Drugging an undruggable pocket on KRAS.

The 3 human RAS genes, KRAS, NRAS, and HRAS, encode 4 different RAS proteins which belong to the protein family of small GTPases that function as binary molecular switches involved in cell signaling. Activating mutations in RAS are among the most common oncogenic drivers in human cancers, with KRAS being the most frequently mutated oncogene. Although KRAS is an excellent drug discovery target for many cancers, and despite decades of research, no therapeutic agent directly targeting RAS has been clinically approved. Using structure-based drug design, we have discovered BI-2852 (1), a KRAS inhibitor that binds with nanomolar affinity to a pocket, thus far perceived to be "undruggable," between switch I and II on RAS; 1 is mechanistically distinct from covalent KRASG12C inhibitors because it binds to a different pocket present in both the active and inactive forms of KRAS. In doing so, it blocks all GEF, GAP, and effector interactions with KRAS, leading to inhibition of downstream signaling and an antiproliferative effect in the low micromolar range in KRAS mutant cells. These findings clearly demonstrate that this so-called switch I/II pocket is indeed druggable and provide the scientific community with a chemical probe that simultaneously targets the active and inactive forms of KRAS.

Clinical impact of studying epithelial-mesenchymal plasticity in pluripotent stem cells.

BACKGROUND: The ability of cells to travel long distances in order to form tissues and organs is inherently connected to embryogenesis. The process in which epithelial-like embryonic cells become motile and invasive is termed 'epithelial-to-mesenchymal transition' (EMT), while the reversion of this programme--yielding differentiated cells and organs--is called 'mesenchymal-to-epithelial transition' (MET). DESIGN: Here, we review the processes of EMT and MET in development and cancer and combine them with knowledge from pluripotent stem cell research. RESULTS: Research has shown that these processes are activated in many cancers leading to dissemination of cancer cells throughout the body and formation of metastasis. While the regulation of EMT during cancer progression has been extensively studied for decades, many fundamental processes that govern normal development are only poorly understood. Recent discoveries, such as reprogramming to pluripotent stem cells and identification of ground and primed states of pluripotent stem cells, have redirected much attention to EMT and MET. CONCLUSION: Findings from pluripotent stem cell research and EMT/MET should be combined in order to design future strategies aimed to improve our understanding of cancer progression and to help develop novel anticancer strategies.

Phosphorylation of nuclear and cytoplasmic pools of ribosomal protein S6 during cell cycle progression.

Of all known ribosomal proteins, the 40S ribosomal protein S6 is by far the most extensively studied. Still, little is known about some basic aspects of S6 regulation including its cell cycle-related expression and localization. Using a flow cytometric single cell approach applied to whole cells and isolated nuclei, we monitored nucleocytoplasmic expression of total and S240/4 phosphorylated S6 during unperturbed cell cycle progression, providing first evidence for a S6-specific spatiotemporal pattern and its deregulation under conditions of hyperactivated mTOR.

Renal differentiation of amniotic fluid stem cells: perspectives for clinical application and for studies on specific human genetic diseases.

BACKGROUND: Owing to growing rates of diabetes, hypertension and the ageing population, the prevalence of end-stage renal disease, developed from earlier stages of chronic kidney disease, and of acute renal failure is dramatically increasing. Dialysis and preferable renal transplantation are widely applied therapies for this incurable condition. However these options are limited because of morbidity, shortage of compatible organs and costs. Therefore, stem cell-based approaches are becoming increasingly accepted as an alternative therapeutic strategy. DESIGN: This review summarizes the current findings on the nephrogenic potential of amniotic fluid stem (AFS) cells and their putative implications for clinical applications and for studies on specific human genetic diseases. RESULTS: Since their discovery in 2003, AFS cells have been shown to be pluripotent with the potential to form embryoid bodies. Compared to adult stem cells, induced pluripotent stem cells or embryonic stem cells, AFS cells harbour a variety of advantages, such as their high differentiation and proliferative potential, no need for ectopic induction of pluripotency and no somatic mutations and epigenetic memory of source cells, and no tumourigenic potential and associated ethical controversies, respectively. CONCLUSIONS: Recently, the results of different independent studies provided evidence that AFS cells could indeed be a powerful tool for renal regenerative medicine.

BI-3406, a Potent and Selective SOS1-KRAS Interaction Inhibitor, Is Effective in KRAS-Driven Cancers through Combined MEK Inhibition.

