Developmental basis of SHH medulloblastoma heterogeneity

Many genes that drive normal cellular development also contribute to oncogenesis. Medulloblastoma (MB) tumors likely arise from neuronal progenitors in the cerebellum, and we hypothesized that the heterogeneity observed in MBs with sonic hedgehog (SHH) activation could be due to differences in developmental pathways. To investigate this question, here we perform single-nucleus RNA sequencing on highly differentiated SHH MBs with extensively nodular histology and observed malignant cells resembling each stage of canonical granule neuron development. Through innovative computational approaches, we connect these results to published datasets and find that some established molecular subtypes of SHH MB appear arrested at different developmental stages. Additionally, using multiplexed proteomic imaging and MALDI imaging mass spectrometry, we identify distinct histological and metabolic profiles for highly differentiated tumors. Our approaches are applicable to understanding the interplay between heterogeneity and differentiation in other cancers and can provide important insights for the design of targeted therapies.

Failure of human rhombic lip differentiation underlies medulloblastoma formation

Medulloblastoma (MB) comprises a group of heterogeneous paediatric embryonal neoplasms of the hindbrain with strong links to early development of the hindbrain^1-4. Mutations that activate Sonic hedgehog signalling lead to Sonic hedgehog MB in the upper rhombic lip (RL) granule cell lineage^5-8. By contrast, mutations that activate WNT signalling lead to WNT MB in the lower RL^9,10. However, little is known about the more commonly occurring group 4 (G4) MB, which is thought to arise in the unipolar brush cell lineage^3,4. Here we demonstrate that somatic mutations that cause G4 MB converge on the core binding factor alpha (CBFA) complex and mutually exclusive alterations that affect CBFA2T2, CBFA2T3, PRDM6, UTX and OTX2. CBFA2T2 is expressed early in the progenitor cells of the cerebellar RL subventricular zone in Homo sapiens, and G4 MB transcriptionally resembles these progenitors but are stalled in developmental time. Knockdown of OTX2 in model systems relieves this differentiation blockade, which allows MB cells to spontaneously proceed along normal developmental differentiation trajectories. The specific nature of the split human RL, which is destined to generate most of the neurons in the human brain, and its high level of susceptible EOMES⁺KI67⁺ unipolar brush cell progenitor cells probably predisposes our species to the development of G4 MB.

Metabolic Regulation of the Epigenome Drives Lethal Infantile Ependymoma

Posterior fossa A (PFA) ependymomas are lethal malignancies of the hindbrain in infants and toddlers. Lacking highly recurrent somatic mutations, PFA ependymomas are proposed to be epigenetically driven tumors for which model systems are lacking. Here we demonstrate that PFA ependymomas are maintained under hypoxia, associated with restricted availability of specific metabolites to diminish histone methylation, and increase histone demethylation and acetylation at histone 3 lysine 27 (H3K27). PFA ependymomas initiate from a cell lineage in the first trimester of human development that resides in restricted oxygen. Unlike other ependymomas, transient exposure of PFA cells to ambient oxygen induces irreversible cellular toxicity. PFA tumors exhibit a low basal level of H3K27me3, and, paradoxically, inhibition of H3K27 methylation specifically disrupts PFA tumor growth. Targeting metabolism and/or the epigenome presents a unique opportunity for rational therapy for infants with PFA ependymoma.

Isospin Mixing Reveals ^{30}P(p,γ)^{31}S Resonance Influencing Nova Nucleosynthesis

The thermonuclear ^{30}P(p,γ)^{31}S reaction rate is critical for modeling the final elemental and isotopic abundances of ONe nova nucleosynthesis, which affect the calibration of proposed nova thermometers and the identification of presolar nova grains, respectively. Unfortunately, the rate of this reaction is essentially unconstrained experimentally, because the strengths of key ^{31}S proton capture resonance states are not known, largely due to uncertainties in their spins and parities. Using the β decay of ^{31}Cl, we have observed the β-delayed γ decay of a ^{31}S state at E_{x}=6390.2(7)  keV, with a ^{30}P(p,γ)^{31}S resonance energy of E_{r}=259.3(8)  keV, in the middle of the ^{30}P(p,γ)^{31}S Gamow window for peak nova temperatures. This state exhibits isospin mixing with the nearby isobaric analog state at E_{x}=6279.0(6)  keV, giving it an unambiguous spin and parity of 3/2^{+} and making it an important l=0 resonance for proton capture on ^{30}P.

