Precise mutagenesis in zebrafish using cytosine base editors

Base editing is a powerful CRISPR-based technology for introducing precise substitutions into the genome. This technology greatly advances mutagenesis possibilities in vivo, particularly in zebrafish, for which the generation of precise point mutations is still challenging. Zebrafish have emerged as an important model for genetic studies and in vivo disease modeling. With the development of different base editor variants that recognize protospacer-adjacent motifs (PAMs) other than the classical 5'-NGG-3' PAM, it is now possible to design and test several guide RNAs to find the most efficient way to precisely introduce the desired substitution. Here, we describe the experimental design strategies and protocols for cytosine base editing in zebrafish, from guide RNA design and selection of base editor variants to generation of the zebrafish mutant line carrying the substitution of interest. By using co-selection by introducing a loss-of-function mutation in genes necessary for the formation of pigments, injected embryos with highly efficient base editing can be directly analyzed to determine the phenotypic impact of the targeted substitution. The generation of mutant embryos after base editor injections in zebrafish can be completed within 2 weeks.

De novo missense variants in phosphatidylinositol kinase PIP5KIγ underlie a neurodevelopmental syndrome associated with altered phosphoinositide signaling

Phosphoinositides (PIs) are membrane phospholipids produced through the local activity of PI kinases and phosphatases that selectively add or remove phosphate groups from the inositol head group. PIs control membrane composition and play key roles in many cellular processes including actin dynamics, endosomal trafficking, autophagy, and nuclear functions. Mutations in phosphatidylinositol 4,5 bisphosphate [PI(4,5)P2] phosphatases cause a broad spectrum of neurodevelopmental disorders such as Lowe and Joubert syndromes and congenital muscular dystrophy with cataracts and intellectual disability, which are thus associated with increased levels of PI(4,5)P2. Here, we describe a neurodevelopmental disorder associated with an increase in the production of PI(4,5)P2 and with PI-signaling dysfunction. We identified three de novo heterozygous missense variants in PIP5K1C, which encodes an isoform of the phosphatidylinositol 4-phosphate 5-kinase (PIP5KIγ), in nine unrelated children exhibiting intellectual disability, developmental delay, acquired microcephaly, seizures, visual abnormalities, and dysmorphic features. We provide evidence that the PIP5K1C variants result in an increase of the endosomal PI(4,5)P2 pool, giving rise to ectopic recruitment of filamentous actin at early endosomes (EEs) that in turn causes dysfunction in EE trafficking. In addition, we generated an in vivo zebrafish model that recapitulates the disorder we describe with developmental defects affecting the forebrain, including the eyes, as well as craniofacial abnormalities, further demonstrating the pathogenic effect of the PIP5K1C variants.

A minimally invasive fin scratching protocol for fast genotyping and early selection of zebrafish embryos

Current genetic modification and phenotyping methods in teleost fish allow detailed investigation of vertebrate mechanisms of development, modeling of specific aspects of human diseases and efficient testing of drugs at an organ/organismal level in an unparalleled fast and large-scale mode. Fish-based experimental approaches have boosted the in vivo verification and implementation of scientific advances, offering the quality guaranteed by animal models that ultimately benefit human health, and are not yet fully replaceable by even the most sophisticated in vitro alternatives. Thanks to highly efficient and constantly advancing genetic engineering as well as non-invasive phenotyping methods, the small zebrafish is quickly becoming a popular alternative to large animals' experimentation. This approach is commonly associated to invasive procedures and increased burden. Here, we present a rapid and minimally invasive method to obtain sufficient genomic material from single zebrafish embryos by simple and precise tail fin scratching that can be robustly used for at least two rounds of genotyping already from embryos within 48 h of development. The described protocol betters currently available methods (such as fin clipping), by minimizing the relative animal distress associated with biopsy at later or adult stages. It allows early selection of embryos with desired genotypes for strategizing culturing or genotype-phenotype correlation experiments, resulting in a net reduction of "surplus" animals used for mutant line generation.

