Germline Elongator mutations in Sonic Hedgehog medulloblastoma.

Cancer genomics has revealed many genes and core molecular processes that contribute to human malignancies, but the genetic and molecular bases of many rare cancers remains unclear. Genetic predisposition accounts for 5 to 10% of cancer diagnoses in children1,2, and genetic events that cooperate with known somatic driver events are poorly understood. Pathogenic germline variants in established cancer predisposition genes have been recently identified in 5% of patients with the malignant brain tumour medulloblastoma3. Here, by analysing all protein-coding genes, we identify and replicate rare germline loss-of-function variants across ELP1 in 14% of paediatric patients with the medulloblastoma subgroup Sonic Hedgehog (MBSHH). ELP1 was the most common medulloblastoma predisposition gene and increased the prevalence of genetic predisposition to 40% among paediatric patients with MBSHH. Parent-offspring and pedigree analyses identified two families with a history of paediatric medulloblastoma. ELP1-associated medulloblastomas were restricted to the molecular SHHα subtype4 and characterized by universal biallelic inactivation of ELP1 owing to somatic loss of chromosome arm 9q. Most ELP1-associated medulloblastomas also exhibited somatic alterations in PTCH1, which suggests that germline ELP1 loss-of-function variants predispose individuals to tumour development in combination with constitutive activation of SHH signalling. ELP1 is the largest subunit of the evolutionarily conserved Elongator complex, which catalyses translational elongation through tRNA modifications at the wobble (U34) position5,6. Tumours from patients with ELP1-associated MBSHH were characterized by a destabilized Elongator complex, loss of Elongator-dependent tRNA modifications, codon-dependent translational reprogramming, and induction of the unfolded protein response, consistent with loss of protein homeostasis due to Elongator deficiency in model systems7-9. Thus, genetic predisposition to proteome instability may be a determinant in the pathogenesis of paediatric brain cancers. These results support investigation of the role of protein homeostasis in other cancer types and potential for therapeutic interference.

Deconstructing Sonic Hedgehog Medulloblastoma: Molecular Subtypes, Drivers, and Beyond.

Medulloblastoma (MB) is a highly malignant cerebellar tumor predominantly diagnosed during childhood. Driven by pathogenic activation of sonic hedgehog (SHH) signaling, SHH subgroup MB (SHH-MB) accounts for nearly one-third of diagnoses. Extensive molecular analyses have identified biologically and clinically relevant intertumoral heterogeneity among SHH-MB tumors, prompting the recognition of novel subtypes. Beyond germline and somatic mutations promoting constitutive SHH signaling, driver alterations affect a multitude of pathways and molecular processes, including TP53 signaling, chromatin modulation, and post-transcriptional gene regulation. Here, we review recent advances in the underpinnings of SHH-MB in the context of molecular subtypes, clarify novel somatic and germline drivers, highlight cellular origins and developmental hierarchies, and describe the composition of the tumor microenvironment and its putative role in tumorigenesis.

Crystal, Solution, and Computational Study of the Structure of Ortho-Lithium N,N-Diisopropyl-P,P-Diphenylphosphinothioic Amide.

The first crystal structure of an ortho-lithium phosphinothioic amide complexed with tetramethylethylenediamine 12 is reported. The complex consists of a spirane in which the spiro-lithium is N,N- and C,S-chelated by the diamine and organophosphorus ligands, respectively. The analogous ortho anion 14 obtained by Sn(IV)/Li transmetallation in THF has also been synthesized. Nuclear magnetic resonance study of both anions showed that they exist as monomers in solution and are involved in dynamic processes including the restricted rotation around the P-N bond. 14 is converted at room temperature by nucleophilic cyclization to the dearomatized anion 15, which evolves after a few hours to the benzophosphindole sulfide 16. Density functional theory calculations supported the aggregation state in solution and were used to explore the conformational space of anion 12, the mechanism of ortho-lithiation directed by P(X)-N (X=O, S) groups, and the mechanism of formation of 15.

Solvent- and functional-group-assisted tautomerism of 3-alkyl substituted 5-(2-pyridyl)-1,2,4-triazoles in DMSO-water.

