became quantified on the foundation of consequences proven in (B). (D) HeLa cells expressing HA-tagged WT or G383D-mutant NHE6 were incubated with Alexa Fluor 568–conjugated transferrin (pink) for 10 min and as a result immunostained for HA (eco-friendly) and imaged the usage of super-decision structured illumination microscopy. Arrows (white) in the magnified photographs point out areas of colocalization between transferrin and NHE6 in endosomes. Scale bars, 5 μm. (E) Colocalization of NHE6 WT protein versus NHE6 G383D-mutant protein with transferrin became quantified the use of ImageJ, and a Mander’s coefficient was determined. facts represent ability ± SEM. Unpaired pupil’s t checks were used. *P < 0.05, **P < 0.01, and ***P < 0.001.

To dissect the biochemical mechanism of the dominant-poor exercise exerted by way of the G383D protein, we investigated no matter if the G383D protein may kind heterodimers with wild-classification NHE6 protein in HEK293T cells. We found that exogenously expressed G383D protein could form homodimers with itself and heterodimers with exogenously expressed wild-class NHE6 protein (Fig. 4, B and C). the usage of tremendous-decision structured illumination microscopy in cells expressing exogenous wild-classification NHE6 or G383D-mutant NHE6, the mobile localization of G383D protein turned into altered relative to manage. control protein showed a robust colocalization with fluorescent-conjugated transferrin in early endosomes, whereas G383D-mutant NHE6 protein proven minimal colocalization with transferrin-high quality early endosomes (Fig. 4, D and E). In abstract, we find that the NHE6 G383D mutant doesn't function in the alkalization of endosomes, reflecting the loss-of-feature nature of this mutation. in addition, our dimerization and pH studies additionally show that the G383D-mutant protein features as a dominant-bad, probably with the aid of inhibiting the wild-category NHE6 protein function upon formation of (nonfunctional) heterodimers.

affected person neurons exhibit rescue of neuronal arborization with the aid of exogenous trophic ingredient medication (BDNF or IGF-1) regardless of mutation

right here, we've based a substantial mobile resource that can be used in cell-based mostly assays for preclinical development of therapeutics. moreover a gene remedy approach, we regarded two choice techniques for cellphone rescue that may serve as advantage CS cures: (i) brokers that alkalinize the early endosome, akin to quinolines (corresponding to chloroquine), weak bases, or V-ATPase inhibitors, and (ii) growth factors equivalent to BDNF, which we now have shown to have efficacy in NHE6-null simple mouse cultures (9). To verify the premise for gaining knowledge of brokers that alkalinize the endosome, we performed huge studies of intraendosomal pH throughout all obtainable subclonal traces derived from sufferers with CS the use of two methods: ratiometric analysis of cells after endocytosis of pH-sensitive and pH-insensitive fluorescent conjugates of transferrin; and ratiometric evaluation of cells expressing vesicle-associated membrane protein 3 (VAMP3)–pHluorin2. in the context of either formula, we recognized decreases in intraendosomal pH that had been recoverable through correction of the mutation using CRISPR-Cas9 (Fig. 5, A to C, and figs. S25 to S27) (see the Supplementary substances and methods and figs. S25 to S31 for distinct strategies and additional effects on intraendosomal pH reports, including studies in affected person-derived strains, and in strains in which NHE6 mutations have been brought on in a founder cellphone line.) although, we did observe variability in the power of the effect of overacidification of the endosome across different households. Some households showed mighty consequences, whereas different households did not demonstrate a phenotype of endosome overacidification (figs. S27 to S29). Given this variability, we did not pursue the alkalinizing brokers extra as a rescue approach.

Fig. 5 Correction of endosomal pH defects in genome-edited CS iPSCs.