Base-editing-mediated dissection of a γ-globin cis-regulatory element for the therapeutic reactivation of fetal hemoglobin expression

Sickle cell disease and β-thalassemia affect the production of the adult β-hemoglobin chain. The clinical severity is lessened by mutations that cause fetal γ-globin expression in adult life (i.e., the hereditary persistence of fetal hemoglobin). Mutations clustering ~200 nucleotides upstream of the HBG transcriptional start sites either reduce binding of the LRF repressor or recruit the KLF1 activator. Here, we use base editing to generate a variety of mutations in the -200 region of the HBG promoters, including potent combinations of four to eight γ-globin-inducing mutations. Editing of patient hematopoietic stem/progenitor cells is safe, leads to fetal hemoglobin reactivation and rescues the pathological phenotype. Creation of a KLF1 activator binding site is the most potent strategy - even in long-term repopulating hematopoietic stem/progenitor cells. Compared with a Cas9-nuclease approach, base editing avoids the generation of insertions, deletions and large genomic rearrangements and results in higher γ-globin levels. Our results demonstrate that base editing of HBG promoters is a safe, universal strategy for treating β-hemoglobinopathies.

Dominantly acting KIF5B variants with pleiotropic cellular consequences cause variable clinical phenotypes

Kinesins are motor proteins involved in microtubule (MT)-mediated intracellular transport. They contribute to key cellular processes, including intracellular trafficking, organelle dynamics and cell division. Pathogenic variants in kinesin-encoding genes underlie several human diseases characterized by an extremely variable clinical phenotype, ranging from isolated neurodevelopmental/neurodegenerative disorders to syndromic phenotypes belonging to a family of conditions collectively termed as 'ciliopathies.' Among kinesins, kinesin-1 is the most abundant MT motor for transport of cargoes towards the plus end of MTs. Three kinesin-1 heavy chain isoforms exist in mammals. Different from KIF5A and KIF5C, which are specifically expressed in neurons and established to cause neurological diseases when mutated, KIF5B is an ubiquitous protein. Three de novo missense KIF5B variants were recently described in four subjects with a syndromic skeletal disorder characterized by kyphomelic dysplasia, hypotonia and DD/ID. Here, we report three dominantly acting KIF5B variants (p.Asn255del, p.Leu498Pro and p.Leu537Pro) resulting in a clinically wide phenotypic spectrum, ranging from dilated cardiomyopathy with adult-onset ophthalmoplegia and progressive skeletal myopathy to a neurodevelopmental condition characterized by severe hypotonia with or without seizures. In vitro and in vivo analyses provide evidence that the identified disease-associated KIF5B variants disrupt lysosomal, autophagosome and mitochondrial organization, and impact cilium biogenesis. All variants, and one of the previously reported missense changes, were shown to affect multiple developmental processes in zebrafish. These findings document pleiotropic consequences of aberrant KIF5B function on development and cell homeostasis, and expand the phenotypic spectrum resulting from altered kinesin-mediated processes.

First Measurement of the Z→μ^{+}μ^{-} Angular Coefficients in the Forward Region of pp Collisions at sqrt[s]=13 TeV

The first study of the angular distribution of μ^{+}μ^{-} pairs produced in the forward rapidity region via the Drell-Yan reaction pp→γ^{*}/Z+X→ℓ^{+}ℓ^{-}+X is presented, using data collected with the LHCb detector at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 5.1  fb^{-1}. The coefficients of the five leading terms in the angular distribution are determined as a function of the dimuon transverse momentum and rapidity. The results are compared to various theoretical predictions of the Z-boson production mechanism and can also be used to probe transverse-momentum-dependent parton distributions within the proton.

Apoptosis and cell proliferation during metamorphosis of the planula larva of Clytia hemisphaerica (Hydrozoa, Cnidaria)

BACKGROUND

Metamorphosis in marine species is characterized by profound changes at the ecophysiological, morphological, and cellular levels. The cnidarian Clytia hemisphaerica exhibits a triphasic life cycle that includes a planula larva, a colonial polyp, and a sexually reproductive medusa. Most studies so far have focused on the embryogenesis of this species, whereas its metamorphosis has been only partially studied.