The tautomerism of a series of 5-alkyl substituted 3-(2-pyridyl)-1,2,4-triazoles in DMSO-d6-containing water has been investigated by 1H, 13C and 15N NMR spectroscopy. The populations of the three possible regioisomers in the tautomeric equilibrium (A [3-alkyl-5-(2-pyridyl)-1H], B [5-alkyl-3-(2-pyridyl)-1H] and C [5-alkyl-3-(2-pyridyl)-4H]) were determined. Isomers A (17-40%) and B (54-79%) are the major components and their ratio is insensitive to the substitution pattern, except for the unsubstituted and the methoxymethyl substituted derivatives. The isomer C (3-5%) has been fully characterised for the first time by NMR spectroscopy. Activation energies of tautomerisation (14.74-16.78 kcal mol-1) were determined by EXSY experiments, which also supported the involvement of water in the tautomerisation. Substituent effects on the 15N chemical shifts are relatively small. The DFT study of the tautomerism in DMSO-water showed that both A/B and B/C interconversions are assisted by the pyridine substituent and catalysed by solvent molecules. The NH-A/NH-B tautomerisation takes place via a relayed quadruple proton transfer mediated by three water molecules in the hydrogen-bonded cyclic substructure of a triazole·4H2O complex. The equilibrium B ⇄ C involves three steps: NH-B transfer to the pyridyl nitrogen mediated by a water molecule in a 1 : 1 cyclic complex, rotamerisation to bring the pyridinium NH close to N4 of the triazole catalysed by complexation to a DMSO molecule and transfer of the NH from the pyridinium donor to the N4 acceptor via a 1 : 1 complex with a bridging water molecule. This mechanism of 1,3-prototropic shift in triazoles is unprecedented in the literature.

Spiro[1,2]oxaphosphetanes of Nonstabilized and Semistabilized Phosphorus Ylide Derivatives: Synthesis and Kinetic and Computational Study of Their Thermolysis.

A series of tri- and tetrasubstituted spiro-oxaphosphetanes stabilized by ortho-benzamide (oBA) and N-methyl ortho-benzamide (MoBA) ligands have been synthesized by the reaction of Cα,Cortho-dilithiated phosphazenes with aldehydes and ketones. They include enantiopure products and the first example of an isolated oxaphosphetane having a phenyl substituent at C3 of the ring. Kinetic studies of their thermal decomposition showed that the process takes place irreversibly through a polar transition state (ρ = -0.22) under the influence of electronic, [1,2], [1,3] steric, and solvent effects, with C3/P-[1,2] interactions as the largest contribution to ΔG⧧ of olefination. Inversion of the phosphorus configuration through stereomutation has been observed in a number of cases. DFT calculations showed that oBA derivatives olefinated through the isolated (N, O)(Ph, C6H4, C) oxaphosphetanes (Channel A), whereas MoBA compounds decomposed faster via the isomer (C6H4, O)(C, N, Ph) formed by P-stereomutation involving a MB2 permutational mechanism (Channel B). The energy barrier of P-isomerization is lower than that of olefination. Fragmentation takes place in a concerted asynchronous reaction. The thermal stability of oxaphosphetanes is determined by strong C3/P-[1,2] interactions destabilizing the transition state of olefination. The effect of charge distribution and C3/C4-[1,2] and C4/P-[1,3] steric and solvent interactions on ΔG⧧ was also evaluated.

Diversity and functional convergence of small noncoding RNAs in male germ cell differentiation and fertilization.

The small noncoding RNAs (sncRNAs) are considered as post-transcriptional key regulators of male germ cell development. In addition to microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), other sncRNAs generated from small nucleolar RNAs (snoRNAs), tRNAs, or rRNAs processing may also play important regulatory roles in spermatogenesis. By next-generation sequencing (NGS), we characterized the sncRNA populations detected at three milestone stages in male germ differentiation: primordial germ cells (PGCs), pubertal spermatogonia cells, and mature spermatozoa. To assess their potential transmission through the spermatozoa during fertilization, the sncRNAs of mouse oocytes and zygotes were also analyzed. Both, microRNAs and snoRNA-derived small RNAs are abundantly expressed in PGCs but transiently replaced by piRNAs in spermatozoa and endo-siRNAs in oocytes and zygotes. Exhaustive analysis of miRNA sequence variants also shows an increment of noncanonical microRNA forms along male germ cell differentiation. RNAs-derived from tRNAs and rRNAs interacting with PIWI proteins are not generated by the ping-pong pathway and could be a source of primary piRNAs. Moreover, our results strongly suggest that the small RNAs-derived from tRNAs and rRNAs are interacting with PIWI proteins, and specifically with MILI. Finally, computational analysis revealed their potential involvement in post-transcriptional regulation of mRNA transcripts suggesting functional convergence among different small RNA classes in germ cells and zygotes.