(A) Western blotting become carried out to confirm expression of NHE6 protein in CS iPSCs that had undergone genome editing to suitable the R472fsX4 mutation. Lysates of paired manage, CS, and genome-corrected iPSCs from family unit 1 had been immunoprecipitated the usage of a customized-made anti-NHE6 antibody and because of this analyzed by Western blot the use of the equal antibody. Blotting towards tubulin was used as a loading manage. IgG, immunoglobulin G. (B and C) even if correction of the NHE6 R472fsX4 mutation may rescue endosomal pH defects latest in mutant iPSCs turned into decided. Endosomal pH was assayed the use of two different ratiometric strategies: a transferrin-primarily based formula (B) and a VAMP3-pHluorin2-based mostly formula (C). For the transferrin-based formulation, cells had been incubated with pH-sensitive and pH-insensitive fluorescent conjugates of transferrin and then analyzed via movement cytometry. For the VAMP3-pHluorin2–primarily based components, cells have been transfected with a construct enabling for expression of VAMP3-pHluorin2 after which analyzed with the aid of circulate cytometry. Endosomal pH changed into measured in paired control, R472fsX4-mutant, and genome-corrected iPSCs. statistics are offered as individual statistics features in which each dot represents a technical replicate. n ≥ 3 experiments. facts symbolize means ± SEM. Unpaired scholar’s t tests had been used. *P < 0.05, **P < 0.01, and ****P < 0.0001.

We subsequent confirmed the extent to which neuronal arborization may well be restored in patient-derived neurons pharmacologically via medicine with exogenous BDNF or IGF-1. We proven these two boom factors as proof-of-precept molecules, as we now have in the past shown that BDNF signaling by way of TrkB is diminished and the connected arborization defects may be rescued by using exogenous software of excess BDNF (9). extra nonetheless, IGF-1 is additionally a trophic component that augments neurite increase, and this agent is at the moment in scientific trials for a couple of neurodevelopmental issues (20, 21).

When CS and handle neurons were treated for 3 days with exogenous addition of either BDNF or IGF-1, we accompanied gigantic rescue of the arborization defect in all household traces tested, even with mutation (Fig. 6, A and B). treatment with BDNF or IGF-1 accelerated the mean size per neurite and the number of branch points per neurite in all CS lines tested, as in comparison with untreated CS neurons (Fig. 6B). for this reason, neurite morphology defects in CS cultures may be restored by exogenous trophic aspect treatment. collectively, these consequences suggest that impartial exposure to BDNF or IGF-1 can rescue the neuronal arborization phenotype in CS neurons and that these growth ingredient treatments warrant extra exploration in current animal models and other preclinical reviews. in contrast to the gene switch experiments above, these exogenous trophic elements show efficacy in vitro throughout affected person-derived neurons with diverse mutations.

Fig. 6 Rescue of deficiencies in neuronal arborization, despite mutation class, by BDNF or IGF-1 remedy.

(A) Immunostaining of manage and CS iPSC–derived neurons left untreated or treated with BDNF or IGF-1 changed into carried out for MAP2 (crimson), a marker of dendrites, and TAU (green), a marker of axons. Nuclei had been labeled the usage of DAPI (blue). consultant photos are shown from the CS and matched control strains for family 2, W523X. Scale bar, 50 μm. (B) The recuperation of deficiencies in neuronal arborization existing in CS iPSC–derived neurons by means of growth aspect remedy become quantified. regular length (proper panels) and variety of department elements per neurite (backside panels) have been measured using Neurolucida tracing utility for control and CS iPSC–derived neurons left untreated (UNT) or handled with BDNF or IGF-1 (IGF). Neurites stained with either MAP2 or TAU have been analyzed; no distinction become made between dendrites or axons right through measurements. handle family unit 1: n = 18 (UNT), 35 (BDNF), and 26 (IGF) neurites; family 1, R472fsX4: n = 24 (UNT),19 (BDNF), and 36 (IGF) neurites; manage family unit 2: n = 54 (UNT), forty eight (BDNF), and 28 (IGF) neurites; family 2, W523X: n = fifty three (UNT), 37 (BDNF), and 37 (IGF) neurites; handle family 3: n = 30 (UNT), 35 (BDNF), and 32 (IGF) neurites; household 3, G383D: n = 32 (UNT), 31 (BDNF), and 35 (IGF) neurites. statistics characterize skill ± SEM. Welch’s t tests were used. *P < 0.05, **P < 0.005, and ***P < 0.0005.