RESULTS

We investigated the main morphological changes of the planula larva of Clytia during the metamorphosis, and the associated cell proliferation and apoptosis. Based on our observations of planulae at successive times following artificial metamorphosis induction using GLWamide, we subdivided the Clytia's metamorphosis into a series of eight morphological stages occurring during a pre-settlement phase (from metamorphosis induction to planula ready for settlement) and the post-settlement phase (from planula settlement to primary polyp). Drastic morphological changes prior to definitive adhesion to the substrate were accompanied by specific patterns of stem-cell proliferation as well as apoptosis in both ectoderm and endoderm. Further waves of apoptosis occurring once the larva has settled were associated with morphogenesis of the primary polyp.

CONCLUSION

Clytia larval metamorphosis is characterized by distinct patterns of apoptosis and cell proliferation during the pre-settlement phase and the settled planula-to-polyp transformation.

Precise base editing for the in vivo study of developmental signaling and human pathologies in zebrafish

While zebrafish is emerging as a new model system to study human diseases, an efficient methodology to generate precise point mutations at high efficiency is still lacking. Here we show that base editors can generate C-to-T point mutations with high efficiencies without other unwanted on-target mutations. In addition, we established a new editor variant recognizing an NAA protospacer adjacent motif, expanding the base editing possibilities in zebrafish. Using these approaches, we first generated a base change in the ctnnb1 gene, mimicking oncogenic an mutation of the human gene known to result in constitutive activation of endogenous Wnt signaling. Additionally, we precisely targeted several cancer-associated genes including cbl. With this last target, we created a new zebrafish dwarfism model. Together our findings expand the potential of zebrafish as a model system allowing new approaches for the endogenous modulation of cell signaling pathways and the generation of precise models of human genetic disease-associated mutations.

Zebrafish as a Model for the Study of Live in vivo Processive Transport in Neurons

Motor proteins are responsible for transport of vesicles and organelles within the cell cytoplasm. They interact with the actin cytoskeleton and with microtubules to ensure communication and supply throughout the cell. Much work has been done in vitro and in silico to unravel the key players, including the dynein motor complex, the kinesin and myosin superfamilies, and their interacting regulatory complexes, but there is a clear need for in vivo data as recent evidence suggests previous models might not recapitulate physiological conditions. The zebrafish embryo provides an excellent system to study these processes in intact animals due to the ease of genetic manipulation and the optical transparency allowing live imaging. We present here the advantages of the zebrafish embryo as a system to study live in vivo processive transport in neurons and provide technical recommendations for successful analysis.

Observation of excited Λ(b)(0) baryons

Using pp collision data corresponding to 1.0 fb(-1) integrated luminosity collected by the LHCb detector, two narrow states are observed in the Λ(b)(0)π(+)π(-) spectrum with masses 5911.97±0.12(stat)±0.02(syst)±0.66(Λ(b)(0) mass) MeV/c(2) and 5919.77±0.08(stat)±0.02(syst)±0.66(Λ(b)(0) mass) MeV/c(2). The significances of the observations are 5.2 and 10.2 standard deviations, respectively. These states are interpreted as the orbitally excited Λ(b)(0) baryons, Λ(b)(*0)(5912) and Λ(b)(*0)(5920).

Measurement of the B¯(s)(0) effective lifetime in the J/ψf0(980) final state

The effective lifetime of the B ¯(s)(0) meson in the decay mode B¯(s)(0)→J/ψf(0)(980) is measured using 1.0 fb(-1) of data collected in pp collisions at √s=7 TeV with the LHCb detector. The result is 1.700±0.040±0.026 ps, where the first uncertainty is statistical and the second systematic. As the final state is CP-odd, and CP violation in this mode is measured to be small, the lifetime measurement can be translated into a measurement of the decay width of the heavy B¯(s)(0) mass eigenstate, Γ(H)=0.588±0.014±0.009 ps(-1).