Diastereoselective Ortho Lithiation of Phosphinimidic Amides: A Multinuclear Magnetic Resonance and Computational Study.

The structure of the dianion (SP,RC)-10 formed in the diastereoselective N,Cortho dilithiation of the phosphinimidic amide (RC)-Ph2P(═NCO2Me)NHCH(Me)Ph (5; dr of 95:5) with tert-butyllithium in THF has been elucidated using multinuclear magnetic resonance methods, including 2D 7Li,nX-HMQC (nX = 15N, 31P) correlations. (SP,RC)-10 consists of a monomer in which C,N and N,O chelation of the lithium cations generates a system containing a five- and a six-membered metallacycle, respectively, sharing a P-N bond with the lithium atoms connected through the NCO moiety of the phosphazenyl group. Selective deprotonation of the pro-S P-phenyl ring of 5 was ascertained through NOE measurements. DFT computations at the M06-2X(SMD,THF)/6-311+G(d,p)//M06-2X/6-31G(d) level showed that the stereoselective ortho deprotonation process fulfills the features of the CIPE model. The P═N linkage of the N-lithiated species (RC)-8 acts as a directing metalation group via N···LitBu coordination. The mixed complex that is formed evolves to a more stabilized species due to the intramolecular coordination of the OMe group to the lithium cation of the base. Abstraction of the ortho proton proceeds with energy barriers of 12.4 and 13.3 kcal/mol for the pro-R and pro-S phenyl rings. The preference for the latter is explained in terms of the Curtin-Hammett principle.

Global characterization and target identification of piRNAs and endo-siRNAs in mouse gametes and zygotes.

A set of small RNAs known as rasRNAs (repeat-associated small RNAs) have been related to the down-regulation of Transposable Elements (TEs) to safeguard genome integrity. Two key members of the rasRNAs group are piRNAs and endo-siRNAs. We have performed a comparative analysis of piRNAs and endo-siRNAs present in mouse oocytes, spermatozoa and zygotes, identified by deep sequencing and bioinformatic analysis. The detection of piRNAs and endo-siRNAs in the spermatozoa and revealed also in zygotes, hints to their potential delivery to oocytes during fertilization. However, a comparative assessment of the three cell types indicates that both piRNAs and endo-siRNAs are mainly maternally inherited. Finally, we have assessed the role of the different rasRNA molecules in connection with amplification processes by way of the "ping-pong cycle". Our results suggest that the ping-pong cycle can act on other rasRNAs, such as tRNA- and rRNA-derived fragments, thus not only being restricted to TEs during gametogenesis.

Reprogramming of microRNAs by adenosine-to-inosine editing and the selective elimination of edited microRNA precursors in mouse oocytes and preimplantation embryos.

Adenosine deaminases-acting-on-RNA (ADAR) proteins induce adenosine-to-inosine editing in double-stranded RNA molecules. This editing generates RNA diversity at the post-transcriptional level, and it has been implicated in the control of cell differentiation and development. The editing of microRNA (miRNA) precursors, along with Tudor-SN (Snd1) activity, could lead to the elimination of selected miRNAs and reprogram miRNA activity. Here, we report the dynamics of adenosine-to-inosine editing in miRNA precursors and their selected elimination during mouse preimplantation development. Adar1p110 and Snd1 were found to be strongly but differentially expressed in oocytes and zygotes with respect to later pre-implantation stages. When the biogenesis of miR-151 was assessed, the majority of miR-151 precursors was edited and subsequently eliminated during early development. Deep sequencing of this and other miRNAs confirmed that, in general, edited precursors were selectively eliminated at early post-zygotic stages. Moreover, in oocytes and throughout the zygote-to-blastocyst stages, Tudor-SN accumulated in newly discovered aggregates termed 'T bodies'. These results provide new insight into how editing and Tudor-SN-mediated elimination of miRNA precursors is regulated during early development.