KRAS is the most frequently mutated driver of pancreatic, colorectal, and non-small cell lung cancers. Direct KRAS blockade has proved challenging, and inhibition of a key downstream effector pathway, the RAF-MEK-ERK cascade, has shown limited success because of activation of feedback networks that keep the pathway in check. We hypothesized that inhibiting SOS1, a KRAS activator and important feedback node, represents an effective approach to treat KRAS-driven cancers. We report the discovery of a highly potent, selective, and orally bioavailable small-molecule SOS1 inhibitor, BI-3406, that binds to the catalytic domain of SOS1, thereby preventing the interaction with KRAS. BI-3406 reduces formation of GTP-loaded RAS and limits cellular proliferation of a broad range of KRAS-driven cancers. Importantly, BI-3406 attenuates feedback reactivation induced by MEK inhibitors and thereby enhances sensitivity of KRAS-dependent cancers to MEK inhibition. Combined SOS1 and MEK inhibition represents a novel and effective therapeutic concept to address KRAS-driven tumors. SIGNIFICANCE: To date, there are no effective targeted pan-KRAS therapies. In-depth characterization of BI-3406 activity and identification of MEK inhibitors as effective combination partners provide an attractive therapeutic concept for the majority of KRAS-mutant cancers, including those fueled by the most prevalent mutant KRAS oncoproteins, G12D, G12V, G12C, and G13D.See related commentary by Zhao et al., p. 17.This article is highlighted in the In This Issue feature, p. 1.

Assessing high-resolution melt curve analysis for accurate detection of gene variants in complex DNA fragments.

Mutation detection has, until recently, relied heavily on the use of gel-based methods that can be both time consuming and difficult to design. Nongel-based systems are therefore important to increase simplicity and improve turn around time without compromising assay sensitivity and accuracy, especially in the diagnostic/clinical setting. In this study, we assessed the latest of the nongel-based methods, namely high-resolution melt (HRM) curve analysis. HRM is a closed-tube method that incorporates a saturating dye during DNA amplification followed by a monitoring of the change in fluorescence as the DNA duplex is denatured by an increasing temperature. We assessed 10 amplicons derived from eight genes, namely SERPINA1, CXCR7, MBL, VDR, NKX3A, NPY, TP53, and HRAS using two platforms, the LightScanner System using LC Green PLUS DNA binding dye (Idaho Technology, Salt Lake City, UT, USA) and the LightCycler 480 using the HRM Master dye (Roche Diagnostics, Indianapolis, IN, USA). DNA variants (mutations or polymorphims) were previously identified using denaturing gradient gel electrophoresis (DGGE) a method, similarly to HRM, based upon the different melting properties of double-stranded DNA. Fragments were selected based on variant and fragment complexity. This included the presence of multiple sequence variants, variants in alternate orientations, and single or multiple variants (constitutional or somatic) in GC-rich fragments. We demonstrate current limitations of the HRM method for the analysis of complex DNA regions and call for caution when using HRM as the sole method to make a clinical diagnosis based on genetic analysis.

eIF3 controls cell size independently of S6K1-activity.

All multicellular organisms require a life-long regulation of the number and the size of cells, which build up their organs. mTOR acts as a signaling nodule for the regulation of protein synthesis and growth. To activate the translational cascade, mTOR phosphorylates S6 kinase (S6K1), which is liberated from the eIF3-complex and mobilized for activation of its downstream targets. How S6K1 regulates cell size remains unclear. Here, we challenged cell size control through S6K1 by specifically depleting its binding partner eIF3 in normal and transformed cell lines. We show that loss of eIF3 leads to a massive reduction of cell size and cell number accompanied with an unexpected increase in S6K1-activity. The hyperactive S6K1-signaling was rapamycin-sensitive, suggesting an upstream mTOR-regulation. A selective S6K1 inhibitor (PF-4708671) was unable to interfere with the reduced size, despite efficiently inhibiting S6K1-activity. Restoration of eIF3 expression recovered size defects, without affecting the p-S6 levels. We further show that two, yet uncharacterized, cancer-associated mutations in the eIF3-complex, have the capacity to recover from reduced size phenotype, suggesting a possible role for eIF3 in regulating cancer cell size. Collectively, our results uncover a role for eIF3-complex in maintenance of normal and neoplastic cell size - independent of S6K1-signaling.

The decision on the "optimal" human pluripotent stem cell.

