Reconstructing Gene Regulatory Networks That Control Hematopoietic Commitment.

Hematopoietic stem cells (HSCs) reside at the apex of the hematopoietic hierarchy, possessing the ability to self-renew and differentiate toward all mature blood lineages. Along with more specialized progenitor cells, HSCs have an essential role in maintaining a healthy blood system. Incorrect regulation of cell fate decisions in stem/progenitor cells can lead to an imbalance of mature blood cell populations-a situation seen in diseases such as leukemia. Transcription factors, acting as part of complex regulatory networks, are known to play an important role in regulating hematopoietic cell fate decisions. Yet, discovering the interactions present in these networks remains a big challenge. Here, we discuss a computational method that uses single-cell gene expression data to reconstruct Boolean gene regulatory network models and show how this technique can be applied to enhance our understanding of transcriptional regulation in hematopoiesis.Work in the author’s laboratory is supported by grants from the Wellcome, Bloodwise, Cancer Research UK, NIH-NIDDK and core support grants by the Wellcome to the Cambridge Institute for Medical Research and Wellcome & MRC Cambridge Stem Cell Institute. F.K.H. is a recipient of a Medical Research Council PhD Studentship

An integrative approach for building personalized gene regulatory networks for precision medicine

Only a small fraction of patients respond to the drug prescribed to treat their disease, which means that most are at risk of unnecessary exposure to side effects through ineffective drugs. This inter-individual variation in drug response is driven by differences in gene interactions caused by each patient's genetic background, environmental exposures, and the proportions of specific cell types involved in disease. These gene interactions can now be captured by building gene regulatory networks, by taking advantage of RNA velocity (the time derivative of the gene expression state), the ability to study hundreds of thousands of cells simultaneously, and the falling price of single-cell sequencing. Here, we propose an integrative approach that leverages these recent advances in single-cell data with the sensitivity of bulk data to enable the reconstruction of personalized, cell-type- and context-specific gene regulatory networks. We expect this approach will allow the prioritization of key driver genes for specific diseases and will provide knowledge that opens new avenues towards improved personalized healthcare

Cumulative dietary exposure to a selected group of pesticides of the trazole group in different European countries according to the EFSA guidance on Probabilistic modelling

The practicality was examined of performing a cumulative dietary exposure assessment according to the requirements of the EFSA guidance on probabilistic modelling. For this the acute and chronic cumulative exposure to triazole pesticides was estimated using national food consumption and monitoring data of eight European countries. Both the acute and chronic cumulative dietary exposures were calculated according to two model runs (optimistic and pessimistic) as recommended in the EFSA guidance. The exposures obtained with these model runs differed substantially for all countries, with the highest exposures obtained with the pessimistic model run. In this model run, animal commodities including cattle milk and different meat types, entered in the exposure calculations at the level of the maximum residue limit (MRL), contributed most to the exposure. We conclude that application of the optimistic model run on a routine basis for cumulative assessments is feasible. The pessimistic model run is laborious and the exposure results could be too far from reality. More experience with this approach is needed to stimulate the discussion of the feasibility of all the requirements, especially the inclusion of MRLs of animal commodities which seem to result in unrealistic conclusions regarding their contribution to the dietary exposure

Vers une révision des objectifs et méthodes de sélection de la luzerne

La recherche d’une autonomie protéique, la réduction des dépenses énergétiques et des sources depollution, en premier lieu celles engendrées par la fabrication d’engrais azotés, et la prise en compte de tous lesservices écosystémiques favorisent l’introduction de légumineuses fourragères pérennes dans la plupart desagroécosystèmes, en culture pure et en culture associée. Parallèlement, le changement climatique nécessitedes variétés adaptées à des épisodes de sécheresse et de chaleur. L’accroissement (en surface et pardiversification des systèmes fourragers ou de culture) de la culture de légumineuses et le changementclimatique conduisent aussi à étendre les zones de culture des espèces, et par exemple de considérer laculture de la luzerne beaucoup plus largement dans la moitié nord de la France (bassin parisien, ouest) en plusdes zones traditionnelles (moitié sud de la France, Champagne). La sélection de nouvelles variétés vise àassurer le maintien de la production et de la qualité dans des situations de stress hydrique et thermique, et àpromouvoir l’adaptation de l’espèce à de plus larges zones de culture. Les nouvelles techniques de séquençageet de génotypage offrent des outils prometteurs pour faciliter cette sélection et ainsi accélérer le progrèsgénétique. Nous développerons les perspectives de sélection, en ce qui concerne la luzerne