Expression dynamics of microRNA biogenesis during preimplantation mouse development.

The role of microRNAs (miRNAs) in early development, and particularly in the post-transcriptional regulation of maternal mRNAs remains controversial. Hence, we have assessed how miRNA processing is regulated during preimplantation mouse development, from the fully-grown oocyte to the blastocyst, quantifying the expression of genes whose proteins are involved in miRNAs biogenesis and function. The expression of the Drosha, Dgcr8, Exportin 5, Dicer, Ago1, Ago2, Ago3, Ago4 and Ago5 genes was downregulated from the zygotic cleavage stage, except for the increase of Ago1, Ago3 and Ago4 expression in the 2-cell embryo, and of Ago2 in 4- and 8-cell embryos. These findings suggest that the capacity to process miRNAs, by the considered canonical pathway, diminishes after fertilization, primarily reducing miRNA activity in the later stages of preimplantation development. However, by analyzing the different precursor and mature forms of specific miRNAs that are abundantly expressed in the blastocyst, such as miR-292-3p and miR-292-5p, we identified miRNA-duplexes and/or miRNAs bound to target mRNAs that may serve as potential stockpiles of miRNAs. In response to the demand, such stockpile could directly provide functional and mature miRNAs.

Cell-type-specific regulation of genes involved in testicular lipid metabolism: fatty acid-binding proteins, diacylglycerol acyltransferases, and perilipin 2.

Male germ cell differentiation entails the synthesis and remodeling of membrane polar lipids and the formation of triacylglycerols (TAGs). This requires fatty acid-binding proteins (FABPs) for intracellular fatty acid traffic, a diacylglycerol acyltransferase (DGAT) to catalyze the final step of TAG biosynthesis, and a TAG storage mode. We examined the expression of genes encoding five members of the FABP family and two DGAT proteins, as well as the lipid droplet protein perilipin 2 (PLIN2), during mouse testis development and in specific cells from seminiferous epithelium. Fabp5 expression was distinctive of Sertoli cells and consequently was higher in prepubertal than in adult testis. The expression of Fabp3 increased in testis during postnatal development, associated with the functional differentiation of interstitial cells, but was low in germ cells. Fabp9, together with Fabp12, was prominently expressed in the latter. Their transcripts increased from spermatocytes to spermatids and, interestingly, were highest in spermatid-derived residual bodies (RB). Both Sertoli and germ cells, which produce neutral lipids and store them in lipid droplets, expressed Plin2. Yet, while Dgat1 was detected in Sertoli cells, Dgat2 accumulated in germ cells with a similar pattern of expression as Fabp9. These results correlated with polyunsaturated fatty acid-rich TAG levels also increasing with mouse germ cell differentiation highest in RB, connecting DGAT2 with the biosynthesis of such TAGs. The age- and germ cell type-associated increases in Fabp9, Dgat2, and Plin2 levels are thus functionally related in the last stages of germ cell differentiation.

Exploring through the use of physiological and isotopic techniques the potential of a PGPR-based biofertilizer to improve nitrogen fertilization practices efficiency in strawberry cultivation.

The use of microorganisms as a biofertilizer in strawberry has focused mainly on pathogen biocontrol, which has led to the underestimation of the potential of microorganisms for the improvement of nutritional efficiency in this crop. A study was established to investigate the impact of a plant growth-promoting rhizobacteria (PGPR) based biofertilizer integrated by self-compatible stress tolerant strains with multiple PGP properties, including atmospheric nitrogen fixation, on strawberry (Fragaria × ananassa cv. Rociera) tolerance to N deficiency in terms of growth and physiological performance. After 40 days of nitrogen fertilization shortage, inoculated plants were able to maintain root development and fertility structures (i.e. fruits and flowers) at a level similar to plants properly fertilized. In addition, inoculation lessened the negative impact of nitrogen deficiency on leaves' dry weight and relative water content. This effect was mediated by a higher root/shoot ratio, which would have allowed them to explore larger volumes of soil for the acquisition of water. Moreover, inoculation was able to buffer up to 50% of the reduction in carbon assimilation capacity, due to its positive effect on the diffusion efficiency of CO2 and the biochemical capacity of photosynthesis, as well as on the activity of photosystem II light harvesting. Furthermore, the higher leaf C/N ratio and the maintained δ15N values close to control plants were related to positive bacterial effects at the level of the plant nutritional balance. Despite these positive effects, the application of the bacterial inoculum was unable to completely counteract the restriction of fertilization, being necessary to apply a certain amount of synthetic fertilizer for the strawberry nutrition. However, according to our results, the complementary effect of this PGPR-based biofertilizer could provide a higher efficiency in environmental and economic yields on this crop.

