Multimodal spatiotemporal phenotyping of human retinal organoid development

Organoids generated from human pluripotent stem cells provide experimental systems to study development and disease, but quantitative measurements across different spatial scales and molecular modalities are lacking. In this study, we generated multiplexed protein maps over a retinal organoid time course and primary adult human retinal tissue. We developed a toolkit to visualize progenitor and neuron location, the spatial arrangements of extracellular and subcellular components and global patterning in each organoid and primary tissue. In addition, we generated a single-cell transcriptome and chromatin accessibility timecourse dataset and inferred a gene regulatory network underlying organoid development. We integrated genomic data with spatially segmented nuclei into a multimodal atlas to explore organoid patterning and retinal ganglion cell (RGC) spatial neighborhoods, highlighting pathways involved in RGC cell death and showing that mosaic genetic perturbations in retinal organoids provide insight into cell fate regulation.

Heterozygous carriage of a dysfunctional Toll-like receptor 9 allele affects CpG oligonucleotide responses in B cells

Toll-like receptors (TLR) are employed by the innate immune system to detect microbial pathogens based on conserved microbial pathogen molecules. For example, TLR9 is a receptor for CpG-containing microbial DNA, and its activation results in the production of cytokines and type I interferons from human B cells and plasmacytoid dendritic cells, respectively. Both are required for mounting an efficient antibacterial or antiviral immune response. These effects are mimicked by synthetic CpG oligodeoxynucleotides (ODN). Although several hyporesponsive TLR9 variants have been reported, their functional relevance in human primary cells has not been addressed. Here we report a novel TLR9 allele, R892W, which is hyporesponsive to CpG ODN and acts as a dominant-negative in a cellular model system. The R892W variant is characterized by increased MyD88 binding and defective co-localization with CpG ODN. Whereas primary plasmacytoid dendritic cells isolated from a heterozygous R892W carrier responded normally to CpG by interferon-α production, carrier B cells showed impaired IL-6 and IL-10 production. This suggests that heterozygous carriage of a hyporesponsive TLR9 allele is not associated with complete loss of TLR9 function but that TLR9 signals elicited in different cell types are regulated differently in human primary cells.

Down syndrome: parental origin, recombination, and maternal age

The aims of the present study were to assess (1) the parental origin of trisomy 21 and the stage in which nondisjunction occurs and (2) the relationship between altered genetic recombination and maternal age as risk factors for trisomy 21. The study included 102 cases with Down syndrome from the Croatian population. Genotyping analyses were performed by polymerase chain reaction using 11 short tandem repeat markers along chromosome 21q. The vast majority of trisomy 21 was of maternal origin (93%), followed by paternal (5%) and mitotic origin (2%). The frequencies of maternal meiotic I (MI) and meiotic II errors were 86% and 14%, respectively. The highest proportion of cases with zero recombination was observed among those with maternal MI derived trisomy 21. A higher proportion of telomeric exchanges were presented in cases with maternal MI errors and cases with young mothers, although these findings were not statistically significant. The present study is the first report examining parental origin and altered genetic recombination as a risk factor for trisomy 21 in a Croatian population. The results support that trisomy 21 has a universal genetic etiology across different human populations.

The relationship between interferon-γ gene polymorphism and acute kidney allograft rejection

Cytokine gene polymorphisms have been associated with modified gene expression and cytokine production. Gamma interferon (IFN-γ) plays an important role in the pathogenesis of kidney transplant rejection. This study evaluated the association between IFN-γ gene polymorphisms and the history of acute allograft rejection in 53 adult first-transplant recipients receiving cadaveric kidney grafts. They were followed up in a single centre until 2006, for a median time of 4 years after transplantation (1-22 years). IFN-γ gene polymorphisms +874 T/A (rs2430561) were determined by polymerase chain reaction (PCR). T/T high IFN-γ genotype was found in 12, intermediate T/A in 29 and low A/A in 12 patients. Twenty-six acute kidney rejection episodes were evidenced in 20 patients, of which none occurred in the 12 patients with low IFN-γ genotype A/A. Age, gender, number of HLA (human leukocyte antigen) mismatches, ABO blood groups, HLA, time after transplantation, creatinine clearance and immunosuppressive regimens were excluded as confounding factors associated with IFN-γ genotype distribution between rejectors and non-rejectors. IFN-γ gene polymorphisms could be an important risk factor for acute kidney transplant rejection, whereas the low A/A IFN-γ genotype could be protective against rejection.

Evaluation of the reliability of DNA typing in the process of identification of war victims in Croatia

Aiming to estimate the frequency of various types of errors that can occur in the large-scale process of identification, we identified and compared genotypes of 911 parent-child pairs in the database of 3498 relatives of people that disappeared during the 1991/1992 war in Croatia. Genotypes of 891 pairs (97.8%) were matching, while 20 pairs did not match in one or more loci. Reanalysis of these samples revealed that out of 1822 analyzed genotypes, one genotype was completely wrong, and two genotypes had one wrong allele because of human errors. Five genotypes had a single wrong allele due to either polymerase chain reaction or electrophoresis errors. In five genotypes mutations were the cause of mismatch. Genetic inconsistencies with parentage were found in four "fathers" (4.2%) and three "mothers" (0.36%). As the majority of observed single-locus errors were caused by nonhuman errors, all databases produced with similar technology would probably have comparable level of errors.