Spin-imbalanced quasi-two-dimensional Fermi gases

We measure the density profiles for a Fermi gas of (6)Li containing N(1) spin-up atoms and N(2) spin-down atoms, confined in a quasi-two-dimensional geometry. The spatial profiles are measured as a function of spin imbalance N(2)/N(1) and interaction strength, which is controlled by means of a collisional (Feshbach) resonance. The measured cloud radii and central densities are in disagreement with mean-field Bardeen-Cooper-Schrieffer theory for a true two-dimensional system. We find that the data for normal-fluid mixtures are reasonably well fit by a simple two-dimensional polaron model of the free energy. Not predicted by the model is a phase transition to a spin-balanced central core, which is observed above a critical value of N(2)/N(1). Our observations provide important benchmarks for predictions of the phase structure of quasi-two-dimensional Fermi gases.

Population structure, mitochondrial polyphyly and the repeated loss of human biting ability in anopheline mosquitoes from the southwest Pacific

Australia and New Guinea contain high levels of endemism and biodiversity, yet there have been few evaluations of population-level genetic diversity in fauna occurring throughout the Australo-Papuan region. Using extensive geographical sampling, we examined and compared the phylogenetic relationships, phylogeography and population structure of Anopheles farauti, An. hinesorum and An. irenicus throughout their ranges in the southwest Pacific using mitochondrial (mtDNA COI) and nuclear (ribosomal protein S9 and ribosomal DNA ITS2) loci. Phylogenetic analyses suggest that the ability to utilize humans as hosts has been lost repeatedly, coincident with independent colonizations of the Solomon Islands. As some of the species under investigation transmit malaria in the region, this is a medically important finding. Maximum likelihood and Bayesian phylogenetic analyses of nuclear loci also showed that the three species are monophyletic. However, putative introgression of An. hinesorum mtDNA onto a nuclear background of An. farauti was evident in populations from Queensland, Torres Strait and southern New Guinea. Haplotype networks and pairwise F(ST) values show that there is significant genetic structure within New Guinea and Australia in both An. farauti and An. hinesorum, consistent with a long-term history of low gene flow among populations.

Polaron-to-polaron transitions in the radio-frequency spectrum of a quasi-two-dimensional Fermi gas

We measure radio-frequency spectra for a two-component mixture of a 6Li atomic Fermi gas in a quasi-two-dimensional regime with the Fermi energy comparable to the energy level spacing in the tightly confining potential. Near the Feshbach resonance, we find that the observed resonances do not correspond to transitions between confinement-induced dimers. The spectral shifts can be fit by assuming transitions between noninteracting polaron states in two dimensions.

Properties of cartilage engineered from elderly human chondrocytes for articular surface repair