dialogue

despite increasing CS diagnoses in the health center, an awful lot continues to be to be understood in regards to the pathogenesis of CS, and there are currently no selected treatments. The generation of iPSCs derived from sufferers with CS gifts a brand new opportunity to analyze the pathogenesis of CS and to enhance medication techniques. in this examine, we examined the residences of affected person-derived neurons that underlie deficits in circuit construction as well as two rescue recommendations. We show that human neurons derived from sufferers with CS have reduced complexity of neuronal arbors in spite of the nature of the mutation. These deficits in neuronal boom and arborization may additionally underlie the postnatal microcephaly pronounced in CS (2). We also show that the neuronal arborization defect may be rescued by way of expression of wild-category NHE6 in cells with an NHE6 nonsense mutation and loss of protein as a result of NMD; youngsters, cells from a patient with residual, nonfunctional NHE6 protein, particularly, cells from a patient with the recurrent G383D missense mutation, could not be rescued. We additional supply biochemical facts that residual, nonfunctional G383D protein can act as a dominant-poor via heterodimerization with the exogenously introduced wild-type protein. by contrast, the neuronal arborization defect could be rescued in vitro by way of exogenous addition of BDNF or IGF-1 even with mutation.

Our analyses of iPSCs from patients with CS spanning a sequence of mutations exhibit at the least two mechanistic courses of mutations. Most commonly used mutations in sufferers with CS (classification 1 mutations) are estimated to be loss of function in keeping with disruption of coding through introduction of nonsense mutations (2). Loss-of-feature mutations by the use of splicing mutations are additionally usual and can act in a similar way, yielding complete loss of protein. We show here via size of mRNA expression in affected person-derived cells, together with in human neurons, that the mRNA is absent in CS cells, in keeping with nonsense-mediated mRNA decay. We implicate NMD without delay via healing of mRNA after inhibition of NMD by way of CHX or siRNA-mediated reduction in expression of distinctive add-ons of the NMD equipment.

Our stories also investigate the G383D mutation intensive as a model of a 2nd class of mutations wherein residual, nonfunctional protein remains (type 2 mutations). We display right here that the G383D mutation is recurrent in CS, as we right here file two households with this mutation (Supplementary materials). In patient cells, we show that this mutation has advanced outcomes on mRNA and protein coding: First, we find that the G-to-A mutation on the first base of exon 9 results in exon skipping and construction of an mRNA with a nonsense mutation that's recoverable with CHX treatment. We estimate that this mechanism reduces mRNA amounts via about 50% in comparison with control. 2d, this mutation leads to residual protein with the G383D mutation, which is anticipated to perturb exchanger function in line with our structural predictions. We also locate that this residual protein seems to change the mobile distribution of NHE6, with mutant NHE6 exhibiting reduced colocalization to transferrin-fine endosomes. ultimate, we locate that the G383D protein can heterodimerize with wild-class NHE6 protein. The G383D protein can't characteristic in the alkalization of endosomes, and when coexpressed with wild-type NHE6 protein, the G383D protein can intervene with wild-type NHE6 feature within the alkalization of endosomes. Thereby, this G383D mutation represents a definite type of NHE6 mutations in which the mutation has each loss-of-characteristic residences and also dominant-poor homes through residual expression of a mutant protein. at present, there are several published examples of mutations in sufferers with CS that might healthy this second class of NHE6 mutations in which residual dominant-interfering protein is likely (22).

