First identified in the early 1980s as retroviral oncogenes, the Raf proteins have been the objects of intense research. The discoveries 10 years later that the Raf family members (Raf-1, B-Raf, and A-Raf) are bona fide Ras effectors and upstream activators of the ubiquitous ERK pathway increased the interest in these proteins primarily because of the central role that this cascade plays in cancer development. The important role of Raf in cancer was corroborated in 2002 with the discovery of B-Raf genetic mutations in a large number of tumors. This led to intensified drug development efforts to target Raf signaling in cancer. This work yielded not only recent clinical successes but also surprising insights into the regulation of Raf proteins by homodimerization and heterodimerization. Surprising insights also came from the hunt for new Raf targets. Although MEK remains the only widely accepted Raf substrate, new kinase-independent roles for Raf proteins have emerged. These include the regulation of apoptosis by suppressing the activity of the proapoptotic kinases, ASK1 and MST2, and the regulation of cell motility and differentiation by controlling the activity of Rok-α. In this review, we discuss the regulation of Raf proteins and their role in cancer, with special focus on the interacting proteins that modulate Raf signaling. We also describe the new pathways controlled by Raf proteins and summarize the successes and failures in the development of efficient anticancer therapies targeting Raf. Finally, we also argue for the necessity of more systemic approaches to obtain a better understanding of how the Ras-Raf signaling network generates biological specificity.

Summary Turnover and exchange of nucleosomal histones and their variants, a process long believed to be static in post-replicative cells, remains largely unexplored in brain. Here, we describe a novel mechanistic role for HIRA (histone cell cycle regulator) and proteasomal degradation associated histone dynamics in the regulation of activity-dependent transcription, synaptic connectivity and behavior. We uncover a dramatic developmental profile of nucleosome occupancy across the lifespan of both rodents and humans, with the histone variant H3.3 accumulating to near saturating levels throughout the neuronal genome by mid-adolescence. Despite such accumulation, H3.3 containing nucleosomes remain highly dynamic–in a modification independent manner–to control neuronal- and glial-specific gene expression patterns throughout life. Manipulating H3.3 dynamics in both embryonic and adult neurons confirmed its essential role in neuronal plasticity and cognition. Our findings establish histone turnover as a critical, and previously undocumented, regulator of cell-type specific transcription and plasticity in mammalian brain.

One-sentence summary: Analysis of the ERK circuitry suggests the most effective targets in the pathway for inhibition, which may aid in drug development Editor's Summary: Biological Circuits Inform Drug Development The mitogen-activated protein kinase (MAPK) pathway involves a three-tiered kinase module, which amplifies the signal. Many cells also have negative feedback loops from the last kinase in the module back to various points upstream in the pathway. Sturm et al. show that the MAPK module with negative feedback loops results in a system like that of a negative feedback amplifier (NFA), which is an engineering design that smoothens the output to changes in input and makes a system robust to change. These NFA-like properties may explain why some cells are sensitive to inhibition of the second kinase in the cascade (they lack the feedback loops); whereas other cells are resistant to inhibition at this point (their feedback loops are intact). These results also have implications for drug development, because inhibitors that target components that are outside the NFA are more effective at inhibiting the pathway. Abstract Three-tiered kinase modules, such as the Raf-MEK-ERK mitogen-activated protein kinase pathway, are widespread in biology suggesting that this structure conveys evolutionary advantageous properties. Here, we show that the three-tiered kinase amplifier module combined with negative feedback recapitulates the design principles of a negative feedback amplifier (NFA), which is used in electronic circuits to convey robustness, output stabilization, and linearization of nonlinear signal amplification. With mathematical modelling and experimental validation, we demonstrated that the ERK pathway has properties of a NFA that (i) converts intrinsic switch-like activation kinetics into graded linear responses; (ii) conveys robustness to changes in rates of reactions within the NFA module; and (iii) stabilizes outputs in response to drug-induced perturbations of the amplifier. These properties determine biological behavior, including activation kinetics and the response to drugs.

Summary Activation of ErbB receptors by epidermal growth factor (EGF) or heregulin (HRG) determines distinct cell fate decisions, although signals propagate through shared pathways. Using modeling and experiments, we unravel how EGF and HRG generate distinct, all-or-none responses of the phosphorylated transcription factor c-Fos. In the cytosol, EGF induces transient and HRG induces sustained ERK activation. In the nucleus, however, ERK activity and c-fos mRNA expression are transient for both ligands. Knockdown of dual-specificity phosphatases extends HRG-stimulated nuclear ERK activation, but not c-fos mRNA expression, implying the existence of a HRG-induced repressor of c-fos transcription. Further experiments confirmed that this repressor is mainly induced by HRG, but not EGF, and requires new protein synthesis. We show how a spatially distributed, signaling-transcription cascade robustly discriminates between transient and sustained ERK activities at the c-Fos system level. The proposed control mechanisms are general and operate in different cell types, stimulated by various ligands.