Numerous studies on engineering cartilage utilizing chondrocytes from juvenile animal sources have been reported. However, there are many unknown aspects of engineering cartilage using human chondrocytes-especially from middle-aged or elderly adults-which are critical for clinical application of tissue engineering in the field of orthopedic surgery. The primary aim of this study was to engineer neocartilage tissue from 50-60-year-old human chondrocytes in comparison to engineered cartilage made from juvenile swine chondrocytes (JSCs). Articular chondrocytes from middle-aged, nonarthritic humans and juvenile swine were isolated and placed in culture for expansion. The chondrocytes (passage 1) were mixed in fibrin gel at 40-60×10(6) cells/mL until polymerization. Cells/nodule constructs and devitalized cartilage-cells/hydrogel-devitalized cartilage constructs (three-layered model) were implanted into subcutaneous pockets of nude mice for 12, 18, and 24 weeks. The specimens were evaluated histologically, biochemically, and biomechanically. This allowed for direct comparison of the cartilage engineered from human versus swine cells. Histological analysis demonstrated that samples engineered utilizing chondrocytes from middle-aged adults accumulated basophilic, sulfated glycosaminoglycans (sGAG), and abundant type II collagen around the cells in a manner similar to that seen in samples engineered using JSCs at all time points. Biochemical analysis revealed that samples made with human cells had about 40%-60% of the amount hydroxyproline of native human cartilage, a trend parallel to that observed in the specimens made with swine chondrocytes. The amount of sGAG in the human chondrocyte specimens was about one-and-a-half times the amount in native human cartilage, whereas the amount in the samples made with swine chondrocytes was always less than native cartilage. The biomechanical analysis revealed that the stiffness and tensile of samples made with human cells were in a pattern similar to that seen with swine chondrocytes. This study demonstrates that chondrogenesis using articular chondrocytes from middle-aged adults can be achieved in a predictable and reliable manner similar to that shown in studies using cells from juvenile animals and can form the basis of engineering cartilage with degradable scaffolds in this patient population.

Phase transfer of hydrophilic, cyclodextrin-modified gold nanoparticles to chloroform solutions

The preparation and characterization of gold nanoparticles (approximately 3 nm in diameter) capped with thiolated alpha- and beta-cyclodextrins (alpha and beta-CD) is described. The CD-capped nanoparticles are hydrophilic and bind ferrocene derivatives as evidenced by electrochemical and (1)H NMR spectroscopic measurements. The binding interactions of the CD-capped nanoparticles with a series of five alkyldimethyl(ferrocenylmethyl)ammonium ions (the alkyl group is propyl for compound 1, heptyl for 2, dodecyl for 3, hexadecyl for 4, and docosyl for 5) can be utilized for the phase transfer of the hydrophilic, CD-capped nanoparticles into a nonpolar chloroform phase. Only 3, 4, and 5 act as effective phase transfer agents, since 1 and 2 do not have enough amphiphilic character. The structure of the aggregates formed upon transfer of the CD-capped nanoparticles to the chloroform solution is postulated to resemble that of reverse micelles, as the nanoparticles template the peripheral arrangement of the cationic ferrocene amphiphiles, counterions and water molecules around their surfaces.

Production of human type I collagen in yeast reveals unexpected new insights into the molecular assembly of collagen trimers

Substantial evidence supports the role of the procollagen C-propeptide in the initial association of procollagen polypeptides and for triple helix formation. To evaluate the role of the propeptide domains on triple helix formation, human recombinant type I procollagen, pN-collagen (procollagen without the C-propeptides), pC-collagen (procollagen without the N-propeptides), and collagen (minus both propeptide domains) heterotrimers were expressed in Saccharomyces cerevisiae. Deletion of the N- or C-propeptide, or both propeptide domains, from both proalpha-chains resulted in correctly aligned triple helical type I collagen. Protease digestion assays demonstrated folding of the triple helix in the absence of the N- and C-propeptides from both proalpha-chains. This result suggests that sequences required for folding of the triple helix are located in the helical/telopeptide domains of the collagen molecule. Using a strain that does not contain prolyl hydroxylase, the same folding mechanism was shown to be operative in the absence of prolyl hydroxylase. Normal collagen fibrils were generated showing the characteristic banding pattern using this recombinant collagen. This system offers new opportunities for the study of collagen expression and maturation.

Cytonic acids A and B: novel tridepside inhibitors of hCMV protease from the endophytic fungus Cytonaema species

Two novel human cytomegalovirus protease inhibitors, cytonic acids A (1) and B (2), have been isolated from the solid-state fermentation of the endophytic fungi Cytonaema sp. Their structures as p-tridepside isomers were elucidated by MS and NMR methods.