Observation of B0→D¯(0)K(+)K(-) and evidence for B(s)(0)→D¯(0)K(+)K(-)

The first observation of the decay B0→D¯(0)K(+)K(-) is reported from an analysis of 0.62 fb(-1) of pp collision data collected with the LHCb detector. Its branching fraction is measured relative to that of the topologically similar decay B(0)→D ¯(0)π(+)π(-) to be (B(B(0)→D¯(0)K(+)K(-))/B(B(0)→D¯(0)π(+)π(-))=0.056±0.011±0.007,where the first uncertainty is statistical and the second is systematic. The significance of the signal is 5.8σ. Evidence, with 3.8σ significance, for B(s)(0)→D¯(0)K(+)K(-) decays is also presented. The relative branching fraction is measured to be B(B(s)(0)→D¯(0)K(+)K(-))/B(B(0)→D¯(0)K(+)K(-))=0.90±0.27±0.20. These channels are of interest to study the mechanisms behind hadronic B decays, and open new possibilities for CP violation analyses with larger data sets.

Measurement of relative branching fractions of B decays to ψ(2S) and J/ψ mesons

The relative rates of B-meson decays into J/ψ and ψ(2S) mesons are measured for the three decay modes in pp collisions recorded with the LHCb detector. The ratios of branching fractions ([Formula: see text]) are measured to be [Formula: see text] where the third uncertainty is from the ratio of the ψ(2S) and J/ψ branching fractions to μ⁺μ^-.

Measurement of ψ(2S) meson production in pp collisions at [Formula: see text]

The differential cross-section for the inclusive production of ψ(2S) mesons in pp collisions at [Formula: see text] has been measured with the LHCb detector. The data sample corresponds to an integrated luminosity of 36 pb^-1. The ψ(2S) mesons are reconstructed in the decay channels ψ(2S)→μ⁺μ^- and ψ(2S)→J/ψπ⁺π^-, with the J/ψ meson decaying into two muons. Results are presented both for promptly produced ψ(2S) mesons and for those originating from b-hadron decays. In the kinematic range p_T(ψ(2S))≤16 GeV/c and 2<y(ψ(2S))≤4.5 we measure [Formula: see text] where the last uncertainty on the prompt cross-section is due to the unknown ψ(2S) polarization. Recent QCD calculations are found to be in good agreement with our measurements. Combining the present result with the LHCb J/ψ measurements we determine the inclusive branching fraction [Formula: see text] where the last uncertainty is due to the [Formula: see text], [Formula: see text] and [Formula: see text] branching fraction uncertainties.

First observation of the decay B(c)+ → J/ψπ(+) π- π+

The decay B(c)(+) → J/ψπ(+) π(-) π(+) is observed for the first time, using 0.8 fb(-1) of pp collisions at sqrt[s] = 7 TeV collected by the LHCb experiment. The ratio of branching fractions B(B(c)(+) → J/ψπ(+) π(-) π(+))/B(B(c)(+)→J/ψπ^{+}) is measured to be 2.41 ± 0.30 ± 0.33, where the first uncertainty is statistical and the second is systematic. The result is in agreement with theoretical predictions.

Determination of the sign of the decay width difference in the B(s)(0) system

The interference between the K+ K- S-wave and P-wave amplitudes in B(s)(0) → J/ψK+ K- decays with the K+ K- pairs in the region around the ϕ(1020) resonance is used to determine the variation of the difference of the strong phase between these amplitudes as a function of K+ K- invariant mass. Combined with the results from our CP asymmetry measurement in B(s)(0) → J/ψϕ decays, we conclude that the B(s)(0) mass eigenstate that is almost CP = +1 is lighter and decays faster than the mass eigenstate that is almost CP = -1. This determines the sign of the decay width difference ΔΓ(s) ≡ Γ(L) - Γ(H) to be positive. Our result also resolves the ambiguity in the past measurements of the CP violating phase ϕ(s) to be close to zero rather than π. These conclusions are in agreement with the standard model expectations.