The indisputable fact that CS has distinct mechanistic courses of pathogenic mutations has crucial therapeutic magnitude. Our information show mutation-particular responses to cures with regard to gene switch the usage of DNA transfection. Neurons with nonsense mutations in NHE6 show clear rescue of arborization phenotypes via cDNA switch; besides the fact that children, cells expressing the G383D missense mutation fail to be rescued by way of this method. This outcome suggests that gene remedy primarily based in gene switch techniques is unlikely to be helpful in patients with mutations of this category with residual protein. Mutation-particular mechanisms of medicine response may additionally smartly be greater the guideline than the exception in genetic ailment, as has been studied in depth in cystic fibrosis (eleven). youngsters, exogenous treatments of CS neurons with increase components akin to BDNF or IGF-1 rescue arborization defects inspite of the mutation class. BDNF agonists have been discipline to efforts in preclinical experiences of neurological disorder with combined results (23). on the other hand, IGF-1 has been shown currently to be a potential therapy for the autism-linked syndromes Rett syndrome and Phelan-McDermid syndrome. Preclinical reports in Rett syndrome showed that medication of iPSC-derived neurons with IGF-1 extended numbers of glutamatergic synapses (24). moreover, medication of a Rett syndrome mouse mannequin with IGF-1 rescued mind dimension, synapse density, and excitatory synapse transmission to control values (25). In a phase 1 medical trial for IGF-1 in Rett syndrome, patients showed development in indicators of anxiety and breathing difficulty (20). furthermore, IGF-1 medication of iPSC-derived neurons from patients with Phelan-McDermid syndrome superior deficits in mature excitatory synapses, as in comparison with controls (26). A preliminary clinical trial of IGF-1 in Phelan-McDermid syndrome confirmed improvement of social withdrawal and restricted behaviors (21). in addition, a part 2 medical trial for IGF-1 is in development with respect to a potential treatment for autism spectrum sickness (NCT01970345), and section 2 trials were achieved with appreciate to the use of an IGF-1 analog (NNZ-2566) as a possible remedy for Fragile X syndrome (NCT01894958) and Rett syndrome (NCT02715115). careful attention assessing the efficacy of IGF-1 in these different problems might also have relevance to therapeutic development in CS. moreover, further research into efficacy of IGF-1 remedy may also also be warranted in CS mouse fashions in vivo.

effects of our look at of intraendosomal pH across a various range of affected person-derived and affected person-brought on (via genome editing) mutations also deliver new insights into the feature of NHE6 as an endosomal proton/cation exchanger. Prior statistics from our laboratory and others have confirmed rate reductions in organellar luminal pH in the context of NHE6 mutation or deficiency in inbred, laboratory lines in mouse (9) and in immortalized, mammalian phone strains (27, 28). the same phenotype is observed upon Nhx1 mutation in yeast (17, 29). right here, we accompanied the predictable responses, it truly is, elevation of endosomal pH with correction of the NHE6 mutation using CRISPR-Cas9; besides the fact that children, using patient-derived strains, compared with biologically connected controls from human populations, we accompanied a range within the energy of the impact on intraendosomal pH. There can be a few explanations for this, amongst them are that cells in lifestyle undergo genetic changes that compensate for the impact of the NHE6 mutation. furthermore, it is feasible that there is extra redundancy or induction of compensatory mechanisms in some strains as compared with others, given the wide selection in historical past genomic variation in these human lines. Our transcriptome information guide a link between lack of NHE6 and skills compensatory alterations in expression of V-ATPase genes (figs. S19 to S21, desk S2, and statistics data S2 to S5), thereby additional implicating a task for NHE6 in go-membrane proton transport.

although it is likely that mutation of NHE6 influences proton leak, the faulty mechanisms may additionally additionally contain protein functions that don't seem to be ultimate exemplified through measurable alterations in proton awareness in the endosome lumen. at the identical time, the defects observed in neuronal development, such as in arborization, don't seem to evidently correlate with the energy of the results on acidification of the endosome lumen. typical, the weight of the information right here means that NHE6 additionally services in a manner yet to be decided (no longer interestingly attributable fully to transformations in intraendosomal pH) that perturbs neuronal construction. These outcomes additionally might have therapeutic relevance, as they elevate the query as as to whether alkalinizing agents (equivalent to V-ATPase inhibitors or vulnerable bases) may be effective in treating CS. In constructing capabilities option remedies, in this description of this new iPSC resource, we demonstrated that there are distinct mutational classes in CS and, further, that these courses need to be considered carefully as we embark on studies of medicine construction. Our statistics point out that CS mutations with residual protein are unlikely to reply to gene transfer suggestions, whereas growth element remedies may additionally symbolize a extra fruitful approach to treatments.

through the consequences of our studies described right here, we existing deserves and doubtlessly some obstacles in using iPSC systems. Our experiences have examined tremendously penetrant pathogenic mutations, yet there is still version in the prominence of some mobile phenotypes seemingly as a result of modulation by means of history genetic adaptation. different boundaries of this analyze include that our experiments are in vitro and that the iPSC-derived neurons signify early embryonic differentiating neurons. additional nonetheless, we now have examined only 1 neuron class, excitatory neurons, in monolayer cultures. in the future, cellular phenotypes in distinct neural phone varieties, as well as in additional complex tissue models corresponding to organoids, can be examined. additionally, relocating forward, a hit rescue ideas introduced right here could be ideally corroborated in animal reviews in vivo.

