Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia

Over a decade ago, the Atacama humanoid skeleton (Ata) was discovered in the Atacama region of Chile. The Ata specimen carried a strange phenotype-6-in stature, fewer than expected ribs, elongated cranium, and accelerated bone age-leading to speculation that this was a preserved nonhuman primate, human fetus harboring genetic mutations, or even an extraterrestrial. We previously reported that it was human by DNA analysis with an estimated bone age of about 6-8 yr at the time of demise. To determine the possible genetic drivers of the observed morphology, DNA from the specimen was subjected to whole-genome sequencing using the Illumina HiSeq platform with an average 11.5× coverage of 101-bp, paired-end reads. In total, 3,356,569 single nucleotide variations (SNVs) were found as compared to the human reference genome, 518,365 insertions and deletions (indels), and 1047 structural variations (SVs) were detected. Here, we present the detailed whole-genome analysis showing that Ata is a female of human origin, likely of Chilean descent, and its genome harbors mutations in genes (COL1A1, COL2A1, KMT2D, FLNB, ATR, TRIP11, PCNT) previously linked with diseases of small stature, rib anomalies, cranial malformations, premature joint fusion, and osteochondrodysplasia (also known as skeletal dysplasia). Together, these findings provide a molecular characterization of Ata's peculiar phenotype, which likely results from multiple known and novel putative gene mutations affecting bone development and ossification.

High-throughput precision measurement of subcellular localization in single cells

To quantify visual and spatial information in single cells with a throughput of thousands of cells per second, we developed Subcellular Localization Assay (SLA). This adaptation of Proximity Ligation Assay expands the capabilities of flow cytometry to include data relating to localization of proteins to and within organelles. We used SLA to detect the nuclear import of transcription factors across cell subsets in complex samples. We further measured intranuclear re-localization of target proteins across the cell cycle and upon DNA damage induction. SLA combines multiple single-cell methods to bring about a new dimension of inquiry and analysis in complex cell populations. © 2017 International Society for Advancement of Cytometry.

Human colon fibroblasts induce differentiation and proliferation of intestinal epithelial cells through the direct paracrine action of keratinocyte growth factor

The effects exerted by the keratinocyte growth factor (KGF) on intestinal epithelial cells cultured in vitro are influenced by cell confluence and differentiation through the modulation of keratinocyte growth factor receptor (KGFR) expression. In order to better define the contribution of KGF on the intestinal epithelial cell differentiation and proliferation, here we developed a coculture model, able to mimick in vitro the epithelial-mesenchymal interactions of the bowel. In consequence of its ability to produce KGF, demonstrated by real-time PCR and Western blot analysis, the human colon fibroblast cell line CCD-18 has been selected as coculture partner for the intestinal epithelial Caco-2 cell line. Analysis of the expression of the differentiation and proliferation markers CEA and Ki67, through double immunofluorescence assays, showed that either the coculture with CCD-18 cells or the incubation with primary colon fibroblast-derived conditioned media (CM-F and CM-F2) induced an increase in differentiation and proliferation of confluent intestinal epithelial Caco-2 or HT29 cells, parallel to that obtained by KGF treatment. Use of anti-KGF blocking antibodies and of a tyrosine kinase KGFR inhibitor demonstrated the contribution of KGF and the direct role of its receptor in the regulation of epithelial growth and differentiation, indicating that KGF is a crucial paracrine factor involved in promoting these effects.