Cumulative dietary exposure to a selected group of pesticides of the trazole group in different European countries according to the EFSA guidance on Probabilistic modelling

The practicality was examined of performing a cumulative dietary exposure assessment according to the requirements of the EFSA guidance on probabilistic modelling. For this the acute and chronic cumulative exposure to triazole pesticides was estimated using national food consumption and monitoring data of eight European countries. Both the acute and chronic cumulative dietary exposures were calculated according to two model runs (optimistic and pessimistic) as recommended in the EFSA guidance. The exposures obtained with these model runs differed substantially for all countries, with the highest exposures obtained with the pessimistic model run. In this model run, animal commodities including cattle milk and different meat types, entered in the exposure calculations at the level of the maximum residue limit (MRL), contributed most to the exposure. We conclude that application of the optimistic model run on a routine basis for cumulative assessments is feasible. The pessimistic model run is laborious and the exposure results could be too far from reality. More experience with this approach is needed to stimulate the discussion of the feasibility of all the requirements, especially the inclusion of MRLs of animal commodities which seem to result in unrealistic conclusions regarding their contribution to the dietary exposure

Proteogenomic Discovery of a Small, Novel Protein in Yeast Reveals a Strategy for the Detection of Unannotated Short Open Reading Frames

In recent years, proteomic data have contributed to genome annotation efforts, most notably in humans and mice, and spawned a field termed “proteogenomics”. Yeast, in contrast with higher eukaryotes, has a small genome, which has lent itself to simpler ORF prediction. Despite this, continual advances in mass spectrometry suggest that proteomics should be able to improve genome annotation even in this well-characterized species. Here we applied a proteogenomics workflow to yeast to identify novel protein-coding genes. Specific databases were generated, from intergenic regions of the genome, which were then queried with MS/MS data. This suggested the existence of several putative novel ORFs of <100 codons, one of which we chose to validate. Synthetic peptides, RNA-Seq analysis, and evidence of evolutionary conservation allowed for the unequivocal definition of a new protein of 78 amino acids encoded on chromosome X, which we dub YJR107C-A. It encodes a new type of domain, which ab initio modeling suggests as predominantly α-helical. We show that this gene is nonessential for growth; however, deletion increases sensitivity to osmotic stress. Finally, from the above discovery process, we discuss a generalizable strategy for the identification of short ORFs and small proteins, many of which are likely to be undiscovered

A novel model of human lympho-myeloid progenitor hierarchy based on single cell functional and transcriptional analysis

Human hemopoiesis produces 10 billion new, terminally mature, blood cells daily; a production that is also rapidly responsive to external change. Dysregulation of this complex process can lead to hemopoietic and immune deficiencies and blood cancers. In humans the hemopoietic progenitor hierarchy producing lymphoid and granulocytic-monocytic (myeloid) lineages is unclear. Multiple progenitor populations give rise to lymphoid and myeloid cells but they remain incompletely characterized at the immunophenotypic, transcriptional and functional level

Hematopoietic stem cells retain functional potential and molecular identity in hibernation cultures.

Advances in the isolation and gene expression profiling of single hematopoietic stem cells (HSCs) have permitted in-depth resolution of their molecular program. However, long-term HSCs can only be isolated to near purity from adult mouse bone marrow, thereby precluding studies of their molecular program in different physiological states. Here, we describe a powerful 7-day HSC hibernation culture system that maintains HSCs as single cells in the absence of a physical niche. Single hibernating HSCs retain full functional potential compared with freshly isolated HSCs with respect to colony-forming capacity and transplantation into primary and secondary recipients. Comparison of hibernating HSC molecular profiles to their freshly isolated counterparts showed a striking degree of molecular similarity, further resolving the core molecular machinery of HSC self-renewal while also identifying key factors that are potentially dispensable for HSC function, including members of the AP1 complex (Jun, Fos, and Ncor2), Sult1a1 and Cish. Finally, we provide evidence that hibernating mouse HSCs can be transduced without compromising their self-renewal activity and demonstrate the applicability of hibernation cultures to human HSCs