final, a massive strength of our look at is the institution and validation of those iPSC substances for the examine of mobile mechanisms of ailment and preclinical drug building in CS. Our resource, which might be extensively shared, in part during the national Institute of mental fitness Repository and Genomics aid (analyze 200), has established affected person-derived cells with each linked (unaffected brother) and isogenic (from mutation correction) controls, as well as induced mutations in a traditional male founder iPSC line and in HEK293T cells. a crucial energy of those iPSC techniques is the access to dissimilar human mutations, which are often tough to mannequin within the genome of experimental animals. As we have carried out right here, this kind of affected person phone aid makes it possible for in-depth study of the consequences of sickness-causing mutations and competencies rescue ideas during this mobile context.

SUPPLEMENTARY materials

stm.sciencemag.org/cgi/content material/full/13/580/eaaw0682/DC1

materials and methods

Fig. S1. household 1 to household 5 pathogenic mutations in NHE6 cDNA.

Fig. S2. Sanger sequencing chromatograms of paired manage and CS iPSCs.

Fig. S3. Morphological characterization of paired control and CS iPSCs.

Fig. S4. Karyotype evaluation of paired handle and CS iPSC traces.

Fig. S5. Staining for alkaline phosphatase exercise in paired handle and CS iPSC lines.

Fig. S6. Immunostaining of paired manage and CS iPSC colonies for pluripotency markers.

Fig. S7. Fluorescence-activated mobile sorting evaluation of paired control and CS iPSCs for stem mobilephone–particular markers.

Fig. S8. Quantitative reverse transcription polymerase chain reaction analyses of pluripotency markers in undifferentiated iPSCs as in comparison with hESC-derived embryoid bodies.

Fig. S9. In vitro differentiation abilities of paired handle and CS iPSCs.

Fig. S10. In vivo differentiation skills of paired control and CS iPSCs.

Fig. S11. Northern blot analysis of family 4 and household 5 paired handle and CS iPSCs.

Fig. S12. Conservation of the G383 residue throughout NHE homologs.

Fig. S13. Protocol for neuronal differentiation from iPSCs.

Fig. S14. Neuronal and cortical marker expression in iPSC-derived neurons.

Fig. S15. Gene expression of mobile fate markers in iPSC-derived neurons.

Fig. S16. Unsupervised hierarchical clustering of iPSCs and iPSC-derived neurons via gene expression.

Fig. S17. Volcano plot of gene expression adjustments in iPSCs as in comparison with iPSC-derived neurons.

Fig. S18. Volcano plots of gene expression alterations in CS versus manage iPSCs and iPSC-derived neurons.

Fig. S19. NHE family member gene expression alterations in CS iPSCs and iPSC-derived neurons.

Fig. S20. V-ATPase gene expression alterations in CS iPSCs and iPSC-derived neurons.

Fig. S21. Weighted Gene Co-expression network evaluation (WGCNA)–primarily based network development and module detection in CS iPSCs.

Fig. S22. analysis of iPSC-derived neuronal cultures for proliferation and apoptosis.

Fig. S23. Rescue of deficits in neuronal arborization complexity by way of reexpression of NHE6 in CS lines with frameshift or nonsense mutations however now not within the CS missense mutation line.

Fig. S24. Validation of handle and CRISPR-Cas9–caused NHE6-null HEK293T mobilephone lines and characterization of endosomal pH.

Fig. S25. establishment of isogenic, genome-corrected iPSCs for household 1 the use of genome enhancing.

Fig. S26. Calibration curve and stream cytometer profiles for ratiometric analysis of endosomal pH the use of pH-sensitive and pH-insensitive fluorescent conjugates of transferrin.

Fig. S27. evaluation of endosomal pH in paired manage and CS iPSCs from household 1 to household 5 the usage of the transferrin formulation.