Strong constraints on the rare decays B(s)(0) → μ+ μ- and B0 → μ+ μ-

A search for B(s)(0) → μ+ μ- and B0 → μ+ μ decays is performed using 1.0  fb(-1) of pp collision data collected at sqrt[s] = 7  TeV with the LHCb experiment at the Large Hadron Collider. For both decays, the number of observed events is consistent with expectation from background and standard model signal predictions. Upper limits on the branching fractions are determined to be B(B(s)(0) → μ+ μ-) < 4.5(3.8)×10(-9) and B(B0 → μ+ μ-) < 1.0(0.81)×10(-9) at 95% (90%) confidence level.

Opposite-side flavour tagging of B mesons at the LHCb experiment

The calibration and performance of the opposite-side flavour tagging algorithms used for the measurements of time-dependent asymmetries at the LHCb experiment are described. The algorithms have been developed using simulated events and optimized and calibrated with B⁺→J/ψK⁺, B⁰→J/ψK^∗0 and B⁰→D^∗-μ⁺ν_μ decay modes with 0.37 fb^-1 of data collected in pp collisions at [Formula: see text] during the 2011 physics run. The opposite-side tagging power is determined in the B⁺→J/ψK⁺ channel to be (2.10±0.08±0.24) %, where the first uncertainty is statistical and the second is systematic.

Measurement of production in collisions at [Formula: see text]

The production of ϒ(1S), ϒ(2S) and ϒ(3S) mesons in proton-proton collisions at the centre-of-mass energy of [Formula: see text] is studied with the LHCb detector. The analysis is based on a data sample of 25 pb-1 collected at the Large Hadron Collider. The ϒ mesons are reconstructed in the decay mode ϒ→μ+μ- and the signal yields are extracted from a fit to the μ+μ- invariant mass distributions. The differential production cross-sections times dimuon branching fractions are measured as a function of the ϒ transverse momentum pT and rapidity y, over the range pT <15 GeV/c and 2.0 Collapse

Key Words Collapse

MESH Headings Collapse

Grants Collapse

First evidence of direct CP violation in charmless two-body decays of Bs0 mesons

Using a data sample corresponding to an integrated luminosity of 0.35  fb-1 collected by LHCb in 2011, we report the first evidence of CP violation in the decays of Bs0} mesons to K±π∓ pairs, ACP(Bs0→Kπ)=0.27±0.08(stat)±0.02(syst), with a significance of 3.3σ. Furthermore, we report the most precise measurement of CP violation in the decays of B0 mesons to K±π∓ pairs, ACP(B0→Kπ)=-0.088±0.011(stat)±0.008(syst), with a significance exceeding 6σ.

Differential branching fraction and angular analysis of the decay B0 → K*0 μ+ μ-

The angular distributions and the partial branching fraction of the decay B0 → K*0 μ+ μ- are studied by using an integrated luminosity of 0.37  fb(-1) of data collected with the LHCb detector. The forward-backward asymmetry of the muons, A(FB), the fraction of longitudinal polarization, F(L), and the partial branching fraction dB/dq2 are determined as a function of the dimuon invariant mass. The measurements are in good agreement with the standard model predictions and are the most precise to date. In the dimuon invariant mass squared range 1.00-6.00  GeV2/c4, the results are A(FB)=-0.06(-0.14)(+0.13)±0.04, F(L)=0.55±0.10±0.03, and dB/dq2=(0.42±0.06±0.03)×10(-7)  c4/GeV2. In each case, the first error is statistical and the second systematic.

First observation of the decays B(0) → D(+)K(-)π(+)π(-) and B(-) → D(0)K(-)π(+)π(-)

First observations of the Cabibbo-suppressed decays B(0) → D(+)K(-)π(+)π(-) and B(-) → D(0)K(-)π(+)π(-) are reported using 35 pb(-1) of data collected with the LHCb detector. Their branching fractions are measured with respect to the corresponding Cabibbo-favored decays, from which we obtain B(B(0) → D(+)K(-)π(+)π(-))/B(B(0) → D(+)π(-)π(+)π(-))=(5.9±1.1±0.5)×10(-2) and B(B(-) → D(0)K(-)π(+)π(-))/B(B(-) → D(0)π(-)π(+)π(-))=(9.4±1.3±0.9)×10(-2), where the uncertainties are statistical and systematic, respectively. The B(-) → D(0)K(-)π(+)π(-) decay is particularly interesting, as it can be used in a similar way to B(-) → D(0)K(-) to measure the Cabibbo-Kobayashi-Maskawa phase γ.