Because of recent advances, the array of human pluripotent stem cells now contains embryonic stem cells, derived from "surplus" in vitro fertilization embryos or from cloned embryos; induced pluripotent stem cells; and amniotic fluid stem cells. Here, we compare these stem cell types regarding ethical and legal concerns, cultivation conditions, genomic stability, tumor developing potentials, and applicability for disease modeling and human therapy. This overview highlights that in the future appropriate methodological management must include a decision on the "optimal" stem cell to use before the specific application.

Merging high-quality biochemical fractionation with a refined flow cytometry approach to monitor nucleocytoplasmic protein expression throughout the unperturbed mammalian cell cycle.

This protocol describes a method for nucleocytoplasmic protein tracking during normal cell cycle progression using unmanipulated, asynchronous cells. In contrast with prevalent traditional methods, our approach does not require time-consuming, perturbing cell synchronization or separation. To this end, we chose a single-cell approach and developed a flow cytometry assay that is applied to whole cells and isolated nuclei. Our protocol involves a stepwise biochemical fractionation procedure to purify nuclei from whole cells, conventional DNA and indirect immunostaining techniques for the dual labeling of cells and nuclei for DNA and protein, and a refined concept of flow cytometric data processing and calculation: through the specific combination of DNA and cell size analyses, G1, S and G2/M phases of the cell cycle are further dissected to establish a high-resolution map of cell cycle progression, to which protein expression in cells or nuclei is correlated. In a final data analysis step, cell cycle-related, cytoplasmic protein expression is calculated on the basis of results obtained for whole cells and isolated nuclei. A minimum of 8 h is required to complete the procedure. As the approach does not require cell type-restricting pretreatments, numerous cell types of different origin can be readily studied. Human amniotic fluid stem cells, primary human fibroblasts, immortalized mouse fibroblasts and transformed tumor cells are analyzed at comparable efficiencies, demonstrating low intercell assay variability.

Circadian and circalunar clock interactions in a marine annelid.

Life is controlled by multiple rhythms. Although the interaction of the daily (circadian) clock with environmental stimuli, such as light, is well documented, its relationship to endogenous clocks with other periods is little understood. We establish that the marine worm Platynereis dumerilii possesses endogenous circadian and circalunar (monthly) clocks and characterize their interactions. The RNAs of likely core circadian oscillator genes localize to a distinct nucleus of the worm's forebrain. The worm's forebrain also harbors a circalunar clock entrained by nocturnal light. This monthly clock regulates maturation and persists even when circadian clock oscillations are disrupted by the inhibition of casein kinase 1δ/ε. Both circadian and circalunar clocks converge on the regulation of transcript levels. Furthermore, the circalunar clock changes the period and power of circadian behavior, although the period length of the daily transcriptional oscillations remains unaltered. We conclude that a second endogenous noncircadian clock can influence circadian clock function.

Amniotic fluid stem cells: future perspectives.

The existence of stem cells in human amniotic fluid was reported for the first time almost ten years ago. Since this discovery, the knowledge about these cells has increased dramatically. Today, amniotic fluid stem (AFS) cells are widely accepted as a new powerful tool for basic research as well as for the establishment of new stem-cell-based therapy concepts. It is possible to generate monoclonal genomically stable AFS cell lines harboring high proliferative potential without raising ethical issues. Many different groups have demonstrated that AFS cells can be differentiated into all three germ layer lineages, what is of relevance for both, the scientific and therapeutical usage of these cells. Of special importance for the latter is the fact that AFS cells are less tumorigenic than other pluripotent stem cell types. In this paper, we have summarized the current knowledge about this relatively young scientific field. Furthermore, we discuss the relevant future perspectives of this promising area of stem cell research focusing on the next important questions, which need to be answered.

Amniotic fluid stem cells to study mTOR signaling in differentiation.

The protein kinase mTOR is the central player within a pathway, which is known to be involved in the regulation of e.g., cell size, cell cycle, apoptosis, autophagy, aging and differentiation. mTOR activity responds to many signals, including cellular stress, oxygen, nutrient availability, energy status and growth factors. Deregulation of this enzyme is causatively involved in the molecular development of monogenic human diseases, cancer, obesity, type 2 diabetes or neurodegeneration. Recently, mTOR has also been demonstrated to control stem cell homeostasis. A more detailed investigation of this new mTOR function will be of highest relevance to provide more explicit insights into stem cell regulation in the near future. Different cellular tools, including adult stem cells, embryonic stem cells or induced pluripotent stem cells could be used to investigate the role of mTOR in mammalian stem cell biology. Here we discuss the potential of amniotic fluid stem cells to become a promising cellular model to study the role of signaling cascades in stem cell homeostasis.