Mechanisms of stereomutation and thermolysis of spiro-1,2-oxaphosphetanes: new insights into the second step of the Wittig reaction.

The experimentally observed stereomutation of spiro-1,2-oxaphosphetanes is shown by DFT calculations to proceed through successive M(B2) or M(B4) and M(B3) mechanisms involving two, four, and three Berry pseudorotations at phosphorus, respectively. Oxaphosphetane decomposition takes place in a single step via a polar transition state. The calculated activation parameters for this reaction are in good agreement with those determined experimentally.

Transformations of diphenylphosphinothioic acid tertiary amides mediated by directed ortho metallation.

ortho-Lithiation of N,N-diisopropyl-P,P-diphenylphosphinothioic amide using n-BuLi in the presence of TMEDA in diethyl ether followed by electrophilic trapping is described as an efficient method for the synthesis of ortho-functionalised derivatives in high yields. The structural modification of the phosphinothioic amide includes C-X (X = P, S, Si, Sn, I) and C-C bond forming reactions with a large variety of electrophiles. Additional applications based on functional group transformations are also reported. They include imine formation, desulfurization and Suzuki cross-coupling reactions on selected compounds.

Chelation-Assisted Interrupted Copper(I)-Catalyzed Azide-Alkyne-Azide Domino Reactions: Synthesis of Fully Substituted 5-Triazenyl-1,2,3-triazoles.

We describe the synthesis of 1,4-(disubstituted)-5-triazenyl-1,2,3-triazoles through a ligand-free domino copper(I)-catalyzed azide-alkyne-azide process of chelating aryl azides bearing N-P═O, P═O, and SO3H groups at the ortho position with a wide variety of acetylenes. DFT calculations reveal that Cu-chelation is a crucial factor in the interception of the CuAAC intermediate by the azide. The crystal structure of the catalytic species has been determined by X-ray diffraction.

Synthesis and characterization of a coupled binuclear Cu(I)/Cu(III) complex.

The synthesis through reaction of a C(alpha),C(ortho) dilithiated phosphazene with CuBr and structural characterization of the first example of a binuclear mixed valence [Cu(I)(N(2))/Cu(III)(C(4))] complex showing a metal-metal bond, as well as its applications in cyclopropanation and oxidation reactions, are described.

Large 1p36 Deletions Affecting Arid1a Locus Facilitate Mycn-Driven Oncogenesis in Neuroblastoma.

Loss of heterozygosity (LOH) at 1p36 occurs in multiple cancers, including neuroblastoma (NBL). MYCN amplification and 1p36 deletions tightly correlate with markers of tumor aggressiveness in NBL. Although distal 1p36 losses associate with single-copy MYCN tumors, larger deletions correlate with MYCN amplification, indicating two tumor suppressor regions in 1p36, only one of which facilitates MYCN oncogenesis. To better define this region, we genome-edited the syntenic 1p36 locus in primary mouse neural crest cells (NCCs), a putative NBL cell of origin. In in vitro cell transformation assays, we show that Chd5 loss confers most of the MYCN-independent tumor suppressor effects of 1p36 LOH. In contrast, MYCN-driven tumorigenesis selects for NCCs with Arid1a deletions from a pool of NCCs with randomly sized 1p36 deletions, establishing Arid1a as the MYCN-associated tumor suppressor. Our findings reveal that Arid1a loss collaborates with oncogenic MYCN and better define the tumor suppressor functions of 1p36 LOH in NBL.

Activation of Estrogen Receptor Alpha by Decitabine Inhibits Osteosarcoma Growth and Metastasis.

