Analysis of Ras-effector interaction competition in large intestine and colorectal cancer context

Abstract

Cancer is the second leading cause of death globally, and colorectal cancer (CRC) is among the five most common cancers. The small GTPase KRAS is an oncogene that is mutated in~30% of all CRCs. Pharmacological treatments of CRC are currently unsatisfactory, but much hope rests on network-centric approaches to drug development and cancer treatment. These approaches, however, require a better understanding of how networks downstream of Ras oncoproteins are connected in a particular tissue contexthere colon and CRC. Previously we have shown that competition for binding to a 'hub' protein, such as Ras, can induce a rewiring of signal transduction networks. In this study, we analysed 56 established and predicted effectors that contain a structural domain with the potential ability to bind to Ras oncoproteins and their link to pathways coordinating intestinal homoeostasis and barrier function. Using protein concentrations in colon tissue and Ras-effector binding affinities, a computational network model was generated that predicted how effectors differentially and competitively bind to Ras in colon context. The model also predicted both qualitative and quantitative changes in Ras-effector complex formations with increased levels of active Rasto simulate its upregulation in cancersimply as an emergent property of competition for the same binding interface on the surface of Ras. We also considered how the number of Ras-effector complexes at the membrane can be increased by additional domains present in some effectors that are recruited to the membrane in response to specific conditions (inputs/stimuli/growth factors) in colon context and CRC.

The Ins and Outs of RAS Effector Complexes

“…Although, on the basis of different consensus amino acid sequences, three different domain types exist that can bind to RAS oncoproteins, the RBD (SMART accession number: SM00455), the RA (SM00314), and the PI3K_rbd (SM00144), we collectively refer to these domains as RBDs here. Based on sequence similarities and domain prediction tools, the human genome is predicted to contain 56 RBD-containing effector proteins, which fall into 12 effector pathways [15]. Noteworthy, the binding affinities of individual effector RBDs in complex with RAS•GTP measured either in vitro using biophysical techniques [16][17][18] or calculated in silico using 3D structural modeling and energy calculations [19,20] span a wide range from low nanomolar to high micromolar Kd values [15] ( Fig.…”

“…Indeed, we have shown earlier that increasing the concentration of the effector RIN1 in cultured cells decreased the phosphorylation of CRAF and its downstream targets, which was enhanced even further when RIN1 was artificially localized to the plasma membrane (PM) using a CAAX box [21]. Another consequence of the competition of effectors for binding to RAS is that increasing the levels of active RAS•GTP, such as in the case of cancer mutants that prevent efficient hydrolysis of RAS•GTP, is predicted to not only increase the overall amount of effectors in complex with RAS (quantitative change), but also qualitatively change the binding profile, where low affinity effectors proportionally engage more with the additional amount of RAS•GTP available [15,22]. Thus, understanding RAS-effector signaling requires studying all effectors present in a biological system as the cellular output depends on the concentrations (and affinities) of all players present.…”

“…Our recent investigation using quantitative computational modelling of RAS signaling complexes in colon tissue [15] suggested that at physiologically low RAS . GTP levels high affinity RAS-RAF complexes dominate.…”

“…Many RAS effectors, in addition to their RBD, contain domains with affinity to membranes including the PM or to proteins localized at the PM [15]. Indeed, 28 RAS effectors contain membranebinding domains (Fig.…”

<p>Aloperine Exerts Antitumor Effects on Bladder Cancer in vitro</p>

“…Ras protein is an important component of cell growth and proliferation signaling pathways. 40,41 If the Ras protein is continuously activated, it can bind to the downstream effective protein and transmit the signal to the downstream signal element, which may lead to the abnormal proliferation of cells and the development of tumors. Therefore, we evaluated the role of ALO in Ras and its downstream signals.…”