The completion of the Mammalian Gene Collection (MGC)

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide

Novel Avian Influenza H7N3 Strain Outbreak, British Columbia

Genome sequences of chicken (low pathogenic avian influenza [LPAI] and highly pathogenic avian influenza [HPAI]) and human isolates from a 2004 outbreak of H7N3 avian influenza in Canada showed a novel insertion in the HA0 cleavage site of the human and HPAI isolate. This insertion likely occurred by recombination between the hemagglutination and matrix genes in the LPAI virus

Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy

Human glioblastomas (GBMs) harbour a subpopulation of glioblastoma stem cells (GSCs) that drive tumourigenesis. However, the origin of intra-tumoural functional heterogeneity between GBM cells remains poorly understood. Here we study the clonal evolution of barcoded GBM cells in an unbiased way following serial xenotransplantation to define their individual fate behaviours. Independent of an evolving mutational signature, we show that the growth of GBM clones in vivo is consistent with a remarkably neutral process involving a conserved proliferative hierarchy rooted in GSCs. In this model, slow-cycling stem-like cells give rise to a more rapidly cycling progenitor population with extensive self-maintenance capacity, that in turn generates non-proliferative cells. We also identify rare “outlier” clones that deviate from these dynamics, and further show that chemotherapy facilitates the expansion of pre-existing drug-resistant GSCs. Finally, we show that functionally distinct GSCs can be separately targeted using epigenetic compounds, suggesting new avenues for GBM targeted therapy.This study was supported by the Canadian Institutes of Health Research (funding reference number 142434), the Ontario Institute for Cancer Research through funding provided by the Government of Ontario, and Stand Up To Cancer (SU2C) Canada. P.B.D. is also supported by the Terry Fox Research Institute, the Canadian Cancer Society, the Hospital for Sick Children Foundation, Jessica’s Footprint Foundation, the Hopeful Minds Foundation, the Bresler family, and B.R.A.I.N. Child. P.B.D. holds a Garron Family Chair in Childhood Cancer Research at The Hospital for Sick Children. B.D.S. acknowledges the support of the Wellcome Trust (grant number 098357/Z/12/Z). C.J.E. acknowledges grant support from the Canadian Cancer Society and the Terry Fox Run. Research was supported by SU2C Canada Cancer Stem Cell Dream Team Research Funding (SU2C-AACR-DT-19-15) provided by the Government of Canada through Genome Canada and the Canadian Institutes of Health Research, with supplementary support from the Ontario Institute for Cancer Research through funding provided by the Government of Ontario. Stand Up To Cancer Canada is a program of the Entertainment Industry Foundation Canada. Research funding is administered by the American Association for Cancer Research International – Canada, the scientific partner of SU2C Canada. The Structural Genomics Consortium is funded by AbbVie, Bayer, Boehringer Ingelheim, GSK, Genome Canada, Ontario Genomics Institute, Janssen, Lilly, Merck, Novartis, the government of Ontario, Pfizer, Takeda, and the Wellcome Trust

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

Follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) are the two most common non-Hodgkin lymphomas (NHLs). Here we sequenced tumour and matched normal DNA from 13 DLBCL cases and one FL case to identify genes with mutations in B-cell NHL. We analysed RNA-seq data from these and another 113 NHLs to identify genes with candidate mutations, and then re-sequenced tumour and matched normal DNA from these cases to confirm 109 genes with multiple somatic mutations. Genes with roles in histone modification were frequent targets of somatic mutation. For example, 32% of DLBCL and 89% of FL cases had somatic mutations in MLL2, which encodes a histone methyltransferase, and 11.4% and 13.4% of DLBCL and FL cases, respectively, had mutations in MEF2B, a calcium-regulated gene that cooperates with CREBBP and EP300 in acetylating histones. Our analysis suggests a previously unappreciated disruption of chromatin biology in lymphomagenesis

Draft Genome Sequences of Bordetella hinzii and Bordetella trematum.

International audienceBordetella hinzii colonizes the respiratory tracts of poultry but can also infect immunocompromised humans. Bordetella trematum, however, only infects humans, causing ear and wound infections. Here, we present the first draft genome sequences of strains B. hinzii ATCC 51730 and B. trematum CCUG 13902

The [PSI +] yeast prion does not wildly affect proteome composition whereas selective pressure exerted on [PSI +] cells can promote aneuploidy

AbstractThe yeast Sup35 protein is a subunit of the translation termination factor, and its conversion to the [PSI+] prion state leads to more translational read-through. Although extensive studies have been done on [PSI+], changes at the proteomic level have not been performed exhaustively. We therefore used a SILAC-based quantitative mass spectrometry approach and identified 4187 proteins from both [psi−] and [PSI+] strains. Surprisingly, there was very little difference between the two proteomes under standard growth conditions. We found however that several [PSI+] strains harbored an additional chromosome, such as chromosome I. Albeit, we found no evidence to support that [PSI+] induces chromosomal instability (CIN). Instead we hypothesized that the selective pressure applied during the establishment of [PSI+]-containing strains could lead to a supernumerary chromosome due to the presence of the ade1-14 selective marker for translational read-through. We therefore verified that there was no prevalence of disomy among newly generated [PSI+] strains in absence of strong selection pressure. We also noticed that low amounts of adenine in media could lead to higher levels of mitochondrial DNA in [PSI+] in ade1-14 cells. Our study has important significance for the establishment and manipulation of yeast strains with the Sup35 prion.</jats:p

Depletion of SCFA-fermenting gut bacteria alters the epigenome of hematopoietic stem and progenitor cells

Abstract Gut dysbiosis alters the development and severity of atopic disease. We previously demonstrated that nursing dams and newborn mice treated with low-dose vancomycin alters gut microbial diversity with a marked loss of bacteria that produce short-chain fatty acids (including butyrate). Vancomycin-induced gut dysbiosis enhances the TH2 response to lung allergens due to altered dendritic cell trafficking and activation in addition to modifying the behavior of other mature leukocyte lineages. Butyrate supplementation reverses the vancomycin-induced TH2 pro-inflammatory phenotype. Butyrate is known to exert some of its effects on target cells by inhibiting histone deacetylases (HDACs) with consequent effects on gene expression. Consistent with a role for epigenetic skewing of the hematopoietic compartment, we found that engraftment of total bone marrow from dysbiotic mice transferred enhanced TH2 proclivity in normobiotic recipients. Strikingly, we found unique regulatory states (H3K27ac marks) in purified hematopoietic stem and progenitor cells (HSPC) of TH2-skewed recipient mice. Single cell RNA sequence analyses identified a distinct transcriptomic signature in HSPC of dysbiotic mice that was reversed by butyrate supplementation. Together, these data suggest that the gut microbiome alters gene expression in blood progenitor cells with long term consequences on the immune response to peripheral allergens.</jats:p

Polycomb contraction differentially regulates terminal human hematopoietic differentiation programs

AbstractLifelong production of the many types of mature blood cells from less differentiated progenitors is a hierarchically ordered process that spans multiple cell divisions. The nature and timing of the molecular events required to integrate the environmental signals, transcription factor activity, epigenetic modifications, and changes in gene expression involved are thus complex and still poorly understood. We now show that the more primitive types of human cells in this system display a unique repressive H3K27me3 signature that is retained by mature lymphoid cells but is lost in terminally differentiated monocytes and erythroblasts. Additional intervention data implicate that control of this chromatin state change is a requisite part of the process, whereby normal human hematopoietic progenitor cells make lymphoid and myeloid fate decisions.</jats:p