Osteosarcoma is a malignant tumor in the bone, which originates from normal osteoblasts or osteoblast precursors. Normal osteoblasts express estrogen receptor alpha (ERα); however, osteosarcomas do not express ERα due to promoter DNA methylation. Here we show that treatment of 143B osteosarcoma cells with decitabine (DAC, 5-Aza-2'-deoxycytidine) induces expression of ERα and leads to decreased proliferation and concurrent induction of osteoblast differentiation. DAC exposure reduced protein expression of metastasis-associated markers VIMENTIN, SLUG, ZEB1, and MMP9, with a concurrent decrease in mRNA expression of known stem cell markers SOX2, OCT4, and NANOG. Treatment with 17ß-estradiol (E2) synergized with DAC to reduce proliferation. Overexpression of ERα inhibited proliferation and induced osteoblast differentiation, whereas knockout of ERα by CRISPR/Cas9 prevented the effects of DAC. In an orthotopic model of osteosarcoma, DAC inhibited tumor growth and metastasis of 143B cells injected into the tibia of NOD SCID gamma mice. Furthermore, ERα overexpression reduced tumor growth and metastasis, and ERα knockout prevented the effects of DAC in vivo. Together, these experiments provide preclinical evidence that the FDA-approved DNA methylation inhibitor DAC may be repurposed to treat patients with osteosarcoma based on its efficacy to decrease proliferation, to induce osteoblast differentiation, and to reduce metastasis to visceral organs.Significance: These findings describe the effects of DNA methyltransferase inhibition on ERα and its potential role as a tumor suppressor in osteosarcoma.See related commentary by Roberts, p. 1034 See related article by El Ayachi and colleagues; Cancer Res 79(5);982-93.

Detection and Characterization of Small Noncoding RNAs in Mouse Gametes and Embryos Prior to Zygotic Genome Activation.

Small noncoding RNAs (ncRNAs) are regulatory elements of gene expression in all cell types and tissues. An ever-increasing number of studies have implicated ncRNAs in differentiation and developmental processes. In mammals, as a consequence of fertilization, the content of ncRNAs in the zygote is mostly the result of the maternal material included on oocytes and the potential sperm-borne paternal contributions. The genetic identity program of any individual is the reprogramming of each parental contribution to the zygotic genome activation. In mouse, this activation occurs at 2-cell stage. In this program of early development the small ncRNAs can play important roles. Here, we describe protocols for collection of oocytes, spermatozoa, and zygotes in mouse, followed by RNA purification to analyze the different types of small ncRNA by next-generation sequencing approaches (NGS). Bioinformatics protocols also describe the methodology able to characterize microRNAs (miRNAs) as the most well-known and widespread regulatory small ncRNA. The comparative analysis allows identifying the changes and background previous to zygotic genome activation.

Synthesis of P-stereogenic diarylphosphinic amides by directed lithiation: transformation into tertiary phosphine oxides via methanolysis, aryne chemistry and complexation behaviour toward zinc(ii).

The highly diastereoselective synthesis of P-stereogenic phosphinic amides via directed ortho lithiation (DoLi) of (SC)-P,P-diphenylphosphinic amides with t-BuLi followed by electrophilic quench reactions is described. Functionalised derivatives containing a wide variety of ortho substituents (Cl, Br, I, OH, N3, SiMe3, SnMe3, P(O)Ph2, Me, allyl, (t)BuOCO) have been prepared in high yields with diastereomeric ratios up to 98 : 2. The X-ray diffraction structure of the ortho-stannylated and ortho-iodo compounds showed that the pro-S P-phenyl ring was stereoselectively ortho-deprotonated by the organolithium base. The usefulness of the method is supported by two key transformations, the synthesis of P-stereogenic methyl phosphinates through replacement of the chiral auxiliary by a methoxy group and the first example of the insertion of benzyne into the P-N bond of a P-stereogenic phosphinic amide. A DFT study of this reaction showed that the insertion proceeds through a [2 + 2] cycloaddition and a subsequent ring-opening with retention of the P-configuration. Explorative coordination chemistry of the new P-stereogenic ligands provided access to a chiral phosphinic amide-phosphine oxide Zn(ii) complex, the crystal structure of which is reported.