Determining PTEN functional status by network component deduced transcription factor activities

T-ALL leukemia stem cell 'stemness' is epigenetically controlled by the master regulator SPI1

Leukemia stem cells (LSCs) are regarded as the origins and key therapeutic targets of leukemia, but limited knowledge is available on the key determinants of LSC 'stemness'. Using single-cell RNA-seq analysis, we identify a master regulator, SPI1, the LSC-specific expression of which determines the molecular signature and activity of LSCs in the murine Pten-null T-ALL model. Although initiated by PTEN-controlled β-catenin activation, Spi1 expression and LSC 'stemness' are maintained by a β-catenin-SPI1-HAVCR2 regulatory circuit independent of the leukemogenic driver mutation. Perturbing any component of this circuit either genetically or pharmacologically can prevent LSC formation or eliminate existing LSCs. LSCs lose their 'stemness' when Spi1 expression is silenced by DNA methylation, but Spi1 expression can be reactivated by 5-AZ treatment. Importantly, similar regulatory mechanisms may be also present in human T-ALL.

Targeting the MYC and PI3K pathways eliminates leukemia-initiating cells in T-cell acute lymphoblastic leukemia

Disease relapse remains the major clinical challenge in treating T-cell acute lymphoblastic leukemia (T-ALL), particularly those with PTEN loss. We hypothesized that leukemia-initiating cells (LIC) are responsible for T-ALL development and treatment relapse. In this study, we used a genetically engineered mouse model of Pten(-/-) T-ALL with defined blast and LIC-enriched cell populations to demonstrate that LICs are responsible for therapeutic resistance. Unlike acute and chronic myelogenous leukemia, LICs in T-ALL were actively cycling, were distinct biologically, and responded differently to targeted therapies in comparison with their differentiated blast cell progeny. Notably, we found that T-ALL LICs could be eliminated by cotargeting the deregulated pathways driven by PI3K and Myc, which are altered commonly in human T-ALL and are associated with LIC formation. Our findings define critical events that may be targeted to eliminate LICs in T-ALL as a new strategy to treat the most aggressive relapsed forms of this disease.

Stem cell quiescence acts as a tumour suppressor in squamous tumours

In some organs, adult stem cells are uniquely poised to serve as cancer cells of origin. It is unclear, however, whether tumorigenesis is influenced by the activation state of the adult stem cell. Hair follicle stem cells (HFSCs) act as cancer cells of origin for cutaneous squamous cell carcinoma (SCC) and undergo defined cycles of quiescence and activation. The data presented here show that HFSCs are unable to initiate tumors during the quiescent phase of the hair cycle, indicating that the mechanisms that keep HFSCs dormant are dominant to the gain of oncogenes (Ras) or the loss of tumor suppressors (p53). Furthermore, Pten activity is necessary for quiescence based tumor suppression, as its deletion alleviates tumor suppression without affecting proliferation. These data demonstrate that stem cell quiescence is a form of tumor suppression in HFSCs, and that Pten plays a role in maintaining quiescence in the presence of tumorigenic stimuli.

Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network

Background

Gene regulatory networks (GRNs) are models of molecule-gene interactions instrumental in the coordination of gene expression. Transcription factor (TF)-GRNs are an important subset of GRNs that characterize gene expression as the effect of TFs acting on their target genes. Although such networks can qualitatively summarize TF-gene interactions, it is highly desirable to quantitatively determine the strengths of the interactions in a TF-GRN as well as the magnitudes of TF activities. To our knowledge, such analysis is rare in plant biology. A computational methodology developed for this purpose is network component analysis (NCA), which has been used for studying large-scale microbial TF-GRNs to obtain nontrivial, mechanistic insights. In this work, we employed NCA to quantitatively analyze a plant TF-GRN important in floral development using available regulatory information from AGRIS, by processing previously reported gene expression data from four shoot apical meristem cell types.

Results

The NCA model satisfactorily accounted for gene expression measurements in a TF-GRN of seven TFs (LFY, AG, SEPALLATA3 [SEP3], AP2, AGL15, HY5 and AP3/PI) and 55 genes. NCA found strong interactions between certain TF-gene pairs including LFY → MYB17, AG → CRC, AP2 → RD20, AGL15 → RAV2 and HY5 → HLH1, and the direction of the interaction (activation or repression) for some AGL15 targets for which this information was not previously available. The activity trends of four TFs - LFY, AG, HY5 and AP3/PI as deduced by NCA correlated well with the changes in expression levels of the genes encoding these TFs across all four cell types; such a correlation was not observed for SEP3, AP2 and AGL15.

Conclusions

For the first time, we have reported the use of NCA to quantitatively analyze a plant TF-GRN important in floral development for obtaining nontrivial information about connectivity strengths between TFs and their target genes as well as TF activity. However, since NCA relies on documented connectivity information about the underlying TF-GRN, it is currently limited in its application to larger plant networks because of the lack of documented connectivities. In the future, the identification of interactions between plant TFs and their target genes on a genome scale would allow the use of NCA to provide quantitative regulatory information about plant TF-GRNs, leading to improved insights on cellular regulatory programs.

PTPs emerge as PIPs: protein tyrosine phosphatases with lipid-phosphatase activities in human disease

Protein tyrosine phosphatases (PTPs) constitute a family of key homeostatic regulators, with wide implications on physiology and disease. Recent findings have unveiled that the biological activity of PTPs goes beyond the dephosphorylation of phospho-proteins to shut down protein tyrosine kinase-driven signaling cascades. Substrates dephosphorylated by clinically relevant PTPs extend to phospholipids and phosphorylated carbohydrates as well. In addition, non-catalytic functions are also used by PTPs to regulate essential cellular functions. Consequently, PTPs have emerged as novel potential therapeutic targets for human diseases, including cancer predispositions, myopathies and neuropathies. In this review, we highlight recent advances on the multifaceted role of lipid-phosphatase PTPs in human pathology, with an emphasis on hereditary diseases. The involved PTP regulatory networks and PTP modulatory strategies with potential therapeutic application are discussed.

Targeting the PI3K/AKT/mTOR and Raf/MEK/ERK pathways in the treatment of breast cancer

Alterations of signal transduction pathways leading to uncontrolled cellular proliferation, survival, invasion, and metastases are hallmarks of the carcinogenic process. The phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) and the Raf/mitogen-activated and extracellular signal-regulated kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) signaling pathways are critical for normal human physiology, and also commonly dysregulated in several human cancers, including breast cancer (BC). In vitro and in vivo data suggest that the PI3K/AKT/mTOR and Raf/MEK/ERK cascades are interconnected with multiple points of convergence, cross-talk, and feedback loops. Raf/MEK/ERK and PI3K/AKT/mTOR pathway mutations may co-exist. Inhibition of one pathway can still result in the maintenance of signaling via the other (reciprocal) pathway. The existence of such "escape" mechanisms implies that dual targeting of these pathways may lead to superior efficacy and better clinical outcome in selected patients. Several clinical trials targeting one or both pathways are already underway in BC patients. The toxicity profile of this novel approach of dual pathway inhibition needs to be closely monitored, given the important physiological role of PI3K/AKT/mTOR and Raf/MEK/ERK signaling. In this article, we present a review of the current relevant pre-clinical and clinical data and discuss the rationale for dual inhibition of these pathways in the treatment of BC patients.