Mtor Restricts Chromatin Access And Genomic Activity To Maintain Hematopoietic Stem Cell Quiescence And Engraftment

mTOR kinase is an anti-cancer drug target that integrates signals from nutrients, growth factors, and cellular energy status to control cell growth and proliferation, but its biological function in hematopoietic stem cells remains unclear. Numerous studies by using rapamycin or mTOR kinase inhibitors have indicated that mTOR inhibition suppresses chromatin access and gene expression and inhibits cell growth. Consistent with the notion that mTOR targeting suppresses gene activation, hyperactivation of mTOR by deletion of negative regulators of mTOR, TSC1/TSC2 or PTEN, causes a loss of quiescence and exhaustion of HSCs. To directly examine the function of mTOR and its kinase activity in HSC regulation, we used the conditional Mx-Cre;mTORflox/flox and the Mx-Cre;mTORflox/knockin mice that produce the mTOR-/- and the mTOR kinase-activity deficient D2338A mutant knockin genotype, respectively, upon poly I:C induced Cre recombination. We have determined the phenotypic, genomic and molecular effects of their HSCs. Our previous studies have found that depletion of mTOR drastically affected hematopoiesis, with a marked reduction in total BM cellularity and transient increase in the number of HSCs in bone marrow. Remarkably, mTOR-/- HSCs displayed a loss of quiescence, increased proliferation and a normal survival index (Guo et al., Haematologic a 98:1353). Our current study has found similar phenotypes of the HSCs in increased number and proliferation in the Mx-Cre;mTORflox/knockin mice where the mTOR kinase activity is abolished. Both mTOR-/- and mTORKI/- HSCs are defective in engraftment upon competitive transplant into recipient mice, with a clear molecular signature of drastically reduced downstream effectors p-S6K and p-4E-BP. ATAC-seq reveals that loss of mTOR or mTOR kinase activity results in selectively increased chromatin access and global gene activation, in contrast to the reported effects by mTOR inhibitors such as rapamycin or pp242/AZD2014. ChIP-seq of two active histone markers, H3K27Ac and H3K4Me3, yields consistent results that chromosome of the HSCs are activated upon the loss of mTOR or its kinase activity. In particular, increased H3K27Ac and H3K4Me3 ChIP-seq activities are observed in both the upstream and downstream region of c-myc locus, consistent with an activated c-myc expression. RNA-seq analysis reveals that upon mTOR KO or KI, thousands of genes exhibit differential expression. The up-regulated genes are particularly enriched in functions involved in ribosome biogenesis/protein translation, cell cycle progression, cell fate determination, and survival. Analysis using the STRING functional interaction network to search for the compensatory genes/pathways discovers a number of likely compensatorily upregulated genes, upon mTOR KO or KI, that share a significant number of interacting genes with mTOR, including c-myc, Fos, and Jun. These genes are enriched in pathways such as EGFR-MAPK pathway, PI3K-Akt pathway, Jak-Stat pathway, and NFkB pathway, which may compensate for mTOR loss. RT-PCR and Western blotting further verify that loss of mTOR or its kinase activity causes elevated mRNA and protein expression of selected compensatory genes, including c-myc, Fos, Jun, and Pik3cd. In addition, broad compensatory elevations in ribosome and translation machinery gene expression, activation of RNA pol-II, and activation of several interesting compensatory pathways are seen. The BET inhibitor, JQ1, that inhibits c-myc activity readily suppresses the hyper-proliferative phenotype of mTOR-/- and mTORKI/-HSCs. Thus, contrary to dogma established mostly by transient rapamycin or kinase inhibitor usages, our genetic and genomic studies demonstrate that mTOR, through its kinase activity, plays a restrictive role to maintain chromosomal access and genomic activity of HSCs. Loss of mTOR or its kinase activity unleashes a compensatory chromosomal and gene activation effects that involve master regulators of gene activities such as c-myc and Fos, protein translation and ribosomal proteins, and cell growth signaling pathways. These genomic changes may cause the HSC loss of quiescence and engraftment phenotypes seen upon mTOR loss, and need to be taken into consideration in the development of new generations of mTOR targeted therapy and combinatory therapy.