Fig. S28. Analyses of endosomal pH in paired manage and CS iPSCs from family 1 to family unit 5 the usage of the VAMP3-pHluorin2 method.

Fig. S29. evaluation of endosomal pH in paired handle and CS iPSC–derived neurons.

Fig. S30. establishment of iPSCs with NHE6 mutations and isogenic controls the use of genome enhancing of a traditional founder line.

Fig. S31. evaluation of endosomal pH in paired isogenic handle iPSCs and iPSCs with caused NHE6 mutations the use of the transferrin system.

table S1. Characterization of peripheral blood mononuclear mobile–derived iPSC traces.

table S2. Statistical analysis of genes protected in the blue module the usage of a hypergeometric examine.

records file S1. NanoString custom-made probe set.

information file S2. usual normalized NanoString count number facts of gene regulation in iPSCs and iPSC-derived neurons from patients with CS and controls.

facts file S3. by-pattern normalized NanoString count facts of gene regulation in iPSCs and iPSC-derived neurons from patients with CS and controls.

statistics file S4. via-sample raw NanoString count records of gene legislation in iPSCs and iPSC-derived neurons from patients with CS and controls.

information file S5. Genes in each and every gene module from the WGCNA-primarily based analyses.

records file S6. basic information for main text figures.

facts file S7. fundamental information for supplementary figures.

References (32–51)

Acknowledgments: We thank the households who participated during this look at. Funding: The study turned into supported by means of here: Aspire I Junior school Award (to S.B.L.), center of Biomedical Excellence Dietary dietary supplements and irritation-NIGMS P20GM103641 Pilot undertaking Award (to S.B.L.), and SC INBRE NIGMS P20GM103499 Pilot Award (to S.B.L.); NIGMS Postbaccalaureate research schooling application (PREP) R25GM064118 (to S.A.); Brown Institute for brain Science Pilot Award and Brown university Seed Award (to D.H.-ok.); NIGMS R01GM108911 (to A.S.); and Burroughs Wellcome Fund profession Award for clinical Scientists 1006815.01 (to E.M.M.), NIMH R01MH105442 (to E.M.M.), NIMH R01MH102418 (to E.M.M.), NIMH R21MH115392 (to E.M.M.), NINDS/NIA R01NS113141 (to E.M.M.), and Angelman Syndrome foundation customary analysis furnish (to E.M.M.). This study became additionally supported through the Hassenfeld child health Innovation Institute at Brown college, the Brown institution stream Cytometry and Sorting Facility, and the Cincinnati little ones’s clinic scientific center Pluripotent Stem cellphone Facility. writer contributions: S.B.L., A.M.M., and E.M.M. designed the examine. S.B.L., A.M.M., L.M., L.I.v.D., and Q.O. performed experiments and analyses. L.M. and M.S. contributed to characterization of the iPSC lines, in specific the genome-edited strains. L.M. performed studies regarding analysis of HEK293T cells. Q.W. and E.D.G.U. contributed to the bioinformatics-based mostly evaluation of NanoString statistics. B.C.k. performed patient assessments. D.N., M.H.C., and P.B.-V. contributed to evaluation of information relating to the iPSC strains. L.L.L. and D.H.-k. contributed to the time-lapse imaging. M.F.P. contributed to the recruitment of sufferers and acquiring samples for producing the iPSC strains. S.A. and A.S. performed the structural modeling. R.N.J. contributed to statistical design and carried out statistical analyses. S.B.L., A.M.M., and E.M.M. wrote the manuscript. All authors reviewed and approved the manuscript. Competing pursuits: A.S. is a cofounder of AIchemy and a Scientific Advisory Board Member of Trilogy Sciences and Parthenon Therapeutics. The other authors declare that they have no competing hobbies. information and materials availability: The CS and coupled control iPSC lines are available in the course of the NIMH Repository and Genomics aid (look at 200). Constructs and different telephone strains newly described in this examine are available from the corresponding author upon inexpensive request and may be shared upon implementation of a Uniform biological fabric switch agreement. All statistics linked to this look at are latest in the paper or the Supplementary substances. See statistics data S6 and S7 for basic statistics for leading textual content and supplemental figures, respectively, by which experiments had an n < 20.


References


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