Observation of B(s)(0) → J/ψf(2)'(1525) in J/ψK+ K- final states

The decay B(s)(0) → J/ψK+ K- is investigated using 0.16  fb(-1) of data collected with the LHCb detector using 7 TeV pp collisions. Although the J/ψϕ channel is well known, final states at higher K+ K- masses have not previously been studied. In the K+ K- mass spectrum we observe a significant signal in the f(2)'(1525) region as well as a nonresonant component. After subtracting the nonresonant component, we find B(B(s)(0) → J/ψf(2)'(1525))/B(B(s)(0) → J/ψϕ) = (26.4 ± 2.7 ± 2.4)%.

Evidence for CP violation in time-integrated D0→h(-)h(+) decay rates

A search for time-integrated CP violation in D(0)→h(-)h(+) (h=K, π) decays is presented using 0.62 fb(-1) of data collected by LHCb in 2011. The flavor of the charm meson is determined by the charge of the slow pion in the D(*+)→D(0)π(+) and D(*-)→D[over ¯](0)π(-) decay chains. The difference in CP asymmetry between D(0)→K(-)K(+) and D(0)→π(-)π(+), ΔA(CP)≡A(CP)(K(-)K(+))-A(CP)(π(-)π(+)), is measured to be [-0.82±0.21(stat)±0.11(syst)]%. This differs from the hypothesis of CP conservation by 3.5 standard deviations.

Search for lepton number violating decays B+ → π- μ+ μ+ and B+ → K- μ+ μ+

A search is performed for the lepton number violating decay B+ → h- μ+ μ+, where h- represents a K- or a π-, using an integrated luminosity of 36  pb(-1) of data collected with the LHCb detector. The decay is forbidden in the standard model but allowed in models with a Majorana neutrino. No signal is observed in either channel and limits of B(B+ → K- μ+ μ+) < 5.4×10(-8) and B(B+ → π- μ+ μ+) < 5.8×10(-8) are set at the 95% confidence level. These improve the previous best limits by factors of 40 and 30, respectively.

Measurement of the CP-violating phase ϕ(s) in the decay B(s)(0) → J/ψϕ

We present a measurement of the time-dependent CP-violating asymmetry in B(s)(0) → J/ψϕ decays, using data collected with the LHCb detector at the LHC. The decay time distribution of B(s)(0) → J/ψϕ is characterized by the decay widths Γ(H) and Γ(L) of the heavy and light mass eigenstates, respectively, of the B(s)(0) - B(s)(0) system and by a CP-violating phase ϕ(s). In a sample of about 8500 B(s)(0) → J/ψϕ events isolated from 0.37  fb(-1) of pp collisions at sqrt[s] = 7  TeV, we measure ϕ(s) = 0.15 ± 0.18(stat) ± 0.06(syst)  rad. We also find an average B(s)(0) decay width Γ(s) ≡ (Γ(L) + Γ(H))/2 = 0.657 ± 0.009(stat) ± 0.008(syst)  ps(-1) and a decay width difference ΔΓ(s) ≡ Γ(L) - Γ(H) = 0.123 ± 0.029(stat) ± 0.011(syst)  ps(-1). Our measurement is insensitive to the transformation (ϕ(s),ΔΓ(s)) ↦ (π - ϕ(s), -ΔΓ(s)).

[The labor test under epidural analgesia. Apropos of 87 cases]

Two series of trials of labour are compared: the first series without any particular analgesia and the second under epidural analgesia. The caesarian rate was significantly less in the second series because the trial of labour was able to be pursued for a longer period of time without any danger to the foetus. The authors consider that, provided cases of mechanical dystocia and maternal agitation are eliminated, trial of labour under epidural anaesthesia can result in a real cephalopelvic engagement.