Blocking mTORC1 activity by rapamycin leads to impairment of spatial memory retrieval but not acquisition in C57BL/6J mice.

Although the involvement of the mTOR (mammalian target of rapamycin) system in memory processes has been reported, information on the effect of rapamycin on spatial learning and memory is limited. It was therefore the aim of the study to show the effect of parenteral rapamycin administration to C57BL/6J mice on performance in the multiple T-maze (MTM) and to determine hippocampal mTOR activity. Rapamycin-treated and -untreated/trained/probed mice are the main part of the experiment considering retrieval and acquisition or consolidation of spatial memory. Six hours following euthanasia hippocampi were extirpated and used for evaluation of mTOR activity as represented by hippocampal levels of S6 protein and its phosphorylated active form (phospho S6 protein, S240,244), a read out of mTOR complex 1 activity. Mice given i.p. rapamycin learned the task of the MTM but failed at the probe trial, showing absence of the phosphorylated active form of S6 protein, indicating inhibition of mTOR activity. Herein, impairing effects of rapamycin on retrieval but not on acquisition or consolidation of spatial memory are shown. Deficient memory retrieval was paralleled by inhibition of mTOR complex 1 activity. The current study extends knowledge on rapamycin in memory mechanisms and challenges work on deeper insights into the role of mTOR in different phases of memory formation and retrieval.

Human amniotic fluid stem cells as a model for functional studies of genes involved in human genetic diseases or oncogenesis.

Besides their putative usage for therapies, stem cells are a promising tool for functional studies of genes involved in human genetic diseases or oncogenesis. For this purpose induced pluripotent stem (iPS) cells can be derived from patients harbouring specific mutations. In contrast to adult stem cells, iPS cells are pluripotent and can efficiently be grown in culture. However, iPS cells are modulated due to the ectopic induction of pluripotency, harbour other somatic mutations accumulated during the life span of the source cells, exhibit only imperfectly cleared epigenetic memory of the source cell, and are often genomically instable. In addition, iPS cells from patients only allow the investigation of mutations, which are not prenatally lethal. Embryonic stem (ES) cells have a high proliferation and differentiation potential, but raise ethical issues. Human embryos, which are not transferred in the course of in vitro fertilization, because of preimplantation genetic diagnosis of a genetic defect, are still rarely donated for the establishment of ES cell lines. In addition, their usage for studies on gene functions for oncogenesis is hampered by the fact the ES cells are already tumorigenic per se. In 2003 amniotic fluid stem (AFS) cells have been discovered, which meanwhile have been demonstrated to harbour the potential to differentiate into cells of all three germ layers. Monoclonal human AFS cell lines derived from amniocenteses have a high proliferative potential, are genomically stable and are not associated with ethical controversies. Worldwide amniocenteses are performed for routine human genetic diagnosis. We here discuss how generation and banking of monoclonal human AFS cell lines with specific chromosomal aberrations or monogenic disease mutations would allow to study the functional consequences of disease causing mutations. In addition, recently a protocol for efficient and highly reproducible siRNA-mediated long-term knockdown of endogenous gene functions in AFS cells was established. Since AFS cells are not tumorigenic, gene modulations not only allow to investigate the role of endogenous genes involved in human genetic diseases but also may help to reveal putative oncogenic gene functions in different biological models, both in vitro and in vivo. This concept is discussed and a "proof of principle", already obtained via modulating genes involved in the mammalian target of rapamycin (mTOR) pathway in AFS cells, is presented.

Hedgehog signaling regulates segment formation in the annelid Platynereis.

Annelids and arthropods share a similar segmented organization of the body whose evolutionary origin remains unclear. The Hedgehog signaling pathway, prominent in arthropod embryonic segment patterning, has not been shown to have a similar function outside arthropods. We show that the ligand Hedgehog, the receptor Patched, and the transcription factor Gli are all expressed in striped patterns before the morphological appearance of segments in the annelid Platynereis dumerilii. Treatments with small molecules antagonistic to Hedgehog signaling disrupt segment formation. Platynereis Hedgehog is not necessary to establish early segment patterns but is required to maintain them. The molecular similarity of segment patterning functions of the Hedgehog pathway in an annelid and in arthropods supports a common origin of segmentation in protostomes.