(RB1)-negative retinal organoids display proliferation of cone photoreceptors and loss of retinal differentiation

Retinoblastoma is a tumor of the eye in children under the age of five caused by biallelic inactivation of the (RB1) tumor suppressor gene in maturing retinal cells. Cancer models are essential for understanding tumor development and in preclinical research. Because of the complex organization of the human retina, such models were challenging to develop for retinoblastoma. Here, we present an organoid model based on differentiation of human embryonic stem cells into neural retina after inactivation of (RB1) by CRISPR/Cas9 mutagenesis. Wildtype and (RB1) heterozygous mutant retinal organoids were indistinguishable with respect to morphology, temporal development of retinal cell types and global mRNA expression. However, loss of pRB resulted in spatially disorganized organoids and aberrant differentiation, indicated by disintegration of organoids beyond day 130 of differentiation and depletion of most retinal cell types. Only cone photoreceptors were abundant and continued to proliferate, supporting these as candidate cells-of-origin for retinoblastoma. Transcriptome analysis of (RB1) knockout organoids and primary retinoblastoma revealed gain of a retinoblastoma expression signature in the organoids, characterized by upregulation of (RBL1) (p107), (MDM2), (DEK), (SYK) and (HELLS). In addition, genes related to immune response and extracellular matrix were specifically upregulated in (RB1)-negative organoids. In vitro retinal organoids therefore display some features associated with retinoblastoma and, so far, represent the only valid human cancer model for the development of this disease

Unstable TTTTA/TTTCA expansions in MARCH6 are associated with Familial Adult Myoclonic Epilepsy type 3

Familial Adult Myoclonic Epilepsy (FAME) is a genetically heterogeneous disorder characterized by cortical tremor and seizures. Intronic TTTTA/TTTCA repeat expansions in SAMD12 (FAME1) are the main cause of FAME in Asia. Using genome sequencing and repeat-primed PCR, we identify another site of this repeat expansion, in MARCH6 (FAME3) in four European families. Analysis of single DNA molecules with nanopore sequencing and molecular combing show that expansions range from 3.3 to 14 kb on average. However, we observe considerable variability in expansion length and structure, supporting the existence of multiple expansion configurations in blood cells and fibroblasts of the same individual. Moreover, the largest expansions are associated with micro-rearrangements occurring near the expansion in 20% of cells. This study provides further evidence that FAME is caused by intronic TTTTA/TTTCA expansions in distinct genes and reveals that expansions exhibit an unexpectedly high somatic instability that can ultimately result in genomic rearrangements

Comprehensive characterization of RB1 mutant and MYCN amplified retinoblastoma cell lines

In retinoblastoma research tumor-derived cell lines remain an important model to investigate tumorigenesis and new therapy options, due to limited tumor material and lack of adequate animal models. A panel of 10 retinoblastoma cell lines was characterized with respect to mutation, methylation and expression of RB1 and MYCN. These established retinoblastoma cell lines represent the most frequent types of RB1 inactivation and together with the MYCN amplification status, three classes can be distinguished: RB1(mut)/MYCNnonA,RB1(mut)/MYCNA and RB1(wt)/MYCNA. MYCN amplification was identified in five cell lines, whereby two of them, RB522 and RB3823, harbor no aberration in RB1. Targeted sequencing of 160 genes often mutated in cancer identified only few variants in tumor-associated genes other than in RB1. None of these variants was recurrent. mRNA expression analyses of retinal markers, cell cycle regulators and members of the TP53 signaling pathway revealed a high variability between cell lines but no class-specific differences. The here presented thorough validation of retinoblastoma cell lines, including microsatellite analysis for cell line authentication, provides the basis for further in vitro studies on retinoblastoma

Temporal Downscaling of Soil Carbon Dioxide Efflux Measurements Based on Time-Stable Spatial Patterns

Soil CO2 efflux at a field site is often computed as the average of successive chamber measurements at several points to overcome the effects of spatial variability and microclimatic disturbances. As a consequence, the resulting data set has a coarser resolution in space (one average per site) and time than the raw data set. The deviations between raw measurements and the field average may provide additional insights, however, if they can be decomposed into a time-stable part, characterizing the spatial pattern of emission strengths, and a dynamic part, characterizing rapid changes in soil CO2 efflux. We evaluated data from several measurement campaigns in an agricultural landscape. First, we determined the persistence of spatial CO2 efflux patterns and found that >= 50% of spatial variance was stable for at least 1 d in all examined crop and field types. For fields where vegetation and gradients in soil properties determined the spatial variation in CO2 efflux, some correlation was still found after 10 d. In a next step, we removed the time-stable patterns from the raw time series. The resulting estimate of instantaneous area-average soil respiration closely resembled the conventional spatiotemporal field average on days without rapid changes in meteorologic conditions. On days with fluctuations of radiation and temperature, in contrast, soil respiration reacted on a time scale from instantaneous to about 1 h. Based on a discussion of potential mechanisms underlying these reactions for a wheat (Triticum aestivum L.) and a sugarbeet (Beta vulgaris L. ssp. vulgaris) stand, we suggest that the proposed downscaling methodology, in combination with existing decomposition techniques, may help to examine the short-term dependence of heterotrophic and root respiration on radiation, temperature, and rain

Unstable TTTTA/TTTCA expansions in MARCH6 are associated with Familial Adult Myoclonic Epilepsy type 3

Familial Adult Myoclonic Epilepsy (FAME) is a genetically heterogeneous disorder characterized by cortical tremor and seizures. Intronic TTTTA/TTTCA repeat expansions in SAMD12 (FAME1) are the main cause of FAME in Asia. Using genome sequencing and repeat-primed PCR, we identify another site of this repeat expansion, in MARCH6 (FAME3) in four European families. Analysis of single DNA molecules with nanopore sequencing and molecular combing show that expansions range from 3.3 to 14 kb on average. However, we observe considerable variability in expansion length and structure, supporting the existence of multiple expansion configurations in blood cells and fibroblasts of the same individual. Moreover, the largest expansions are associated with micro-rearrangements occurring near the expansion in 20% of cells. This study provides further evidence that FAME is caused by intronic TTTTA/TTTCA expansions in distinct genes and reveals that expansions exhibit an unexpectedly high somatic instability that can ultimately result in genomic rearrangements